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Sample records for multiple chlamydiaceae species

  1. Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans.

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    Joseph, Sandeep J; Marti, Hanna; Didelot, Xavier; Castillo-Ramirez, Santiago; Read, Timothy D; Dean, Deborah

    2015-10-27

    Chlamydiaceae are obligate intracellular bacteria that cause a diversity of severe infections among humans and livestock on a global scale. Identification of new species since 1989 and emergence of zoonotic infections, including abortion in women, underscore the need for genome sequencing of multiple strains of each species to advance our knowledge of evolutionary dynamics across Chlamydiaceae. Here, we genome sequenced isolates from avian, lower mammalian and human hosts. Based on core gene phylogeny, five isolates previously classified as Chlamydia abortus were identified as members of Chlamydia psittaci and Chlamydia pecorum. Chlamydia abortus is the most recently emerged species and is a highly monomorphic group that lacks the conserved virulence-associated plasmid. Low-level recombination and evidence for adaptation to the placenta echo evolutionary processes seen in recently emerged, highly virulent niche-restricted pathogens, such as Bacillus anthracis. In contrast, gene flow occurred within C. psittaci and other Chlamydiaceae species. The C. psittaci strain RTH, isolated from a red-tailed hawk (Buteo jamaicensis), is an outlying strain with admixture of C. abortus, C. psittaci, and its own population markers. An average nucleotide identity of less than 94% compared with other Chlamydiaceae species suggests that RTH belongs to a new species intermediary between C. psittaci and C. abortus. Hawks, as scavengers and predators, have extensive opportunities to acquire multiple species in their intestinal tract. This could facilitate transformation and homologous recombination with the potential for new species emergence. Our findings indicate that incubator hosts such as birds-of-prey likely promote Chlamydiaceae evolution resulting in novel pathogenic lineages. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  2. Chlamydiaceae Genomics Reveals Interspecies Admixture and the Recent Evolution of Chlamydia abortus Infecting Lower Mammalian Species and Humans

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    Joseph, Sandeep J.; Marti, Hanna; Didelot, Xavier; Castillo-Ramirez, Santiago; Read, Timothy D.; Dean, Deborah

    2015-01-01

    Chlamydiaceae are obligate intracellular bacteria that cause a diversity of severe infections among humans and livestock on a global scale. Identification of new species since 1989 and emergence of zoonotic infections, including abortion in women, underscore the need for genome sequencing of multiple strains of each species to advance our knowledge of evolutionary dynamics across Chlamydiaceae. Here, we genome sequenced isolates from avian, lower mammalian and human hosts. Based on core gene ...

  3. Chlamydiaceae infections in pig

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    Schautteet Katelijn

    2011-02-01

    Full Text Available Abstract Chlamydiaceae are Gram-negative obligate intracellular bacteria. They are responsible for a broad range of diseases in animals and humans. In pigs, Chlamydia suis, Chlamydia abortus, Chlamydia pecorum and Chlamydia psittaci have been isolated. Chlamydiaceae infections in pigs are associated with different pathologies such as conjunctivitis, pneumonia, pericarditis, polyarthritis, polyserositis, pseudo-membranous or necrotizing enteritis, periparturient dysgalactiae syndrome, vaginal discharge, return to oestrus, abortion, mummification, delivery of weak piglets, increased perinatal and neonatal mortality and inferior semen quality, orchitis, epididymitis and urethritis in boars. However, Chlamydiaceae are still considered as non-important pathogens because reports of porcine chlamydiosis are rare. Furthermore, Chlamydiaceae infections are often unnoticed because tests for Chlamydiaceae are not routinely performed in all veterinary diagnostic laboratories and Chlamydiaceae are often found in association with other pathogens, which are sometimes more easily to detect. However, recent studies have demonstrated that Chlamydiaceae infections in breeding sows, boars and piglets occur more often than thought and are economically important. This paper presents an overview on: the taxonomy of Chlamydiaceae occurring in pigs, diagnostic considerations, epidemiology and pathology of infections with Chlamydiaceae in pigs, public health significance and finally on prevention and treatment of Chlamydiaceae infections in pigs.

  4. Emendation of the family Chlamydiaceae: proposal of a single genus, Chlamydia, to include all currently recognized species.

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    Sachse, Konrad; Bavoil, Patrik M; Kaltenboeck, Bernhard; Stephens, Richard S; Kuo, Cho-Chou; Rosselló-Móra, Ramon; Horn, Matthias

    2015-03-01

    The family Chlamydiaceae (order Chlamydiales, phylum Chlamydiae) comprises important, obligate intracellular bacterial pathogens of humans and animals. Subdivision of the family into the two genera Chlamydia and Chlamydophila has been discussed controversially during the past decade. Here, we have revisited the current classification in the light of recent genomic data and in the context of the unique biological properties of these microorganisms. We conclude that neither generally used 16S rRNA sequence identity cut-off values nor parameters based on genomic similarity consistently separate the two genera. Notably, no easily recognizable phenotype such as host preference or tissue tropism is available that would support a subdivision. In addition, the genus Chlamydophila is currently not well accepted and not used by a majority of research groups in the field. Therefore, we propose the classification of all 11 currently recognized Chlamydiaceae species in a single genus, the genus Chlamydia. Finally, we provide emended descriptions of the family Chlamydiaceae, the genus Chlamydia, as well as the species Chlamydia abortus, Chlamydia caviae and Chlamydia felis. Copyright © 2015 Elsevier GmbH. All rights reserved.

  5. ATYPICAL CHLAMYDIACEAE IN WILD POPULATIONS OF HAWKS ( BUTEO SPP.) IN CALIFORNIA.

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    Luján-Vega, Charlene; Hawkins, Michelle G; Johnson, Christine K; Briggs, Christopher; Vennum, Chris; Bloom, Peter H; Hull, Joshua M; Cray, Carolyn; Pesti, Denise; Johnson, Lisa; Ciembor, Paula; Ritchie, Branson R

    2018-03-01

    Chlamydiaceae bacteria infect many vertebrate hosts, and previous reports based on polymerase chain reaction (PCR) assays and serologic assays that are prone to cross-reaction among chlamydial organisms have been used to describe the prevalence of either DNA fragments or antibodies to Chlamydia spp. in wild raptorial populations. This study reports the PCR-based prevalence of Chlamydiaceae DNA that does not 100% match any avian or mammalian Chlamydiaceae in wild populations of hawks in California Buteo species. In this study, multimucosal swab samples ( n = 291) for quantitative PCR (qPCR) and plasma ( n = 78) for serology were collected from wild hawks. All available plasma samples were negative for antibodies using a C. psittaci-specific elementary body agglutination test (EBA; n = 78). For IgY antibodies all 51 available samples were negative using the indirect immunofluorescent assay. The overall prevalence of Chlamydiaceae DNA detection in wild Buteo species sampled was 1.37% (4/291) via qPCR-based analysis. Two fledgling Swainson's hawks ( Buteo swainsoni) and two juvenile red-tailed hawks ( Buteo jamaicensis) were positive by qPCR-based assay for an atypical chlamydial sequence that did not 100% match any known C. psittaci genotype. Positive swab samples from these four birds were sequenced based on the ompA gene and compared by high-resolution melt analysis with all known avian and mammalian Chlamydiaceae. The amplicon sequence did not 100% match any known avian chlamydial sequence; however, it was most similar (98.6%) to C. psittaci M56, a genotype that is typically found in muskrats and hares. Culture and full genome sequence analysis of Chlamydia spp. isolated from diseased hawks will be necessary to classify this organism and to better understand its epizootiology and potential health impact on wild Buteo populations in California.

  6. A real-time PCR assay for the detection of atypical strains of Chlamydiaceae from pigeons.

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    Aleksandar Zocevic

    Full Text Available Recent evidence of the occurrence of atypical Chlamydiaceae strains in pigeons, different from the established Chlamydiaceae, requires the development of a specific and rapid detection tool to investigate their prevalence and significance. Here is described a new real-time PCR assay that allows specific detection of atypical Chlamydiaceae from pigeons. The assay has been used to assess the dissemination of these strains in field samples collected from Parisian pigeon populations in 2009. The results suggest a limited dissemination compared to the usually higher prevalence of Chlamydia psittaci that is the main species associated with avian chlamydiosis.

  7. Natural Products for the Treatment of Chlamydiaceae Infections

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    Mika A. Brown

    2016-10-01

    Full Text Available Due to the global prevalence of Chlamydiae, exploring studies of diverse antichlamydial compounds is important in the development of effective treatment strategies and global infectious disease management. Chlamydiaceae is the most widely known bacterial family of the Chlamydiae order. Among the species in the family Chlamydiaceae, Chlamydia trachomatis and Chlamydia pneumoniae cause common human diseases, while Chlamydia abortus, Chlamydia psittaci, and Chlamydia suis represent zoonotic threats or are endemic in human food sources. Although chlamydial infections are currently manageable in human populations, chlamydial infections in livestock are endemic and there is significant difficulty achieving effective treatment. To combat the spread of Chlamydiaceae in humans and other hosts, improved methods for treatment and prevention of infection are needed. There exist various studies exploring the potential of natural products for developing new antichlamydial treatment modalities. Polyphenolic compounds can inhibit chlamydial growth by membrane disruption, reestablishment of host cell apoptosis, or improving host immune system detection. Fatty acids, monoglycerides, and lipids can disrupt the cell membranes of infective chlamydial elementary bodies (EBs. Peptides can disrupt the cell membranes of chlamydial EBs, and transferrins can inhibit chlamydial EBs from attachment to and permeation through the membranes of host cells. Cellular metabolites and probiotic bacteria can inhibit chlamydial infection by modulating host immune responses and directly inhibiting chlamydial growth. Finally, early stage clinical trials indicate that polyherbal formulations can be effective in treating chlamydial infections. Herein, we review an important body of literature in the field of antichlamydial research.

  8. Chlamydiaceae family, Parachlamydia spp., and Waddlia spp. in porcine abortion.

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    Koschwanez, Maria; Meli, Marina; Vögtlin, Andrea; Greub, Gilbert; Sidler, Xaver; Handke, Martin; Sydler, Titus; Kaiser, Carmen; Pospischil, Andreas; Borel, Nicole

    2012-09-01

    At present, despite extensive laboratory investigations, most cases of porcine abortion remain without an etiological diagnosis. Due to a lack of recent data on the abortigenic effect of order Chlamydiales, 286 fetuses and their placentae of 113 abortion cases (1-5 fetuses per abortion case) were investigated by polymerase chain reaction (PCR) methods for family Chlamydiaceae and selected Chlamydia-like organisms such as Parachlamydia acanthamoebae and Waddlia chondrophila. In 0.35% of the cases (1/286 fetuses), the Chlamydiaceae real-time PCR was positive. In the Chlamydiaceae-positive fetus, Chlamydia abortus was detected by a commercial microarray and 16S ribosomal RNA PCR followed by sequencing. The positive fetus had a Porcine circovirus-2 coinfection. By the Parachlamydia real-time PCR, 3.5% (10/286 fetuses of 9 abortion cases) were questionable positive (threshold cycle values: 35.0-45.0). In 2 of these 10 cases, a confirmation by Chlamydiales-specific real-time PCR was possible. All samples tested negative by the Waddlia real-time PCR. It seems unlikely that Chlamydiaceae, Parachlamydia, and Waddlia play an important role as abortigenic agents in Swiss sows.

  9. BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species

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    Gupta Radhey S

    2006-01-01

    Full Text Available Abstract Background Chlamydiae species are of much importance from a clinical viewpoint. Their diversity both in terms of their numbers as well as clinical involvement are presently believed to be significantly underestimated. The obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. Thus, it is of importance to develop additional means for their identification and characterization. Results We have carried out analyses of available chlamydiae genomes to identify sets of unique proteins that are either specific for all Chlamydiales genomes, or different Chlamydiaceae family members, or members of the Chlamydia and Chlamydophila genera, or those unique to Protochlamydia amoebophila, but which are not found in any other bacteria. In total, 59 Chlamydiales-specific proteins, 79 Chlamydiaceae-specific proteins, 20 proteins each that are specific for both Chlamydia and Chlamydophila and 445 ORFs that are Protochlamydia-specific were identified. Additionally, 33 cases of possible gene loss or lateral gene transfer were also detected. Conclusion The identified chlamydiae-lineage specific proteins, many of which are highly conserved, provide novel biomarkers that should prove of much value in the diagnosis of these bacteria and in exploration of their prevalence and diversity. These conserved protein sequences (CPSs also provide novel therapeutic targets for drugs that are specific for these bacteria. Lastly, functional studies on these chlamydiae or chlamydiae subgroup-specific proteins should lead to important insights into lineage-specific adaptations with regards to development, infectivity and pathogenicity.

  10. Prevalence of antibodies to Chlamydiaceae in pet dogs in Shenzhen, Guangdong Province, China

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    Tian Cheng

    2015-01-01

    Full Text Available The prevalence of chlamydiosis in pet dogs was surveyed in Shenzhen, Guangdong Province, China. A total of 442 serum samples were collected from three districts of Shenzhen, namely the Futian, Nanshan, and Luohu Districts, and assayed for Chlamydiaceae antibodies by indirect haemagglutination assay. The results showed that the mean positive rate was 6.11%, and the positive rate for the Futian District was the highest (9.52%, followed by the Nanshan District (7.08%, and the Luohu District (4.02%. The positive rate for male dogs was 6.08%, and for female dogs 6.16%. Out of all the 38 breeds of dogs examined, 14 breeds were positive. The positive rate for the Cocker Spaniel dog was the highest (14.2%, followed by the Pekinese dog (10.71%, and the Border Collie dog (10.34%. This is the first time that the seroprevalence of Chlamydiaceae infection in pet dogs in Shenzhen, Guangdong province, China was reported, and the results indicated that pet dogs may be an important source for human infection by Chlamydiaceae in Shenzhen and other areas of China.

  11. Chlamydiaceae and Chlamydia-like organisms in the koala (Phascolarctos cinereus)--organ distribution and histopathological findings.

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    Burach, Fabienne; Pospischil, Andreas; Hanger, Jon; Loader, Jo; Pillonel, Trestan; Greub, Gilbert; Borel, Nicole

    2014-08-06

    Chlamydial infections in koalas can cause life-threatening diseases leading to blindness and sterility. However, little is known about the systemic spread of chlamydiae in the inner organs of the koala, and data concerning related pathological organ lesions are limited. The aim of this study was to perform a thorough investigation of organs from 23 koalas and to correlate their histopathological lesions to molecular chlamydial detection. To reach this goal, 246 formalin-fixed and paraffin embedded organ samples from 23 koalas were investigated by histopathology, Chlamydiaceae real-time PCR and immunohistochemistry, ArrayTube Microarray for Chlamydiaceae species identification as well as Chlamydiales real-time PCR and sequencing. By PCR, two koalas were positive for Chlamydia pecorum whereas immunohistochemical labelling for Chlamydiaceae was detected in 10 tissues out of nine koalas. The majority of these (n=6) had positive labelling in the urogenital tract related to histopathological lesions such as cystitis, endometritis, pyelonephritis and prostatitis. Somehow unexpected was the positive labelling in the gastrointestinal tract including the cloaca as well as in lung and spleen indicating systemic spread of infection. Uncultured Chlamydiales were detected in several organs of seven koalas by PCR, and four of these suffered from plasmacytic enteritis of unknown aetiology. Whether the finding of Chlamydia-like organisms in the gastrointestinal tract is linked to plasmacytic enteritis is unclear and remains speculative. However, as recently shown in a mouse model, the gastrointestinal tract might play a role being the site for persistent chlamydial infections and being a source for reinfection of the genital tract. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. Chlamydiaceae in North Atlantic Seabirds Admitted to a Wildlife Rescue Center in Western France.

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    Aaziz, R; Gourlay, P; Vorimore, F; Sachse, K; Siarkou, V I; Laroucau, K

    2015-07-01

    Birds are the primary hosts of Chlamydia psittaci, a bacterium that can cause avian chlamydiosis in birds and psittacosis in humans. Wild seabirds are frequently admitted to wildlife rescue centers (WRC) at European Atlantic coasts, for example, in connection with oil spills. To investigate the extent of chlamydial shedding by these birds and the resulting risk for animals in care and the medical staff, seabirds from a French WRC were sampled from May 2011 to January 2014. By use of a quantitative PCR (qPCR), 195 seabirds belonging to 4 orders, 5 families and 13 species were examined, of which 18.5% proved to be Chlamydiaceae positive. The highest prevalence of shedders was found in northern gannets (Morus bassanus) (41%), followed by European herring gulls (Larus argentatus) (14%) and common murres (Uria aalge) (7%). Molecular characterization and phylogenetic analysis of qPCR-positive northern gannet samples revealed two variants of a strain closely related to C. psittaci. In European herring gulls and in one common murre, strains showing high sequence similarity to the atypical Chlamydiaceae-like C122 previously found in gulls were detected. Our study shows that seabirds from the northeastern Atlantic Ocean carry several chlamydial organisms, including C. psittaci-related strains. The staff in WRCs should take protective measures, particularly in the case of mass admissions of seabirds. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  13. Rapid Detection of the Chlamydiaceae and Other Families in the Order Chlamydiales: Three PCR Tests

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    Everett, Karin D. E.; Hornung, Linda J.; Andersen, Arthur A.

    1999-01-01

    Few identification methods will rapidly or specifically detect all bacteria in the order Chlamydiales, family Chlamydiaceae. In this study, three PCR tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. Two tests exclusively recognized the Chlamydiaceae: a multiplex test targeting the ompA gene and the rRNA intergenic spacer and a TaqMan test targeting the 23S ribosomal DNA. The multiplex test was able to detect as few as 200 inclusion-forming units (IFU), while the TaqMan test could detect 2 IFU. The amplicons produced in these tests ranged from 132 to 320 bp in length. The third test, targeting the 23S rRNA gene, produced a 600-bp amplicon from strains belonging to several families in the order Chlamydiales. Direct sequence analysis of this amplicon has facilitated the identification of new chlamydial strains. These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation. PMID:9986815

  14. Real-Time Detection and Identification of Chlamydophila Species in Veterinary Specimens by Using SYBR Green-Based PCR Assays

    DEFF Research Database (Denmark)

    Nordentoft, Steen; Kabell, Susanne; Pedersen, Karl

    2011-01-01

    of Chlamydiaceae and differentiate the most prevalent veterinary Chlamydophila species: Cp. psittaci, Cp. abortus, Cp. felis, and Cp. caviae. By adding bovine serum albumin to the master mixes, target DNA could be detected directly in crude lysates of enzymatically digested conjunctival or pharyngeal swabs...... or tissue specimens from heart, liver, and spleen without further purification. The assays were evaluated on veterinary specimens where all samples were screened using a family-specific PCR, and positive samples were further tested using species-specific PCRs. Cp. psittaci was detected in 47 birds, Cp...... with a highly sensitive family-specific PCR, we were able to screen for Chlamydiaceae in veterinary specimens and confirm the species in positive samples with additional PCR assays....

  15. HinT proteins and their putative interaction partners in Mollicutes and Chlamydiaceae

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    Hegemann Johannes H

    2005-05-01

    Full Text Available Background HinT proteins are found in prokaryotes and eukaryotes and belong to the superfamily of HIT proteins, which are characterized by an histidine-triad sequence motif. While the eukaryotic variants hydrolyze AMP derivates and modulate transcription, the function of prokaryotic HinT proteins is less clearly defined. In Mycoplasma hominis, HinT is concomitantly expressed with the proteins P60 and P80, two domains of a surface exposed membrane complex, and in addition interacts with the P80 moiety. Results An cluster of hitABL genes, similar to that of M. hominis was found in M. pulmonis, M. mycoides subspecies mycoides SC, M. mobile and Mesoplasma florum. RT-PCR analyses provided evidence that the P80, P60 and HinT homologues of M. pulmonis were polycistronically organized, suggesting a genetic and physical interaction between the proteins encoded by these genes in these species. While the hit loci of M. pneumoniae and M. genitalium encoded, in addition to HinT, a protein with several transmembrane segments, the hit locus of Ureaplasma parvum encoded a pore-forming protein, UU270, a P60 homologue, UU271, HinT, UU272, and a membrane protein of unknown function, UU273. Although a full-length mRNA spanning the four genes was not detected, amplification of all intergenic regions from the center of UU270 to the end of UU273 by RT-PCR may be indicative of a common, but unstable mRNA. In Chlamydiaceae the hit gene is flanked upstream by a gene predicted to encode a metal dependent hydrolase and downstream by a gene putatively encoding a protein with ARM-repeats, which are known to be involved in protein-protein interactions. In RT-PCR analyses of C. pneumoniae, regions comprising only two genes, Cp265/Cp266 and Cp266/Cp267 were able to be amplified. In contrast to this in vivo interaction analysis using the yeast two-hybrid system and in vitro immune co-precipitation revealed an interaction between Cp267, which contains the ARM repeats, Cp265, the

  16. Chlamydia species in free-living Cattle Egret (Bubulcus ibis and Hoopoe (Upupa epops in Egypt

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    Jakeen K. El-Jakee

    2014-06-01

    Full Text Available Little information is available on the presence of chlamydia infection in wildlife. This study was conducted to assess the occurrence of chlamydiae in asymptomatic birds from two species of wild birds (Cattle Egret and Hoopoe in Egypt. In the present study Chlamydiaceae was analyzed using Giemsa stain, Giménez stain, fluorescent antibody test (FAT and PCR. The results of these techniques were compared with CFT for detecting Chlamydia psittaci antibodies among the examined birds. The results reveal that 96.4%, 81.8%, 89.1%, 80.0% and 58.2% of the examined samples were positive for chlamydiosis using PCR, Giemsa stain, Giménez stain, FA, and CFT respectively among Hoopoe. The percentages were 90.6%, 77.4%, 83.0%, 75.5% and 66.0% respectively for the previous tests among Cattle Egret birds. The results suggest that Cattle Egret and Hoopoe may be reservoir of Chlamydiaceae species and thus shed the organisms in their excreta. The shedding of chlamydiae by free living birds in Egypt may expose humans that come in contact with these birds to zoonotic risks.

  17. Natural cross chlamydial infection between livestock and free-living bird species.

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    Jesús A Lemus

    Full Text Available The study of cross-species pathogen transmission is essential to understanding the epizootiology and epidemiology of infectious diseases. Avian chlamydiosis is a zoonotic disease whose effects have been mainly investigated in humans, poultry and pet birds. It has been suggested that wild bird species play an important role as reservoirs for this disease. During a comparative health status survey in common (Falco tinnunculus and lesser (Falco naumanni kestrel populations in Spain, acute gammapathies were detected. We investigated whether gammapathies were associated with Chlamydiaceae infections. We recorded the prevalence of different Chlamydiaceae species in nestlings of both kestrel species in three different study areas. Chlamydophila psittaci serovar I (or Chlamydophila abortus, an ovine pathogen causing late-term abortions, was isolated from all the nestlings of both kestrel species in one of the three studied areas, a location with extensive ovine livestock enzootic of this atypical bacteria and where gammapathies were recorded. Serovar and genetic cluster analysis of the kestrel isolates from this area showed serovars A and C and the genetic cluster 1 and were different than those isolated from the other two areas. The serovar I in this area was also isolated from sheep abortions, sheep faeces, sheep stable dust, nest dust of both kestrel species, carrion beetles (Silphidae and Orthoptera. This fact was not observed in other areas. In addition, we found kestrels to be infected by Chlamydia suis and Chlamydia muridarum, the first time these have been detected in birds. Our study evidences a pathogen transmission from ruminants to birds, highlighting the importance of this potential and unexplored mechanism of infection in an ecological context. On the other hand, it is reported a pathogen transmission from livestock to wildlife, revealing new and scarcely investigated anthropogenic threats for wild and endangered species.

  18. [Detection of Chlamydia abortus in bovine reproductive losses in the province of La Pampa, Argentina].

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    Rojas, María Del C; Fort, Marcelo; Bettermann, Simone; Entrocassi, Carolina; Costamagna, Sixto R; Sachse, Konrad; Rodríguez Fermepin, Marcelo

    2018-01-16

    Reproductive losses linked to an infectious etiology in bovine cattle are a major economic concern worldwide. In Argentina, more than 50% of abortion cases have unknown causes. Species belonging to Chlamydiaceae family are frequent etiologic agents of abortion around the world; however, there is yet no information on their prevalence in Argentina. The objective of this work was to identify Chlamydia spp., and particularly C. abortus in reproductive losses from bovine cattle in La Pampa, Argentina. Real time PCR targeting Chlamydiaceae-specific DNA fragments was performed on 251 samples obtained from bovine abortions and stillborns, and ArrayTube was used for species identification on positive samples. Chlamydiaceae DNA was detected in 12 samples of aborted fetuses (4.78%), 83.33% (10/12) accounting for abortions and 16.66% (2/12) for stillborns. C. abortus was detected by ArrayTube in 5 cases (1.99% of all samples, and 41.67% of Chlamydiaceae positive samples). This study shows the first detection of Chlamydiaceae and C. abortus DNA on reproductive losses of bovine cattle in Argentina, and the described prevalence value (4.78%) should be taken as baseline value due to the type of samples analyzed. Detection of genetic material from Chlamydiaceae not matching any of the studied species could be due to intraspecies variants or local species not yet described. Further research on Chlamydia infections in bovine cattle in Argentina is imperative to describe their range, to analyze their economic and zoonotic implications and to make recommendations about prevention and control measures. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

  19. Simultaneous presence of multiple Campylobacter species in dogs

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    Koene, M.G.J.; Houwers, D.J.; Dijkstra, J.R.; Duim, B.; Wagenaar, J.A.

    2004-01-01

    The prevalence of coinfection of Campylobacter species in dogs was determined using four isolation methods. In 26% of the positive-testing stools, multiple Campylobacter species were identified. The use of multiple isolation methods as well as the time lapse between sampling and processing are

  20. Multiple mechanisms enable invasive species to suppress native species.

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    Bennett, Alison E; Thomsen, Meredith; Strauss, Sharon Y

    2011-07-01

    Invasive plants represent a significant threat to ecosystem biodiversity. To decrease the impacts of invasive species, a major scientific undertaking of the last few decades has been aimed at understanding the mechanisms that drive invasive plant success. Most studies and theories have focused on a single mechanism for predicting the success of invasive plants and therefore cannot provide insight as to the relative importance of multiple interactions in predicting invasive species' success. We examine four mechanisms that potentially contribute to the success of invasive velvetgrass Holcus lanatus: direct competition, indirect competition mediated by mammalian herbivores, interference competition via allelopathy, and indirect competition mediated by changes in the soil community. Using a combination of field and greenhouse approaches, we focus on the effects of H. lanatus on a common species in California coastal prairies, Erigeron glaucus, where the invasion is most intense. We found that H. lanatus had the strongest effects on E. glaucus via direct competition, but it also influenced the soil community in ways that feed back to negatively influence E. glaucus and other native species after H. lanatus removal. This approach provided evidence for multiple mechanisms contributing to negative effects of invasive species, and it identified when particular strategies were most likely to be important. These mechanisms can be applied to eradication of H. lanatus and conservation of California coastal prairie systems, and they illustrate the utility of an integrated set of experiments for determining the potential mechanisms of invasive species' success.

  1. Free-living and captive turtles and tortoises as carriers of new Chlamydia spp.

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    Mitura, Agata; Niemczuk, Krzysztof; Zaręba, Kinga; Zając, Magdalena; Laroucau, Karine; Szymańska-Czerwińska, Monika

    2017-01-01

    A variety of Chlamydia species belonging to the Chlamydiaceae family have been reported in reptilian hosts but scarce data about their occurrence in turtles and tortoises are available. In this study, research was conducted to acquire information on invasive alien species (IAS) of turtles and indigenous turtles and tortoises, living both free and in captivity, as possible reservoirs of Chlamydiaceae. Analysis of specimens (pharyngeal and cloacal swabs and tissues) from 204 turtles and tortoises revealed an overall Chlamydiaceae prevalence of 18.3% and 28.6% among free-living and captive animals respectively, with variable levels of shedding. Further testing conducted with a species-specific real-time PCR and microarray test was unsuccessful. Subsequently sequencing was applied to genotype the Chlamydiaceae-positive samples. Almost the full lengths of the 16S rRNA and ompA genes as well as the 16S-23S intergenic spacer (IGS) and 23S rRNA domain I were obtained for 14, 20 and 8 specimens respectively. Phylogenetic analysis of 16S rRNA amplicons revealed two distinct branches. Group 1 (10 specimens), specific to freshwater turtles and reported here for the first time, was most closely related to Chlamydia (C.) pneumoniae strains and the newly described Candidatus C. sanzinia. Group 2 (four specimens), detected in Testudo spp. samples, showed highest homology to C. pecorum strains but formed a separate sub-branch. Finally, molecular analysis conducted on positive samples together with their geographical distribution in places distant from each other strongly suggest that Group 1 specimens correspond to a new species in the Chlamydiaceae family. In-depth studies of Chlamydia spp. from turtles and tortoises are needed to further characterise these atypical strains and address arising questions about their pathogenicity and zoonotic potential.

  2. Free-living and captive turtles and tortoises as carriers of new Chlamydia spp.

    Directory of Open Access Journals (Sweden)

    Agata Mitura

    Full Text Available A variety of Chlamydia species belonging to the Chlamydiaceae family have been reported in reptilian hosts but scarce data about their occurrence in turtles and tortoises are available. In this study, research was conducted to acquire information on invasive alien species (IAS of turtles and indigenous turtles and tortoises, living both free and in captivity, as possible reservoirs of Chlamydiaceae. Analysis of specimens (pharyngeal and cloacal swabs and tissues from 204 turtles and tortoises revealed an overall Chlamydiaceae prevalence of 18.3% and 28.6% among free-living and captive animals respectively, with variable levels of shedding. Further testing conducted with a species-specific real-time PCR and microarray test was unsuccessful. Subsequently sequencing was applied to genotype the Chlamydiaceae-positive samples. Almost the full lengths of the 16S rRNA and ompA genes as well as the 16S-23S intergenic spacer (IGS and 23S rRNA domain I were obtained for 14, 20 and 8 specimens respectively. Phylogenetic analysis of 16S rRNA amplicons revealed two distinct branches. Group 1 (10 specimens, specific to freshwater turtles and reported here for the first time, was most closely related to Chlamydia (C. pneumoniae strains and the newly described Candidatus C. sanzinia. Group 2 (four specimens, detected in Testudo spp. samples, showed highest homology to C. pecorum strains but formed a separate sub-branch. Finally, molecular analysis conducted on positive samples together with their geographical distribution in places distant from each other strongly suggest that Group 1 specimens correspond to a new species in the Chlamydiaceae family. In-depth studies of Chlamydia spp. from turtles and tortoises are needed to further characterise these atypical strains and address arising questions about their pathogenicity and zoonotic potential.

  3. Optimal design of compact and connected nature reserves for multiple species.

    Science.gov (United States)

    Wang, Yicheng; Önal, Hayri

    2016-04-01

    When designing a conservation reserve system for multiple species, spatial attributes of the reserves must be taken into account at species level. The existing optimal reserve design literature considers either one spatial attribute or when multiple attributes are considered the analysis is restricted only to one species. We built a linear integer programing model that incorporates compactness and connectivity of the landscape reserved for multiple species. The model identifies multiple reserves that each serve a subset of target species with a specified coverage probability threshold to ensure the species' long-term survival in the reserve, and each target species is covered (protected) with another probability threshold at the reserve system level. We modeled compactness by minimizing the total distance between selected sites and central sites, and we modeled connectivity of a selected site to its designated central site by selecting at least one of its adjacent sites that has a nearer distance to the central site. We considered structural distance and functional distances that incorporated site quality between sites. We tested the model using randomly generated data on 2 species, one ground species that required structural connectivity and the other an avian species that required functional connectivity. We applied the model to 10 bird species listed as endangered by the state of Illinois (U.S.A.). Spatial coherence and selection cost of the reserves differed substantially depending on the weights assigned to these 2 criteria. The model can be used to design a reserve system for multiple species, especially species whose habitats are far apart in which case multiple disjunct but compact and connected reserves are advantageous. The model can be modified to increase or decrease the distance between reserves to reduce or promote population connectivity. © 2015 Society for Conservation Biology.

  4. Detection of all Chlamydophila and Chlamydia spp. of veterinary interest using species-specific real-time PCR assays.

    Science.gov (United States)

    Pantchev, Alexandra; Sting, Reinhard; Bauerfeind, Rolf; Tyczka, Judith; Sachse, Konrad

    2010-12-01

    The aim of the present study was to analyse the occurrence of chlamydiae in several mammalian host species. Clinical samples that previously tested positive in a Chlamydiaceae-specific real-time PCR were retested using six species-specific real-time PCR assays to identify the chlamydial species involved. Chlamydophila (Cp.) abortus was the agent most frequently found in cattle, sheep, horses, goats, and pigs. Detection in cattle of Cp. psittaci (11% of samples) and Chlamydia (C.) suis (9%), as well as Cp. psittaci in a goat sample was somewhat unexpected. DNA of two different chlamydiae was identified in 56 (12.7%) of 440 samples tested. Cp. felis was the predominant species found in cats, while in guinea pigs and rabbits only Cp. caviae was detected. Interestingly, the latter two pathogens were also identified in samples from dogs. The data show that mixed chlamydial infections are not rare and suggest an extended host range of individual species. Copyright © 2009 Elsevier Ltd. All rights reserved.

  5. Intraguild predation reduces redundancy of predator species in multiple predator assemblage.

    Science.gov (United States)

    Griffen, Blaine D; Byers, James E

    2006-07-01

    1. Interference between predator species frequently decreases predation rates, lowering the risk of predation for shared prey. However, such interference can also occur between conspecific predators. 2. Therefore, to understand the importance of predator biodiversity and the degree that predator species can be considered functionally interchangeable, we determined the degree of additivity and redundancy of predators in multiple- and single-species combinations. 3. We show that interference between two invasive species of predatory crabs, Carcinus maenas and Hemigrapsus sanguineus, reduced the risk of predation for shared amphipod prey, and had redundant per capita effects in most multiple- and single-species predator combinations. 4. However, when predator combinations with the potential for intraguild predation were examined, predator interference increased and predator redundancy decreased. 5. Our study indicates that trophic structure is important in determining how the effects of predator species combine and demonstrates the utility of determining the redundancy, as well as the additivity, of multiple predator species.

  6. Genus delineation of Chlamydiales by analysis of the percentage of conserved proteins justifies the reunifying of the genera Chlamydia and Chlamydophila into one single genus Chlamydia.

    Science.gov (United States)

    Pannekoek, Yvonne; Qi-Long, Qin; Zhang, Yu-Zhong; van der Ende, Arie

    2016-08-01

    Many studies have aimed to set up boundaries for the classification and definition of prokaryotic genus and species classification; however, studies that focused on genus-level genomic differences for existing taxonomy systems are limited. Recently, a novel method was described for prokaryotic genus delineation using the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance (Qin et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196: :2210-5). Here, we extended the POCP analysis of the order Chlamydiales and pairwise compared all currently recognized species and candidate species of the family Chlamydiaceae as well as some species from other families. Using the taxonomy advised by the International Committee on Systematics of Prokaryotes, subcommittee on the taxonomy of the Chlamydiae, POCP analysis revealed that all pairwise comparisons of species from different families resulted in values lower than 50%, the proposed threshold for genus boundary. In contrast, all interspecies pairwise comparisons of species from the single genus within the family Chlamydiaceae resulted in POCP values higher than 70%. We conclude that the recommended genus classification of the family Chlamydiaceae is rational and that POCP analyses can provide a robust genomic index for the taxonomy of members of the order Chlamydiales in terms of genus demarcation. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Evidence for Chlamydia in wild mammals of the Serengeti.

    Science.gov (United States)

    Pospischil, Andreas; Kaiser, Carmen; Hofmann-Lehmann, Regina; Lutz, Hans; Hilbe, Monika; Vaughan, Lloyd; Borel, Nicole

    2012-10-01

    Only limited information is available on the presence of Chlamydiaceae in wildlife, a deficit that is particularly acute concerning mammalian wildlife in Africa. In a retrospective analysis of organ material from an earlier study on wild mammals from the Seregenti National Park, 521 samples from 54 animals of 14 mammalian species were investigated. The presence of Chlamydiaceae was analyzed using molecular methods and immunohistochemistry. Chlamydial DNA was detected by real-time polymerase chain reaction in formalin-fixed and paraffin-embedded tissues from large ruminants (African buffaloes, Syncerus caffer, n=4) and a large predator (spotted hyena, Crocuta crocuta, n=1). Microarray results revealed Chlamydia abortus in all cases, confirmed by sequencing of selected samples, and a mixed infection with Chlamydia abortus and Chlamydia pneumoniae in an African buffalo. This is the first report of Chlamydiaceae in African wildlife of the Serengeti area.

  8. Chlamydiae in febrile children with respiratory tract symptoms and age-matched controls, Ghana

    Directory of Open Access Journals (Sweden)

    H. Bühl

    2018-03-01

    Full Text Available Members of the Chlamydiales order are obligate intracellular pathogens causing acute and chronic infectious diseases. Chlamydiaceae are established agents of community- and zoonotically acquired respiratory tract infections, and emerging pathogens among the Chlamydia-related bacteria have been implicated in airway infections. The role of both in airway infections in Africa is underexplored. We performed a case -control study on the prevalence of Chlamydiaceae and Chlamydia-related emerging pathogens in children with febrile respiratory tract infections in West Africa, Ghana. Using a pan-Chlamydiales broad-range real-time PCR, we detected chlamydial DNA in 11 (1.9% of 572 hospitalized febrile children with respiratory tract symptoms and in 24 (4.3% of 560 asymptomatic age-matched controls (p 0.03. Chlamydiaceae were found to be common among both symptomatic and healthy Ghanaian children, with Chlamydia pneumoniae being the most prevalent species. Parachlamydiaceae were detected in two children without symptoms but not in the symptomatic group. We identified neither Chlamydia psittaci nor Simkania negevensis but a member of a new chlamydial family that shared 90.2% sequence identity with the 16S rRNA gene of the zoonotic pathogen Chlamydia pecorum. In addition, we found a new Chlamydia-related species that belonged to a novel family sharing 91.3% 16S rRNA sequence identity with Candidatus Syngnamydia venezia. The prevalence and spectrum of chlamydial species differed from previous results obtained from children of other geographic regions and our study indicates that both, Chlamydiaceae and Chlamydia-related bacteria, are not clearly linked to clinical symptoms in Ghanaian children. Keywords: Children, Chlamydia, Chlamydia-related bacteria, febrile respiratory tract infection, Ghana

  9. Flow cytometry as an improved method for the titration of Chlamydiaceae and other intracellular bacteria.

    Science.gov (United States)

    Käser, T; Pasternak, J A; Hamonic, G; Rieder, M; Lai, K; Delgado-Ortega, M; Gerdts, V; Meurens, F

    2016-05-01

    Chlamydiaceae is a family of intracellular bacteria causing a range of diverse pathological outcomes. The most devastating human diseases are ocular infections with C. trachomatis leading to blindness and genital infections causing pelvic inflammatory disease with long-term sequelae including infertility and chronic pelvic pain. In order to enable the comparison of experiments between laboratories investigating host-chlamydia interactions, the infectious titer has to be determined. Titer determination of chlamydia is most commonly performed via microscopy of host cells infected with a serial dilution of chlamydia. However, other methods including fluorescent ELISpot (Fluorospot) and DNA Chip Scanning Technology have also been proposed to enumerate chlamydia-infected cells. For viruses, flow cytometry has been suggested as a superior alternative to standard titration methods. In this study we compared the use of flow cytometry with microscopy and Fluorospot for the titration of C. suis as a representative of other intracellular bacteria. Titer determination via Fluorospot was unreliable, while titration via microscopy led to a linear read-out range of 16 - 64 dilutions and moderate reproducibility with acceptable standard deviations within and between investigators. In contrast, flow cytometry had a vast linear read-out range of 1,024 dilutions and the lowest standard deviations given a basic training in these methods. In addition, flow cytometry was faster and material costs were lower compared to microscopy. Flow cytometry offers a fast, cheap, precise, and reproducible alternative for the titration of intracellular bacteria like C. suis. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

  10. Optimal Foraging for Multiple Resources in Several Food Species

    NARCIS (Netherlands)

    Hengeveld, G.M.; Langevelde, van F.; Groen, T.A.; Knegt, de H.J.

    2009-01-01

    The concentrations of resources in forage are not perfectly balanced to the needs of an animal, and food species differ in these concentrations. Under many circumstances, animals should thus forage on multiple food species to attain the maximum and most balanced intake of several resources. In this

  11. Optimal foraging for multiple resources in several food species

    NARCIS (Netherlands)

    Hengeveld, G.M.; van Langevelde, F.; Groen, T.A.; de Knegt, H.J.

    2009-01-01

    The concentrations of resources in forage are not perfectly balanced to the needs of an animal, and food species differ in these concentrations. Under many circumstances, animals should thus forage on multiple food species to attain the maximum and most balanced intake of several resources. In this

  12. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    . aeruginosa were found to be significantly larger than ulcers without the presence of P. aeruginosa (P wound is colonised by multiple bacterial species and that once they are established many of them persist in the wound. Our results suggest that the presence...... of P. aeruginosa in venous leg ulcers can induce ulcer enlargement and/or cause delayed healing....

  13. Influence of predator density on nonindependent effects of multiple predator species.

    Science.gov (United States)

    Griffen, Blaine D; Williamson, Tucker

    2008-02-01

    Interactions between multiple predator species are frequent in natural communities and can have important implications for shared prey survival. Predator density may be an important component of these interactions between predator species, as the frequency of interactions between species is largely determined by species density. Here we experimentally examine the importance of predator density for interactions between predator species and subsequent impacts on prey. We show that aggressive interactions between the predatory shore crabs Carcinus maenas and Hemigrapsus sanguineus increased with predator density, yet did not increase as fast as negative interactions between conspecifics. At low density, interactions between conspecific and heterospecific predators had similar inhibitory impacts on predator function, whereas conspecific interference was greater than interference from heterospecifics at high predator density. Thus the impact of conspecific interference at high predator density was sufficient in itself that interactions with a second predator species had no additional impact on per capita predation. Spatial and temporal variability in predator density is a ubiquitous characteristic of natural systems that should be considered in studies of multiple predator species.

  14. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

    Science.gov (United States)

    Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

    2015-09-15

    There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

  15. Identification of Phylogenetic Position in the Chlamydiaceae Family for Chlamydia Strains Released from Monkeys and Humans with Chlamydial Pathology

    Directory of Open Access Journals (Sweden)

    Alexander Karaulov

    2010-01-01

    Full Text Available Based on the results of the comparative analysis concerning relatedness and evolutional difference of the 16S–23S nucleotide sequences of the middle ribosomal cluster and 23S rRNA I domain, and based on identification of phylogenetic position for Chlamydophila pneumoniae and Chlamydia trichomatis strains released from monkeys, relatedness of the above stated isolates with similar strains released from humans and with strains having nucleotide sequences presented in the GenBank electronic database has been detected for the first time ever. Position of these isolates in the Chlamydiaceae family phylogenetic tree has been identified. The evolutional position of the investigated original Chlamydia and Chlamydophila strains close to analogous strains from the Gen-Bank electronic database has been demonstrated. Differences in the 16S–23S nucleotide sequence of the middle ribosomal cluster and 23S rRNA I domain of plasmid and nonplasmid Chlamydia trachomatis strains released from humans and monkeys relative to different genotype groups (group B-B, Ba, D, Da, E, L1, L2, L2a; intermediate group-F, G, Ga have been revealed for the first time ever. Abnormality in incA chromosomal gene expression resulting in Chlamydia life development cycle disorder, and decrease of Chlamydia virulence can be related to probable changes in the nucleotide sequence of the gene under consideration

  16. Selection of multiple umbrella species for functional and taxonomic diversity to represent urban biodiversity.

    Science.gov (United States)

    Sattler, T; Pezzatti, G B; Nobis, M P; Obrist, M K; Roth, T; Moretti, M

    2014-04-01

    Surrogates, such as umbrella species, are commonly used to reduce the complexity of quantifying biodiversity for conservation purposes. The presence of umbrella species is often indicative of high taxonomic diversity; however, functional diversity is now recognized as an important metric for biodiversity and thus should be considered when choosing umbrella species. We identified umbrella species associated with high taxonomic and functional biodiversity in urban areas in Switzerland. We analyzed 39,752 individuals of 574 animal species from 96 study plots and 1397 presences of 262 plant species from 58 plots. Thirty-one biodiversity measures of 7 taxonomic groups (plants, spiders, bees, ground beetles, lady bugs, weevils and birds) were included in within- and across-taxa analyses. Sixteen measures were taxonomical (species richness and species diversity), whereas 15 were functional (species traits including mobility, resource use, and reproduction). We used indicator value analysis to identify umbrella species associated with single or multiple biodiversity measures. Many umbrella species were indicators of high biodiversity within their own taxonomic group (from 33.3% in weevils to 93.8% in birds), to a lesser extent they were indicators across taxa. Principal component analysis revealed that umbrella species for multiple measures of biodiversity represented different aspects of biodiversity, especially with respect to measures of taxonomic and functional diversity. Thus, even umbrella species for multiple measures of biodiversity were complementary in the biodiversity aspects they represented. Thus, the choice of umbrella species based solely on taxonomic diversity is questionable and may not represent biodiversity comprehensively. Our results suggest that, depending on conservation priorities, managers should choose multiple and complementary umbrella species to assess the state of biodiversity. © 2013 Society for Conservation Biology.

  17. Diffusion of multiple species with excluded-volume effects

    KAUST Repository

    Bruna, Maria; Chapman, S. Jonathan

    2012-01-01

    Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results. © 2012 American Institute of Physics.

  18. Effects of biotic interactions and dispersal on the presence-absence of multiple species

    International Nuclear Information System (INIS)

    Mohd, Mohd Hafiz; Murray, Rua; Plank, Michael J.; Godsoe, William

    2017-01-01

    One of the important issues in ecology is to predict which species will be present (or absent) across a geographical region. Dispersal is thought to have an important influence on the range limits of species, and understanding this problem in a multi-species community with priority effects (i.e. initial abundances determine species presence-absence) is a challenging task because dispersal also interacts with biotic and abiotic factors. Here, we propose a simple multi-species model to investigate the joint effects of biotic interactions and dispersal on species presence-absence. Our results show that dispersal can substantially expand species ranges when biotic and abiotic forces are present; consequently, coexistence of multiple species is possible. The model also exhibits ecologically interesting priority effects, mediated by intense biotic interactions. In the absence of dispersal, competitive exclusion of all but one species occurs. We find that dispersal reduces competitive exclusion effects that occur in no-dispersal case and promotes coexistence of multiple species. These results also show that priority effects are still prevalent in multi-species communities in the presence of dispersal process. We also illustrate the existence of threshold values of competitive strength (i.e. transcritical bifurcations), which results in different species presence-absence in multi-species communities with and without dispersal.

  19. Defining hotspots of characteristic species for multiple taxonomic groups in the Netherlands

    NARCIS (Netherlands)

    Schouten, M.A.; Barendregt, A.; Verweij, P.A.; Kalkman, V.J.; Kleukers, R.J.M.C.; Lenders, H.J.R.; Siebel, H.N.

    2010-01-01

    Biogeographical zonation based on single taxa poses major limitations on planning for nature conservation. This paper identifies biogeographical patterns of multiple taxa in the Netherlands, where no endemics are present at species level, on the basis of characteristic species. We used occurrence

  20. Molecular evidence for high frequency of multiple paternity in a freshwater shrimp species Caridina ensifera.

    Directory of Open Access Journals (Sweden)

    Gen Hua Yue

    2010-09-01

    Full Text Available Molecular genetic analyses of parentage provide insights into mating systems. Although there are 22,000 members in Malacostraca, not much has been known about mating systems in Malacostraca. The freshwater shrimp Caridina ensifera blue, is a new species belonging to Malacostraca which was discovered recently in Sulawesi, Indonesia. Due to its small body size and low fecundity, this species is an ideal species to study the occurrence and frequency of multiple paternity and to understand of how the low fecundity species persist and evolve.In this study, we developed four polymorphic microsatellites from C. ensifera and applied them to investigate the occurrence and frequency of multiple paternity in 20 C. ensifera broods caught from Lake Matano, Sulawesi. By genotyping the mother and all offspring from each brood we discovered multiple paternity in all 20 broods. In most of the 20 broods, fathers contributed skewed numbers of offspring and there was an apparent inverse correlation between reproductive success of sires and their relatedness to mothers.Our results in combination with recent reports on multiple paternity in crayfish, crab and lobster species suggests that multiple paternity is common in Malacostraca. Skewed contribution of fathers to the numbers of offspring and inverse correlation between reproductive success of sires and their relatedness to mothers suggest that sperm competition occurred and/or pre- and postcopulatory female choice happen, which may be important for avoiding the occurrence of inbreeding and optimize genetic variation in offspring and for persistence and evolution of low fecundity species.

  1. Blends of Pheromones, With and Without Host Plant Volatiles, Can Attract Multiple Species of Cerambycid Beetles Simultaneously

    Science.gov (United States)

    L.M. Hanks; J.A. Mongold-Diers; T.H. Atkinson; M.K. Fierke; M.D. Ginzel; E.E. Graham; T.M. Poland; A.B. Richards; M.L. Richardson; J.G. Millar

    2018-01-01

    Pheromone components of cerambycid beetles are often conserved, with a given compound serving as a pheromone component for multiple related species, including species native to different continents. Consequently, a single synthesized compound may attract multiple species to a trap simultaneously. Furthermore, our previous research in east-central Illinois had...

  2. Mapping habitat for multiple species in the Desert Southwest

    Science.gov (United States)

    Inman, Richard D.; Nussear, Kenneth E.; Esque, Todd C.; Vandergast, Amy G.; Hathaway, Stacie A.; Wood, Dustin A.; Barr, Kelly R.; Fisher, Robert N.

    2014-01-01

    Many utility scale renewable energy projects are currently proposed across the Mojave Ecoregion. Agencies that manage biological resources throughout this region need to understand the potential impacts of these renewable energy projects and their associated infrastructure (for example, transmission corridors, substations, access roads, etc.) on species movement, genetic exchange among populations, and species’ abilities to adapt to changing environmental conditions. Understanding these factors will help managers’ select appropriate project sites and possibly mitigate for anticipated effects of management activities. We used species distribution models to map habitat for 15 species across the Mojave Ecoregion to aid regional land-use management planning. Models were developed using a common 1 × 1 kilometer resolution with maximum entropy and generalized additive models. Occurrence data were compiled from multiple sources, including VertNet (http://vertnet.org/), HerpNET (http://www.herpnet.org), and MaNIS (http://manisnet.org), as well as from internal U.S. Geological Survey databases and other biologists. Background data included 20 environmental covariates representing terrain, vegetation, and climate covariates. This report summarizes these environmental covariates and species distribution models used to predict habitat for the 15 species across the Mojave Ecoregion.

  3. Where and how to manage: optimal selection of conservation actions for multiple species

    NARCIS (Netherlands)

    Teeffelen, van A.J.A.; Moilanen, A.

    2008-01-01

    Multiple alternative options are frequently available for the protection, maintenance or restoration of conservation areas. The choice of a particular management action can have large effects on the species occurring in the area, because different actions have different effects on different species.

  4. Whole genome phylogenies for multiple Drosophila species

    Directory of Open Access Journals (Sweden)

    Seetharam Arun

    2012-12-01

    Full Text Available Abstract Background Reconstructing the evolutionary history of organisms using traditional phylogenetic methods may suffer from inaccurate sequence alignment. An alternative approach, particularly effective when whole genome sequences are available, is to employ methods that don’t use explicit sequence alignments. We extend a novel phylogenetic method based on Singular Value Decomposition (SVD to reconstruct the phylogeny of 12 sequenced Drosophila species. SVD analysis provides accurate comparisons for a high fraction of sequences within whole genomes without the prior identification of orthologs or homologous sites. With this method all protein sequences are converted to peptide frequency vectors within a matrix that is decomposed to provide simplified vector representations for each protein of the genome in a reduced dimensional space. These vectors are summed together to provide a vector representation for each species, and the angle between these vectors provides distance measures that are used to construct species trees. Results An unfiltered whole genome analysis (193,622 predicted proteins strongly supports the currently accepted phylogeny for 12 Drosophila species at higher dimensions except for the generally accepted but difficult to discern sister relationship between D. erecta and D. yakuba. Also, in accordance with previous studies, many sequences appear to support alternative phylogenies. In this case, we observed grouping of D. erecta with D. sechellia when approximately 55% to 95% of the proteins were removed using a filter based on projection values or by reducing resolution by using fewer dimensions. Similar results were obtained when just the melanogaster subgroup was analyzed. Conclusions These results indicate that using our novel phylogenetic method, it is possible to consult and interpret all predicted protein sequences within multiple whole genomes to produce accurate phylogenetic estimations of relatedness between

  5. Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L. Moench and related model species.

    Directory of Open Access Journals (Sweden)

    Adugna Abdi Woldesemayat

    Full Text Available Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations.In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO, Trait Ontology (TO, Plant Ontology (PO, Growth Ontology (GRO and Environment Ontology (EO were used to semantically integrate drought related information.Target genes linked to Quantitative Trait Loci (QTLs controlling yield and stress tolerance in sorghum (Sorghum bicolor (L. Moench and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%, salt (32%, cold (20%, heat (8% and oxidative stress (25% were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs

  6. Where and how to manage: Optimal selection of conservation actions for multiple species.

    Directory of Open Access Journals (Sweden)

    Astrid van Teeffelen

    2008-01-01

    Full Text Available Multiple alternative options are frequently available for the protection, maintenance or restoration of conservation areas. The choice of a particular management action can have large effects on the species occurring in the area, because different actions have different effects on different species. Together with the fact that conservation funds are limited and particular management actions are costly, it would be desirable to be able to identify where, and what kind of management should be applied to maximize conservation benefits. Currently available site-selection algorithms can identify the optimal set of sites for a reserve network. However, these algorithms have not been designed to answer what kind of action would be most beneficial at these sites when multiple alternative actions are available. We describe an algorithm capable of solving multi-species planning problems with multiple management options per site. The algorithm is based on benefit functions, which translate the effect of a management action on species representation levels into a value, in order to identify the most beneficial option. We test the performance of this algorithm with simulated data for different types of benefit functions and show that the algorithm’s solutions are optimal, or very near globally optimal, partially depending on the type of benefit function used. The good performance of the proposed algorithm suggests that it could be profitably used for large multi-action multi-species conservation planning problems.

  7. New and emerging chlamydial infections of creatures great and small

    Directory of Open Access Journals (Sweden)

    A. Taylor-Brown

    2017-07-01

    Full Text Available Until recently, our knowledge of the host range and diversity of members of the Chlamydiaceae, obligate intracellular bacterial pathogens of humans and animals, was thought to be nearly complete. Aided by advances in molecular diagnostics, a new picture is emerging, however, that the host barriers may be looser than previously thought for many chlamydial species. While cross-host transmission of chlamydial species is a concern for animal health, new reports highlight an emerging zoonotic risk for several species associated with intensification of farming and the widespread popularity of companion animals. The description of an expanded cohort of new species within this family from avian and reptilian hosts has also highlighted how much we still have to learn about the biology and pathogenicity of the Chlamydiaceae as a whole. Reports emerging about these relatives of the traditional chlamydial pathogens are matched by the continued identification of novel Chlamydia-related bacteria in the phylum Chlamydiae, providing evidence that many may be pathogenic to humans or animals and pose a zoonotic or vector-borne risk. The review examines the new hosts described for well-characterized chlamydial veterinary pathogens, emerging novel chlamydial species and the potential for these to cause disease in their respective hosts.

  8. Genetic components to caste allocation in a multiple-queen ant species

    NARCIS (Netherlands)

    Libbrecht, Romain; Schwander, Tanja; Keller, Laurent

    2011-01-01

    Reproductive division of labor and the coexistence of distinct castes are hallmarks of insect societies. In social insect species with multiple queens per colony, the fitness of nestmate queens directly depends on the process of caste allocation (i.e., the relative investment in queen, sterile

  9. CARS Spectral Fitting with Multiple Resonant Species using Sparse Libraries

    Science.gov (United States)

    Cutler, Andrew D.; Magnotti, Gaetano

    2010-01-01

    The dual pump CARS technique is often used in the study of turbulent flames. Fast and accurate algorithms are needed for fitting dual-pump CARS spectra for temperature and multiple chemical species. This paper describes the development of such an algorithm. The algorithm employs sparse libraries, whose size grows much more slowly with number of species than a conventional library. The method was demonstrated by fitting synthetic "experimental" spectra containing 4 resonant species (N2, O2, H2 and CO2), both with noise and without it, and by fitting experimental spectra from a H2-air flame produced by a Hencken burner. In both studies, weighted least squares fitting of signal, as opposed to least squares fitting signal or square-root signal, was shown to produce the least random error and minimize bias error in the fitted parameters.

  10. Phylogenetic analysis reveals multiple introductions of Cynodon species in Australia.

    Science.gov (United States)

    Jewell, M; Frère, C H; Harris-Shultz, K; Anderson, W F; Godwin, I D; Lambrides, C J

    2012-11-01

    The distinction between native and introduced flora within isolated land masses presents unique challenges. The geological and colonisation history of Australia, the world's largest island, makes it a valuable system for studying species endemism, introduction, and phylogeny. Using this strategy we investigated Australian cosmopolitan grasses belonging to the genus Cynodon. While it is believed that seven species of Cynodon are present in Australia, no genetic analyses have investigated the origin, diversity and phylogenetic history of Cynodon within Australia. To address this gap, 147 samples (92 from across Australia and 55 representing global distribution) were sequenced for a total of 3336bp of chloroplast DNA spanning six genes. Data showed the presence of at least six putatively introduced Cynodon species (C. transvaalensis, C. incompletus, C. hirsutus, C. radiatus, C. plectostachyus and C. dactylon) in Australia and suggested multiple recent introductions. C. plectostachyus, a species often confused with C. nlemfuensis, was not previously considered to be present in Australia. Most significantly, we identified two common haplotypes that formed a monophyletic clade diverging from previously identified Cynodon species. We hypothesise that these two haplotypes may represent a previously undescribed species of Cynodon. We provide further evidence that two Australian native species, Brachyachne tenella and B. convergens belong in the genus Cynodon and, therefore, argue for the taxonomic revision of the genus Cynodon. Copyright © 2012 Elsevier Inc. All rights reserved.

  11. Prevalence of Chlamydial Infections in Fattening Pigs and Their Influencing Factors.

    Directory of Open Access Journals (Sweden)

    Karolin Hoffmann

    Full Text Available Chlamydial infections in pigs are associated with respiratory disease, diarrhea, conjunctivitis and other pathologies. The aim of this study was to define the prevalence of Chlamydiaceae in Swiss fattening pigs by applying sensitive and specific detection methods and to correlate prior antibiotic treatment and farm related factors with differences in prevalence. Conjunctival and fecal swabs were collected from 636 pigs in 29 Swiss fattening pig farms with and without antibiotic treatment, at the beginning and the end of the fattening period. The swabs were screened by real-time PCR for Chlamydiaceae. For the chlamydial detection and species-identification, a DNA-microarray analysis was performed. All farms were positive for Chlamydiaceae with 94.3 and 92.0% prevalence in fecal swabs as well as 45.9 and 32.6% in conjunctival swabs at the first and second time points, respectively. Antibiotic treatment could not clear the infection on herd level. Potential contact with wild boars was a significant risk factor, while hygiene criteria did not influence chlamydial prevalence. A correlation of chlamydial positivity to diarrhea, but not to conjunctivitis was evident. Chlamydia suis was the predominant species. Mixed infections with C. suis and C. pecorum were common, with a substantial increase in C. pecorum positivity at the end of the fattening period, and this finding was associated with ruminant contact. C. abortus was detected in one conjunctival swab. In this study, C. suis inhabited the intestinal tract of nearly all examined pigs, implying a long-term infection. C. pecorum was also common and might be transmitted to pigs by ruminants.

  12. Prevalence of Chlamydial Infections in Fattening Pigs and Their Influencing Factors

    Science.gov (United States)

    Hoffmann, Karolin; Schott, Franziska; Donati, Manuela; Di Francesco, Antonietta; Hässig, Michael; Wanninger, Sabrina; Sidler, Xaver; Borel, Nicole

    2015-01-01

    Chlamydial infections in pigs are associated with respiratory disease, diarrhea, conjunctivitis and other pathologies. The aim of this study was to define the prevalence of Chlamydiaceae in Swiss fattening pigs by applying sensitive and specific detection methods and to correlate prior antibiotic treatment and farm related factors with differences in prevalence. Conjunctival and fecal swabs were collected from 636 pigs in 29 Swiss fattening pig farms with and without antibiotic treatment, at the beginning and the end of the fattening period. The swabs were screened by real-time PCR for Chlamydiaceae. For the chlamydial detection and species-identification, a DNA-microarray analysis was performed. All farms were positive for Chlamydiaceae with 94.3 and 92.0% prevalence in fecal swabs as well as 45.9 and 32.6% in conjunctival swabs at the first and second time points, respectively. Antibiotic treatment could not clear the infection on herd level. Potential contact with wild boars was a significant risk factor, while hygiene criteria did not influence chlamydial prevalence. A correlation of chlamydial positivity to diarrhea, but not to conjunctivitis was evident. Chlamydia suis was the predominant species. Mixed infections with C. suis and C. pecorum were common, with a substantial increase in C. pecorum positivity at the end of the fattening period, and this finding was associated with ruminant contact. C. abortus was detected in one conjunctival swab. In this study, C. suis inhabited the intestinal tract of nearly all examined pigs, implying a long-term infection. C. pecorum was also common and might be transmitted to pigs by ruminants. PMID:26619187

  13. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species

    Directory of Open Access Journals (Sweden)

    Messeguer Xavier

    2006-10-01

    Full Text Available Abstract Background Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic sequencing projects. This increase in related genomic data will allow for in depth studies of evolution in closely related species through multiple whole genome comparisons. Results To facilitate such comparisons, we present an interactive multiple genome comparison and alignment tool, M-GCAT, that can efficiently construct multiple genome comparison frameworks in closely related species. M-GCAT is able to compare and identify highly conserved regions in up to 20 closely related bacterial species in minutes on a standard computer, and as many as 90 (containing 75 cloned genomes from a set of 15 published enterobacterial genomes in an hour. M-GCAT also incorporates a novel comparative genomics data visualization interface allowing the user to globally and locally examine and inspect the conserved regions and gene annotations. Conclusion M-GCAT is an interactive comparative genomics tool well suited for quickly generating multiple genome comparisons frameworks and alignments among closely related species. M-GCAT is freely available for download for academic and non-commercial use at: http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html.

  14. Characterization of serine hydroxymethyltransferase GlyA as a potential source of D-alanine in Chlamydia pneumoniae.

    Science.gov (United States)

    De Benedetti, Stefania; Bühl, Henrike; Gaballah, Ahmed; Klöckner, Anna; Otten, Christian; Schneider, Tanja; Sahl, Hans-Georg; Henrichfreise, Beate

    2014-01-01

    For intracellular Chlamydiaceae, there is no need to withstand osmotic challenges, and a functional cell wall has not been detected in these pathogens so far. Nevertheless, penicillin inhibits cell division in Chlamydiaceae resulting in enlarged aberrant bodies, a phenomenon known as chlamydial anomaly. D-alanine is a unique and essential component in the biosynthesis of bacterial cell walls. In free-living bacteria like Escherichia coli, penicillin-binding proteins such as monofunctional transpeptidases PBP2 and PBP3, the putative targets of penicillin in Chlamydiaceae, cross-link adjacent peptidoglycan strands via meso-diaminopimelic acid and D-Ala-D-Ala moieties of pentapeptide side chains. In the absence of genes coding for alanine racemase Alr and DadX homologs, the source of D-Ala and thus the presence of substrates for PBP2 and PBP3 activity in Chlamydiaceae has puzzled researchers for years. Interestingly, Chlamydiaceae genomes encode GlyA, a serine hydroxymethyltransferase that has been shown to exhibit slow racemization of D- and L-alanine as a side reaction in E. coli. We show that GlyA from Chlamydia pneumoniae can serve as a source of D-Ala. GlyA partially reversed the D-Ala auxotrophic phenotype of an E. coli racemase double mutant. Moreover, purified chlamydial GlyA had racemase activity on L-Ala in vitro and was inhibited by D-cycloserine, identifying GlyA, besides D-Ala ligase MurC/Ddl, as an additional target of this competitive inhibitor in Chlamydiaceae. Proof of D-Ala biosynthesis in Chlamydiaceae helps to clarify the structure of cell wall precursor lipid II and the role of chlamydial penicillin-binding proteins in the development of non-dividing aberrant chlamydial bodies and persistence in the presence of penicillin.

  15. Characterization of serine hydroxymethyltransferase GlyA as a potential source of D-alanine in Chlamydia pneumoniae

    Directory of Open Access Journals (Sweden)

    Stefania eDe Benedetti

    2014-02-01

    Full Text Available For intracellular Chlamydiaceae, there is no need to withstand osmotic challenges, and a functional cell wall has not been detected in these pathogens so far. Nevertheless, penicillin inhibits cell division in Chlamydiaceae resulting in enlarged aberrant bodies, a phenomenon known as chlamydial anomaly.D-alanine is a unique and essential component in the biosynthesis of bacterial cell walls. In free-living bacteria like Escherichia coli, penicillin-binding proteins such as monofunctional transpeptidases PBP2 and PBP3, the putative targets of penicillin in Chlamydiaceae, cross-link adjacent peptidoglycan strands via meso-diaminopimelic acid and D-Ala-D-Ala moieties of pentapeptide side chains. In the absence of genes coding for alanine racemase Alr and DadX homologs, the source of D-Ala and thus the presence of substrates for PBP2 and PBP3 activity in Chlamydiaceae has puzzled researchers for years. Interestingly, Chlamydiaceae genomes encode GlyA, a serine hydroxymethyltransferase that has been shown to exhibit slow racemization of D- and L- alanine as a side reaction in E. coli. We show that GlyA from Chlamydia pneumoniae can serve as a source of D-Ala. GlyA partially reversed the D-Ala auxotrophic phenotype of an E. coli racemase double mutant. Moreover, purified chlamydial GlyA had racemase activity on L-Ala in vitro and was inhibited by D-cycloserine, identifying GlyA, besides D-Ala ligase MurC/Ddl, as an additional target of this competitive inhibitor in Chlamydiaceae. Proof of D-Ala biosynthesis in Chlamydiaceae helps to clarify the structure of cell wall precursor lipid II and the role of chlamydial penicillin-binding proteins in the development of non-dividing aberrant chlamydial bodies and persistence in the presence of penicillin.

  16. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterization of currently unrecognized taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 573 cox1 sequences from 110 currently recognized species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognized taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g., morphology, life history, ecology) are necessary before any taxonomic changes are formalized.

  17. Multiple endmember spectral-angle-mapper (SAM) analysis improves discrimination of Savanna tree species

    CSIR Research Space (South Africa)

    Cho, Moses A

    2009-08-01

    Full Text Available of this paper was to evaluate the classification performance of a multiple-endmember spectral angle mapper (SAM) classification approach in discriminating seven common African savanna tree species and to compare the results with the traditional SAM classifier...

  18. The Pleurobemini (Bivalvia: Unionida) revisited: Molecular species delineation using a mitochondrial DNA gene reveals multiple conspecifics and undescribed species

    Science.gov (United States)

    Inoue, Kentaro; Hayes, David M.; Harris, John L.; Johnson, Nathan A.; Morrison, Cheryl L.; Eackles, Michael S.; King, Tim; Jones, Jess W.; Hallerman, Eric M.; Christian, Alan D.; Randklev, Charles R.

    2018-01-01

    The Pleurobemini (Bivalvia: Unionida) represent approximately one-third of freshwater mussel diversity in North America. Species identification within this group is challenging due to morphological convergence and phenotypic plasticity. Accurate species identification, including characterisation of currently unrecognised taxa, is required to develop effective conservation strategies because many species in the group are imperiled. We examined 575 cox1 sequences from 110 currently recognised species (including 13 Fusconaia and 21 Pleurobema species) to understand phylogenetic relationships among pleurobemine species (mainly Fusconaia and Pleurobema) and to delineate species boundaries. The results of phylogenetic analyses showed no geographic structure within widespread species and illustrated a close relationship between Elliptio lanceolata and Parvaspina collina. Constraint tests supported monophyly of the genera Fusconaia and Pleurobema, including the subgenus P. (Sintoxia). Furthermore, results revealed multiple conspecifics, including P. hanleyianum and P. troschelianum, P. chattanoogaense and P. decisum, P. clava and P. oviforme, P. rubrum and P. sintoxia, F. askewi and F. lananensis, and F. cerina and F. flava. Species delimitation analyses identified three currently unrecognised taxa (two in Fusconaia and one in Pleurobema). Further investigation using additional genetic markers and other lines of evidence (e.g. morphology, life history, ecology) are necessary before any taxonomic changes are formalised.

  19. Bayesian estimation applied to multiple species

    International Nuclear Information System (INIS)

    Kunz, Martin; Bassett, Bruce A.; Hlozek, Renee A.

    2007-01-01

    Observed data are often contaminated by undiscovered interlopers, leading to biased parameter estimation. Here we present BEAMS (Bayesian estimation applied to multiple species) which significantly improves on the standard maximum likelihood approach in the case where the probability for each data point being ''pure'' is known. We discuss the application of BEAMS to future type-Ia supernovae (SNIa) surveys, such as LSST, which are projected to deliver over a million supernovae light curves without spectra. The multiband light curves for each candidate will provide a probability of being Ia (pure) but the full sample will be significantly contaminated with other types of supernovae and transients. Given a sample of N supernovae with mean probability, , of being Ia, BEAMS delivers parameter constraints equal to N spectroscopically confirmed SNIa. In addition BEAMS can be simultaneously used to tease apart different families of data and to recover properties of the underlying distributions of those families (e.g. the type-Ibc and II distributions). Hence BEAMS provides a unified classification and parameter estimation methodology which may be useful in a diverse range of problems such as photometric redshift estimation or, indeed, any parameter estimation problem where contamination is an issue

  20. Lepidopteran larva consumption of soybean foliage: basis for developing multiple-species economic thresholds for pest management decisions.

    Science.gov (United States)

    Bueno, Regiane Cristina Oliveira de Freitas; Bueno, Adeney de Freitas; Moscardi, Flávio; Parra, José Roberto Postali; Hoffmann-Campo, Clara Beatriz

    2011-02-01

    Defoliation by Anticarsia gemmatalis (Hübner), Pseudoplusia includens (Walker), Spodoptera eridania (Cramer), S. cosmioides (Walker) and S. frugiperda (JE Smith) (Lepidoptera: Noctuidae) was evaluated in four soybean genotypes. A multiple-species economic threshold (ET), based upon the species' feeding capacity, is proposed with the aim of improving growers' management decisions on when to initiate control measures for the species complex. Consumption by A. gemmatalis, S. cosmioides or S. eridania on different genotypes was similar. The highest consumption of P. includens was 92.7 cm(2) on Codetec 219RR; that of S. frugiperda was 118 cm(2) on Codetec 219RR and 115.1 cm(2) on MSoy 8787RR. The insect injury equivalent for S. cosmoides, calculated on the basis of insect consumption, was double the standard consumption by A. gemmatalis, and statistically different from the other species tested, which were similar to each other. As S. cosmioides always defoliated nearly twice the leaf area of the other species, the injury equivalent would be 2 for this lepidopteran species and 1 for the other species. The recommended multiple-species ET to trigger the beginning of insect control would then be 20 insect equivalents per linear metre. Copyright © 2010 Society of Chemical Industry.

  1. Recombination in liquid filled ionisation chambers with multiple charge carrier species: Theoretical and numerical results

    International Nuclear Information System (INIS)

    Aguiar, P.; González-Castaño, D.M.; Gómez, F.; Pardo-Montero, J.

    2014-01-01

    Liquid-filled ionisation chambers (LICs) are used in radiotherapy for dosimetry and quality assurance. Volume recombination can be quite important in LICs for moderate dose rates, causing non-linearities in the dose rate response of these detectors, and needs to be corrected for. This effect is usually described with Greening and Boag models for continuous and pulsed radiation respectively. Such models assume that the charge is carried by two different species, positive and negative ions, each of those species with a given mobility. However, LICs operating in non-ultrapure mode can contain different types of electronegative impurities with different mobilities, thus increasing the number of different charge carriers. If this is the case, Greening and Boag models can be no longer valid and need to be reformulated. In this work we present a theoretical and numerical study of volume recombination in parallel-plate LICs with multiple charge carrier species, extending Boag and Greening models. Results from a recent publication that reported three different mobilities in an isooctane-filled LIC have been used to study the effect of extra carrier species on recombination. We have found that in pulsed beams the inclusion of extra mobilities does not affect volume recombination much, a behaviour that was expected because Boag formula for charge collection efficiency does not depend on the mobilities of the charge carriers if the Debye relationship between mobilities and recombination constant holds. This is not the case in continuous radiation, where the presence of extra charge carrier species significantly affects the amount of volume recombination. - Highlights: • Analytical extension of Greening and Boag theories to multiple charge carriers. • Detailed numerical study of process of volume recombination in LICs. • Recombination in pulsed beams is independent of number and mobilities of carriers. • Multiple charge carriers have a significant effect in continuous

  2. Low genetic diversity despite multiple introductions of the invasive plant species Impatiens glandulifera in Europe.

    Science.gov (United States)

    Hagenblad, Jenny; Hülskötter, Jennifer; Acharya, Kamal Prasad; Brunet, Jörg; Chabrerie, Olivier; Cousins, Sara A O; Dar, Pervaiz A; Diekmann, Martin; De Frenne, Pieter; Hermy, Martin; Jamoneau, Aurélien; Kolb, Annette; Lemke, Isgard; Plue, Jan; Reshi, Zafar A; Graae, Bente Jessen

    2015-08-20

    Invasive species can be a major threat to native biodiversity and the number of invasive plant species is increasing across the globe. Population genetic studies of invasive species can provide key insights into their invasion history and ensuing evolution, but also for their control. Here we genetically characterise populations of Impatiens glandulifera, an invasive plant in Europe that can have a major impact on native plant communities. We compared populations from the species' native range in Kashmir, India, to those in its invaded range, along a latitudinal gradient in Europe. For comparison, the results from 39 other studies of genetic diversity in invasive species were collated. Our results suggest that I. glandulifera was established in the wild in Europe at least twice, from an area outside of our Kashmir study area. Our results further revealed that the genetic diversity in invasive populations of I. glandulifera is unusually low compared to native populations, in particular when compared to other invasive species. Genetic drift rather than mutation seems to have played a role in differentiating populations in Europe. We find evidence of limitations to local gene flow after introduction to Europe, but somewhat less restrictions in the native range. I. glandulifera populations with significant inbreeding were only found in the species' native range and invasive species in general showed no increase in inbreeding upon leaving their native ranges. In Europe we detect cases of migration between distantly located populations. Human activities therefore seem to, at least partially, have facilitated not only introductions, but also further spread of I. glandulifera across Europe. Although multiple introductions will facilitate the retention of genetic diversity in invasive ranges, widespread invasive species can remain genetically relatively invariant also after multiple introductions. Phenotypic plasticity may therefore be an important component of the

  3. Using AVIRIS data and multiple-masking techniques to map urban forest trees species

    Science.gov (United States)

    Q. Xiao; S.L. Ustin; E.G. McPherson

    2004-01-01

    Tree type and species information are critical parameters for urban forest management, benefit cost analysis and urban planning. However, traditionally, these parameters have been derived based on limited field samples in urban forest management practice. In this study we used high-resolution Airborne Visible Infrared Imaging Spectrometer (AVIRIS) data and multiple-...

  4. Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

    Science.gov (United States)

    Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

    2016-11-01

    It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

  5. Electron tomography and cryo-SEM characterization reveals novel ultrastructural features of host-parasite interaction during Chlamydia abortus infection.

    Science.gov (United States)

    Wilkat, M; Herdoiza, E; Forsbach-Birk, V; Walther, P; Essig, A

    2014-08-01

    Chlamydia (C.) abortus is a widely spread pathogen among ruminants that can be transmitted to women during pregnancy leading to severe systemic infection with consecutive abortion. As a member of the Chlamydiaceae, C. abortus shares the characteristic feature of an obligate intracellular biphasic developmental cycle with two morphological forms including elementary bodies (EBs) and reticulate bodies (RBs). In contrast to other chlamydial species, C. abortus ultrastructure has not been investigated yet. To do so, samples were fixed by high-pressure freezing and processed by different electron microscopic methods. Freeze-substituted samples were analysed by transmission electron microscopy, scanning transmission electron microscopical tomography and immuno-electron microscopy, and freeze-fractured samples were analysed by cryo-scanning electron microscopy. Here, we present three ultrastructural features of C. abortus that have not been reported up to now. Firstly, the morphological evidence that C. abortus is equipped with the type three secretion system. Secondly, the accumulation and even coating of whole inclusion bodies by membrane complexes consisting of multiple closely adjacent membranes which seems to be a C. abortus specific feature. Thirdly, the formation of small vesicles in the periplasmic space of RBs in the second half of the developmental cycle. Concerning the time point of their formation and the fact that they harbour chlamydial components, these vesicles might be morphological correlates of an intermediate step during the process of redifferentiation of RBs into EBs. As this feature has also been shown for C. trachomatis and C. pneumoniae, it might be a common characteristic of the family of Chlamydiaceae.

  6. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

    Science.gov (United States)

    Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

    2012-01-01

    Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

  7. Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus in China with multiple gene markers.

    Directory of Open Access Journals (Sweden)

    Qing-Yan Dai

    Full Text Available Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI gene and two alternative internal transcribed spacer (ITS genes (ITS1 and ITS2. Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML/Neighbor-joining (NJ, "best close match" (BCM, Minimum distance (MD, and BP-based method (BP, representing commonly used methodology (tree-based and non-tree based in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In

  8. Species delimitation in lemurs: multiple genetic loci reveal low levels of species diversity in the genus Cheirogaleus

    Directory of Open Access Journals (Sweden)

    Rasoloarison Rodin M

    2009-02-01

    Full Text Available Abstract Background Species are viewed as the fundamental unit in most subdisciplines of biology. To conservationists this unit represents the currency for global biodiversity assessments. Even though Madagascar belongs to one of the top eight biodiversity hotspots of the world, the taxonomy of its charismatic lemuriform primates is not stable. Within the last 25 years, the number of described lemur species has more than doubled, with many newly described species identified among the nocturnal and small-bodied cheirogaleids. Here, we characterize the diversity of the dwarf lemurs (genus Cheirogaleus and assess the status of the seven described species, based on phylogenetic and population genetic analysis of mtDNA (cytb + cox2 and three nuclear markers (adora3, fiba and vWF. Results This study identified three distinct evolutionary lineages within the genus Cheirogaleus. Population genetic cluster analyses revealed a further layer of population divergence with six distinct genotypic clusters. Conclusion Based on the general metapopulation lineage concept and multiple concordant data sets, we identify three exclusive groups of dwarf lemur populations that correspond to three of the seven named species: C. major, C. medius and C. crossleyi. These three species were found to be genealogically exclusive in both mtDNA and nDNA loci and are morphologically distinguishable. The molecular and morphometric data indicate that C. adipicaudatus and C. ravus are synonymous with C. medius and C. major, respectively. Cheirogaleus sibreei falls into the C. medius mtDNA clade, but in morphological analyses the membership is not clearly resolved. We do not have sufficient data to assess the status of C. minusculus. Although additional patterns of population differentiation are evident, there are no clear subdivisions that would warrant additional specific status. We propose that ecological and more geographic data should be collected to confirm these results.

  9. Phylogeographic and population genetic analyses reveal multiple species of Boa and independent origins of insular dwarfism.

    Science.gov (United States)

    Card, Daren C; Schield, Drew R; Adams, Richard H; Corbin, Andrew B; Perry, Blair W; Andrew, Audra L; Pasquesi, Giulia I M; Smith, Eric N; Jezkova, Tereza; Boback, Scott M; Booth, Warren; Castoe, Todd A

    2016-09-01

    Boa is a Neotropical genus of snakes historically recognized as monotypic despite its expansive distribution. The distinct morphological traits and color patterns exhibited by these snakes, together with the wide diversity of ecosystems they inhabit, collectively suggest that the genus may represent multiple species. Morphological variation within Boa also includes instances of dwarfism observed in multiple offshore island populations. Despite this substantial diversity, the systematics of the genus Boa has received little attention until very recently. In this study we examined the genetic structure and phylogenetic relationships of Boa populations using mitochondrial sequences and genome-wide SNP data obtained from RADseq. We analyzed these data at multiple geographic scales using a combination of phylogenetic inference (including coalescent-based species delimitation) and population genetic analyses. We identified extensive population structure across the range of the genus Boa and multiple lines of evidence for three widely-distributed clades roughly corresponding with the three primary land masses of the Western Hemisphere. We also find both mitochondrial and nuclear support for independent origins and parallel evolution of dwarfism on offshore island clusters in Belize and Cayos Cochinos Menor, Honduras. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Characters with multiple usages- phenotypic variability analysis at Echinacea purpurea (L. Moench species

    Directory of Open Access Journals (Sweden)

    Mihai Radu POP

    2010-11-01

    Full Text Available Merging aesthetics with utility, some medicinal plants can benefit both of a high production and decoration potential. This calls for diversification of improvement directions of the species. Through this article we suggest one of these species, Echinacea purpurea (L. Moench. This is considered to be important at this time, acquisition of new biological forms - varieties in this species, which show multiple attributes utility based on key biological characteristics, agronomic, physiological, biochemical and agrochemical (medicinal, decorative, culinary etc.. To achieve this goal, studies were undertaken, given in this article, which is the starting point for selecting characters representative for our targets.The results presented in this study reveal a pronounced genetic polymorphism showing the selection operation can use the original material for a quantitative and qualitative differentiation of valuable genotypes that could be approved.

  11. Optimising the application of multiple-capture traps for invasive species management using spatial simulation.

    Science.gov (United States)

    Warburton, Bruce; Gormley, Andrew M

    2015-01-01

    Internationally, invasive vertebrate species pose a significant threat to biodiversity, agricultural production and human health. To manage these species a wide range of tools, including traps, are used. In New Zealand, brushtail possums (Trichosurus vulpecula), stoats (Mustela ermine), and ship rats (Rattus rattus) are invasive and there is an ongoing demand for cost-effective non-toxic methods for controlling these pests. Recently, traps with multiple-capture capability have been developed which, because they do not require regular operator-checking, are purported to be more cost-effective than traditional single-capture traps. However, when pest populations are being maintained at low densities (as is typical of orchestrated pest management programmes) it remains uncertain if it is more cost-effective to use fewer multiple-capture traps or more single-capture traps. To address this uncertainty, we used an individual-based spatially explicit modelling approach to determine the likely maximum animal-captures per trap, given stated pest densities and defined times traps are left between checks. In the simulation, single- or multiple-capture traps were spaced according to best practice pest-control guidelines. For possums with maintenance densities set at the lowest level (i.e. 0.5/ha), 98% of all simulated possums were captured with only a single capacity trap set at each site. When possum density was increased to moderate levels of 3/ha, having a capacity of three captures per trap caught 97% of all simulated possums. Results were similar for stoats, although only two potential captures per site were sufficient to capture 99% of simulated stoats. For rats, which were simulated at their typically higher densities, even a six-capture capacity per trap site only resulted in 80% kill. Depending on target species, prevailing density and extent of immigration, the most cost-effective strategy for pest control in New Zealand might be to deploy several single

  12. Multiple factors contribute to reproductive isolation between two co-existing Habenaria species (Orchidaceae.

    Directory of Open Access Journals (Sweden)

    Wenliu Zhang

    Full Text Available Reproductive isolation is a key feature that forms barriers to gene flow between distinct plants. In orchids, prezygotic reproductive isolation has been considered to be strong, because their associations with highly specific pollinators. In this study, the reproductive ecology and reproductive isolation of two sympatric Habenaria species, H. davidii and H. fordii, was investigated by floral phenology and morphology, hand-pollination experiments and visitor observation in southwest China. The two species were dependent on insects for pollination and completely self-compatible. A number of factors have been identified to limit gene flow between the two species and achieved full reproductive isolation. Ecogeographic isolation was a weak barrier. H. fordii and H. davidii had completely overlapped flowering periods, and floral morphology plays an important role in floral isolation. The two species shared the same hawkmoth pollinator, Cechenena lineosa, but the pollinaria of the two orchids were attached on different body parts of pollinators. Prezygotic isolation was not complete, but the interspecific pollination treatments of each species resulted in no seed sets, indicating that unlike many other orchid species, in which the postzygotic reproductive isolation is very weak or complete absence, the post-zygotic isolation strongly acted in the stage of seed production between two species. The results illustrate the reproductive isolation between two species involves multiple plant life-history stages and a variety of reproductive barriers can contribute to overall isolation.

  13. Transport of a multiple ion species plasma in the Pfirsch--Schluter regime

    International Nuclear Information System (INIS)

    Hirshman, S.P.

    1976-10-01

    The classical parallel friction coefficients, which relate the collisional friction forces to the flow of particles and heat along the magnetic field, are calculated for a multiple ion species plasma. In the short mean free path regime, the neoclassical Pfirsch--Schlueter transport coefficients for a toroidally confined multispecies plasma are computed in terms of the classical friction coefficients. The dependence of the neoclassical cross-field transport on the equilibration of the parallel ion temperature profiles is determined

  14. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    International Nuclear Information System (INIS)

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-01-01

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries

  15. Hybrid approaches for multiple-species stochastic reaction–diffusion models

    Energy Technology Data Exchange (ETDEWEB)

    Spill, Fabian, E-mail: fspill@bu.edu [Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215 (United States); Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Guerrero, Pilar [Department of Mathematics, University College London, Gower Street, London WC1E 6BT (United Kingdom); Alarcon, Tomas [Centre de Recerca Matematica, Campus de Bellaterra, Edifici C, 08193 Bellaterra (Barcelona) (Spain); Departament de Matemàtiques, Universitat Atonòma de Barcelona, 08193 Bellaterra (Barcelona) (Spain); Maini, Philip K. [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Byrne, Helen [Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG (United Kingdom); Computational Biology Group, Department of Computer Science, University of Oxford, Oxford OX1 3QD (United Kingdom)

    2015-10-15

    Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.

  16. Suppression of Stimulated Brillouin Scattering in multiple-ion species inertial confinement fusion Hohlraum Plasmas

    International Nuclear Information System (INIS)

    Neumayer, P

    2007-01-01

    A long-standing problem in the field of laser-plasma interactions is to successfully employ multiple-ion species plasmas to reduce stimulated Brillouin scattering (SBS) in inertial confinement fusion (ICF) hohlraum conditions. Multiple-ion species increase significantly the linear Landau damping for acoustic waves. Consequently, recent hohlraum designs for indirect-drive ignition on the National Ignition Facility investigate wall liner material options so that the liner gain for parametric instabilities will be below threshold for the onset SBS. Although the effect of two-ion species plasmas on Landau damping has been directly observed with Thomson scattering, early experiments on SBS in these plasmas have suffered from competing non-linear effects or laser beam filamentation. In this study, a reduction of SBS scattering to below the percent level has been observed in hohlraums at Omega that emulate the plasma conditions in an indirect drive ICF experiments. These experiments have measured the laser-plasma interaction processes in ignition-relevant high-electron temperature regime demonstrating Landau damping as a controlling process for SBS. The hohlraums have been filled with various fractions of CO 2 and C 3 H 8 varying the ratio of the light (H) to heavy (C and O) ion density from 0 to 2.6. They have been heated by 14.5 kJ of 351-nm light, thus increasing progressively Landau damping by an order of magnitude at constant electron density and temperature. A delayed 351-nm interaction beam, spatially smoothed to produce a 200-(micro)m laser spot at best focus, has propagated along the axis of the hohlraum. The backscattered light, both into the lens and outside, the transmitted light through the hohlraum plasma and the radiation temperature of the hohlraum has been measured. For ignition relevant laser intensities (3-9 10 14 Wcm -2 ), we find that the SBS reflectivity scales as predicted with Landau damping from >30% to <1%. Simultaneously, the hohlraum radiation

  17. Multiple species of scuttle flies (Diptera: Phoridae) as contaminants in forensic entomology laboratory insect colony.

    Science.gov (United States)

    Zuha, R M; Jenarthanan, L X Q; Disney, R H L; Omar, B

    2015-09-01

    In forensic entomology, larval rearing usually includes the presence of biological contaminants including scuttle flies (Diptera: Phoridae). Scuttle flies are recognized as forensically important insects and have been reported causing nuisance and contamination in laboratory environments. This paper reports for the first time the finding of multiple scuttle fly species affecting colonies of third instar larvae of the Oriental latrine blowfly, Chrysomya megacephala (Fabricius) (Diptera: Calliphoridae), reared indoors at the Forensic Science Simulation Site, Universiti Kebangsaan Malaysia. Adult scuttle flies were discovered inside a rearing container after the emergence of adult C. megacephala., The scuttle fly species are Megaselia scalaris (Loew), M. spiracularis Schmitz and Puliciphora borinquenensis (Wheeler). Notes on the life history and biology of these species are discussed herein.

  18. Beyond Streptococcus mutans: Dental Caries Onset Linked to Multiple Species by 16S rRNA Community Analysis

    Science.gov (United States)

    Gross, Erin L.; Beall, Clifford J.; Kutsch, Stacey R.; Firestone, Noah D.; Leys, Eugene J.; Griffen, Ann L.

    2012-01-01

    Dental caries in very young children may be severe, result in serious infection, and require general anesthesia for treatment. Dental caries results from a shift within the biofilm community specific to the tooth surface, and acidogenic species are responsible for caries. Streptococcus mutans, the most common acid producer in caries, is not always present and occurs as part of a complex microbial community. Understanding the degree to which multiple acidogenic species provide functional redundancy and resilience to caries-associated communities will be important for developing biologic interventions. In addition, microbial community interactions in health and caries pathogenesis are not well understood. The purpose of this study was to investigate bacterial community profiles associated with the onset of caries in the primary dentition. In a combination cross-sectional and longitudinal design, bacterial community profiles at progressive stages of caries and over time were examined and compared to those of health. 16S rRNA gene sequencing was used for bacterial community analysis. Streptococcus mutans was the dominant species in many, but not all, subjects with caries. Elevated levels of S. salivarius, S. sobrinus, and S. parasanguinis were also associated with caries, especially in subjects with no or low levels of S. mutans, suggesting these species are alternative pathogens, and that multiple species may need to be targeted for interventions. Veillonella, which metabolizes lactate, was associated with caries and was highly correlated with total acid producing species. Among children without previous history of caries, Veillonella, but not S. mutans or other acid-producing species, predicted future caries. Bacterial community diversity was reduced in caries as compared to health, as many species appeared to occur at lower levels or be lost as caries advanced, including the Streptococcus mitis group, Neisseria, and Streptococcus sanguinis. This may have

  19. Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism

    Directory of Open Access Journals (Sweden)

    McLeish Michael J

    2012-01-01

    Full Text Available Abstract Background The interaction between insects and plants takes myriad forms in the generation of spectacular diversity. In this association a species host range is fundamental and often measured using an estimate of phylogenetic concordance between species. Pollinating fig wasps display extreme host species specificity, but the intraspecific variation in empirical accounts of host affiliation has previously been underestimated. In this investigation, lineage delimitation and codiversification tests are used to generate and discuss hypotheses elucidating on pollinating fig wasp associations with Ficus. Results Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies. Conclusions The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution.

  20. Impact of Vertical Canopy Position on Leaf Spectral Properties and Traits across Multiple Species

    Directory of Open Access Journals (Sweden)

    Tawanda W. Gara

    2018-02-01

    Full Text Available Understanding the vertical pattern of leaf traits across plant canopies provide critical information on plant physiology, ecosystem functioning and structure and vegetation response to climate change. However, the impact of vertical canopy position on leaf spectral properties and subsequently leaf traits across the entire spectrum for multiple species is poorly understood. In this study, we examined the ability of leaf optical properties to track variability in leaf traits across the vertical canopy profile using Partial Least Square Discriminatory Analysis (PLS-DA. Leaf spectral measurements together with leaf traits (nitrogen, carbon, chlorophyll, equivalent water thickness and specific leaf area were studied at three vertical canopy positions along the plant stem: lower, middle and upper. We observed that foliar nitrogen (N, chlorophyll (Cab, carbon (C, and equivalent water thickness (EWT were higher in the upper canopy leaves compared with lower shaded leaves, while specific leaf area (SLA increased from upper to lower canopy leaves. We found that leaf spectral reflectance significantly (P ≤ 0.05 shifted to longer wavelengths in the ‘red edge’ spectrum (685–701 nm in the order of lower > middle > upper for the pooled dataset. We report that spectral bands that are influential in the discrimination of leaf samples into the three groups of canopy position, based on the PLS-DA variable importance projection (VIP score, match with wavelength regions of foliar traits observed to vary across the canopy vertical profile. This observation demonstrated that both leaf traits and leaf reflectance co-vary across the vertical canopy profile in multiple species. We conclude that canopy vertical position has a significant impact on leaf spectral properties of an individual plant’s traits, and this finding holds for multiple species. These findings have important implications on field sampling protocols, upscaling leaf traits to canopy level

  1. Attempted integration of multiple species of turaco into a mixed-species aviary.

    Science.gov (United States)

    Valuska, Annie J; Leighty, Katherine A; Ferrie, Gina M; Nichols, Valerie D; Tybor, Cheryl L; Plassé, Chelle; Bettinger, Tamara L

    2013-03-01

    Mixed-species exhibits offer a variety of benefits but can be challenging to maintain due to difficulty in managing interspecific interactions. This is particularly true when little has been documented on the behavior of the species being mixed. This was the case when we attempted to house three species of turaco (family: Musophagidae) together with other species in a walk-through aviary. To learn more about the behavior of great blue turacos, violaceous turacos, and white-bellied gray go-away birds, we supplemented opportunistic keeper observations with systematic data collection on their behavior, location, distance from other birds, and visibility to visitors. Keepers reported high levels of aggression among turacos, usually initiated by a go-away bird or a violaceous turaco. Most aggression occurred during feedings or when pairs were defending nest sites. Attempts to reduce aggression by temporarily removing birds to holding areas and reintroducing them days later were ineffective. Systematic data collection revealed increased social behavior, including aggression, during breeding season in the violaceous turacos, as well as greater location fidelity. These behavioral cues may be useful in predicting breeding behavior in the future. Ultimately, we were only able to house three species of turaco together for a short time, and prohibitively high levels of conflict occurred when pairs were breeding. We conclude that mixing these three turaco species is challenging and may not be the most appropriate housing situation for them, particularly during breeding season. However, changes in turaco species composition, sex composition, or exhibit design may result in more compatible mixed-turaco species groups. © 2012 Wiley Periodicals, Inc.

  2. Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species.

    Science.gov (United States)

    Baker, Kate S; Dallman, Timothy J; Field, Nigel; Childs, Tristan; Mitchell, Holly; Day, Martin; Weill, François-Xavier; Lefèvre, Sophie; Tourdjman, Mathieu; Hughes, Gwenda; Jenkins, Claire; Thomson, Nicholas

    2018-04-13

    Horizontal gene transfer has played a role in developing the global public health crisis of antimicrobial resistance (AMR). However, the dynamics of AMR transfer through bacterial populations and its direct impact on human disease is poorly elucidated. Here, we study parallel epidemic emergences of multiple Shigella species, a priority AMR organism, in men who have sex with men to gain insight into AMR emergence and spread. Using genomic epidemiology, we show that repeated horizontal transfer of a single AMR plasmid among Shigella enhanced existing and facilitated new epidemics. These epidemic patterns contrasted with slighter, slower increases in disease caused by organisms with vertically inherited (chromosomally encoded) AMR. This demonstrates that horizontal transfer of AMR directly affects epidemiological outcomes of globally important AMR pathogens and highlights the need for integration of genomic analyses into all areas of AMR research, surveillance and management.

  3. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

    Science.gov (United States)

    Genome wide analysis of orthologous clusters is an important component of comparative genomics studies. Identifying the overlap among orthologous clusters can enable us to elucidate the function and evolution of proteins across multiple species. Here, we report a web platform named OrthoVenn that i...

  4. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization

    CSIR Research Space (South Africa)

    Gcebe, N

    2017-04-01

    Full Text Available Journal of Systematic and Evolutionary Microbiology: DOI 10.1099/ijsem.0.001678 Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization Gcebe N Rutten V Gey...

  5. More than classical Chlamydia psittaci in urban pigeons.

    Science.gov (United States)

    Sachse, Konrad; Kuehlewind, Simone; Ruettger, Anke; Schubert, Evelyn; Rohde, Gernot

    2012-06-15

    In the literature, studies of Chlamydia infection in birds have usually been confined to the search for Chlamydia (C., formerly Chlamydophila) psittaci, so that little is known about the presence of other chlamydial agents. In the present study, cloacal swabs and faeces samples of urban pigeons have been examined by real-time PCR, DNA microarray assays and partial ompA sequencing. Whilst C. psittaci was the predominant chlamydial agent in this pigeon population (75.8% of all Chlamydiaceae positives), the combined use of highly specific and sensitive molecular assays facilitated the detection of atypical serovars of C. psittaci, as well as other species of Chlamydia, such as C. abortus. Detection of C. pecorum and C. trachomatis from an avian host is reported here for the first time. Rather unexpectedly, 19.5% of all Chlamydiaceae-positive cases turned out to be infected with non-classified organisms. The considerable prevalence of these novel agents raises the question of their epidemiological importance and possible role as pathogens. Future surveys in domestic and wild birds will have to take the extended variety of chlamydial organisms into account. Copyright © 2012 Elsevier B.V. All rights reserved.

  6. Functional traits drive the contribution of solar radiation to leaf litter decomposition among multiple arid-zone species.

    Science.gov (United States)

    Pan, Xu; Song, Yao-Bin; Liu, Guo-Fang; Hu, Yu-Kun; Ye, Xue-Hua; Cornwell, William K; Prinzing, Andreas; Dong, Ming; Cornelissen, Johannes H C

    2015-08-18

    In arid zones, strong solar radiation has important consequences for ecosystem processes. To better understand carbon and nutrient dynamics, it is important to know the contribution of solar radiation to leaf litter decomposition of different arid-zone species. Here we investigated: (1) whether such contribution varies among plant species at given irradiance regime, (2) whether interspecific variation in such contribution correlates with interspecific variation in the decomposition rate under shade; and (3) whether this correlation can be explained by leaf traits. We conducted a factorial experiment to determine the effects of solar radiation and environmental moisture for the mass loss and the decomposition constant k-values of 13 species litters collected in Northern China. The contribution of solar radiation to leaf litter decomposition varied significantly among species. Solar radiation accelerated decomposition in particular in the species that already decompose quickly under shade. Functional traits, notably specific leaf area, might predict the interspecific variation in that contribution. Our results provide the first empirical evidence for how the effect of solar radiation on decomposition varies among multiple species. Thus, the effect of solar radiation on the carbon flux between biosphere and atmosphere may depend on the species composition of the vegetation.

  7. Multiple bacterial species reside in chronic wounds

    DEFF Research Database (Denmark)

    Gjødsbøl, Kristine; Christensen, Jens Jørgen; Karlsmark, Tonny

    2006-01-01

    species present were identified. More than one bacterial species were detected in all the ulcers. The most common bacteria found were Staphylococcus aureus (found in 93.5% of the ulcers), Enterococcus faecalis (71.7%), Pseudomonas aeruginosa (52.2%), coagulase-negative staphylococci (45.7%), Proteus...

  8. Chlamydiaceae in cattle: commensals, trigger organisms, or pathogens?

    Science.gov (United States)

    Reinhold, Petra; Sachse, Konrad; Kaltenboeck, Bernhard

    2011-09-01

    Epidemiological data indicate that infection of cattle with chlamydiae such as Chlamydophila (C.) pecorum, C. abortus, C. psittaci and Chlamydia suis, is ubiquitous with mixed infections occurring frequently. The apparent lack of association between infection and clinical disease has resulted in debate as to the pathogenic significance of these organisms, and their tendency to sub-clinical and/or persistent infection presents a challenge to the study of their potential effects. However, recent evidence indicates that chlamydial infections have a substantial and quantifiable impact on livestock productivity with chronic, recurrent infections associated with pulmonary disease in calves and with infertility and sub-clinical mastitis in dairy cows. Data also suggest these infections manifest clinically when they coincide with a number of epidemiological risk factors. Future research should: (1) use relevant animal models to clarify the pathogenesis of bovine chlamydioses; (2) quantify the impact of chlamydial infection at a herd level and identify strategies for its control, including sub-unit vaccine development; and (3) evaluate the zoonotic risk of bovine chlamydial infections which will require the development of species-specific serodiagnostics. Copyright © 2010 Elsevier Ltd. All rights reserved.

  9. Sequence-specific electrochemical recognition of multiple species using nanoparticle labels

    International Nuclear Information System (INIS)

    Cai Hong; Shang, Chii; Hsing, I.-Ming

    2004-01-01

    In this work, we report an electrochemical methodology that enables the rapid identification of different DNA sequences on the microfabricated electrodes. Our approach starts with an electropolymerization process on a patterned indium tin oxide (ITO)-coated glass electrode, followed by a selective immobilization of biotin-tagged probes on individually addressable spots via the biotin-streptavidin linkage. An exemplary target mixture containing E. coli and Stachybotrys Chartarum, an airborne pathogen, is then introduced. Recognition of the DNA hybridization event of the immobilized probes with the target pathogen PCR products or synthetic oligonucleotides is achieved by a novel electrochemistry-based technique utilizing the preferential catalytic silver electrodeposition process on the DNA-linked nanogold shells. The ability to selectively immobilize different oligonucleotide probes together with a sensitive electrochemistry-based detection for multiple species, as demonstrated in this study, is an important step forward for the realization of a portable bioanalytical microdevice for the rapid detection of pathogens

  10. Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.

    Science.gov (United States)

    Schröder, Markus S; Martinez de San Vicente, Kontxi; Prandini, Tâmara H R; Hammel, Stephen; Higgins, Desmond G; Bagagli, Eduardo; Wolfe, Kenneth H; Butler, Geraldine

    2016-11-01

    Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B) that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.

  11. Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species.

    Directory of Open Access Journals (Sweden)

    Markus S Schröder

    2016-11-01

    Full Text Available Mating between different species produces hybrids that are usually asexual and stuck as diploids, but can also lead to the formation of new species. Here, we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis. We find that most isolates are diploid hybrids, products of mating between two unknown parental species (A and B that are 5% divergent in sequence. Isolates vary greatly in the extent of homogenization between A and B, making their genomes a mosaic of highly heterozygous regions interspersed with homozygous regions. Separate phylogenetic analyses of SNPs in the A- and B-derived portions of the genome produces almost identical trees of the isolates with four major clades. However, the presence of two mutually exclusive genotype combinations at the mating type locus, and recombinant mitochondrial genomes diagnostic of inter-clade mating, shows that the species C. orthopsilosis does not have a single evolutionary origin but was created at least four times by separate interspecies hybridizations between parents A and B. Older hybrids have lost more heterozygosity. We also identify two isolates with homozygous genomes derived exclusively from parent A, which are pure non-hybrid strains. The parallel emergence of the same hybrid species from multiple independent hybridization events is common in plant evolution, but is much less documented in pathogenic fungi.

  12. Welding fumes from stainless steel gas metal arc processes contain multiple manganese chemical species.

    Science.gov (United States)

    Keane, Michael; Stone, Samuel; Chen, Bean

    2010-05-01

    Fumes from a group of gas metal arc welding (GMAW) processes used on stainless steel were generated using three different metal transfer modes and four different shield gases. The objective was to identify and measure manganese (Mn) species in the fumes, and identify processes that are minimal generators of Mn species. The robotic welding system was operated in short-circuit (SC) mode (Ar/CO2 and He/Ar), axial spray (AXS) mode (Ar/O2 and Ar/CO2), and pulsed axial-spray (PAXS) mode (Ar/O2). The fumes were analyzed for Mn by a sequential extraction process followed by inductively coupled plasma-atomic emission spectroscopy (ICP-AES) analysis, and by X-ray diffraction (XRD). Total elemental Mn, iron (Fe), chromium (Cr) and nickel (Ni) were separately measured after aqua regia digestion and ICP-AES analysis. Soluble Mn2+, Fe2+, Fe3+, and Ni2+ in a simple biological buffer (phosphate-buffered saline) were determined at pH 7.2 and 5.0 after 2 h incubation at 37 C by ion chromatography. Results indicate that Mn was present in soluble form, acid-soluble form, and acid-soluble form after reduction by hydroxylamine, which represents soluble Mn0 and Mn2+ compounds, other Mn2+ compounds, and (Mn3+ and Mn4+) compounds, respectively. The dominant fraction was the acid-soluble Mn2+ fraction, but results varied with the process and shield gas. Soluble Mn mass percent in the fume ranged from 0.2 to 0.9%, acid-soluble Mn2+ compounds ranged from 2.6 to 9.3%, and acid plus reducing agent-soluble (Mn3+ and Mn4+) compounds ranged from 0.6 to 5.1%. Total Mn composition ranged from 7 to 15%. XRD results showed fumes had a crystalline content of 90-99% Fe3O4, and showed evidence of multiple Mn oxides, but overlaps and weak signals limited identification. Small amounts of the Mn2+ in the fume (welding process. Mn generation rates for the fractions were tabulated, and the influence of ozone is discussed. The conclusions are that exposures to welding fumes include multiple Mn species, both

  13. Extension of the Si:C Stressor Thickness by Using Multiple ClusterCarbon Species

    International Nuclear Information System (INIS)

    Sekar, Karuppanan; Krull, Wade

    2011-01-01

    ClusterCarbon implantation is now well established as an attractive alternative for producing stress in advanced NMOS devices. ClusterCarbon has the advantage over monomer carbon implant in it's self-amorphization feature, eliminating the need for PAI implantation while producing highly substitutional carbon incorporation. To date, the limitation of this approach has been the high energy limit, due to the extraction limit of the available production tools for the preferred carbon species, which has been the C7Hx molecule. It is noted that the C7 species is produced by the breakup of the parent C14H14 molecule in the ion source. It is further noted that the preferred method of producing the Si:C stress layer is a multiple implant sequence with ClusterCarbon implants at various energies and doses designed to produce a carbon profile which is constant in-depth. The stressor thickness limit using C7 is known to be about 40 nm, which is less than the stressor thickness used in the conventional SiGe process for PMOS. In this work, it is shown that utilizing the C5 molecule which is also available from the breakup of C14H14 enables the stressor layer thickness to be extended to at least 60 nm, which is consistent with the conventional SiGe process. It will be shown that one additional C5 implant, performed after a standard C7 multiple implant sequence, can produce the extension of the stressor thickness while maintaining the flat depth profile. A detailed process characterization will be shown for this new process sequence.

  14. Using empirical models of species colonization under multiple threatening processes to identify complementary threat-mitigation strategies.

    Science.gov (United States)

    Tulloch, Ayesha I T; Mortelliti, Alessio; Kay, Geoffrey M; Florance, Daniel; Lindenmayer, David

    2016-08-01

    Approaches to prioritize conservation actions are gaining popularity. However, limited empirical evidence exists on which species might benefit most from threat mitigation and on what combination of threats, if mitigated simultaneously, would result in the best outcomes for biodiversity. We devised a way to prioritize threat mitigation at a regional scale with empirical evidence based on predicted changes to population dynamics-information that is lacking in most threat-management prioritization frameworks that rely on expert elicitation. We used dynamic occupancy models to investigate the effects of multiple threats (tree cover, grazing, and presence of an hyperaggressive competitor, the Noisy Miner (Manorina melanocephala) on bird-population dynamics in an endangered woodland community in southeastern Australia. The 3 threatening processes had different effects on different species. We used predicted patch-colonization probabilities to estimate the benefit to each species of removing one or more threats. We then determined the complementary set of threat-mitigation strategies that maximized colonization of all species while ensuring that redundant actions with little benefit were avoided. The single action that resulted in the highest colonization was increasing tree cover, which increased patch colonization by 5% and 11% on average across all species and for declining species, respectively. Combining Noisy Miner control with increasing tree cover increased species colonization by 10% and 19% on average for all species and for declining species respectively, and was a higher priority than changing grazing regimes. Guidance for prioritizing threat mitigation is critical in the face of cumulative threatening processes. By incorporating population dynamics in prioritization of threat management, our approach helps ensure funding is not wasted on ineffective management programs that target the wrong threats or species. © 2016 Society for Conservation Biology.

  15. Bias correction in species distribution models: pooling survey and collection data for multiple species.

    Science.gov (United States)

    Fithian, William; Elith, Jane; Hastie, Trevor; Keith, David A

    2015-04-01

    Presence-only records may provide data on the distributions of rare species, but commonly suffer from large, unknown biases due to their typically haphazard collection schemes. Presence-absence or count data collected in systematic, planned surveys are more reliable but typically less abundant.We proposed a probabilistic model to allow for joint analysis of presence-only and survey data to exploit their complementary strengths. Our method pools presence-only and presence-absence data for many species and maximizes a joint likelihood, simultaneously estimating and adjusting for the sampling bias affecting the presence-only data. By assuming that the sampling bias is the same for all species, we can borrow strength across species to efficiently estimate the bias and improve our inference from presence-only data.We evaluate our model's performance on data for 36 eucalypt species in south-eastern Australia. We find that presence-only records exhibit a strong sampling bias towards the coast and towards Sydney, the largest city. Our data-pooling technique substantially improves the out-of-sample predictive performance of our model when the amount of available presence-absence data for a given species is scarceIf we have only presence-only data and no presence-absence data for a given species, but both types of data for several other species that suffer from the same spatial sampling bias, then our method can obtain an unbiased estimate of the first species' geographic range.

  16. Comparative Proteomics of Rubber Latex Revealed Multiple Protein Species of REF/SRPP Family Respond Diversely to Ethylene Stimulation among Different Rubber Tree Clones

    Directory of Open Access Journals (Sweden)

    Zheng Tong

    2017-05-01

    Full Text Available Rubber elongation factor (REF and small rubber particle protein (SRPP are two key factors for natural rubber biosynthesis. To further understand the roles of these proteins in rubber formation, six different genes for latex abundant REF or SRPP proteins, including REF138,175,258 and SRPP117,204,243, were characterized from Hevea brasiliensis Reyan (RY 7-33-97. Sequence analysis showed that REFs have a variable and long N-terminal, whereas SRPPs have a variable and long C-terminal beyond the REF domain, and REF258 has a β subunit of ATPase in its N-terminal. Through two-dimensional electrophoresis (2-DE, each REF/SRPP protein was separated into multiple protein spots on 2-DE gels, indicating they have multiple protein species. The abundance of REF/SRPP proteins was compared between ethylene and control treatments or among rubber tree clones with different levels of latex productivity by analyzing 2-DE gels. The total abundance of each REF/SRPP protein decreased or changed a little upon ethylene stimulation, whereas the abundance of multiple protein species of the same REF/SRPP changed diversely. Among the three rubber tree clones, the abundance of the protein species also differed significantly. Especially, two protein species of REF175 or REF258 were ethylene-responsive only in the high latex productivity clone RY 8-79 instead of in RY 7-33-97 and PR 107. Some individual protein species were positively related to ethylene stimulation and latex productivity. These results suggested that the specific protein species could be more important than others for rubber production and post-translational modifications might play important roles in rubber biosynthesis.

  17. A Distributed Agent Implementation of Multiple Species Flocking Model for Document Partitioning Clustering

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Xiaohui [ORNL; Potok, Thomas E [ORNL

    2006-01-01

    The Flocking model, first proposed by Craig Reynolds, is one of the first bio-inspired computational collective behavior models that has many popular applications, such as animation. Our early research has resulted in a flock clustering algorithm that can achieve better performance than the Kmeans or the Ant clustering algorithms for data clustering. This algorithm generates a clustering of a given set of data through the embedding of the highdimensional data items on a two-dimensional grid for efficient clustering result retrieval and visualization. In this paper, we propose a bio-inspired clustering model, the Multiple Species Flocking clustering model (MSF), and present a distributed multi-agent MSF approach for document clustering.

  18. A comparison of multiple indicator kriging and area-to-point Poisson kriging for mapping patterns of herbivore species abundance in Kruger National Park, South Africa.

    Science.gov (United States)

    Kerry, Ruth; Goovaerts, Pierre; Smit, Izak P J; Ingram, Ben R

    Kruger National Park (KNP), South Africa, provides protected habitats for the unique animals of the African savannah. For the past 40 years, annual aerial surveys of herbivores have been conducted to aid management decisions based on (1) the spatial distribution of species throughout the park and (2) total species populations in a year. The surveys are extremely time consuming and costly. For many years, the whole park was surveyed, but in 1998 a transect survey approach was adopted. This is cheaper and less time consuming but leaves gaps in the data spatially. Also the distance method currently employed by the park only gives estimates of total species populations but not their spatial distribution. We compare the ability of multiple indicator kriging and area-to-point Poisson kriging to accurately map species distribution in the park. A leave-one-out cross-validation approach indicates that multiple indicator kriging makes poor estimates of the number of animals, particularly the few large counts, as the indicator variograms for such high thresholds are pure nugget. Poisson kriging was applied to the prediction of two types of abundance data: spatial density and proportion of a given species. Both Poisson approaches had standardized mean absolute errors (St. MAEs) of animal counts at least an order of magnitude lower than multiple indicator kriging. The spatial density, Poisson approach (1), gave the lowest St. MAEs for the most abundant species and the proportion, Poisson approach (2), did for the least abundant species. Incorporating environmental data into Poisson approach (2) further reduced St. MAEs.

  19. Taxonaut: an application software for comparative display of multiple taxonomies with a use case of GBIF Species API.

    Science.gov (United States)

    Ytow, Nozomi

    2016-01-01

    The Species API of the Global Biodiversity Information Facility (GBIF) provides public access to taxonomic data aggregated from multiple data sources. Each data source follows its own classification which can be inconsistent with classifications from other sources. Even with a reference classification e.g. the GBIF Backbone taxonomy, a comprehensive method to compare classifications in the data aggregation is essential, especially for non-expert users. A Java application was developed to compare multiple taxonomies graphically using classification data acquired from GBIF's ChecklistBank via the GBIF Species API. It uses a table to display taxonomies where each column represents a taxonomy under comparison, with an aligner column to organise taxa by name. Each cell contains the name of a taxon if the classification in that column contains the name. Each column also has a cell showing the hierarchy of the taxonomy by a folder metaphor where taxa are aligned and synchronised in the aligner column. A set of those comparative tables shows taxa categorised by relationship between taxonomies. The result set is also available as tables in an Excel format file.

  20. Mitochondrial genome analyses suggest multiple Trichuris species in humans, baboons, and pigs from different geographical regions

    DEFF Research Database (Denmark)

    Hawash, Mohamed B. F.; Andersen, Lee O.; Gasser, Robin B.

    2015-01-01

    Trichuris from françois' leaf monkey, suggesting multiple whipworm species circulating among non-human primates. The genetic and protein distances between pig Trichuris from Denmark and other regions were roughly 9% and 6%, respectively, while Chinese and Ugandan whipworms were more closely related......) suggesting that they represented different species. Trichuris from the olive baboon in US was genetically related to human Trichuris in China, while the other from the hamadryas baboon in Denmark was nearly identical to human Trichuris from Uganda. Baboon-derived Trichuris was genetically distinct from......BACKGROUND: The whipworms Trichuris trichiura and Trichuris suis are two parasitic nematodes of humans and pigs, respectively. Although whipworms in human and non-human primates historically have been referred to as T. trichiura, recent reports suggest that several Trichuris spp. are found...

  1. Evaluation of a multiple-species approach to monitoring species at the ecoregional scale

    Science.gov (United States)

    Patricia N. Manley; William J. Zielinski; Matthew D. Schlesinger; Sylvia R. Mori

    2004-01-01

    Monitoring is required of land managers and conservation practitioners to assess the success of management actions. "Shortcuts" are sought to reduce monitoring costs, most often consisting of the selection of a small number of species that are closely monitored to represent the status of many associated species and environmental correlates. Assumptions...

  2. Genomic resources for multiple species in the Drosophila ananassae species group.

    Science.gov (United States)

    Signor, Sarah; Seher, Thaddeus; Kopp, Artyom

    2013-01-01

    The development of genomic resources in non-model taxa is essential for understanding the genetic basis of biological diversity. Although the genomes of many Drosophila species have been sequenced, most of the phenotypic diversity in this genus remains to be explored. To facilitate the genetic analysis of interspecific and intraspecific variation, we have generated new genomic resources for seven species and subspecies in the D. ananassae species subgroup. We have generated large amounts of transcriptome sequence data for D. ercepeae, D. merina, D. bipectinata, D. malerkotliana malerkotliana, D. m. pallens, D. pseudoananassae pseudoananassae, and D. p. nigrens. de novo assembly resulted in contigs covering more than half of the predicted transcriptome and matching an average of 59% of annotated genes in the complete genome of D. ananassae. Most contigs, corresponding to an average of 49% of D. ananassae genes, contain sequence polymorphisms that can be used as genetic markers. Subsets of these markers were validated by genotyping the progeny of inter- and intraspecific crosses. The ananassae subgroup is an excellent model system for examining the molecular basis of speciation and phenotypic evolution. The new genomic resources will facilitate the genetic analysis of inter- and intraspecific differences in this lineage. Transcriptome sequencing provides a simple and cost-effective way to identify molecular markers at nearly single-gene density, and is equally applicable to any non-model taxa.

  3. In vitro establishment and multiplication of Guettarda clarense, a Cuban endemic species in extinction danger

    Directory of Open Access Journals (Sweden)

    Elisa Quiala

    2005-01-01

    Full Text Available The present work was carried out with the objective of achieving the in vitro establishment and multiplication of Guettarda clarense which is an endemic local of Santa Clara city and it is considered in extinction danger. Seeds of mature fruits collected under field conditions were used. The effect of a concentration of NaOCl (2% during 15, 20 and 25 minutes in the disinfection of the seeds was studied. The seeds were sowed in a culture medium of germination compound by 50% of MS salts. During the multiplication phase of the explants, the effect of three concentrations of 6-BAP (0.2, 0.4 and 0.6 mg. l-1 was studied. The culture medium was compound by the MS salts, 1.0 mg. l-1 of thiamine and 3% of sucrose. The bigger number of seeds free of visible microbial pollutants (50% was obtained when the treatment with 2.0% of NaOCl during 25 minutes was used. The 85% of the seeds germinated in the culture medium compound by the 50% of the MS salts without growth regulators. During the multiplication phase of the explants, the multiplication coefficient and the longitude of the plants were increased in the same proportion as the concentration of 6-BAP was increased. The highest values were obtained (6.1 explants and 6.7 cm respectively in the treatment with 0.6 mg. l-1. Key words: cuabal, in vitro culture, micropropagation, threatened species

  4. VORICONAZOLE TOXICITY IN MULTIPLE PENGUIN SPECIES.

    Science.gov (United States)

    Hyatt, Michael W; Georoff, Timothy A; Nollens, Hendrik H; Wells, Rebecca L; Clauss, Tonya M; Ialeggio, Donna M; Harms, Craig A; Wack, Allison N

    2015-12-01

    Aspergillosis is a common respiratory fungal disease in penguins managed under human care. Triazole antifungal drugs, including itraconazole, are most commonly used for treatment; however, itraconazole treatment failures from drug resistance are becoming more common, requiring newer treatment options. Voriconazole, a newer triazole, is being used more often. Until recently, no voriconazole pharmacokinetic studies had been performed in penguins, leading to empiric dosing based on other avian studies. This has led to increased anecdotal reporting of apparent voriconazole toxicity in penguins. This report describes 18 probable and 6 suspected cases of voriconazole toxicity in six penguin species from nine institutions: 12 African penguins (Spheniscus demersus), 5 Humboldt penguins (Spheniscus humboldti), 3 Magellanic penguins (Spheniscus magellanicus), 2 gentoo penguins (Pygoscelis papua papua), 1 macaroni penguin (Eudyptes chrysolophus), and 1 emperor penguin (Aptenodytes forsteri). Observed clinical signs of toxicity included anorexia, lethargy, weakness, ataxia, paresis, apparent vision changes, seizure-like activity, and generalized seizures. Similar signs of toxicity have also been reported in humans, in whom voriconazole therapeutic plasma concentration for Aspergillus spp. infections is 2-6 μg/ml. Plasma voriconazole concentrations were measured in 18 samples from penguins showing clinical signs suggestive of voriconazole toxicity. The concentrations ranged from 8.12 to 64.17 μg/ml, with penguins having plasma concentrations above 30 μg/ml exhibiting moderate to severe neurologic signs, including ataxia, paresis, and seizures. These concentrations were well above those known to result in central nervous system toxicity, including encephalopathy, in humans. This case series highlights the importance of species-specific dosing of voriconazole in penguins and plasma therapeutic drug monitoring. Further investigation, including pharmacokinetic studies, is

  5. Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

    Science.gov (United States)

    Salzberg, Steven L; Dunning Hotopp, Julie C; Delcher, Arthur L; Pop, Mihai; Smith, Douglas R; Eisen, Michael B; Nelson, William C

    2005-01-01

    The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.

  6. Forward selection for multiple resistance across the non-selective glyphosate, glufosinate and oxyfluorfen herbicides in Lolium weed species.

    Science.gov (United States)

    Fernández, Pablo; Alcántara, Ricardo; Osuna, María D; Vila-Aiub, Martin M; Prado, Rafael De

    2017-05-01

    In the Mediterranean area, Lolium species have evolved resistance to glyphosate after decades of continual use without other alternative chemicals in perennial crops (olive, citrus and vineyards). In recent years, oxyfluorfen alone or mixed with glyphosate and glufosinate has been introduced as a chemical option to control dicot and grass weeds. Dose-response studies confirmed that three glyphosate-resistant Lolium weed species (L. rigidum, L. perenne, L. multiflorum) collected from perennial crops in the Iberian Peninsula have also evolved resistance to glufosinate and oxyfluorfen herbicides, despite their recent introduction. Based on the LD 50 resistance parameter, the resistance factor was similar among Lolium species and ranged from 14- to 21-fold and from ten- to 12-fold for oxyfluorfen and glufosinate respectively. Similarly, about 14-fold resistance to both oxyfluorfen and glufosinate was estimated on average for the three Lolium species when growth reduction (GR 50 ) was assessed. This study identified oxyfluorfen resistance in a grass species for the first time. A major threat to sustainability of perennial crops in the Iberian Peninsula is evident, as multiple resistance to non-selective glyphosate, glufosinate and oxyfluorfen herbicides has evolved in L. rigidum, L. perenne and L. multiflorum weeds. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  7. Genetic diversity and differentiation patterns in Micromeria from the Canary Islands are congruent with multiple colonization dynamics and the establishment of species syngameons.

    Science.gov (United States)

    Curto, M; Puppo, P; Kratschmer, S; Meimberg, H

    2017-08-22

    Especially on islands closer to the mainland, such as the Canary Islands, different lineages that originated by multiple colonization events could have merged by hybridization, which then could have promoted radiation events (Herben et al., J Ecol 93: 572-575, 2005; Saunders and Gibson, J Ecol 93: 649-652, 2005; Caujapé-Castells, Jesters, red queens, boomerangs and surfers: a molecular outlook on the diversity of the Canarian endemic flora, 2011). This is an alternative to the scenario where evolution is mostly driven by drift (Silvertown, J Ecol 92: 168-173, 2004; Silvertown et al., J Ecol 93: 653-657, 2005). In the former case hybridization should be reflected in the genetic structure and diversity patterns of island species. In the present work we investigate Micromeria from the Canary Islands by extensively studying their phylogeographic pattern based on 15 microsatellite loci and 945 samples. These results are interpreted according to the hypotheses outlined above. Genetic structure assessment allowed us to genetically differentiate most Micromeria species and supported their current classification. We found that populations on younger islands were significantly more genetically diverse and less differentiated than those on older islands. Moreover, we found that genetic distance on younger islands was in accordance with an isolation-by-distance pattern, while on the older islands this was not the case. We also found evidence of introgression among species and islands. These results are congruent with a scenario of multiple colonizations during the expansion onto new islands. Hybridization contributes to the grouping of multiple lineages into highly diverse populations. Thus, in our case, islands receive several colonization events from different sources, which are combined into sink populations. This mechanism is in accordance with the surfing syngameon hypothesis. Contrary to the surfing syngameon current form, our results may reflect a slightly different

  8. Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs

    Directory of Open Access Journals (Sweden)

    Jörger Katharina M

    2012-12-01

    Full Text Available Abstract Background Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic and the success rate has never been explored on mesopsammic Mollusca. Results We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH. In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC, statistical parsimony, Bayesian Species Delineation (BPP and Automatic Barcode Gap Discovery (ABGD. The secondary species hypothesis (SSH is gained by relying only on uncontradicted results of the different approaches (‘minimum consensus approach’, resulting in the discovery of a radiation of (at least 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions. Conclusions Our study confirms extensive, morphologically

  9. The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens.

    Directory of Open Access Journals (Sweden)

    Anja Voigt

    Full Text Available Chlamydiaceae are a family of obligate intracellular pathogens causing a wide range of diseases in animals and humans, and facing unique evolutionary constraints not encountered by free-living prokaryotes. To investigate genomic aspects of infection, virulence and host preference we have sequenced Chlamydia psittaci, the pathogenic agent of ornithosis.A comparison of the genome of the avian Chlamydia psittaci isolate 6BC with the genomes of other chlamydial species, C. trachomatis, C. muridarum, C. pneumoniae, C. abortus, C. felis and C. caviae, revealed a high level of sequence conservation and synteny across taxa, with the major exception of the human pathogen C. trachomatis. Important differences manifest in the polymorphic membrane protein family specific for the Chlamydiae and in the highly variable chlamydial plasticity zone. We identified a number of psittaci-specific polymorphic membrane proteins of the G family that may be related to differences in host-range and/or virulence as compared to closely related Chlamydiaceae. We calculated non-synonymous to synonymous substitution rate ratios for pairs of orthologous genes to identify putative targets of adaptive evolution and predicted type III secreted effector proteins.This study is the first detailed analysis of the Chlamydia psittaci genome sequence. It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions.

  10. The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens.

    Science.gov (United States)

    Voigt, Anja; Schöfl, Gerhard; Saluz, Hans Peter

    2012-01-01

    Chlamydiaceae are a family of obligate intracellular pathogens causing a wide range of diseases in animals and humans, and facing unique evolutionary constraints not encountered by free-living prokaryotes. To investigate genomic aspects of infection, virulence and host preference we have sequenced Chlamydia psittaci, the pathogenic agent of ornithosis. A comparison of the genome of the avian Chlamydia psittaci isolate 6BC with the genomes of other chlamydial species, C. trachomatis, C. muridarum, C. pneumoniae, C. abortus, C. felis and C. caviae, revealed a high level of sequence conservation and synteny across taxa, with the major exception of the human pathogen C. trachomatis. Important differences manifest in the polymorphic membrane protein family specific for the Chlamydiae and in the highly variable chlamydial plasticity zone. We identified a number of psittaci-specific polymorphic membrane proteins of the G family that may be related to differences in host-range and/or virulence as compared to closely related Chlamydiaceae. We calculated non-synonymous to synonymous substitution rate ratios for pairs of orthologous genes to identify putative targets of adaptive evolution and predicted type III secreted effector proteins. This study is the first detailed analysis of the Chlamydia psittaci genome sequence. It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions.

  11. Novel Chlamydiales genotypes identified in ticks from Australian wildlife.

    Science.gov (United States)

    Burnard, Delaney; Weaver, Haylee; Gillett, Amber; Loader, Joanne; Flanagan, Cheyne; Polkinghorne, Adam

    2017-01-26

    Members of the order Chlamydiales are known for their potential as human and veterinary bacterial pathogens. Despite this recognition, epidemiological factors such as routes of transmission are yet to be fully defined. Ticks are well known vectors for many other infections with several reports recently describing the presence of bacteria in the order Chlamydiales in these arthropods. Australian wildlife are hosts to an extensive range of tick species. Evidence is also growing that the marsupial hosts these ticks parasitise can also be infected by a number of bacteria in the order Chlamydiales, with at least one species, Chlamydia pecorum, posing a significant conservation threat. In the current study, we investigated the presence and identity of Chlamydiales in 438 ixodid ticks parasitizing wildlife in Australia by screening with a pan-Chlamydiales specific targeting the 16S rRNA gene. Pan-Chlamydiales specific PCR assays confirmed the common presence of Chlamydiales in Australian ticks parasitising a range of native wildlife. Interestingly, we did not detect any Chlamydiaceae, including C. pecorum, the ubiquitous pathogen of the koala. Instead, the Chlamydiales diversity that could be resolved indicated that Australian ticks carry at least six novel Chlamydiales genotypes. Phylogenetic analysis of the 16S rRNA sequences (663 bp) of these novel Chlamydiales suggests that three of these genotypes are associated with the Simkaniaceae and putatively belong to three distinct novel strains of Fritschea spp. and three genotypes are related to the "Ca. Rhabdochlamydiaceae" and putatively belong to a novel genus, Rhabdochlamydia species and strain, respectively. Sequence results suggest Australian wildlife ticks harbour a range of unique Chlamydiales bacteria that belong to families previously identified in a range of arthropod species. The results of this work also suggest that it is unlikely that arthropods act as vectors of pathogenic members of the family

  12. High prevalence of co-infection with multiple Torque teno sus virus species in Italian pig herds.

    Directory of Open Access Journals (Sweden)

    Sylvain Blois

    Full Text Available Torque teno viruses (TTVs are a large group of vertebrate-infecting small viruses with circular single-stranded DNA, classified in the Anelloviridae family. In swine, two genetically distinct species, Torque teno sus virus 1a (TTSuV1a and 1b (TTSuV1b are currently grouped into the genus Iotatorquevirus. More recently, a novel Torque teno sus virus species, named Torque teno sus virus k2b (TTSuVk2b, has been included with Torque teno sus virus k2a (TTSuVk2a into the genus Kappatorquevirus. In the present study, TTSuV1 (TTSuV1a and TTSuV1b, TTSuVk2a and TTSuVk2b prevalence was evaluated in 721 serum samples of healthy pigs from Sardinian farms, insular Italy. This is the largest study to date on the presence of TTSuV in healthy pigs in Italy. The global prevalence of infection was 83.2% (600/721, being 62.3% (449/721, 60.6% (437/721, and 11.5% (83/721 the prevalence of TTSuV1, TTSuVk2a and TTSuVk2b, respectively. The rate of co-infection with two and/or three species was also calculated, and data show that co-infections were significantly more frequent than infections with single species, and that TTSuV1+TTSuVk2a double infection was the prevalent combination (35.4%. Quantitative results obtained using species-specific real time-qPCR evidenced the highest mean levels of viremia in the TTSuV1 subgroup, and the lowest in the TTSuVk2b subgroup. Interestingly, multiple infections with distinct TTSuV species seemed to significantly affect the DNA load and specifically, data highlighted that double infection with TTSuVk2a increased the viral titers of TTSuV1, likewise the co-infection with TTSuVk2b increased the titers of TTSuVk2a.

  13. High prevalence of co-infection with multiple Torque teno sus virus species in Italian pig herds.

    Science.gov (United States)

    Blois, Sylvain; Mallus, Francesca; Liciardi, Manuele; Pilo, Cristian; Camboni, Tania; Macera, Lisa; Maggi, Fabrizio; Manzin, Aldo

    2014-01-01

    Torque teno viruses (TTVs) are a large group of vertebrate-infecting small viruses with circular single-stranded DNA, classified in the Anelloviridae family. In swine, two genetically distinct species, Torque teno sus virus 1a (TTSuV1a) and 1b (TTSuV1b) are currently grouped into the genus Iotatorquevirus. More recently, a novel Torque teno sus virus species, named Torque teno sus virus k2b (TTSuVk2b), has been included with Torque teno sus virus k2a (TTSuVk2a) into the genus Kappatorquevirus. In the present study, TTSuV1 (TTSuV1a and TTSuV1b), TTSuVk2a and TTSuVk2b prevalence was evaluated in 721 serum samples of healthy pigs from Sardinian farms, insular Italy. This is the largest study to date on the presence of TTSuV in healthy pigs in Italy. The global prevalence of infection was 83.2% (600/721), being 62.3% (449/721), 60.6% (437/721), and 11.5% (83/721) the prevalence of TTSuV1, TTSuVk2a and TTSuVk2b, respectively. The rate of co-infection with two and/or three species was also calculated, and data show that co-infections were significantly more frequent than infections with single species, and that TTSuV1+TTSuVk2a double infection was the prevalent combination (35.4%). Quantitative results obtained using species-specific real time-qPCR evidenced the highest mean levels of viremia in the TTSuV1 subgroup, and the lowest in the TTSuVk2b subgroup. Interestingly, multiple infections with distinct TTSuV species seemed to significantly affect the DNA load and specifically, data highlighted that double infection with TTSuVk2a increased the viral titers of TTSuV1, likewise the co-infection with TTSuVk2b increased the titers of TTSuVk2a.

  14. Diversified Native Species Restoration for Recovery of Multiple Ecosystem Services in a Highly Disturbed Tropical Dry Forest Landscape of Southwestern Nicaragua

    Science.gov (United States)

    Williams-Guillen, K.; Otterstrom, S.; Perla, C.

    2015-12-01

    Tropical dry forests have been reduced to a fraction of their original extent in the Neotropics due to conversion to agriculture and cattle pasture. While TDF can recover via natural regeneration, resulting forests are dominated by wind-dispersed pioneer species of limited value for frugivorous wildlife. Additionally, passive restoration can be perceived as "abandonment" resulting in neighbors casually invading property to rear livestock and extract timber. In 2007, the NGO Paso Pacífico initiated restoration in a highly degraded tropical dry forest landscape of southwestern Nicaragua; funded by an ex-ante carbon purchase, the project was designed to integrate multiple native tree species known to provide resources used by local wildlife. We restored roughly 400 hectares spanning a rainfall gradient from dry to transitional moist forest, using reforestation (planting 70 species of tree seedlings in degraded pastures on a 4x4 m grid, leaving occurring saplings) and assisted regeneration (clearing vines and competing vegetation from saplings in natural regeneration and strategically managing canopy cover). In just over seven years, mean carbon increased nearly threefold, from to 21.5±5.0 to 57.9±9.6 SE tonnes/ha. Current carbon stocks match those of 20-year-old forests in the area, accumulated in less than a decade. Stem density per 15-m radius plot decreased from 16.3±2.3 to 12.5±0.9 SE, while species richness increased from 3.9±0.4 to 18.4±1.4 SE. Alpha richness of woody stems across plots increased from 36 to 94 species, and over 20 tree species established as a result of natural dispersal and recruitment. We have observed sensitive species such as spider monkeys and parrots foraging in restoration areas. Managed reforestation is a highly effective method for rapidly restoring the functionality of multiple ecosystem services in degraded TDF, particularly when social and political realities force restoration to coexist with human productive activities

  15. Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

    Science.gov (United States)

    Beauparlant, Marc A; Drouin, Guy

    2014-02-01

    Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

  16. Species turnover drives β-diversity patterns across multiple spatial scales of plant-galling interactions in mountaintop grasslands.

    Science.gov (United States)

    Coelho, Marcel Serra; Carneiro, Marco Antônio Alves; Branco, Cristina Alves; Borges, Rafael Augusto Xavier; Fernandes, Geraldo Wilson

    2018-01-01

    This study describes differences in species richness and composition of the assemblages of galling insects and their host plants at different spatial scales. Sampling was conducted along altitudinal gradients composed of campos rupestres and campos de altitude of two mountain complexes in southeastern Brazil: Espinhaço Range and Mantiqueira Range. The following hypotheses were tested: i) local and regional richness of host plants and galling insects are positively correlated; ii) beta diversity is the most important component of regional diversity of host plants and galling insects; and iii) Turnover is the main mechanism driving beta diversity of both host plants and galling insects. Local richness of galling insects and host plants increased with increasing regional richness of species, suggesting a pattern of unsaturated communities. The additive partition of regional richness (γ) into local and beta components shows that local richnesses (α) of species of galling insects and host plants are low relative to regional richness; the beta (β) component incorporates most of the regional richness. The multi-scale analysis of additive partitioning showed similar patterns for galling insects and host plants with the local component (α) incorporated a small part of regional richness. Beta diversity of galling insects and host plants were mainly the result of turnover, with little contribution from nesting. Although the species composition of galling insects and host plant species varied among sample sites, mountains and even mountain ranges, local richness remained relatively low. In this way, the addition of local habitats with different landscapes substantially affects regional richness. Each mountain contributes fundamentally to the composition of regional diversity of galling insects and host plants, and so the design of future conservation strategies should incorporate multiple scales.

  17. Ring species as demonstrations of the continuum of species formation

    DEFF Research Database (Denmark)

    Pereira, Ricardo José Do Nascimento; Wake, David B.

    2015-01-01

    In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of 'circular overlaps' or 'ring species' as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier......? What conditions favour their formation? Modelling studies have attempted to address these knowledge gaps by estimating the biological parameters that result in stable ring species (Martins et al. 2013), and determining the necessary topographic parameters of the barriers encircled (Monahan et al. 2012......). However, any generalization is undermined by a major limitation: only a handful of ring species are known to exist in nature. In addition, many of them have been broken into multiple species presumed to be evolving independently, usually obscuring the evolutionary dynamics that generate diversity. A paper...

  18. Assessing species boundaries using multilocus species delimitation in a morphologically conserved group of neotropical freshwater fishes, the Poecilia sphenops species complex (Poeciliidae.

    Directory of Open Access Journals (Sweden)

    Justin C Bagley

    Full Text Available Accurately delimiting species is fundamentally important for understanding species diversity and distributions and devising effective strategies to conserve biodiversity. However, species delimitation is problematic in many taxa, including 'non-adaptive radiations' containing morphologically cryptic lineages. Fortunately, coalescent-based species delimitation methods hold promise for objectively estimating species limits in such radiations, using multilocus genetic data. Using coalescent-based approaches, we delimit species and infer evolutionary relationships in a morphologically conserved group of Central American freshwater fishes, the Poecilia sphenops species complex. Phylogenetic analyses of multiple genetic markers (sequences of two mitochondrial DNA genes and five nuclear loci from 10/15 species and genetic lineages recognized in the group support the P. sphenops species complex as monophyletic with respect to outgroups, with eight mitochondrial 'major-lineages' diverged by ≥2% pairwise genetic distances. From general mixed Yule-coalescent models, we discovered (conservatively 10 species within our concatenated mitochondrial DNA dataset, 9 of which were strongly supported by subsequent multilocus Bayesian species delimitation and species tree analyses. Results suggested species-level diversity is underestimated or overestimated by at least ~15% in different lineages in the complex. Nonparametric statistics and coalescent simulations indicate genealogical discordance among our gene tree results has mainly derived from interspecific hybridization in the nuclear genome. However, mitochondrial DNA show little evidence for introgression, and our species delimitation results appear robust to effects of this process. Overall, our findings support the utility of combining multiple lines of genetic evidence and broad phylogeographical sampling to discover and validate species using coalescent-based methods. Our study also highlights the

  19. Multiple glacial refugia of the low-dispersal ground beetle Carabus irregularis: molecular data support predictions of species distribution models.

    Directory of Open Access Journals (Sweden)

    Katharina Homburg

    Full Text Available Classical glacial refugia such as the southern European peninsulas were important for species survival during glacial periods and acted as sources of post-glacial colonisation processes. Only recently, some studies have provided evidence for glacial refugia north of the southern European peninsulas. In the present study, we combined species distribution models (SDMs with phylogeographic analyses (using mitochondrial DNA = mtDNA to investigate if the cold-adapted, stenotopic and flightless ground beetle species, Carabus irregularis, survived the Last Glacial Maximum (LGM in classical and/or other refugia. SDMs (for both a western European and for a Carpathian subgroup were calculated with MAXENT on the basis of 645 species records to predict current and past distribution patterns. Two mtDNA loci (CO1 and ND5, concatenated sequence length: 1785 bp were analyzed from 91 C. irregularis specimens to reconstruct the phylogeography of Central and eastern European populations and to estimate divergence times of the given lineages. Strong intra-specific genetic differentiation (inter-clade ΦST values ranged from 0.92 to 0.99 implied long-term isolation of major clades and subsclades. The high divergence between the nominate subspecies and the Carpathian subspecies C. i. montandoni points to two independent species rather than subspecies (K-2P distance 0.042 ± 0.004; supposed divergence of the maternal lineages dated back 1.6 to 2.5 million years BP differing not only morphologically but also genetically and ecologically from each other. The SDMs also inferred classical as well as other refugia for C. irregularis, especially north of the Alps, in southeastern Europe and in the Carpathians. The coincidences between the results of both methods confirm the assumption of multiple glacial refugia for the studied species and the usefulness of combining methodological approaches for the understanding of the history of low-dispersal insect species.

  20. Reactive Oxygen Species along with Reactive Nitrogen Species (ROS/RNS) as the Main Cause of Multiple Sclerosis

    OpenAIRE

    Somayeh Zaminpira; Sorush Niknamian

    2017-01-01

    Multiple Sclerosis is a condition of demyelination of the nerve cells in the brain and spinal cord. It is possible that multiple factors are involved in causing multiple sclerosis, including DNA defects in nuclear and mitochondrial genomes, viral infection, hypoxia, oxidative stress, lack of sunlight, and increased macrophages and lymphocytes in the brain. This meta-analysis has gone through many researches and reviews to find the similarities and differences in the cause of this disease. The...

  1. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species

    Science.gov (United States)

    Baroncelli, Riccardo; Zapparata, Antonio; Sarrocco, Sabrina; Sukno, Serenella A.; Lane, Charles R.; Thon, Michael R.; Vannacci, Giovanni; Holub, Eric; Sreenivasaprasad, Surapareddy

    2015-01-01

    Fragaria × ananassa (common name: strawberry) is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l.) is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production. PMID:26086351

  2. Molecular Diversity of Anthracnose Pathogen Populations Associated with UK Strawberry Production Suggests Multiple Introductions of Three Different Colletotrichum Species.

    Directory of Open Access Journals (Sweden)

    Riccardo Baroncelli

    Full Text Available Fragaria × ananassa (common name: strawberry is a globally cultivated hybrid species belonging to Rosaceae family. Colletotrichum acutatum sensu lato (s.l. is considered to be the second most economically important pathogen worldwide affecting strawberries. A collection of 148 Colletotrichum spp. isolates including 67 C. acutatum s.l. isolates associated with the phytosanitary history of UK strawberry production were used to characterize multi-locus genetic variation of this pathogen in the UK, relative to additional reference isolates that represent a worldwide sampling of the diversity of the fungus. The evidence indicates that three different species C. nymphaeae, C. godetiae and C. fioriniae are associated with strawberry production in the UK, which correspond to previously designated genetic groups A2, A4 and A3, respectively. Among these species, 12 distinct haplotypes were identified suggesting multiple introductions into the country. A subset of isolates was also used to compare aggressiveness in causing disease on strawberry plants and fruits. Isolates belonging to C. nymphaeae, C. godetiae and C. fioriniae representative of the UK anthracnose pathogen populations showed variation in their aggressiveness. Among the three species, C. nymphaeae and C. fioriniae appeared to be more aggressive compared to C. godetiae. This study highlights the genetic and pathogenic heterogeneity of the C. acutatum s.l. populations introduced into the UK linked to strawberry production.

  3. Invasive species information networks: Collaboration at multiple scales for prevention, early detection, and rapid response to invasive alien species

    Science.gov (United States)

    Simpson, Annie; Jarnevich, Catherine S.; Madsen, John; Westbrooks, Randy G.; Fournier, Christine; Mehrhoff, Les; Browne, Michael; Graham, Jim; Sellers, Elizabeth A.

    2009-01-01

    Accurate analysis of present distributions and effective modeling of future distributions of invasive alien species (IAS) are both highly dependent on the availability and accessibility of occurrence data and natural history information about the species. Invasive alien species monitoring and detection networks (such as the Invasive Plant Atlas of New England and the Invasive Plant Atlas of the MidSouth) generate occurrence data at local and regional levels within the United States, which are shared through the US National Institute of Invasive Species Science. The Inter-American Biodiversity Information Network's Invasives Information Network (I3N), facilitates cooperation on sharing invasive species occurrence data throughout the Western Hemisphere. The I3N and other national and regional networks expose their data globally via the Global Invasive Species Information Network (GISIN). International and interdisciplinary cooperation on data sharing strengthens cooperation on strategies and responses to invasions. However, limitations to effective collaboration among invasive species networks leading to successful early detection and rapid response to invasive species include: lack of interoperability; data accessibility; funding; and technical expertise. This paper proposes various solutions to these obstacles at different geographic levels and briefly describes success stories from the invasive species information networks mentioned above. Using biological informatics to facilitate global information sharing is especially critical in invasive species science, as research has shown that one of the best indicators of the invasiveness of a species is whether it has been invasive elsewhere. Data must also be shared across disciplines because natural history information (e.g. diet, predators, habitat requirements, etc.) about a species in its native range is vital for effective prevention, detection, and rapid response to an invasion. Finally, it has been our

  4. Multiple ion species fluid modeling of sprite halos and the role of electron detachment from O- in their dynamics

    Science.gov (United States)

    Liu, N.

    2011-12-01

    Sprite halos are brief descending glows appearing at the lower ionosphere boundary, which follow impulsive cloud-to-ground lightning discharges [e.g., Barrington-Leigh et al., JGR, 106, 1741, 2001, Wescott et al., JGR, 106, 10467, 2001; Pasko, JGR, 115, A00E35, 2010]. They last for a few milliseconds, with horizontal extension of tens of kilometers and vertical thickness of several kilometers. According to global survey of the occurrence of transient luminous events by the ISUAL instruments on the FORMOSAT-2 satellite, on average sprite halos occur once every minute on Earth [Chen et al., JGR, 113, A08306, 2008]. It has been established that sprite halos are caused by electron heating, and molecule excitation and ionization in the lower ionosphere due to lightning quasi-electrostatic field [e.g., Pasko et al., JGR, 102, 4529, 1997; Barrington-Leigh et al., 2001; Pasko, 2010]. Past modeling work on sprite halos was conducted using either a two dimensional (2D) model of at most three charged species or a zero dimensional model of multiple ion species. In this talk, we report a modeling study of sprite halos using a recently developed 2D fluid model of multiple charged species. The model charged species include the ion species set used in [Lehtinen and Inan, GRL, 34, L08804, 2007] to study the dynamics of ionization perturbations produced by gigantic jets in the middle and upper atmosphere. In addition, another charged species, O-, is added to this set, because electron detachment of O- can proceed very fast under moderate electric field [Rayment and Moruzzi, Int. J. Mass Spectrom., 26, 321, 1978], requiring a separate treatment from the other light negative ions. The modeling results of a sprite halo driven by positive cloud-to-ground lightning indicate that the halo can descend to lower altitude with much higher electron density behind its front when the O- detachment process is included. Electron density ahead of the halo front is not significantly reduced from the

  5. Multiple-level defect species evaluation from average carrier decay

    Science.gov (United States)

    Debuf, Didier

    2003-10-01

    An expression for the average decay is determined by solving the the carrier continuity equations, which include terms for multiple defect recombination. This expression is the decay measured by techniques such as the contactless photoconductance decay method, which determines the average or volume integrated decay. Implicit in the above is the requirement for good surface passivation such that only bulk properties are observed. A proposed experimental configuration is given to achieve the intended goal of an assessment of the type of defect in an n-type Czochralski-grown silicon semiconductor with an unusually high relative lifetime. The high lifetime is explained in terms of a ground excited state multiple-level defect system. Also, minority carrier trapping is investigated.

  6. Phylogeography in Nassarius mud snails: Complex patterns in congeneric species.

    Directory of Open Access Journals (Sweden)

    Chuanliang Pu

    Full Text Available One major goal for phylogeographical studies is to elucidate respective roles of multiple evolutionary and ecological forces that shape the current distribution patterns. In marine and coastal ecosystems, it has been generated a common realization that species with enormous population size and pelagic larval stages can disperse across broad geographical scales, leading to weak or even no phylogeographical structure across large geographical scales. However, the violation of such realization has been frequently reported, and it remains largely unexplored on mechanisms responsible for various phylogeographical patterns observed in different species at varied geographical scales. Here, we used a species-rich genus Nassarius to assess and compare phylogeographical patterns in congeneric species, and discuss causes and consequences underlying varied phylogeographical patterns. Interestingly, we observed complex phylogeographical patterns both within single species and across multiple species, and multiple analyses showed varied levels of genetic heterogeneity among sites within and across species. Available evidence suggests that related species with similar biological characteristics may not be necessary to result in consistent phylogeographical patterns. Multiple factors, including larval ecology, interactions between dispersal and natural selection, and human activity-mediated dispersal, can partially explain the complex patterns observed in this study. Deep investigations should be performed on these factors, particularly their respective roles in determining evolutionary/ecological processes to form phylogeographical patterns in species with high dispersal capacities in marine and coastal ecosystems.

  7. Characterizing lentic freshwater fish assemblages using multiple sampling methods

    Science.gov (United States)

    Fischer, Jesse R.; Quist, Michael C.

    2014-01-01

    Characterizing fish assemblages in lentic ecosystems is difficult, and multiple sampling methods are almost always necessary to gain reliable estimates of indices such as species richness. However, most research focused on lentic fish sampling methodology has targeted recreationally important species, and little to no information is available regarding the influence of multiple methods and timing (i.e., temporal variation) on characterizing entire fish assemblages. Therefore, six lakes and impoundments (48–1,557 ha surface area) were sampled seasonally with seven gear types to evaluate the combined influence of sampling methods and timing on the number of species and individuals sampled. Probabilities of detection for species indicated strong selectivities and seasonal trends that provide guidance on optimal seasons to use gears when targeting multiple species. The evaluation of species richness and number of individuals sampled using multiple gear combinations demonstrated that appreciable benefits over relatively few gears (e.g., to four) used in optimal seasons were not present. Specifically, over 90 % of the species encountered with all gear types and season combinations (N = 19) from six lakes and reservoirs were sampled with nighttime boat electrofishing in the fall and benthic trawling, modified-fyke, and mini-fyke netting during the summer. Our results indicated that the characterization of lentic fish assemblages was highly influenced by the selection of sampling gears and seasons, but did not appear to be influenced by waterbody type (i.e., natural lake, impoundment). The standardization of data collected with multiple methods and seasons to account for bias is imperative to monitoring of lentic ecosystems and will provide researchers with increased reliability in their interpretations and decisions made using information on lentic fish assemblages.

  8. Determinants of species richness patterns in the Netherlands across multiple taxonomic groups

    NARCIS (Netherlands)

    Schouten, M.A.; Verweij, P.A.; Barendrecht, A.; Kleukers, R.

    2009-01-01

    We examined the species richness patterns of five different species groups (mosses, reptiles and amphibians, grasshoppers and crickets, dragonflies, and hoverflies) in the Netherlands (41,500 km2) using sampling units of 5 × 5 km. We compared the spatial patterns of species richness of the five

  9. Detection and genotyping of Chlamydia species responsible for reproductive disorders in Algerian small ruminants.

    Science.gov (United States)

    Merdja, Salah-Eddine; Khaled, Hamza; Aaziz, Rachid; Vorimore, Fabien; Bertin, Claire; Dahmani, Ali; Bouyoucef, Abdallah; Laroucau, Karine

    2015-02-01

    Chlamydiosis in small ruminants is a zoonotic disease mainly related to Chlamydia abortus. This bacterium is responsible for abortions and reproductive disorders in sheep and goats. Stillbirth and infertility, leading to important economic losses, are also associated with this pathology. In Algeria, abortion cases are frequently reported by veterinarians but, except for brucellosis which is a notifiable disease in this country, abortive diseases are in general poorly studied. In order to detect and genotype Chlamydia species in small ruminants in different areas of Algeria, a study was conducted on samples collected from females (164 blood samples and 199 vaginal swabs) between October 2011 and March 2013. Serum samples were tested with a C. abortus-specific indirect ELISA test. Fourteen samples (8.5 %), from six farms (6/20, 30 %) were tested positive. Vaginal swabs were analysed with a real-time PCR targeting all Chlamydiaceae spp. Thirty samples (15 %) were diagnosed positive in 16 farms (16/25, 64 %). Positive samples were all re-tested with a C. abortus- and a C. pecorum-specific real-time PCR. Finally, 13/30 (43.3 %) and 6/30 (20 %) were identified as C. abortus and C. pecorum, respectively. Enough concentrated C. abortus samples were genotyped by multi-loci variable number of tandem repeat (VNTR) analysis (MLVA), and all were related to the genotype [2] group which mainly includes French C. abortus isolates. C. pecorum-positive samples were genotyped by multi-locus sequence typing (MLST). Interestingly, two of them were successfully genotyped and showed identical MLST sequences to VB2, AB10, E58 and SBE, a group which includes C. pecorum isolates considered as highly pathogenic. These findings suggest a possible role of C. abortus and C. pecorum strains in the aetiology of abortion in Algerian small ruminants.

  10. Priority setting for invasive species management: risk assessment of Ponto-Caspian invasive species into Great Britain.

    Science.gov (United States)

    Gallardo, Belinda; Aldridge, David C

    2013-03-01

    Invasive species drive important ecological and economic losses across wide geographies, with some regions supporting especially large numbers of nonnative species and consequently suffering relatively high impacts. For this reason, integrated risk assessments able to screen a suite of multiple invaders over large geographic areas are needed for prioritizing the allocation of limited resources. A total of 16 Ponto-Caspian aquatic species (10 gammarids, one isopod, two mysids, and three fishes) have been short-listed as recent or potential future invaders of British waters, whose introduction and spread is of high concern. In this study, we use multiple modeling techniques to assess their risk of establishment and spread into Great Britain. Climate suitability maps for these 16 species differed depending on the eastern and western distribution of species in continental Europe, which was related to their respective migration corridor: southern (Danube-Rhine rivers), and northern (Don and Volga rivers and Baltic lakes). Species whose suitability was high across large parts of Great Britain included four gammarids (Cheliorophium robustum, Dikerogammarus bispinosus, D. villosus, and Echinogammarus trichiatus) and a mysid (Hemimysis anomala). A climatic "heat map" combining the results of all 16 species together pointed to the southeast of England as the area most vulnerable to multiple invasions, particularly the Thames, Anglian, Severn, and Humber river basin districts. Regression models further suggested that alkalinity concentration > 120 mg/L in southeast England may favor the establishment of Ponto-Caspian invaders. The production of integrated risk maps for future invaders provides a means for the scientifically informed prioritization of resources toward particular species and geographic regions. Such tools have great utility in helping environmental managers focus efforts on the most effective prevention, management, and monitoring programs.

  11. Contaminant Effects on California Bay–Delta Species and Human Health

    Directory of Open Access Journals (Sweden)

    Stephanie Fong

    2016-12-01

    Full Text Available doi: https://doi.org/10.15447/sfews.2016v14iss4art5Many contaminants in the California Bay–Delta (Bay–Delta exceed regulatory standards, affect aquatic species, and potentially affect human health. Recent studies provide multiple lines of evidence that contaminants affect species of concern in the Bay–Delta (e.g., the decline of several important fish species referred to as the “Pelagic Organism Decline” or POD. Contaminants occur as dynamic complex mixtures and exert effects at multiple levels of biological organization. Multiple chemicals impair processes at cellular and physiological levels (measured as growth, development, and behavior abnormalities, and when viability and reproductive output are affected, populations are affected. As an important example, the population decline of the endangered Delta Smelt (Hypomesus transpacificus is significantly associated with multiple stressors, including insecticide use. New analyses presented in this paper show significant correlations between pyrethroid use and declining abundance of POD fish species. Water sampled from the Bay–Delta causes multiple deleterious effects in fish, and Delta Smelt collected from the Bay–Delta exhibit contaminant effects. Fish prey items are also affected by contaminants; this may have an indirect effect on their populations. Co-occurrence with thermal changes or disease can exacerbate contaminant effects. Contaminants also pose threats to human health via consumption of fish and shellfish, drinking water, and contact recreation, in particular, mercury, cyanobacteria toxins, disinfection byproducts, pathogens, pesticides, and pharmaceuticals and personal care products. The role of contaminants in the decline of Bay–Delta species is difficult to accurately assess in a complex, dynamic system. However, tools and approaches are available to evaluate contaminant effects on Bay–Delta species, and separate the effects of multiple stressors. Integrated

  12. Assembled cross-species perchlorate dose-response data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This data set contains dose-response data for perchlorate exposure in multiple species. These data were assembled from peer-reviewed studies. Species included in...

  13. Species limits and relationships within Otidea inferred from multiple gene phylogenies

    NARCIS (Netherlands)

    Hansen, K.; Olariaga, I.

    2015-01-01

    The genus Otidea is one of the more conspicuous members of the Pyronemataceae, with high species diversity in hemiboreal and boreal forests. The genus is morphologically coherent and in previous higher-level multi-gene analyses it formed a highly supported monophyletic group. Species delimitation

  14. Predictions for an invaded world: A strategy to predict the distribution of native and non-indigenous species at multiple scales

    Science.gov (United States)

    Reusser, D.A.; Lee, H.

    2008-01-01

    Habitat models can be used to predict the distributions of marine and estuarine non-indigenous species (NIS) over several spatial scales. At an estuary scale, our goal is to predict the estuaries most likely to be invaded, but at a habitat scale, the goal is to predict the specific locations within an estuary that are most vulnerable to invasion. As an initial step in evaluating several habitat models, model performance for a suite of benthic species with reasonably well-known distributions on the Pacific coast of the US needs to be compared. We discuss the utility of non-parametric multiplicative regression (NPMR) for predicting habitat- and estuary-scale distributions of native and NIS. NPMR incorporates interactions among variables, allows qualitative and categorical variables, and utilizes data on absence as well as presence. Preliminary results indicate that NPMR generally performs well at both spatial scales and that distributions of NIS are predicted as well as those of native species. For most species, latitude was the single best predictor, although similar model performance could be obtained at both spatial scales with combinations of other habitat variables. Errors of commission were more frequent at a habitat scale, with omission and commission errors approximately equal at an estuary scale. ?? 2008 International Council for the Exploration of the Sea. Published by Oxford Journals. All rights reserved.

  15. Projecting future expansion of invasive species: comparing and improving methodologies for species distribution modeling.

    Science.gov (United States)

    Mainali, Kumar P; Warren, Dan L; Dhileepan, Kunjithapatham; McConnachie, Andrew; Strathie, Lorraine; Hassan, Gul; Karki, Debendra; Shrestha, Bharat B; Parmesan, Camille

    2015-12-01

    Modeling the distributions of species, especially of invasive species in non-native ranges, involves multiple challenges. Here, we developed some novel approaches to species distribution modeling aimed at reducing the influences of such challenges and improving the realism of projections. We estimated species-environment relationships for Parthenium hysterophorus L. (Asteraceae) with four modeling methods run with multiple scenarios of (i) sources of occurrences and geographically isolated background ranges for absences, (ii) approaches to drawing background (absence) points, and (iii) alternate sets of predictor variables. We further tested various quantitative metrics of model evaluation against biological insight. Model projections were very sensitive to the choice of training dataset. Model accuracy was much improved using a global dataset for model training, rather than restricting data input to the species' native range. AUC score was a poor metric for model evaluation and, if used alone, was not a useful criterion for assessing model performance. Projections away from the sampled space (i.e., into areas of potential future invasion) were very different depending on the modeling methods used, raising questions about the reliability of ensemble projections. Generalized linear models gave very unrealistic projections far away from the training region. Models that efficiently fit the dominant pattern, but exclude highly local patterns in the dataset and capture interactions as they appear in data (e.g., boosted regression trees), improved generalization of the models. Biological knowledge of the species and its distribution was important in refining choices about the best set of projections. A post hoc test conducted on a new Parthenium dataset from Nepal validated excellent predictive performance of our 'best' model. We showed that vast stretches of currently uninvaded geographic areas on multiple continents harbor highly suitable habitats for parthenium

  16. Biological interactions and cooperative management of multiple species.

    Science.gov (United States)

    Jiang, Jinwei; Min, Yong; Chang, Jie; Ge, Ying

    2017-01-01

    Coordinated decision making and actions have become the primary solution for the overexploitation of interacting resources within ecosystems. However, the success of coordinated management is highly sensitive to biological, economic, and social conditions. Here, using a game theoretic framework and a 2-species model that considers various biological relationships (competition, predation, and mutualism), we compute cooperative (or joint) and non-cooperative (or separate) management equilibrium outcomes of the model and investigate the effects of the type and strength of the relationships. We find that cooperation does not always show superiority to non-cooperation in all biological interactions: (1) if and only if resources are involved in high-intensity predation relationships, cooperation can achieve a win-win scenario for ecosystem services and resource diversity; (2) for competitive resources, cooperation realizes higher ecosystem services by sacrificing resource diversity; and (3) for mutual resources, cooperation has no obvious advantage for either ecosystem services or resource evenness but can slightly improve resource abundance. Furthermore, by using a fishery model of the North California Current Marine Ecosystem with 63 species and seven fleets, we demonstrate that the theoretical results can be reproduced in real ecosystems. Therefore, effective ecosystem management should consider the interconnection between stakeholders' social relationship and resources' biological relationships.

  17. Two competing species in super-diffusive dynamical regimes

    Science.gov (United States)

    La Cognata, A.; Valenti, D.; Spagnolo, B.; Dubkov, A. A.

    2010-09-01

    The dynamics of two competing species within the framework of the generalized Lotka-Volterra equations, in the presence of multiplicative α-stable Lévy noise sources and a random time dependent interaction parameter, is studied. The species dynamics is characterized by two different dynamical regimes, exclusion of one species and coexistence of both, depending on the values of the interaction parameter, which obeys a Langevin equation with a periodically fluctuating bistable potential and an additive α-stable Lévy noise. The stochastic resonance phenomenon is analyzed for noise sources asymmetrically distributed. Finally, the effects of statistical dependence between multiplicative noise and additive noise on the dynamics of the two species are studied.

  18. Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau.

    Science.gov (United States)

    Wang, Bin; Xie, Feng; Li, Jiannan; Wang, Gang; Li, Cheng; Jiang, Jianping

    2017-01-01

    The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

  19. Effects of different dispersal patterns on the presence-absence of multiple species

    Science.gov (United States)

    Mohd, Mohd Hafiz; Murray, Rua; Plank, Michael J.; Godsoe, William

    2018-03-01

    Predicting which species will be present (or absent) across a geographical region remains one of the key problems in ecology. Numerous studies have suggested several ecological factors that can determine species presence-absence: environmental factors (i.e. abiotic environments), interactions among species (i.e. biotic interactions) and dispersal process. While various ecological factors have been considered, less attention has been given to the problem of understanding how different dispersal patterns, in interaction with other factors, shape community assembly in the presence of priority effects (i.e. where relative initial abundances determine the long-term presence-absence of each species). By employing both local and non-local dispersal models, we investigate the consequences of different dispersal patterns on the occurrence of priority effects and coexistence in multi-species communities. In the case of non-local, but short-range dispersal, we observe agreement with the predictions of local models for weak and medium dispersal strength, but disagreement for relatively strong dispersal levels. Our analysis shows the existence of a threshold value in dispersal strength (i.e. saddle-node bifurcation) above which priority effects disappear. These results also reveal a co-dimension 2 point, corresponding to a degenerate transcritical bifurcation: at this point, the transcritical bifurcation changes from subcritical to supercritical with corresponding creation of a saddle-node bifurcation curve. We observe further contrasting effects of non-local dispersal as dispersal distance changes: while very long-range dispersal can lead to species extinctions, intermediate-range dispersal can permit more outcomes with multi-species coexistence than short-range dispersal (or purely local dispersal). Overall, our results show that priority effects are more pronounced in the non-local dispersal models than in the local dispersal models. Taken together, our findings highlight

  20. Small molecule CP-31398 induces reactive oxygen species-dependent apoptosis in human multiple myeloma.

    Science.gov (United States)

    Arihara, Yohei; Takada, Kohichi; Kamihara, Yusuke; Hayasaka, Naotaka; Nakamura, Hajime; Murase, Kazuyuki; Ikeda, Hiroshi; Iyama, Satoshi; Sato, Tsutomu; Miyanishi, Koji; Kobune, Masayoshi; Kato, Junji

    2017-09-12

    Reactive oxygen species (ROS) are normal byproducts of a wide variety of cellular processes. ROS have dual functional roles in cancer cell pathophysiology. At low to moderate levels, ROS act as signaling transducers to activate cell proliferation, migration, invasion, and angiogenesis. In contrast, high levels of ROS induce cell death. In multiple myeloma (MM), ROS overproduction is the trigger for apoptosis induced by several anticancer compounds, including proteasome inhibitors. However, no drugs for which oxidative stress is the main mechanism of action are currently used for treatment of MM in clinical situations. In this study, we demonstrate that the p53-activating small molecule CP-31398 (CP) effectively inhibits the growth of MM cell lines and primary MM isolates from patients. CP also suppresses the growth of MM xenografts in mice. Mechanistically, CP was found to induce intrinsic apoptosis in MM cells via increasing ROS production. Interestingly, CP-induced apoptosis occurs regardless of the p53 status, suggesting that CP has additional mechanisms of action. Our findings thus indicate that CP could be an attractive candidate for treatment of MM patients harboring p53 abnormalities; this satisfies an unmet clinical need, as such individuals currently have a poor prognosis.

  1. Central-marginal population dynamics in species invasions

    Directory of Open Access Journals (Sweden)

    Qinfeng eGuo

    2014-06-01

    Full Text Available The species’ range limits and associated central-marginal (C-M; i.e., from species range center to margin population dynamics continue to draw increasing attention because of their importance for current emerging issues such as biotic invasions and epidemic diseases under global change. Previous studies have mainly focused on species borders and C-M process in natural settings for native species. More recently, growing efforts are devoted to examine the C-M patterns and process for invasive species partly due to their relatively short history, highly dynamic populations, and management implications. Here I examine recent findings and information gaps related to (1 the C-M population dynamics linked to species invasions, and (2 the possible effects of climate change and land use on the C-M patterns and processes. Unlike most native species that are relatively stable (some even having contracting populations or ranges, many invasive species are still spreading fast and form new distribution or abundance centers. Because of the strong nonlinearity of population demographic or vital rates (i.e. birth, death, immigration and emigration across the C-M gradients and the increased complexity of species ranges due to habitat fragmentation, multiple introductions, range-wide C-M comparisons and simulation involving multiple vital rates are needed in the future.

  2. Complex patterns of speciation in cosmopolitan "rock posy" lichens--discovering and delimiting cryptic fungal species in the lichen-forming Rhizoplaca melanophthalma species-complex (Lecanoraceae, Ascomycota).

    Science.gov (United States)

    Leavitt, Steven D; Fankhauser, Johnathon D; Leavitt, Dean H; Porter, Lyndon D; Johnson, Leigh A; St Clair, Larry L

    2011-06-01

    A growing body of evidence indicates that in some cases morphology-based species circumscription of lichenized fungi misrepresents the number of existing species. The cosmopolitan "rock posy" lichen (Rhizoplaca melanophthalma) species-complex includes a number of morphologically distinct species that are both geographically and ecologically widespread, providing a model system to evaluate speciation in lichen-forming ascomycetes. In this study, we assembled multiple lines of evidence from nuclear DNA sequence data, morphology, and biochemistry for species delimitation in the R. melanophthalma species-complex. We identify a total of ten candidate species in this study, four of which were previously recognized as distinct taxa and six previously unrecognized lineages found within what has been thus far considered a single species. Candidate species are supported using inferences from multiple empirical operational criteria. Multiple instances of sympatry support the view that these lineages merit recognition as distinct taxa. Generally, we found little corroboration between morphological and chemical characters, and previously unidentified lineages were morphologically polymorphic. However, secondary metabolite data supported one cryptic saxicolous lineage, characterized by orsellinic-derived gyrophoric and lecanoric acids, which we consider to be taxonomically significant. Our study of the R. melanophthalma species-complex indicates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than originally perceived, and we present our analyses as a working example of species delimitation in morphologically cryptic and recently diverged lichenized fungi. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. San Diego Multiple Species Conservation Program (MSCP) Rare Plant Monitoring Review and Revision

    Science.gov (United States)

    McEachern, Kathryn; Pavlik, Bruce M.; Rebman, Jon; Sutter, Rob

    2007-01-01

    Introduction The San Diego Multiple Species Conservation Program (MSCP) was developed for the conservation of plants and animals in the south part of San Diego County, under the California Natural Community Conservation Planning Act of 1991 (California Department of Fish and Game) and the Federal Endangered Species Act of 1973, as amended (16 U.S. Code 1531-1544.) The Program is on the leading edge of conservation, as it seeks to both guide development and conserve at-risk species with the oversight of both State and Federal agencies. Lands were identified for inclusion in the MSCP based on their value as habitat for at-risk plants or plant communities (Natural Community Conservation Planning, 2005). Since its inception in the mid-1990s the Program has protected over 100,000 acres, involving 15 jurisdictions and the U.S. Fish and Wildlife Service (USFWS) and California Department of Fish and Game (CDFG) in the conservation of 87 taxa. Surveys for covered species have been conducted, and management and monitoring have been implemented at some high priority sites. Each jurisdiction or agency manages and monitors their conservation areas independently, while collaborating regionally for long-term protection. The San Diego MSCP is on the forefront of conservation, in one of the most rapidly growing urban areas of the country. The planning effort that developed the MSCP was state-of-the-art, using expert knowledge, spatial habitat modeling, and principles of preserve design to identify and prioritize areas for protection. Land acquisition and protection are ahead of schedule for most jurisdictions. Surveys have verified the locations of many rare plant populations known from earlier collections, and they provide general information on population size and health useful for further conservation planning. Management plans have been written or are in development for most MSCP parcels under jurisdictional control. Several agencies are developing databases for implementation

  4. Multiple paternity and hybridization in two smooth-hound sharks.

    Science.gov (United States)

    Marino, Ilaria A M; Riginella, Emilio; Gristina, Michele; Rasotto, Maria B; Zane, Lorenzo; Mazzoldi, Carlotta

    2015-08-10

    Multiple paternity appears to be a common trait of elasmobranch mating systems, with its occurrence likely driven by convenience, due to females seeking to minimize the stress of male harassment. Here we use molecular markers to analyse the frequency of multiple paternity in two related viviparous sharks, Mustelus mustelus and Mustelus punctulatus. We first applied molecular methods to assign pregnant females, embryos and additional reference adults (N = 792) to one of the two species. Paternity analysis was performed using a total of 9 polymorphic microsatellites on 19 females and 204 embryos of M. mustelus, and on 13 females and 303 embryos of M. punctulatus. Multiple paternity occurs in both species, with 47% of M. mustelus and 54% of M. punctulatus litters sired by at least two fathers. Female fecundity is not influenced by multiple mating and in 56% of polyandrous litters paternity is skewed, with one male siring most of the pups. Genetic analyses also revealed hybridization between the two species, with a M. punctulatus female bearing pups sired by a M. mustelus male. The frequency of polyandrous litters in these species is consistent with aspects of their reproductive biology, such as synchronous ovulation and possible occurrence of breeding aggregations.

  5. A Physiologically Based Pharmacokinetic (PB/PK) Model for Multiple Exposure Routes of Soman in Multiple Species

    National Research Council Canada - National Science Library

    Sweeney, Richard E; Langenberg, Jan P; Maxwell, Donald M

    2006-01-01

    ...) levels of soman challenge in three species (rat, guinea pig, marmoset). Allometric formulae were used to compute the compartment volumes, blood flow rates, tidal volume and respiratory rate based upon total animal weight...

  6. The Importance of Providing Multiple-Channel Sections in Dredging Activities to Improve Fish Habitat Environments

    Directory of Open Access Journals (Sweden)

    Hung-Pin Chiu

    2016-01-01

    Full Text Available After Typhoon Morakot, dredging engineering was conducted while taking the safety of humans and structures into consideration, but partial stream reaches were formed in the multiple-channel sections in Cishan Stream because of anthropogenic and natural influences. This study mainly explores the distribution of each fish species in both the multiple- and single-channel sections in the Cishan Stream. Parts of the environments did not exhibit significant differences according to a one-way ANOVA comparing the multiple- and single-channel sections, but certain areas of the multiple-channel sections had more diverse habitats. Each fish species was widely distributed by non-metric multidimensional scaling in the multiple-channel sections as compared to those in the single-channel sections. In addition, according to the principal component analysis, each fish species has a preferred environment, and all of them have a wide choice of habitat environments in the multiple-channel sections. Finally, the existence of multiple-channel sections could significantly affect the existence of the fish species under consideration in this study. However, no environmental factors were found to have an influence on fish species in the single-channel sections, with the exception of Rhinogobius nantaiensis. The results show that providing multiple-channel sections in dredging activities could improve fish habitat environments.

  7. Molecular assessment of Podarcis sicula populations in Britain, Greece and Turkey reinforces a multiple-origin invasion pattern in this species

    Directory of Open Access Journals (Sweden)

    Iolanda Silva-Rocha

    2014-12-01

    Full Text Available Biological invasions are a challenge to conservation and constitute a threat to biodiversity worldwide. The Italian wall lizard Podarcis sicula has been widely introduced, and seems capable of adapting to most of the regions where it is established and to impact on native biota. Here we construct a phylogenetic framework to assess the origin of the introduced populations in the United Kingdom, Greece and Turkey comparing cytochrome-b gene sequences of lizards from five locations to published sequences from the native range and other non-native locations. The results support an origin from central Italy for the United Kingdom population, from the Adriatic region for the Greek population and from Calabria for the population from Turkey. These results emphasise the multiple-source pattern of introduction of this species identified in previous studies. The improvement in the knowledge of the origin and pathways by which invaders arrive in new areas, as well as the monitoring of their populations, are crucial for successful strategies to deal with exotic species.

  8. Efficient species-level monitoring at the landscape scale

    Science.gov (United States)

    Barry R. Noon; Larissa L. Bailey; Thomas D. Sisk; Kevin S. McKelvey

    2012-01-01

    Monitoring the population trends of multiple animal species at a landscape scale is prohibitively expensive. However, advances in survey design, statistical methods, and the ability to estimate species presence on the basis of detection­nondetection data have greatly increased the feasibility of species-level monitoring. For example, recent advances in monitoring make...

  9. Genetic assessment of ornamental fish species from North East India.

    Science.gov (United States)

    Dhar, Bishal; Ghosh, Sankar Kumar

    2015-01-25

    Ornamental fishes are traded with multiple names from various parts around the world, including North East India. Most are collected from the wild, due to lack of species-specific culture or breeding, and therefore, such unmanaged collection of the wild and endemic species could lead to severe threats to biodiversity. Despite many regulatory policies, trade of threatened species, including the IUCN listed species have been largely uncontrolled, due to species identification problems arising from the utilization of multiple trade names. So, the development of species-specific DNA marker is indispensable where DNA Barcoding is proved to be helpful in species identification. Here, we investigated, through DNA Barcoding and morphological assessment, the identification of 128 ornamental fish specimens exported from NE India from different exporters. The generated sequences were subjected to similarity match in BOLD-IDS as well as BLASTN, and analysed using MEGA5.2 for species identification through Neighbour-Joining (NJ) clustering, and K2P distance based approach. The analysis revealed straightforward identification of 84 specimens into 35 species, while 44 specimens were difficult to distinguish based on CO1 barcode alone. However, these cases were resolved through morphology, NJ and distanced based method and found to be belonging to 16 species. Among the 51 identified species, 14 species represented multiple trade names; 17 species belonged to threatened category. Species-level identification through DNA Barcoding along with traditional morphotaxonomy reflects its efficacy in regulating ornamental fish trade and therefore, appeals for their conservation in nature. The use of trade names rather than the zoological name created the passage for trafficking of the threatened species and demands immediate attention for sustaining wildlife conservation. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Relating biomarkers to whole-organism effects using species sensitivity distributions : A pilot study for marine species exposed to oil

    NARCIS (Netherlands)

    Smit, M.G.D.; Bechmann, R.K.; Hendriks, A.J.; Skadsheim, A.; Larsen, B.K.; Baussant, T.; Bamber, S.; Sannei, S.

    2009-01-01

    Biomarkers are widely used to measure environmental impacts on marine species. For many biomarkers, it is not clear how the signal levels relate to effects on the whole organism. This paper shows how species sensitivity distributions (SSDs) can be applied to evaluate multiple biomarker responses in

  11. Differential recognition of the multiple banded antigen isoforms across Ureaplasma parvum and Ureaplasma urealyticum species by monoclonal antibodies.

    Science.gov (United States)

    Aboklaish, Ali F; Ahmed, Shatha; McAllister, Douglas; Cassell, Gail; Zheng, Xiaotian T; Spiller, Owen B

    2016-08-01

    Two separate species of Ureaplasma have been identified that infect humans: Ureaplasma parvum and Ureaplasma urealyticum. Most notably, these bacteria lack a cell wall and are the leading infectious organism associated with infection-related induction of preterm birth. Fourteen separate representative prototype bacterial strains, called serovars, are largely differentiated by the sequence of repeating units in the C-terminus of the major surface protein: multiple-banded antigen (MBA). Monoclonal antibodies that recognise single or small groups of serovars have been previously reported, but these reagents remain sequestered in individual research laboratories. Here we characterise a panel of commercially available monoclonal antibodies raised against the MBA and describe the first monoclonal antibody that cross-reacts by immunoblot with all serovars of U. parvum and U. urealyticum species. We also describe a recombinant MBA expressed by Escherichia coli which facilitated further characterisation by immunoblot and demonstrate immunohistochemistry of paraffin-embedded antigens. Immunoblot reactivity was validated against well characterised previously published monoclonal antibodies and individual commercial antibodies were found to recognise all U. parvum strains, only serovars 3 and 14 or only serovars 1 and 6, or all strains belonging to U. parvum and U. urealyticum. MBA mass was highly variable between strains, consistent with variation in the number of C-terminal repeats between strains. Antibody characterisation will enable future investigations to correlate severity of pathogenicity to MBA isoform number or mass, in addition to development of antibody-based diagnostics that will detect infection by all Ureaplasma species or alternately be able to differentiate between U. parvum, U. urealyticum or mixed infections. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Alternaria section Alternaria: Species, formae speciales or pathotypes'

    NARCIS (Netherlands)

    Woudenberg, J.H.C.; Seidl, M.F.; Groenewald, J.Z.; de Vries, M .; Stielow, B.; Thomma, B.P.H.J.; Crous, P.W.

    2015-01-01

    The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated

  13. Alternaria section Alternaria: Species, formae speciales or pathotypes?

    NARCIS (Netherlands)

    Woudenberg, J.H.C.; Seidl, M.F.; Groenewald, J.Z.; Vries, de M.; Stielow, J.B.; Thomma, B.; Crous, P.W.

    2015-01-01

    The cosmopolitan fungal genus Alternaria consists of multiple saprophytic and pathogenic species. Based on phylogenetic and morphological studies, the genus is currently divided into 26 sections. Alternaria sect. Alternaria contains most of the small-spored Alternaria species with concatenated

  14. As multiple fish species in large marine ecosystems are harvested ...

    African Journals Online (AJOL)

    CMPTMAC10

    and of other top predators such as marine mammals. This concern ... whereas single-species fishing theory implies that fishing leads to surplus by removing larger, older, less-productive ...... pools (the “cod is not a tuna” problem, Longhurst.

  15. Multiple Phytophthora species associated with a single riparian ecosystem in South Africa.

    Science.gov (United States)

    Nagel, Jan H; Slippers, Bernard; Wingfield, Michael J; Gryzenhout, Marieka

    2015-01-01

    The diversity of Phytophthora spp. in rivers and riparian ecosystems has received considerable international attention, although little such research has been conducted in South Africa. This study determined the diversity of Phytophthora spp. within a single river in Gauteng province of South Africa. Samples were collected over 1 y including biweekly river baiting with Rhododendron indicum leaves. Phytophthora isolates were identified with phylogenetic analyses of sequences for the internal transcribed spacer (ITS) region of the ribosomal DNA and the mitochondrial cytochrome oxidase c subunit I (coxI) gene. Eight Phytophthora spp. were identified, including a new taxon, P. taxon Sisulu-river, and two hybrid species from Cooke's ITS clade 6. Of these, species from Clade 6 were the most abundant, including P. chlamydospora and P. lacustris. Species residing in Clade 2 also were encountered, including P. multivora, P. plurivora and P. citrophthora. The detection of eight species in this investigation of Phytophthora diversity in a single riparian river ecosystem in northern South Africa adds to the known diversity of this genus in South Africa and globally. © 2015 by The Mycological Society of America.

  16. Semiparametric bivariate zero-inflated Poisson models with application to studies of abundance for multiple species

    Science.gov (United States)

    Arab, Ali; Holan, Scott H.; Wikle, Christopher K.; Wildhaber, Mark L.

    2012-01-01

    Ecological studies involving counts of abundance, presence–absence or occupancy rates often produce data having a substantial proportion of zeros. Furthermore, these types of processes are typically multivariate and only adequately described by complex nonlinear relationships involving externally measured covariates. Ignoring these aspects of the data and implementing standard approaches can lead to models that fail to provide adequate scientific understanding of the underlying ecological processes, possibly resulting in a loss of inferential power. One method of dealing with data having excess zeros is to consider the class of univariate zero-inflated generalized linear models. However, this class of models fails to address the multivariate and nonlinear aspects associated with the data usually encountered in practice. Therefore, we propose a semiparametric bivariate zero-inflated Poisson model that takes into account both of these data attributes. The general modeling framework is hierarchical Bayes and is suitable for a broad range of applications. We demonstrate the effectiveness of our model through a motivating example on modeling catch per unit area for multiple species using data from the Missouri River Benthic Fishes Study, implemented by the United States Geological Survey.

  17. Membrane-based oligonucleotide array developed from multiple markers for the detection of many Phytophthora species.

    Science.gov (United States)

    Chen, Wen; Djama, Zeinab Robleh; Coffey, Michael D; Martin, Frank N; Bilodeau, Guillaume J; Radmer, Lorien; Denton, Geoff; Lévesque, C André

    2013-01-01

    Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5' end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.

  18. Possible pathogenic interplay between Chlamydia suis, Chlamydophila abortus and PCV-2 on a pig production farm.

    Science.gov (United States)

    Schautteet, K; Beeckman, D S A; Delava, P; Vanrompay, D

    2010-03-13

    A concurrent outbreak of chlamydial disease in boars, sows and gilts and postweaning multisystemic wasting syndrome (PMWS) in weaned piglets was investigated on a large pig production farm in Estonia. Chlamydia suis DNA was detected in conjunctival swabs from boars, sows and gilts, but also in the faeces of boars and sows. Chlamydophila abortus DNA was found in semen, and in conjunctival swabs from sows; DNA was demonstrated by microarrays. Serum samples from boars were examined using a Chlamydiaceae-specific recombinant ELISA. All 10 serum samples examined were positive (1:960 to 1:3840). Chlamydiosis was characterised by reproductive failure and conjunctivitis. Piglets were not examined for Chlamydiaceae, as eye problems were not observed. Piglets showed wasting, respiratory signs, diarrhoea, enlargement of lymph nodes and increased mortality (10 per cent). Porcine circovirus type 2 (PCV-2) was detected in the lymph nodes of piglets by immunohistochemistry, and PCV-2 antibodies were demonstrated in all 10 serum samples from sows examined using an immunoperoxidase monolayer assay.

  19. Comparative microbial modules resource: generation and visualization of multi-species biclusters.

    Science.gov (United States)

    Kacmarczyk, Thadeous; Waltman, Peter; Bate, Ashley; Eichenberger, Patrick; Bonneau, Richard

    2011-12-01

    The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures - results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation. © 2011 Kacmarczyk et al.

  20. Comparative microbial modules resource: generation and visualization of multi-species biclusters.

    Directory of Open Access Journals (Sweden)

    Thadeous Kacmarczyk

    2011-12-01

    Full Text Available The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html. The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures - results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation.

  1. Time-domain multiple-quantum NMR

    International Nuclear Information System (INIS)

    Weitekamp, D.P.

    1982-11-01

    The development of time-domain multiple-quantum nuclear magnetic resonance is reviewed through mid 1982 and some prospects for future development are indicated. Particular attention is given to the problem of obtaining resolved, interpretable, many-quantum spectra for anisotropic magnetically isolated systems of coupled spins. New results are presented on a number of topics including the optimization of multiple-quantum-line intensities, analysis of noise in two-dimensional spectroscopy, and the use of order-selective excitation for cross polarization between nuclear-spin species

  2. No Inbreeding depression for low temperature developmental acclimation across multiple drosophila species

    DEFF Research Database (Denmark)

    Kristensen, Torsten Nygård; Loeschcke, Volker; Bilde, Trine

    2011-01-01

    stressful temperatures, but whether adaptation to thermal stress through plastic responses also is affected by inbreeding is so far not clear. In this study, we test inherent cold resistance and the ability to respond plastically to temperature changes through developmental cold acclimation in inbred...... the ability to respond adaptively to temperature acclimation, and (3) tropical species with low basal resistance show stronger adaptive plastic responses to developmental acclimation compared to widespread species...

  3. Method for aquatic multiple species toxicant testing: acute toxicity of 10 chemicals to 5 vertebrates and 2 invertebrates. [Pimephales promelas; Carassius auratus; Ictalurus punctatus; Lepomis macrochirus; Salmo gairdneri; Orconectes immunis; Aplexa hypnorum

    Energy Technology Data Exchange (ETDEWEB)

    Phipps, G.L.; Holcombe, G.W.

    1985-01-01

    A method was developed to simultaneously ascertain 96 h LC/sub 50/ values for seven freshwater species in a single flow through test with measured concentrations. It allows interspecific comparisons, easy determination of the most sensitive species, and cuts cost of labor, materials and chemical analysis for measured concentration tests. Species tested included fathead minnows Pimephales promelas, goldfish Carassius auratus, channel catfish Ictalurus punctatus, bluegill Lepomis macrochirus, rainbow trout Salmo gairdneri, crayfish Orconectes immunis and snails Aplexa hypnorum. Compounds tested were pentachlorophenol, 2-chloroethanol, 2,4-pentanedione, hexachloroethane, ..cap alpha..-bromo-2',5'-dimethoxyacetophenone, benzaldehyde, 1,3-dichloro-4,6-dinitro-benzene, dursban, sevin and cadmium chloride. The LC/sub 50/ values from these multiple species tests compared favourably with those determined using single species tests at this laboratory, usually within 20%.

  4. Cross-species infection trials reveal cryptic parasite varieties and a putative polymorphism shared among host species.

    Science.gov (United States)

    Luijckx, Pepijn; Duneau, David; Andras, Jason P; Ebert, Dieter

    2014-02-01

    A parasite's host range can have important consequences for ecological and evolutionary processes but can be difficult to infer. Successful infection depends on the outcome of multiple steps and only some steps of the infection process may be critical in determining a parasites host range. To test this hypothesis, we investigated the host range of the bacterium Pasteuria ramosa, a Daphnia parasite, and determined the parasites success in different stages of the infection process. Multiple genotypes of Daphnia pulex, Daphnia longispina and Daphnia magna were tested with four Pasteuria genotypes using infection trials and an assay that determines the ability of the parasite to attach to the hosts esophagus. We find that attachment is not specific to host species but is specific to host genotype. This may suggest that alleles on the locus controlling attachment are shared among different host species that diverged 100 million year. However, in our trials, Pasteuria was never able to reproduce in nonnative host species, suggesting that Pasteuria infecting different host species are different varieties, each with a narrow host range. Our approach highlights the explanatory power of dissecting the steps of the infection process and resolves potentially conflicting reports on parasite host ranges. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  5. Federated or cached searches: providing expected performance from multiple invasive species databases

    Science.gov (United States)

    Graham, Jim; Jarnevich, Catherine S.; Simpson, Annie; Newman, Gregory J.; Stohlgren, Thomas J.

    2011-01-01

    Invasive species are a universal global problem, but the information to identify them, manage them, and prevent invasions is stored around the globe in a variety of formats. The Global Invasive Species Information Network is a consortium of organizations working toward providing seamless access to these disparate databases via the Internet. A distributed network of databases can be created using the Internet and a standard web service protocol. There are two options to provide this integration. First, federated searches are being proposed to allow users to search “deep” web documents such as databases for invasive species. A second method is to create a cache of data from the databases for searching. We compare these two methods, and show that federated searches will not provide the performance and flexibility required from users and a central cache of the datum are required to improve performance.

  6. Genetic complexity and multiple infections with more Parvovirus species in naturally infected cats

    Directory of Open Access Journals (Sweden)

    Battilani Mara

    2011-03-01

    Full Text Available Abstract Parvoviruses of carnivores include three closely related autonomous parvoviruses: canine parvovirus (CPV, feline panleukopenia virus (FPV and mink enteritis virus (MEV. These viruses cause a variety of serious diseases, especially in young patients, since they have a remarkable predilection for replication in rapidly dividing cells. FPV is not the only parvovirus species which infects cats; in addition to MEV, the new variants of canine parvovirus, CPV-2a, 2b and 2c have also penetrated the feline host-range, and they are able to infect and replicate in cats, causing diseases indistinguishable from feline panleukopenia. Furthermore, as cats are susceptible to both CPV-2 and FPV viruses, superinfection and co-infection with multiple parvovirus strains may occur, potentially facilitating recombination and high genetic heterogeneity. In the light of the importance of cats as a potential source of genetic diversity for parvoviruses and, since feline panleukopenia virus has re-emerged as a major cause of mortality in felines, the present study has explored the molecular characteristics of parvovirus strains circulating in cat populations. The most significant findings reported in this study were (a the detection of mixed infection FPV/CPV with the presence of one parvovirus variant which is a true intermediate between FPV/CPV and (b the quasispecies cloud size of one CPV sample variant 2c. In conclusion, this study provides new important results about the evolutionary dynamics of CPV infections in cats, showing that CPV has presumably started a new process of readaptation in feline hosts.

  7. Multi-species biofilm of Candida albicans and non-Candida albicans Candida species on acrylic substrate

    Directory of Open Access Journals (Sweden)

    Apurva K Pathak

    2012-02-01

    Full Text Available OBJECTIVE: In polymicrobial biofilms bacteria extensively interact with Candida species, but the interaction among the different species of the Candida is yet to be completely evaluated. In the present study, the difference in biofilm formation ability of clinical isolates of four species of Candida in both single-species and multi-species combinations on the surface of dental acrylic resin strips was evaluated. MATERIAL AND METHODS: The species of Candida, isolated from multiple species oral candidiasis of the neutropenic patients, were used for the experiment. Organisms were cultured on Sabouraud dextrose broth with 8% glucose (SDB. Biofilm production on the acrylic resins strips was determined by crystal violet assay. Student's t-test and ANOVA were used to compare in vitro biofilm formation for the individual species of Candida and its different multi-species combinations. RESULTS: In the present study, differences between the mean values of the biofilm-forming ability of individual species (C. glabrata>C. krusei>C. tropicalis>C. albicans and in its multi-species' combinations (the highest for C. albicans with C. glabrata and the lowest for all the four species combination were reported. CONCLUSIONS: The findings of this study showed that biofilm-forming ability was found greater for non-Candida albicans Candida species (NCAC than for C. albicans species with intra-species variation. Presence of C. albicans in multi-species biofilms increased, whereas; C. tropicalis decreased the biofilm production with all other NCAC species.

  8. Ward identities and consistency relations for the large scale structure with multiple species

    International Nuclear Information System (INIS)

    Peloso, Marco; Pietroni, Massimo

    2014-01-01

    We present fully nonlinear consistency relations for the squeezed bispectrum of Large Scale Structure. These relations hold when the matter component of the Universe is composed of one or more species, and generalize those obtained in [1,2] in the single species case. The multi-species relations apply to the standard dark matter + baryons scenario, as well as to the case in which some of the fields are auxiliary quantities describing a particular population, such as dark matter halos or a specific galaxy class. If a large scale velocity bias exists between the different populations new terms appear in the consistency relations with respect to the single species case. As an illustration, we discuss two physical cases in which such a velocity bias can exist: (1) a new long range scalar force in the dark matter sector (resulting in a violation of the equivalence principle in the dark matter-baryon system), and (2) the distribution of dark matter halos relative to that of the underlying dark matter field

  9. Biological species in the viral world.

    Science.gov (United States)

    Bobay, Louis-Marie; Ochman, Howard

    2018-06-05

    Due to their dependence on cellular organisms for metabolism and replication, viruses are typically named and assigned to species according to their genome structure and the original host that they infect. But because viruses often infect multiple hosts and the numbers of distinct lineages within a host can be vast, their delineation into species is often dictated by arbitrary sequence thresholds, which are highly inconsistent across lineages. Here we apply an approach to determine the boundaries of viral species based on the detection of gene flow within populations, thereby defining viral species according to the biological species concept (BSC). Despite the potential for gene transfer between highly divergent genomes, viruses, like the cellular organisms they infect, assort into reproductively isolated groups and can be organized into biological species. This approach revealed that BSC-defined viral species are often congruent with the taxonomic partitioning based on shared gene contents and host tropism, and that bacteriophages can similarly be classified in biological species. These results open the possibility to use a single, universal definition of species that is applicable across cellular and acellular lifeforms.

  10. Preliminary assessment of the ecological risks to wide-ranging wildlife species on the Oak Ridge Reservation

    Energy Technology Data Exchange (ETDEWEB)

    Sample, B.E.; Baron, L.A.; Jackson, B.L.

    1995-08-01

    Historically, ecological risk assessment at CERCLA sites [such as the Oak Ridge Reservation (ORR)], has focused on species that may be definitively associated with a contaminated area or source operable unit. Consequently the species that are generally considered are those with home ranges small enough such that multiple individuals or a distinct population can be expected to reside within the boundaries of the contaminated site. This approach is adequate for sites with single, discrete areas of contamination that only provide habitat for species with limited requirements. This approach is not adequate however for large sites with multiple, spatially separated contaminated areas that provide habitat for wide-ranging wildlife species. Because wide-ranging wildlife species may travel between and use multiple contaminated sites they may be exposed to and be at risk from contaminants from multiple locations. Use of a particular contaminated site by wide-ranging species will be dependent upon the amount of suitable habitat available at that site. Therefore to adequately evaluate risks to wide-ranging species at the ORR-wide scale, the use of multiple contaminated sites must be weighted by the amount of suitable habitat on OUs. This reservation-wide ecological risk assessment is intended to identify which endpoints are significantly at risk; which contaminants are responsible for this risk; and which OUs significantly contribute to risk.

  11. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

    DEFF Research Database (Denmark)

    Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós; Mollerup, Sarah

    2016-01-01

    have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32...

  12. Hybrid approaches for multiple-species stochastic reaction-diffusion models

    Science.gov (United States)

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  13. Hybrid approaches for multiple-species stochastic reaction-diffusion models.

    KAUST Repository

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K; Byrne, Helen

    2015-01-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  14. Hybrid approaches for multiple-species stochastic reaction-diffusion models.

    KAUST Repository

    Spill, Fabian

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  15. Independent inactivation of arginine decarboxylase genes by nonsense and missense mutations led to pseudogene formation in Chlamydia trachomatis serovar L2 and D strains

    Directory of Open Access Journals (Sweden)

    Graham David E

    2009-07-01

    selection, consistent with the recent inactivation of these genes. Conclusion The ancestor of the Chlamydiaceae had a functional arginine:agmatine exchange system that is decaying through independent, parallel processes in the C. trachomatis lineage. Differences in arginine metabolism among Chlamydiaceae species may be partly associated with their tissue tropism, possibly due to the protection conferred by a functional arginine-agmatine exchange system against host nitric oxide production and innate immunity. The independent loss of AaxB activity in all sequenced C. trachomatis strains indicates continual gene inactivation and illustrates the difficulty of recognizing recent bacterial pseudogenes from sequence comparison, transcriptional profiling or the analysis of nucleotide substitution rates.

  16. The reverse effects of random perturbation on discrete systems for single and multiple population models

    International Nuclear Information System (INIS)

    Kang, Li; Tang, Sanyi

    2016-01-01

    Highlights: • The discrete single species and multiple species models with random perturbation are proposed. • The complex dynamics and interesting bifurcation behavior have been investigated. • The reverse effects of random perturbation on discrete systems have been discussed and revealed. • The main results can be applied for pest control and resources management. - Abstract: The natural species are likely to present several interesting and complex phenomena under random perturbations, which have been confirmed by simple mathematical models. The important questions are: how the random perturbations influence the dynamics of the discrete population models with multiple steady states or multiple species interactions? and is there any different effects for single species and multiple species models with random perturbation? To address those interesting questions, we have proposed the discrete single species model with two stable equilibria and the host-parasitoid model with Holling type functional response functions to address how the random perturbation affects the dynamics. The main results indicate that the random perturbation does not change the number of blurred orbits of the single species model with two stable steady states compared with results for the classical Ricker model with same random perturbation, but it can strength the stability. However, extensive numerical investigations depict that the random perturbation does not influence the complexities of the host-parasitoid models compared with the results for the models without perturbation, while it does increase the period of periodic orbits doubly. All those confirm that the random perturbation has a reverse effect on the dynamics of the discrete single and multiple population models, which could be applied in reality including pest control and resources management.

  17. Multifaceted, cross-generational costs of hybridization in sibling Drosophila species.

    Directory of Open Access Journals (Sweden)

    Erin M Myers

    Full Text Available Maladaptive hybridization, as determined by the pattern and intensity of selection against hybrid individuals, is an important factor contributing to the evolution of prezygotic reproductive isolation. To identify the consequences of hybridization between Drosophila pseudoobscura and D. persimilis, we estimated multiple fitness components for F1 hybrids and backcross progeny and used these to compare the relative fitness of parental species and their hybrids across two generations. We document many sources of intrinsic (developmental and extrinsic (ecological selection that dramatically increase the fitness costs of hybridization beyond the well-documented F1 male sterility in this model system. Our results indicate that the cost of hybridization accrues over multiple generations and reinforcement in this system is driven by selection against hybridization above and beyond the cost of hybrid male sterility; we estimate a fitness loss of >95% relative to the parental species across two generations of hybridization. Our findings demonstrate the importance of estimating hybridization costs using multiple fitness measures from multiple generations in an ecologically relevant context; so doing can reveal intense postzygotic selection against hybridization and thus, an enhanced role for reinforcement in the evolution of populations and diversification of species.

  18. Multifaceted, cross-generational costs of hybridization in sibling Drosophila species.

    Science.gov (United States)

    Myers, Erin M; Harwell, Tiffany I; Yale, Elizabeth L; Lamb, Abigail M; Frankino, W Anthony

    2013-01-01

    Maladaptive hybridization, as determined by the pattern and intensity of selection against hybrid individuals, is an important factor contributing to the evolution of prezygotic reproductive isolation. To identify the consequences of hybridization between Drosophila pseudoobscura and D. persimilis, we estimated multiple fitness components for F1 hybrids and backcross progeny and used these to compare the relative fitness of parental species and their hybrids across two generations. We document many sources of intrinsic (developmental) and extrinsic (ecological) selection that dramatically increase the fitness costs of hybridization beyond the well-documented F1 male sterility in this model system. Our results indicate that the cost of hybridization accrues over multiple generations and reinforcement in this system is driven by selection against hybridization above and beyond the cost of hybrid male sterility; we estimate a fitness loss of >95% relative to the parental species across two generations of hybridization. Our findings demonstrate the importance of estimating hybridization costs using multiple fitness measures from multiple generations in an ecologically relevant context; so doing can reveal intense postzygotic selection against hybridization and thus, an enhanced role for reinforcement in the evolution of populations and diversification of species.

  19. Micropropagation and cytogenetic assessment of Zingiber species of Northeast India.

    Science.gov (United States)

    Das, Archana; Kesari, Vigya; Rangan, Latha

    2013-12-01

    An improved micropropagation protocol was developed for Zingiber moran and Z. zerumbet, two wild species of the genus Zingiber, found in Northeast India. The effects of growth regulators, sugar concentrations, and nutrients were tested on the rate of shoot initiation and multiplication. An increase in proliferation and multiplication occurred in modified Murashige and Skoog (MS) medium supplemented with benzyladenine and kinetin. About 2 % sucrose and 0.7 % agar were found to be the optimum for shoot multiplication and regeneration. Naphthalene acetic acid at 0.5 mg/L produced the best rooting response for both the species. Regenerated plantlets were acclimatized successfully and cytogenetic stability was confirmed by RAPD profiling and ploidy checks.

  20. Redox-Stratified Bacterial Communities in Sediments Associated with Multiple Lucinid Bivalve Species: Implications for Symbiosis in Changing Coastal Habitats

    Science.gov (United States)

    Paterson, A. T.; Fortier, C. M.; Long, B.; Kokesh, B. S.; Lim, S. J.; Campbell, B. J.; Anderson, L. C.; Engel, A. S.

    2017-12-01

    Lucinids, chemosymbiotic marine bivalves, occupy strong redox gradient habitats, including the rhizosphere of coastal seagrass beds and mangrove forests in subtropical to tropical ecosystems. Lucinids and their sulfide-oxidizing gammaproteobacterial endosymbionts, which are acquired from the environment, provide a critical ecosystem service by removing toxic reduced sulfur compounds from the surrounding environment, and lucinids may be an important food source to economically valuable fisheries. The habitats of Phacoides pectinatus, Stewartia floridana, Codakia orbicularis, Ctena orbiculata, and Lucina pensylvanica lucinids in Florida and San Salvador in The Bahamas were evaluated in comprehensive malacological, microbiological, and geochemical surveys. Vegetation cover included different seagrass species or calcareous green macroalgae. All sites were variably affected by anthropogenic activities, as evidenced by visible prop scars in seagrass beds, grain size distributions atypical of low energy environments (i.e., artificial fill or dredge material from nearby channels), and high levels of pyrogenic hydrocarbon compounds in sediment indicative of urbanization impact. Where present, lucinid population densities frequently exceeded 2000 individuals per cubic meter, and were typically more abundant underlying seagrass compared to unvegetated, bare sand. Dissolved oxygen and sulfide levels varied from where lucinids were recovered. The sediment bacterial communities from classified 16S rRNA gene sequences indicated that the diversity of putative anaerobic groups increased with sediment depth, but putative aerobes, including of Gammaproteobacteria related to the lucinid endosymbionts, decreased with depth. Where multiple seagrass species co-occurred, retrieved bacterial community compositions correlated to overlying seagrass species, but diversity differed from bare sand patches, including among putative free-living endosymbiont groups. As such, continued sea

  1. Seroprevalence and genotype of Chlamydia in pet parrots in China.

    Science.gov (United States)

    Zhang, N-Z; Zhang, X-X; Zhou, D-H; Huang, S-Y; Tian, W-P; Yang, Y-C; Zhao, Q; Zhu, X-Q

    2015-01-01

    Parrots are one of the most popular pet birds in China, and can harbour Chlamydia which has significance for human and animal health. We investigated, by indirect haemagglutination assay, the seroprevalence of Chlamydia infection in four species of parrots, namely budgerigars (Melopsittacus undulatus), lovebirds (Agapornis sp.), cockatiels (Nymphicus hollandicus) and Alexandrine parakeets (Psittacula eupatria) that were collected from Weifang and Beijing cities, North China and explored the association between potential risk factors and chlamydial seropositivity. We further determined the genotype of Chlamydia in 21 fresh faecal samples based on the ompA sequence by reconstruction of phylogenetic relationships. Of the 311 parrots examined, 35·37% (95% confidence interval 30·06-40·68) were seropositive, and species, gender, age, season and geographical location were identified as risk factors. Two PCR-positive samples represented Chlamydia psittaci genotype A. The occurrence of C. psittaci genotype A in the droppings of two pet parrots in China suggests potential environmental contamination with Chlamydiaceae and may raise a public health concern.

  2. Cryptosporidium rubeyi n. sp. (Apicomplexa: Cryptosporidiidae in multiple Spermophilus ground squirrel species

    Directory of Open Access Journals (Sweden)

    Xunde Li

    2015-12-01

    Full Text Available Previously we reported the unique Cryptosporidium sp. “c” genotype (e.g., Sbey03c, Sbey05c, Sbld05c, Sltl05c from three species of Spermophilus ground squirrel (Spermophilus beecheyi, Spermophilus beldingi, Spermophilus lateralis located throughout California, USA. This follow-up work characterizes the morphology and animal infectivity of this novel genotype as the final step in proposing it as a new species of Cryptosporidium. Analysis of sequences of 18S rRNA, actin, and HSP70 genes of additional Cryptosporidium isolates from recently sampled California ground squirrels (S. beecheyi confirms the presence of the unique Sbey-c genotype in S. beecheyi. Phylogenetic and BLAST analysis indicates that the c-genotype in Spermophilus ground squirrels is distinct from Cryptosporidium species/genotypes from other host species currently available in GenBank. We propose to name this c-genotype found in Spermophilus ground squirrels as Cryptosporidium rubeyi n. sp. The mean size of C. rubeyi n. sp. oocysts is 4.67 (4.4–5.0 μm × 4.34 (4.0–5.0 μm, with a length/width index of 1.08 (n = 220. Oocysts of C. rubeyi n. sp. are not infectious to neonatal BALB/c mice and Holstein calves. GenBank accession numbers for C. rubeyi n. sp. are DQ295012, AY462233, and KM010224 for the 18S rRNA gene, KM010227 for the actin gene, and KM010229 for the HSP70 gene.

  3. Prevalence of Multiple Antibiotics Resistant (MAR) Pseudomonas Species in the Final Effluents of Three Municipal Wastewater Treatment Facilities in South Africa

    Science.gov (United States)

    Odjadjare, Emmanuel E.; Igbinosa, Etinosa O.; Mordi, Raphael; Igere, Bright; Igeleke, Clara L.; Okoh, Anthony I.

    2012-01-01

    The final effluents of three (Alice, Dimbaza, and East London) wastewater treatment plants (WWTPs) were evaluated to determine their physicochemical quality and prevalence of multiple antibiotics resistant (MAR) Pseudomonas species, between August 2007 and July 2008. The annual mean total Pseudomonas count (TPC) was 1.20 × 104 (cfu/100 mL), 1.08 × 104 (cfu/100 mL), and 2.66 × 104 (cfu/100 mL), for the Alice, Dimbaza, and East London WWTPs respectively. The effluents were generally compliant with recommended limits for pH, temperature, TDS, DO, nitrite and nitrate; but fell short of target standards for turbidity, COD, and phosphate. The tested isolates were highly sensitive to gentamicin (100%), ofloxacin (100%), clindamycin (90%), erythromycin (90%) and nitrofurantoin (80%); whereas high resistance was observed against the penicillins (90–100%), rifampin (90%), sulphamethoxazole (90%) and the cephems (70%). MAR index ranged between 0.26 and 0.58. The study demonstrated that MAR Pseudomonas species were quite prevalent in the final effluents of WWTPs in South Africa; and this can lead to serious health risk for communities that depend on the effluent-receiving waters for sundry purposes. PMID:22829792

  4. Linking Resilience of Aquatic Species to Watershed Condition

    Science.gov (United States)

    Flitcroft, R. L.

    2017-12-01

    Watershed condition means different things to different people. From the perspective of aquatic ecology, watershed condition may be interpreted to mean the capacity of a watershed to support life history diversity of native species. Diversity in expression of life history is thought to confer resilience allowing portions of the broader population to survive stressful conditions. Different species have different life history strategies, many of which were developed through adaptation to regional or local environmental conditions and natural disturbance regimes. By reviewing adaptation strategies for species of interest at regional scales, characteristics of watersheds that confer resilience may be determined. Such assessments must be completed at multiple levels of spatial organization (i.e. sub-watershed, watershed, region) allowing assessments to be inferred across broad spatial extents. In a project on the Wenatchee River watershed, we guided models of wildfire effects on bull trout and spring Chinook from a meta-population perspective to determine risks to survival at local and population scales over multiple extents of spatial organization. In other work in the Oregon Coast Range, we found that historic landslides continue to exert habitat-forming pressure at local scales, leading to patchiness in distribution of habitats for different life stages of coho salmon. Further, climate change work in Oregon estuaries identified different vulnerabilities in terms of juvenile rearing habitat depending on the species of interest and the intensity of future changes in climate. All of these studies point to the importance of considering physical conditions in watersheds at multiple spatial extents from the perspective of native aquatic species in order to understand risks to long-term survival. The broader implications of watershed condition, from this perspective, is the determination of physical attributes that confer resilience to native biota. This may require

  5. Multiple phenological responses to climate change among 42 plant species in Xi'an, China.

    Science.gov (United States)

    Dai, Junhu; Wang, Huanjiong; Ge, Quansheng

    2013-09-01

    Phenological data of 42 woody plants in a temperate deciduous forest from the Chinese Phenological Observation Network (CPON) and the corresponding meteorological data from 1963 to 2011 in Xi'an, Shaanxi Province, China were collected and analyzed. The first leaf date (FLD), leaf coloring date (LCD) and first flower date (FFD) are revealed as strong biological signals of climatic change. The FLD, LCD and FFD of most species are sensitive to average temperature during a certain period before phenophase onset. Regional precipitation also has a significant impact on phenophases of about half of the species investigated. Affected by climate change, the FLD and FFD of these species have advanced by 5.54 days and 10.20 days on average during 2003-2011 compared with the period 1963-1996, respectively. Meanwhile, the LCD has delayed by 10.59 days, and growing season length has extended 16.13 days. Diverse responses of phenology commonly exist among different species and functional groups during the study period. Especially for FFD, the deviations between the above two periods ranged from -20.68 to -2.79 days; biotic pollination species showed a significantly greater advance than abiotic pollination species. These results were conducive to the understanding of possible changes in both the structure of plant communities and interspecific relationships in the context of climate change.

  6. Crustacean zooplankton species richness in Chilean lakes and ponds (23°-51°S

    Directory of Open Access Journals (Sweden)

    Patricio De los Ríos-Escalante

    2013-07-01

    Full Text Available Chilean inland-water ecosystems are characterized by their low species-level biodiversity. This study analyses available data on surface area, maximum depth, conductivity, chlorophyll-α concentration, and zooplankton crustacean species number in lakes and ponds between 23° and 51°S. The study uses multiple regression analysis to identify the potential factors affecting the species number. The partial correlation analysis indicated a direct significant correlation between chlorophyll-α concentration and species number, whereas the multiple regression analysis indicated a direct significant response of species number to latitude and chlorophyll-α concentration. These results agree with findings from comparable ecosystems in Argentina and New Zealand.

  7. Deriving field-based species sensitivity distributions (f-SSDs) from stacked species distribution models (S-SDMs).

    Science.gov (United States)

    Schipper, Aafke M; Posthuma, Leo; de Zwart, Dick; Huijbregts, Mark A J

    2014-12-16

    Quantitative relationships between species richness and single environmental factors, also called species sensitivity distributions (SSDs), are helpful to understand and predict biodiversity patterns, identify environmental management options and set environmental quality standards. However, species richness is typically dependent on a variety of environmental factors, implying that it is not straightforward to quantify SSDs from field monitoring data. Here, we present a novel and flexible approach to solve this, based on the method of stacked species distribution modeling. First, a species distribution model (SDM) is established for each species, describing its probability of occurrence in relation to multiple environmental factors. Next, the predictions of the SDMs are stacked along the gradient of each environmental factor with the remaining environmental factors at fixed levels. By varying those fixed levels, our approach can be used to investigate how field-based SSDs for a given environmental factor change in relation to changing confounding influences, including for example optimal, typical, or extreme environmental conditions. This provides an asset in the evaluation of potential management measures to reach good ecological status.

  8. Global Existence Analysis of Cross-Diffusion Population Systems for Multiple Species

    Science.gov (United States)

    Chen, Xiuqing; Daus, Esther S.; Jüngel, Ansgar

    2018-02-01

    The existence of global-in-time weak solutions to reaction-cross-diffusion systems for an arbitrary number of competing population species is proved. The equations can be derived from an on-lattice random-walk model with general transition rates. In the case of linear transition rates, it extends the two-species population model of Shigesada, Kawasaki, and Teramoto. The equations are considered in a bounded domain with homogeneous Neumann boundary conditions. The existence proof is based on a refined entropy method and a new approximation scheme. Global existence follows under a detailed balance or weak cross-diffusion condition. The detailed balance condition is related to the symmetry of the mobility matrix, which mirrors Onsager's principle in thermodynamics. Under detailed balance (and without reaction) the entropy is nonincreasing in time, but counter-examples show that the entropy may increase initially if detailed balance does not hold.

  9. Partitioning sources of variation in vertebrate species richness

    Science.gov (United States)

    Boone, R.B.; Krohn, W.B.

    2000-01-01

    Aim: To explore biogeographic patterns of terrestrial vertebrates in Maine, USA using techniques that would describe local and spatial correlations with the environment. Location: Maine, USA. Methods: We delineated the ranges within Maine (86,156 km2) of 275 species using literature and expert review. Ranges were combined into species richness maps, and compared to geomorphology, climate, and woody plant distributions. Methods were adapted that compared richness of all vertebrate classes to each environmental correlate, rather than assessing a single explanatory theory. We partitioned variation in species richness into components using tree and multiple linear regression. Methods were used that allowed for useful comparisons between tree and linear regression results. For both methods we partitioned variation into broad-scale (spatially autocorrelated) and fine-scale (spatially uncorrelated) explained and unexplained components. By partitioning variance, and using both tree and linear regression in analyses, we explored the degree of variation in species richness for each vertebrate group that Could be explained by the relative contribution of each environmental variable. Results: In tree regression, climate variation explained richness better (92% of mean deviance explained for all species) than woody plant variation (87%) and geomorphology (86%). Reptiles were highly correlated with environmental variation (93%), followed by mammals, amphibians, and birds (each with 84-82% deviance explained). In multiple linear regression, climate was most closely associated with total vertebrate richness (78%), followed by woody plants (67%) and geomorphology (56%). Again, reptiles were closely correlated with the environment (95%), followed by mammals (73%), amphibians (63%) and birds (57%). Main conclusions: Comparing variation explained using tree and multiple linear regression quantified the importance of nonlinear relationships and local interactions between species

  10. Production of sophorolipids biosurfactants by multiple species of the Starmerella (Candida) bombicola yeast clade

    Science.gov (United States)

    Sophorolipid production was tested for 26 strains representing 19 species of the Starmerella yeast clade, including S. bombicola and Candida apicola, which were previously reported to produce sophorolipids. Five of the 19 species tested showed significant production of sophorolipids: S. bombicola, ...

  11. Functional analysis of the cytoskeleton protein MreB from Chlamydophila pneumoniae.

    Science.gov (United States)

    Gaballah, Ahmed; Kloeckner, Anna; Otten, Christian; Sahl, Hans-Georg; Henrichfreise, Beate

    2011-01-01

    In rod-shaped bacteria, the bacterial actin ortholog MreB is considered to organize the incorporation of cell wall precursors into the side-wall, whereas the tubulin homologue FtsZ is known to tether incorporation of cell wall building blocks at the developing septum. For intracellular bacteria, there is no need to compensate osmotic pressure by means of a cell wall, and peptidoglycan has not been reliably detected in Chlamydiaceae. Surprisingly, a nearly complete pathway for the biosynthesis of the cell wall building block lipid II has been found in the genomes of Chlamydiaceae. In a previous study, we discussed the hypothesis that conservation of lipid II biosynthesis in cell wall-lacking bacteria may reflect the intimate molecular linkage of cell wall biosynthesis and cell division and thus an essential role of the precursor in cell division. Here, we investigate why spherical-shaped chlamydiae harbor MreB which is almost exclusively found in elongated bacteria (i.e. rods, vibrios, spirilla) whereas they lack the otherwise essential division protein FtsZ. We demonstrate that chlamydial MreB polymerizes in vitro and that polymerization is not inhibited by the blocking agent A22. As observed for MreB from Bacillus subtilis, chlamydial MreB does not require ATP for polymerization but is capable of ATP hydrolysis in phosphate release assays. Co-pelleting and bacterial two-hybrid experiments indicate that MreB from Chlamydophila (Chlamydia) pneumoniae interacts with MurF, MraY and MurG, three key components in lipid II biosynthesis. In addition, MreB polymerization is improved in the presence of MurF. Our findings suggest that MreB is involved in tethering biosynthesis of lipid II and as such may be necessary for maintaining a functional divisome machinery in Chlamydiaceae.

  12. Metals and organotins in multiple bivalve species in a one-off global survey

    DEFF Research Database (Denmark)

    Larsen, Martin Mørk; Strand, Jakob; Christensen, Jan H.

    2011-01-01

    contamination levels on a global scale. Metal concentrations in nine bivalve species were normalised to the Mytilidae family using conversion factors based on cosampled species and literature bioconcentration factors. The lowest metal and tributyltin concentrations were below background assessment...... were low, but not always lower than expected impacted areas. The most contaminated areas were harbours, where especially Copenhagen, St Croix and Sydney, can be considered hotspots of tributyltin as well as a number of metals....

  13. Taking a multiple intelligences (MI) perspective.

    Science.gov (United States)

    Gardner, Howard

    2017-01-01

    The theory of multiple intelligences (MI) seeks to describe and encompass the range of human cognitive capacities. In challenging the concept of general intelligence, we can apply an MI perspective that may provide a more useful approach to cognitive differences within and across species.

  14. Sequence Factorization with Multiple References.

    Directory of Open Access Journals (Sweden)

    Sebastian Wandelt

    Full Text Available The success of high-throughput sequencing has lead to an increasing number of projects which sequence large populations of a species. Storage and analysis of sequence data is a key challenge in these projects, because of the sheer size of the datasets. Compression is one simple technology to deal with this challenge. Referential factorization and compression schemes, which store only the differences between input sequence and a reference sequence, gained lots of interest in this field. Highly-similar sequences, e.g., Human genomes, can be compressed with a compression ratio of 1,000:1 and more, up to two orders of magnitude better than with standard compression techniques. Recently, it was shown that the compression against multiple references from the same species can boost the compression ratio up to 4,000:1. However, a detailed analysis of using multiple references is lacking, e.g., for main memory consumption and optimality. In this paper, we describe one key technique for the referential compression against multiple references: The factorization of sequences. Based on the notion of an optimal factorization, we propose optimization heuristics and identify parameter settings which greatly influence 1 the size of the factorization, 2 the time for factorization, and 3 the required amount of main memory. We evaluate a total of 30 setups with a varying number of references on data from three different species. Our results show a wide range of factorization sizes (optimal to an overhead of up to 300%, factorization speed (0.01 MB/s to more than 600 MB/s, and main memory usage (few dozen MB to dozens of GB. Based on our evaluation, we identify the best configurations for common use cases. Our evaluation shows that multi-reference factorization is much better than single-reference factorization.

  15. CSA: An efficient algorithm to improve circular DNA multiple alignment

    Directory of Open Access Journals (Sweden)

    Pereira Luísa

    2009-07-01

    Full Text Available Abstract Background The comparison of homologous sequences from different species is an essential approach to reconstruct the evolutionary history of species and of the genes they harbour in their genomes. Several complete mitochondrial and nuclear genomes are now available, increasing the importance of using multiple sequence alignment algorithms in comparative genomics. MtDNA has long been used in phylogenetic analysis and errors in the alignments can lead to errors in the interpretation of evolutionary information. Although a large number of multiple sequence alignment algorithms have been proposed to date, they all deal with linear DNA and cannot handle directly circular DNA. Researchers interested in aligning circular DNA sequences must first rotate them to the "right" place using an essentially manual process, before they can use multiple sequence alignment tools. Results In this paper we propose an efficient algorithm that identifies the most interesting region to cut circular genomes in order to improve phylogenetic analysis when using standard multiple sequence alignment algorithms. This algorithm identifies the largest chain of non-repeated longest subsequences common to a set of circular mitochondrial DNA sequences. All the sequences are then rotated and made linear for multiple alignment purposes. To evaluate the effectiveness of this new tool, three different sets of mitochondrial DNA sequences were considered. Other tests considering randomly rotated sequences were also performed. The software package Arlequin was used to evaluate the standard genetic measures of the alignments obtained with and without the use of the CSA algorithm with two well known multiple alignment algorithms, the CLUSTALW and the MAVID tools, and also the visualization tool SinicView. Conclusion The results show that a circularization and rotation pre-processing step significantly improves the efficiency of public available multiple sequence alignment

  16. Removal of multiple metallic species from a sludge by electromigration

    Energy Technology Data Exchange (ETDEWEB)

    Ricart, M.T.; Cameselle, C. [Dept. of Chemical Engineering., Univ. of Vigo (Spain); Lema, J.M. [Dept. of Chemical Engineering., Univ. of Vigo (Spain)]|[Dept. of Chemical Engineering, Univ. of Santiago de Compostela (Spain)

    2001-07-01

    This study deals with the treatment of sludge from a wastewater treatment plant contaminated several metallic species. Electromigration laboratory experiments were conducted in an electrokinetic cell with or without cathode solution pH control. A large pH influence has been observed over metals removal. The neutralisation of basic environment at cathode deals with a increasing in current intensity and power consumption, but also in a large removal of Fe, Ca, Mg, Na, Mn, Sr, Zn and Cu from sludge sample. (orig.)

  17. Frequent cross-species transmission of parvoviruses among diverse carnivore hosts

    Science.gov (United States)

    Allison, Andrew B.; Kohler, Dennis J.; Fox, Karen A.; Brown, Justin D.; Gerhold, Richard W.; Shearn-Bochsler, Valerie I.; Dubovi, Edward J.; Parrish, Colin R.; Holmes, Edward C.

    2013-01-01

    Although parvoviruses are commonly described in domestic carnivores, little is known about their biodiversity in nondomestic species. A phylogenetic analysis of VP2 gene sequences from puma, coyote, gray wolf, bobcat, raccoon, and striped skunk revealed two major groups related to either feline panleukopenia virus (“FPV-like”) or canine parvovirus (“CPV-like”). Cross-species transmission was commonplace, with multiple introductions into each host species but, with the exception of raccoons, relatively little evidence for onward transmission in nondomestic species.

  18. DNA barcode detects high genetic structure within neotropical bird species.

    Directory of Open Access Journals (Sweden)

    Erika Sendra Tavares

    Full Text Available BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520 of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21 or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20. Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent

  19. Induction of apoptosis in human multiple myeloma cell lines by ebselen via enhancing the endogenous reactive oxygen species production.

    Science.gov (United States)

    Zhang, Liang; Zhou, Liwei; Du, Jia; Li, Mengxia; Qian, Chengyuan; Cheng, Yi; Peng, Yang; Xie, Jiayin; Wang, Dong

    2014-01-01

    Ebselen a selenoorganic compound showing glutathione peroxidase like activity is an anti-inflammatory and antioxidative agent. Its cytoprotective activity has been investigated in recent years. However, experimental evidence also shows that ebselen causes cell death in several cancer cell types whose mechanism has not yet been elucidated. In this study, we examined the effect of ebselen on multiple myeloma (MM) cell lines in vitro. The results showed that ebselen significantly enhanced the production of reactive oxygen species (ROS) accompanied by cell viability decrease and apoptosis rate increase. Further studies revealed that ebselen can induce Bax redistribution from the cytosol to mitochondria leading to mitochondrial membrane potential ΔΨm changes and cytochrome C release from the mitochondria to cytosol. Furtherly, we found that exogenous addition of N-acetyl cysteine (NAC) completely diminished the cell damage induced by ebselen. This result suggests that relatively high concentration of ebselen can induce MM cells apoptosis in culture by enhancing the production of endogenous ROS and triggering mitochondria mediated apoptotic pathway.

  20. Ribosomal DNA in diploid and polyploid Setaria (Poaceae) species: number and distribution

    OpenAIRE

    Nani, Thaís Furtado; Cenzi, Gisele; Pereira, Daniele Lais; Davide, Lisete Chamma; Techio, Vania Helena

    2015-01-01

    Abstract Setaria Beauvois, 1812 is a genus of economically important forage species, including Setaria italica (Linnaeus, 1753) Beauvois, 1812 and Setaria viridis (Linnaeus, 1753) Beauvois, 1812, closely related species and considered as model systems for studies of C4 plants. However, complications and uncertainties related to taxonomy of other species of the genus are frequent due to the existence of numerous synonyms for the same species or multiple species with the same name, and overlapp...

  1. Engineering a plant community to deliver multiple ecosystem services.

    Science.gov (United States)

    Storkey, Jonathan; Döring, Thomas; Baddeley, John; Collins, Rosemary; Roderick, Stephen; Jones, Hannah; Watson, Christine

    2015-06-01

    The sustainable delivery of multiple ecosystem services requires the management of functionally diverse biological communities. In an agricultural context, an emphasis on food production has often led to a loss of biodiversity to the detriment of other ecosystem services such as the maintenance of soil health and pest regulation. In scenarios where multiple species can be grown together, it may be possible to better balance environmental and agronomic services through the targeted selection of companion species. We used the case study of legume-based cover crops to engineer a plant community that delivered the optimal balance of six ecosystem services: early productivity, regrowth following mowing, weed suppression, support of invertebrates, soil fertility building (measured as yield of following crop), and conservation of nutrients in the soil. An experimental species pool of 12 cultivated legume species was screened for a range of functional traits and ecosystem services at five sites across a geographical gradient in the United Kingdom. All possible species combinations were then analyzed, using a process-based model of plant competition, to identify the community that delivered the best balance of services at each site. In our system, low to intermediate levels of species richness (one to four species) that exploited functional contrasts in growth habit and phenology were identified as being optimal. The optimal solution was determined largely by the number of species and functional diversity represented by the starting species pool, emphasizing the importance of the initial selection of species for the screening experiments. The approach of using relationships between functional traits and ecosystem services to design multifunctional biological communities has the potential to inform the design of agricultural systems that better balance agronomic and environmental services and meet the current objective of European agricultural policy to maintain viable food

  2. Consumer preference for seeds and seedlings of rare species impacts tree diversity at multiple scales.

    Science.gov (United States)

    Young, Hillary S; McCauley, Douglas J; Guevara, Roger; Dirzo, Rodolfo

    2013-07-01

    Positive density-dependent seed and seedling predation, where herbivores selectively eat seeds or seedlings of common species, is thought to play a major role in creating and maintaining plant community diversity. However, many herbivores and seed predators are known to exhibit preferences for rare foods, which could lead to negative density-dependent predation. In this study, we first demonstrate the occurrence of increased predation of locally rare tree species by a widespread group of insular seed and seedling predators, land crabs. We then build computer simulations based on these empirical data to examine the effects of such predation on diversity patterns. Simulations show that herbivore preferences for locally rare species are likely to drive scale-dependent effects on plant community diversity: at small scales these foraging patterns decrease plant community diversity via the selective consumption of rare plant species, while at the landscape level they should increase diversity, at least for short periods, by promoting clustered local dominance of a variety of species. Finally, we compared observed patterns of plant diversity at the site to those obtained via computer simulations, and found that diversity patterns generated under simulations were highly consistent with observed diversity patterns. We posit that preference for rare species by herbivores may be prevalent in low- or moderate-diversity systems, and that these effects may help explain diversity patterns across different spatial scales in such ecosystems.

  3. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

  4. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  5. Delineation of Culicoides species by morphology and barcode exemplified by three new species of the subgenus Culicoides (Diptera: Ceratopogonidae) from Scandinavia

    DEFF Research Database (Denmark)

    Nielsen, Søren Achim; Kristensen, Michael

    2015-01-01

    new species initially separated by DNA barcoding with mitochondrial COI can be distinguished by morphological characters. In this context a key to Scandinavian subgenus Culicoides using wing and maxillary palp characters is presented. The key is including the three new species Culicoides boyi...... is considered, as well as the evolutionary relationships between species within this genus remains problematic. In recent years molecular barcoding has assisted substantially in the identification of biting midges in the multiple entomological survey projects which were initiated in many European countries...... following the bluetongue outbreak in 2006–2009. These studies revealed potentially new species and “species-complexes” with large genetic and morphological variability. Here we use molecular barcoding, together with morphological analysis, to study subgenus Culicoides Latreille from Scandinavia with focus...

  6. Multidrug-resistant Nocardia pseudobrasiliensis presenting as multiple muscle abscesses.

    Science.gov (United States)

    Veerappan Kandasamy, Vimalkumar; Nagabandi, Arun; Horowitz, Edward A; Vivekanandan, Renuga

    2015-05-06

    A 79-year-old Caucasian man presented with multiple leg abscesses due to Nocardia pseudobrasiliensis. He was on chronic steroid therapy for myasthenia gravis. We present the difficulties in diagnosis and treatment of this rare organism. N. pseudobrasiliensis is a new emerging species that was previously thought to belong to the N. brasiliensis species. The distinction between the two species is extremely important given the different antibiotic susceptibility pattern and association of N. pseudobrasiliensis with more invasive and disseminated disease. 2015 BMJ Publishing Group Ltd.

  7. Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia.

    Science.gov (United States)

    Esselstyn, Jacob A; Maharadatunkamsi; Achmadi, Anang S; Siler, Cameron D; Evans, Ben J

    2013-10-01

    In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co-occur and how or whether ecological niches are partitioned. The extent to which species are able to coexist may depend on the degree to which they exploit different features of their habitat, which may in turn influence our ability to recognize them as species. We explored these issues in a biodiversity hotspot, by surveying shrew (genus Crocidura) diversity on the Indonesian island of Java. We sequenced portions of nine unlinked genes in 100-117 specimens of Javan shrews and incorporated homologous data from most known Crocidura species from other parts of island South-East Asia. Current taxonomy recognizes four Crocidura species on Java, including two endemics. However, our phylogenetic, population genetic and species delimitation analyses identify five species on the island, and all are endemic to Java. While the individual ranges of these species may not overlap in their entirety, we found up to four species living syntopically and all five species co-occurring on one mountain. Differences in species' body size, use of above ground-level habitats by one species and habitat partitioning along ecological gradients may have facilitated species diversification and coexistence. © 2013 John Wiley & Sons Ltd.

  8. Novel multiplex PCR reveals multiple trypanosomatid species infecting North American bumble bees (Hymenoptera: Apidae: Bombus).

    Science.gov (United States)

    Tripodi, Amber D; Szalanski, Allen L; Strange, James P

    2018-03-01

    Crithidia bombi and Crithidia expoeki (Trypanosomatidae) are common parasites of bumble bees (Bombus spp.). Crithidia bombi was described in the 1980s, and C. expoeki was recently discovered using molecular tools. Both species have cosmopolitan distributions among their bumble bee hosts, but there have been few bumble bee studies that have identified infections to species since the original description of C. expoeki in 2010. Morphological identification of species is difficult due to variability within each stage of their complex lifecycles, although they can be easily differentiated through DNA sequencing. However, DNA sequencing can be expensive, particularly with many samples to diagnose. In order to reliably and inexpensively distinguish Crithidia species for a large-scale survey, we developed a multiplex PCR protocol using species-specific primers with a universal trypanosomatid primer set to detect unexpected relatives. We applied this method to 356 trypanosomatid-positive bumble bees from North America as a first-look at the distribution and host range of each parasite in the region. Crithidia bombi was more common (90.2%) than C. expoeki (21.3%), with most C. expoeki-positive samples existing as co-infections with C. bombi (13.8%). This two-step detection method also revealed that 2.2% samples were positive for trypanosmatids that were neither C. bombi nor C. expoeki. Sequencing revealed that two individuals were positive for C. mellificae, one for Lotmaria passim, and three for two unclassified trypanosomatids. This two-step method is effective in diagnosing known bumble bee infecting Crithidia species, and allowing for the discovery of unknown potential symbionts. Published by Elsevier Inc.

  9. Swimming with multiple propulsors: measurement and comparison of swimming gaits in three species of neotropical cichlids.

    Science.gov (United States)

    Feilich, Kara L

    2017-11-15

    Comparative studies of fish swimming have been limited by the lack of quantitative definitions of fish gaits. Traditionally, steady swimming gaits have been defined categorically by the fin or region of the body that is used as the main propulsor and named after major fish clades (e.g. carangiform, anguilliform, balistiform, labriform). This method of categorization is limited by the lack of explicit measurements, the inability to incorporate contributions of multiple propulsors and the inability to compare gaits across different categories. I propose an alternative framework for the definition and comparison of fish gaits based on the propulsive contribution of each structure (body and/or fin) being used as a propulsor relative to locomotor output, and demonstrate the effectiveness of this framework by comparing three species of neotropical cichlids with different body shapes. This approach is modular with respect to the number of propulsors considered, flexible with respect to the definition of the propulsive inputs and the locomotor output of interest, and designed explicitly to handle combinations of propulsors. Using this approach, gait can be defined as a trajectory through propulsive space, and gait transitions can be defined as discontinuities in the gait trajectory. By measuring and defining gait in this way, patterns of clustering corresponding to existing categorical definitions of gait may emerge, and gaits can be rigorously compared across categories. © 2017. Published by The Company of Biologists Ltd.

  10. Multiple prismatic calcium phosphate layers in the jaws of present-day sharks (Chondrichthyes; Selachii).

    Science.gov (United States)

    Dingerkus, G; Séret, B; Guilbert, E

    1991-01-15

    Jaws of large individuals, over 2 m in total length, of the shark species Carcharodon carcharias (great white shark) and Isurus oxyrinchus (mako shark) of the family Lamnidae, and Galeocerdo cuvieri (tiger shark) and Carcharhinus leucas (bull shark) of the family Carcharhinidae were found to have multiple, up to five, layers of prismatic calcium phosphate surrounding the cartilages. Smaller individuals of these species and other known species of living chondrichthyans have only one layer of prismatic calcium phosphate surrounding the cartilages, as also do most species of fossil chondrichthyans. Two exceptions are the fossil shark genera Xenacanthus and Tamiobatis. Where it is found in living forms, this multiple layered calcification does not appear to be phylogenetic, as it appears to be lacking in other lamnid and carcharhinid genera and species. Rather it appears to be functional, only appearing in larger individuals and species of these two groups, and hence may be necessary to strengthen the jaw cartilages of such individuals for biting.

  11. The Hyalella (Crustacea: Amphipoda) species cloud of the ancient Lake Titicaca originated from multiple colonizations.

    Science.gov (United States)

    Adamowicz, Sarah J; Marinone, María Cristina; Menu-Marque, Silvina; Martin, Jeffrey W; Allen, Daniel C; Pyle, Michelle N; De Los Ríos, Patricio; Sobel, Crystal N; Ibañez, Carla; Pinto, Julio; Witt, Jonathan D S

    2018-08-01

    Ancient lakes are renowned for their exceptional diversity of endemic species. As model systems for the study of sympatric speciation, it is necessary to understand whether a given hypothesized species flock is of monophyletic or polyphyletic origin. Here, we present the first molecular characterization of the Hyalella (Crustacea: Amphipoda) species complex of Lake Titicaca, using COI and 28S DNA sequences, including samples from the connected Small and Large Lakes that comprise Lake Titicaca as well as from a broader survey of southern South American sites. At least five evolutionarily distant lineages are present within Lake Titicaca, which were estimated to have diverged from one another 12-20 MYA. These major lineages are dispersed throughout the broader South American Hyalella phylogeny, with each lineage representing at least one independent colonization of the lake. Moreover, complex genetic relationships are revealed between Lake Titicaca individuals and those from surrounding water bodies, which may be explained by repeated dispersal into and out of the lake, combined with parallel intralacustrine diversification within two separate clades. Although further work in deeper waters will be required to determine the number of species present and modes of diversification, our results strongly indicate that this amphipod species cloud is polyphyletic with a complex geographic history. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. A Framework for Spatial Risk Assessments: Potential Impacts of Nonindigenous Invasive Species on Native Species

    Directory of Open Access Journals (Sweden)

    Craig R. Allen

    2006-06-01

    Full Text Available Many populations of wild animals and plants are declining and face increasing threats from habitat fragmentation and loss as well as exposure to stressors ranging from toxicants to diseases to invasive nonindigenous species. We describe and demonstrate a spatially explicit ecological risk assessment that allows for the incorporation of a broad array of information that may influence the distribution of an invasive species, toxicants, or other stressors, and the incorporation of landscape variables that may influence the spread of a species or substances. The first step in our analyses is to develop species models and quantify spatial overlap between stressor and target organisms. Risk is assessed as the product of spatial overlap and a hazard index based on target species vulnerabilities to the stressor of interest. We illustrate our methods with an example in which the stressor is the ecologically destructive nonindigenous ant, Solenopsis invicta, and the targets are two declining vertebrate species in the state of South Carolina, USA. A risk approach that focuses on landscapes and that is explicitly spatial is of particular relevance as remaining undeveloped lands become increasingly uncommon and isolated and more important in the management and recovery of species and ecological systems. Effective ecosystem management includes the control of multiple stressors, including invasive species with large impacts, understanding where those impacts may be the most severe, and implementing management strategies to reduce impacts.

  13. Large roads reduce bat activity across multiple species.

    Science.gov (United States)

    Kitzes, Justin; Merenlender, Adina

    2014-01-01

    Although the negative impacts of roads on many terrestrial vertebrate and bird populations are well documented, there have been few studies of the road ecology of bats. To examine the effects of large roads on bat populations, we used acoustic recorders to survey bat activity along ten 300 m transects bordering three large highways in northern California, applying a newly developed statistical classifier to identify recorded calls to the species level. Nightly counts of bat passes were analyzed with generalized linear mixed models to determine the relationship between bat activity and distance from a road. Total bat activity recorded at points adjacent to roads was found to be approximately one-half the level observed at 300 m. Statistically significant road effects were also found for the Brazilian free-tailed bat (Tadarida brasiliensis), big brown bat (Eptesicus fuscus), hoary bat (Lasiurus cinereus), and silver-haired bat (Lasionycteris noctivagans). The road effect was found to be temperature dependent, with hot days both increasing total activity at night and reducing the difference between activity levels near and far from roads. These results suggest that the environmental impacts of road construction may include degradation of bat habitat and that mitigation activities for this habitat loss may be necessary to protect bat populations.

  14. H2DB: a heritability database across multiple species by annotating trait-associated genomic loci.

    Science.gov (United States)

    Kaminuma, Eli; Fujisawa, Takatomo; Tanizawa, Yasuhiro; Sakamoto, Naoko; Kurata, Nori; Shimizu, Tokurou; Nakamura, Yasukazu

    2013-01-01

    H2DB (http://tga.nig.ac.jp/h2db/), an annotation database of genetic heritability estimates for humans and other species, has been developed as a knowledge database to connect trait-associated genomic loci. Heritability estimates have been investigated for individual species, particularly in human twin studies and plant/animal breeding studies. However, there appears to be no comprehensive heritability database for both humans and other species. Here, we introduce an annotation database for genetic heritabilities of various species that was annotated by manually curating online public resources in PUBMED abstracts and journal contents. The proposed heritability database contains attribute information for trait descriptions, experimental conditions, trait-associated genomic loci and broad- and narrow-sense heritability specifications. Annotated trait-associated genomic loci, for which most are single-nucleotide polymorphisms derived from genome-wide association studies, may be valuable resources for experimental scientists. In addition, we assigned phenotype ontologies to the annotated traits for the purposes of discussing heritability distributions based on phenotypic classifications.

  15. A spatial theory for emergent multiple predator-prey interactions in food webs.

    Science.gov (United States)

    Northfield, Tobin D; Barton, Brandon T; Schmitz, Oswald J

    2017-09-01

    Predator-prey interaction is inherently spatial because animals move through landscapes to search for and consume food resources and to avoid being consumed by other species. The spatial nature of species interactions necessitates integrating spatial processes into food web theory and evaluating how predators combine to impact their prey. Here, we present a spatial modeling approach that examines emergent multiple predator effects on prey within landscapes. The modeling is inspired by the habitat domain concept derived from empirical synthesis of spatial movement and interactions studies. Because these principles are motivated by synthesis of short-term experiments, it remains uncertain whether spatial contingency principles hold in dynamical systems. We address this uncertainty by formulating dynamical systems models, guided by core habitat domain principles, to examine long-term multiple predator-prey spatial dynamics. To describe habitat domains, we use classical niche concepts describing resource utilization distributions, and assume species interactions emerge from the degree of overlap between species. The analytical results generally align with those from empirical synthesis and present a theoretical framework capable of demonstrating multiple predator effects that does not depend on the small spatial or temporal scales typical of mesocosm experiments, and help bridge between empirical experiments and long-term dynamics in natural systems.

  16. Model selection in Bayesian segmentation of multiple DNA alignments.

    Science.gov (United States)

    Oldmeadow, Christopher; Keith, Jonathan M

    2011-03-01

    The analysis of multiple sequence alignments is allowing researchers to glean valuable insights into evolution, as well as identify genomic regions that may be functional, or discover novel classes of functional elements. Understanding the distribution of conservation levels that constitutes the evolutionary landscape is crucial to distinguishing functional regions from non-functional. Recent evidence suggests that a binary classification of evolutionary rates is inappropriate for this purpose and finds only highly conserved functional elements. Given that the distribution of evolutionary rates is multi-modal, determining the number of modes is of paramount concern. Through simulation, we evaluate the performance of a number of information criterion approaches derived from MCMC simulations in determining the dimension of a model. We utilize a deviance information criterion (DIC) approximation that is more robust than the approximations from other information criteria, and show our information criteria approximations do not produce superfluous modes when estimating conservation distributions under a variety of circumstances. We analyse the distribution of conservation for a multiple alignment comprising four primate species and mouse, and repeat this on two additional multiple alignments of similar species. We find evidence of six distinct classes of evolutionary rates that appear to be robust to the species used. Source code and data are available at http://dl.dropbox.com/u/477240/changept.zip.

  17. An analysis of species boundaries and biogeographic patterns in a cryptic species complex: the rotifer--Brachionus plicatilis.

    Science.gov (United States)

    Suatoni, Elizabeth; Vicario, Saverio; Rice, Sean; Snell, Terry; Caccone, Adalgisa

    2006-10-01

    Since the advent of molecular phylogenetics, there is increasing evidence that many small aquatic and marine invertebrates--once believed to be single, cosmopolitan species--are in fact cryptic species complexes. Although the application of the biological species concept is central to the identification of species boundaries in these cryptic complexes, tests of reproductive isolation do not frequently accompany phylogenetic studies. Because different species concepts generally identify different boundaries in cryptic complexes, studies that apply multiple species concepts are needed to gain a more detailed understanding of patterns of diversification in these taxa. Here we explore different methods of empirically delimiting species boundaries in the salt water rotifer Brachionus plicatilis by comparing reproductive data (i.e., the traditional biological species concept) to phylogenetic data (the genealogical species concept). Based on a high degree of molecular sequence divergence and largely concordant genetic patterns in COI and ITS1, the genealogical species hypothesis indicates the existence of at least 14 species--the highest estimate for the group thus far. A test of the genealogical species concept with biological crosses shows a fairly high level of concordance, depending on the degree of reproductive success used to draw boundaries. The convergence of species concepts in this group suggests that many of the species within the group may be old. Although the diversity of the group is higher than previously understood, geographic distributions remain broad. Efficient passive dispersal has resulted in global distributions for many species with some evidence of isolation by distance over large geographic scales. These patterns concur with expectations that micro-meiofauna (0.1-1mm) have biogeographies intermediate to microbial organisms and large vertebrates. Sympatry of genetically distant strains is common.

  18. Multiple embryos, multiple nepionts and multiple equatorial layers in Cycloclypeus carpenteri.

    Science.gov (United States)

    Briguglio, Antonino; Kinoshita, Shunichi; Wolfgring, Erik; Hohenegger, Johann

    2016-04-01

    In this study, 17 specimens of Cycloclypeus carpenteri have been analyzed by means of microCT scanning. We used CT scanning technique as it enables the visualization and the quantifications of internal structures of hollow specimens without their destruction. It has been observed that many specimens possessing the natural morphology of this taxon, actually contain multiple embryos (up to 16 in one single specimen) and, in some few cases, multiple nepionts each with its own heterosteginid chambers (up to three separated nepionts). The diameter of each proloculus has been measured, and as a result, they are very variable even within the same specimen, therefore questioning the long known theory that schizonts have smaller proloculi than gamonts and also questioning the fact that proloculi in the same species should all have comparable size. Furthermore, we have observed the presence of additional equatorial planes on several specimens. Such additional planes are always connected to what seems to be the main equatorial plane. Such connections are T-shaped and are located at the junction between two equatorial layers; these junctions are made by a chamberlet, which possesses an unusually higher number of apertures. The connections between equatorial planes are always perfectly synchronized with the relative growth step and the same chamber can be therefore followed along the multiple equatorial planes. Apparently there is a perfect geometric relationship between the creation of additional equatorial planes and the position of the nepionts. Whenever the nepionts are positioned on different planes, additional planes are created and the angle of the nepionts is related to the banding angle of the equatorial planes. The presence of additional planes do not hamper the life of the cell, on the contrary, it seems that the cell is still able to build nicely shaped chamberlets and, after volumetric calculations, it seems all specimens managed to keep their logistic growth

  19. Metabolomic Analyses of Leishmania Reveal Multiple Species Differences and Large Differences in Amino Acid Metabolism.

    Directory of Open Access Journals (Sweden)

    Gareth D Westrop

    Full Text Available Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts.

  20. Induction of Apoptosis in Human Multiple Myeloma Cell Lines by Ebselen via Enhancing the Endogenous Reactive Oxygen Species Production

    Directory of Open Access Journals (Sweden)

    Liang Zhang

    2014-01-01

    Full Text Available Ebselen a selenoorganic compound showing glutathione peroxidase like activity is an anti-inflammatory and antioxidative agent. Its cytoprotective activity has been investigated in recent years. However, experimental evidence also shows that ebselen causes cell death in several cancer cell types whose mechanism has not yet been elucidated. In this study, we examined the effect of ebselen on multiple myeloma (MM cell lines in vitro. The results showed that ebselen significantly enhanced the production of reactive oxygen species (ROS accompanied by cell viability decrease and apoptosis rate increase. Further studies revealed that ebselen can induce Bax redistribution from the cytosol to mitochondria leading to mitochondrial membrane potential ΔΨm changes and cytochrome C release from the mitochondria to cytosol. Furtherly, we found that exogenous addition of N-acetyl cysteine (NAC completely diminished the cell damage induced by ebselen. This result suggests that relatively high concentration of ebselen can induce MM cells apoptosis in culture by enhancing the production of endogenous ROS and triggering mitochondria mediated apoptotic pathway.

  1. A Kolmogorov-type competition model with multiple coexistence states and its applications to plant competition for sunlight

    Science.gov (United States)

    Just, Winfried; Nevai, Andrew L.

    2008-12-01

    It is demonstrated that a Kolmogorov-type competition model featuring species allocation and gain functions can possess multiple coexistence statesE Two examples are constructed: one in which the two competing species possess rectangular allocation functions but distinct gain functions, and the other in which one species has a rectangular allocation function, the second species has a bi-rectangular allocation function, and the two species share a common gain function. In both examples, it is shown that the species nullclines may intersect multiple times within the interior of the first quadrant, thus creating both locally stable and unstable equilibrium points. These results have important applications in the study of plant competition for sunlight, in which the allocation functions describe the vertical placement of leaves for two competing species, and the gain functions represent rates of photosynthesis performed by leaves at different heights when shaded by overlying leaves belonging to either species.

  2. Three novel, multiple recombinant types of species of human mastadenovirus D (HAdV-D 73, 74 & 75) isolated from diarrhoeal faeces of immunocompromised patients.

    Science.gov (United States)

    Hage, Elias; Dhingra, Akshay; Liebert, Uwe G; Bergs, Sandra; Ganzenmueller, Tina; Heim, Albert

    2017-11-02

    Species D is the largest of the seven species of human mastadenoviruses (HAdV), but few of its multiple types are associated with asevere disease, e.g. epidemic keratoconjunctivitis. Many other types are hardly ever associated with significant diseases in immunocompetent patients, but have been isolated from the diarrhoeal faeces of terminal AIDS patients suggesting their role as opportunistic pathogens. Three novel HAdV-D strains were isolated from the faeces of three immunocompromised adult patients (clinical diagnoses: lymphoma, myelodysplastic syndrome and AIDS CDC3B, respectively). These strains were not typeable by imputed serology of the hexon and fibre gene and therefore complete genomic sequences were generated by next-generation sequencing (NGS). All three strains were multiple recombinants and fulfilled the criteria for designation as types 73, 74 and 75 with the penton/hexon/fibre genotype codes P67H45F27, P70H74F51 and P75H26F29, respectively. A novel genomic backbone and also a novel hexon neutralization epitope sequence were discovered in type 74, and a novel penton sequence in type 75. At the complete genome level, types 73, 74 and 75 were closely related neither to each other nor to type 70, which was previously isolated in the same region. However, these four HAdV-D types were closely related to each other in single genes and gene regions, e.g. penton, E1 and E4 due to recombination events in their phylogeny. In conclusion, regional co-circulation of opportunistic HAdV-D types facilitated co- and super-infections, which are essential for homologous recombination, and thus resulted in the evolution of novel genotypes by lateral gene transfer.

  3. Multiple mortality events in bats: a global review

    Science.gov (United States)

    O'Shea, Thomas J.; Cryan, Paul; Hayman, David TH; Plowright, Raina K.; Streicker, Daniel G.

    2016-01-01

    Despite conservation concerns for many species of bats, factors causing mortality in bats have not been reviewed since 1970. Here, we review and qualitatively describe trends in the occurrence and apparent causes of multiple mortality events (MMEs) in bats around the world.

  4. Equilibrium and extraction mechanism from monomeric and polimeric species of zirconium in solution. part. 2

    International Nuclear Information System (INIS)

    Azevedo, H.L.P. de.

    1980-01-01

    The mechanism of extraction and the equilibrium of chemical species from Zirconium solutions was studied. The multiple extraction method was used to show the species envolved in the extraction process and qualitative informations was obtained about the equilibrium between extractable species (monomers) and non-extractable species (polymers) in the aqueous phase. (M.J.C.) [pt

  5. Competitive interactions between co-occurring invaders: identifying asymmetries between two invasive crayfish species

    NARCIS (Netherlands)

    Hudina, S.; Galic, N.G.; Roessink, I.; Hock, K.

    2011-01-01

    Ecosystems today increasingly suffer invasions by multiple invasive species. Complex interactions between invasive species can have different fitness implications for each invader, which can in turn determine the future progression of their invasions and result in differential impacts on native

  6. Species and size diversity in protective services offered by coral guard-crabs

    Directory of Open Access Journals (Sweden)

    C. Seabird McKeon

    2014-09-01

    Full Text Available Coral guard-crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex. The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species.Studies conducted in Mo’orea, French Polynesia showed the Trapezia—coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller-size Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores.We also measured the benefits of this mutualism to corals in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism may positively affect the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that while functional diversity is supported within the genus, some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species.

  7. Preparation of genomic DNA from a single species of uncultured magnetotactic bacterium by multiple-displacement amplification.

    Science.gov (United States)

    Arakaki, Atsushi; Shibusawa, Mie; Hosokawa, Masahito; Matsunaga, Tadashi

    2010-03-01

    Magnetotactic bacteria comprise a phylogenetically diverse group that is capable of synthesizing intracellular magnetic particles. Although various morphotypes of magnetotactic bacteria have been observed in the environment, bacterial strains available in pure culture are currently limited to a few genera due to difficulties in their enrichment and cultivation. In order to obtain genetic information from uncultured magnetotactic bacteria, a genome preparation method that involves magnetic separation of cells, flow cytometry, and multiple displacement amplification (MDA) using phi29 polymerase was used in this study. The conditions for the MDA reaction using samples containing 1 to 100 cells were evaluated using a pure-culture magnetotactic bacterium, "Magnetospirillum magneticum AMB-1," whose complete genome sequence is available. Uniform gene amplification was confirmed by quantitative PCR (Q-PCR) when 100 cells were used as a template. This method was then applied for genome preparation of uncultured magnetotactic bacteria from complex bacterial communities in an aquatic environment. A sample containing 100 cells of the uncultured magnetotactic coccus was prepared by magnetic cell separation and flow cytometry and used as an MDA template. 16S rRNA sequence analysis of the MDA product from these 100 cells revealed that the amplified genomic DNA was from a single species of magnetotactic bacterium that was phylogenetically affiliated with magnetotactic cocci in the Alphaproteobacteria. The combined use of magnetic separation, flow cytometry, and MDA provides a new strategy to access individual genetic information from magnetotactic bacteria in environmental samples.

  8. Are trade-offs among species' ecological interactions scale dependent? A test using pitcher-plant inquiline species.

    Science.gov (United States)

    Kneitel, Jamie M

    2012-01-01

    Trade-offs among species' ecological interactions is a pervasive explanation for species coexistence. The traits associated with trade-offs are typically measured to mechanistically explain species coexistence at a single spatial scale. However, species potentially interact at multiple scales and this may be reflected in the traits among coexisting species. I quantified species' ecological traits associated with the trade-offs expected at both local (competitive ability and predator tolerance) and regional (competitive ability and colonization rate) community scales. The most common species (four protozoa and a rotifer) from the middle trophic level of a pitcher plant (Sarracenia purpurea) inquiline community were used to link species traits to previously observed patterns of species diversity and abundance. Traits associated with trade-offs (competitive ability, predator tolerance, and colonization rate) and other ecological traits (size, growth rate, and carrying capacity) were measured for each of the focal species. Traits were correlated with one another with a negative relationship indicative of a trade-off. Protozoan and rotifer species exhibited a negative relationship between competitive ability and predator tolerance, indicative of coexistence at the local community scale. There was no relationship between competitive ability and colonization rate. Size, growth rate, and carrying capacity were correlated with each other and the trade-off traits: Size was related to both competitive ability and predator tolerance, but growth rate and carrying capacity were correlated with predator tolerance. When partial correlations were conducted controlling for size, growth rate and carrying capacity, the trade-offs largely disappeared. These results imply that body size is the trait that provides the basis for ecological interactions and trade-offs. Altogether, this study showed that the examination of species' traits in the context of coexistence at different scales

  9. Survey of Infectious Etiologies of Bovine Abortion during Mid- to Late Gestation in Dairy Herds

    OpenAIRE

    Barkallah, Mohamed; Gharbi, Yaakoub; Ben Hassena, Amal; Ben Slima, Ahlem; Mallekh, Zouhir; Gautier, Michel; Greub, Gilbert; Gdoura, Radhouane

    2014-01-01

    Bovine abortion of unknown infectious etiology still remains a major economic problem. Thus, we investigated whether Brucella spp., Listeria monocytogenes, Salmonella spp., Campylobacter spp. and Coxiella burnetii are associated with abortion and/or stillbirth in Tunisian dairy cattle. Using a pan-Chlamydiales PCR, we also investigated the role of Chlamydiaceae, Waddlia chondrophila, Parachlamydia acanthamoebae and other members of the Chlamydiales order in this setting. Veterinary samples ta...

  10. Bioeconomic analysis supports the endangered species act.

    Science.gov (United States)

    Salau, Kehinde R; Fenichel, Eli P

    2015-10-01

    The United States Endangered Species Act (ESA) was enacted to protect and restore declining fish, wildlife, and plant populations. The ESA mandates endangered species protection irrespective of costs. This translates to the restriction of activities that harm endangered populations. We discuss criticisms of the ESA in the context of public land management and examine under what circumstance banning non-conservation activity on multiple use federal lands can be socially optimal. We develop a bioeconomic model to frame the species management problem under the ESA and identify scenarios where ESA-imposed regulations emerge as optimal strategies. Results suggest that banning harmful activities is a preferred strategy when valued endangered species are in decline or exposed to poor habitat quality. However, it is not optimal to sustain such a strategy in perpetuity. An optimal plan involves a switch to land-use practices characteristic of habitat conservation plans.

  11. Characterization of Chlamydia MurC-Ddl, a fusion protein exhibiting D-alanyl-D-alanine ligase activity involved in peptidoglycan synthesis and D-cycloserine sensitivity.

    Science.gov (United States)

    McCoy, Andrea J; Maurelli, Anthony T

    2005-07-01

    Recent characterization of chlamydial genes encoding functional peptidoglycan (PG)-synthesis proteins suggests that the Chlamydiaceae possess the ability to synthesize PG yet biochemical evidence for the synthesis of PG has yet to be demonstrated. The presence of D-amino acids in PG is a hallmark of bacteria. Chlamydiaceae do not appear to encode amino acid racemases however, a D-alanyl-D-alanine (D-Ala-D-Ala) ligase homologue (Ddl) is encoded in the genome. Thus, we undertook a genetics-based approach to demonstrate and characterize the D-Ala-D-Ala ligase activity of chlamydial Ddl, a protein encoded as a fusion with MurC. The full-length murC-ddl fusion gene from Chlamydia trachomatis serovar L2 was cloned and placed under the control of the arabinose-inducible ara promoter and transformed into a D-Ala-D-Ala ligase auxotroph of Escherichia coli possessing deletions of both the ddlA and ddlB genes. Viability of the E. coliDeltaddlADeltaddlB mutant in the absence of exogenous D-Ala-D-Ala dipeptide became dependent on the expression of the chlamydial murC-ddl thus demonstrating functional ligase activity. Domain mapping of the full-length fusion protein and site-directed mutagenesis of the MurC domain revealed that the structure of the full fusion protein but not MurC enzymatic activity was required for ligase activity in vivo. Recombinant MurC-Ddl exhibited substrate specificity for D-Ala. Chlamydia growth is inhibited by D-cycloserine (DCS) and in vitro analysis provided evidence for the chlamydial MurC-Ddl as the target for DCS sensitivity. In vivo sensitivity to DCS could be reversed by addition of exogenous D-Ala and D-Ala-D-Ala. Together, these findings further support our hypothesis that PG is synthesized by members of the Chlamydiaceae family and suggest that D-amino acids, specifically D-Ala, are present in chlamydial PG.

  12. Chromatographic speciation of Cr(III)-species, inter-species equilibrium isotope fractionation and improved chemical purification strategies for high-precision isotope analysis

    DEFF Research Database (Denmark)

    Larsen, Kirsten Kolbjørn; Wielandt, Daniel Kim Peel; Schiller, Martin

    2016-01-01

    Chromatographic purification of chromium (Cr), which is required for high-precision isotope analysis, is complicated by the presence of multiple Cr-species with different effective charges in the acid digested sample aliquots. The differing ion exchange selectivity and sluggish reaction rates of ...

  13. Multiple-Parameter, Low-False-Alarm Fire-Detection Systems

    Science.gov (United States)

    Hunter, Gary W.; Greensburg, Paul; McKnight, Robert; Xu, Jennifer C.; Liu, C. C.; Dutta, Prabir; Makel, Darby; Blake, D.; Sue-Antillio, Jill

    2007-01-01

    Fire-detection systems incorporating multiple sensors that measure multiple parameters are being developed for use in storage depots, cargo bays of ships and aircraft, and other locations not amenable to frequent, direct visual inspection. These systems are intended to improve upon conventional smoke detectors, now used in such locations, that reliably detect fires but also frequently generate false alarms: for example, conventional smoke detectors based on the blockage of light by smoke particles are also affected by dust particles and water droplets and, thus, are often susceptible to false alarms. In contrast, by utilizing multiple parameters associated with fires, i.e. not only obscuration by smoke particles but also concentrations of multiple chemical species that are commonly generated in combustion, false alarms can be significantly decreased while still detecting fires as reliably as older smoke-detector systems do. The present development includes fabrication of sensors that have, variously, micrometer- or nanometer-sized features so that such multiple sensors can be integrated into arrays that have sizes, weights, and power demands smaller than those of older macroscopic sensors. The sensors include resistors, electrochemical cells, and Schottky diodes that exhibit different sensitivities to the various airborne chemicals of interest. In a system of this type, the sensor readings are digitized and processed by advanced signal-processing hardware and software to extract such chemical indications of fires as abnormally high concentrations of CO and CO2, possibly in combination with H2 and/or hydrocarbons. The system also includes a microelectromechanical systems (MEMS)-based particle detector and classifier device to increase the reliability of measurements of chemical species and particulates. In parallel research, software for modeling the evolution of a fire within an aircraft cargo bay has been developed. The model implemented in the software can

  14. Density dependence governs when population responses to multiple stressors are magnified or mitigated.

    Science.gov (United States)

    Hodgson, Emma E; Essington, Timothy E; Halpern, Benjamin S

    2017-10-01

    Population endangerment typically arises from multiple, potentially interacting anthropogenic stressors. Extensive research has investigated the consequences of multiple stressors on organisms, frequently focusing on individual life stages. Less is known about population-level consequences of exposure to multiple stressors, especially when exposure varies through life. We provide the first theoretical basis for identifying species at risk of magnified effects from multiple stressors across life history. By applying a population modeling framework, we reveal conditions under which population responses from stressors applied to distinct life stages are either magnified (synergistic) or mitigated. We find that magnification or mitigation critically depends on the shape of density dependence, but not the life stage in which it occurs. Stressors are always magnified when density dependence is linear or concave, and magnified or mitigated when it is convex. Using Bayesian numerical methods, we estimated the shape of density dependence for eight species across diverse taxa, finding support for all three shapes. © 2017 by the Ecological Society of America.

  15. How much variation can one ant species hold? Species delimitation in the Crematogaster kelleri-group in Madagascar.

    Directory of Open Access Journals (Sweden)

    Bonnie B Blaimer

    Full Text Available We investigated the species-level taxonomy of the Malagasy Crematogaster (Crematogaster kelleri-group and an additional more distantly related species of the same subgenus. Morphological data from worker, queen and male ants, as well as genetic data from three nuclear genes (long wavelength rhodopsin, arginine kinase and carbomoylphosphate synthase and one mitochondrial marker (cytochrome oxidase I led to the recognition of six species. Within the C. kelleri-group, three new species are described: C. hazolava Blaimer sp. n., C. hafahafa Blaimer sp. n. and C. tavaratra Blaimer sp. n. The previously described taxa C. kelleri Forel and C. madagascariensis André are validated by our analysis. Conversely, our data suggests synonymy of C. adrepens Forel (with C. kelleri and C. gibba Emery (with C. madagascariensis. A more distantly related and phylogenetically isolated species, C. tsisitsilo Blaimer sp. n., is further described. We report high levels of morphological and molecular variation in C. kelleri and illustrate that this variation can be explained partly by geography. Species descriptions, images, distribution maps and identification keys based on worker ants, as well as on queen and male ants where available, are presented for all six species. Our work highlights the elevated species richness of Crematogaster ants throughout Madagascar's humid forests, especially in the far northern tip of the island, and the need to use multiple data sources to ensure clear demarcation of this diversity.

  16. Accounting for the ecosystem services of migratory species: Quantifying migration support and spatial subsidies

    Science.gov (United States)

    Semmens, Darius J.; Diffendorfer, James E.; López-Hoffman, Laura; Shapiro, Carl D.

    2011-01-01

    Migratory species support ecosystem process and function in multiple areas, establishing ecological linkages between their different habitats. As they travel, migratory species also provide ecosystem services to people in many different locations. Previous research suggests there may be spatial mismatches between locations where humans use services and the ecosystems that produce them. This occurs with migratory species, between the areas that most support the species' population viability – and hence their long-term ability to provide services – and the locations where species provide the most ecosystem services. This paper presents a conceptual framework for estimating how much a particular location supports the provision of ecosystem services in other locations, and for estimating the extent to which local benefits are dependent upon other locations. We also describe a method for estimating the net payment, or subsidy, owed by or to a location that balances benefits received and support provided by locations throughout the migratory range of multiple species. The ability to quantify these spatial subsidies could provide a foundation for the establishment of markets that incentivize cross-jurisdictional cooperative management of migratory species. It could also provide a mechanism for resolving conflicts over the sustainable and equitable allocation of exploited migratory species.

  17. Systematics of Plant-Pathogenic and Related Streptomyces Species Based on Phylogenetic Analyses of Multiple Gene Loci

    Science.gov (United States)

    The 10 species of Streptomyces implicated as the etiological agents in scab disease of potatoes or soft rot disease of sweet potatoes are distributed among 7 different phylogenetic clades in analyses based on 16S rRNA gene sequences, but high sequence similarity of this gene among Streptomyces speci...

  18. Towards an integration of biodiversity-ecosystem functioning and food web theory to evaluate relationships between multiple ecosystem services

    NARCIS (Netherlands)

    Hines, Jes; van der Putten, W.H.; De Deyn, G.B.; Wagg, Cameron; Voigt, Winfried; Mulder, Christian; Weisser, Wolfgang W.; Engel, Jan; Melian, Carlos; Scheu, Stefan; Birkhofer, Klaus; Ebeling, Anne; Scherber, Christoph; Eisenhauer, Nico

    2015-01-01

    Ecosystem responses to changes in species diversity are often studied individually. However, changes in species diversity can simultaneously influence multiple interdependent ecosystem functions. Therefore, an important challenge is to determine when and how changes in species diversity that

  19. In vitro mass multiplication of pomegranate from cotyledonary nodal ...

    African Journals Online (AJOL)

    Maria

    2013-05-15

    May 15, 2013 ... Key words: Establishment, multiplication, rooting, acclimatization, Punica granatum. INTRODUCTION. Pomegranate Punica granatum L. belongs to the family. Punicaceae which comprises only one genus (Punica) and only two species, P. granatum and P. proptopunica. This is popularly known as anar, ...

  20. Telecoupling framework for research on migratory species in the Anthropocene

    Directory of Open Access Journals (Sweden)

    Jacqueline Hulina

    2017-03-01

    Full Text Available Migratory species are an important component of biodiversity and provide essential ecosystem services for humans, but many are threatened and endangered. Numerous studies have been conducted on the biology of migratory species, and there is an increased recognition of the major role of human dimensions in conserving migratory species. However, there is a lack of systematic integration of socioeconomic and environmental factors. Because human activities affect migratory species in multiple places, integrating socioeconomic and environmental factors across space is essential, but challenging. The holistic framework of telecoupling (socioeconomic and environmental interactions over distances has the potential to help meet this challenge because it enables researchers to integrate human and natural interactions across multiple distant places. The use of the telecoupling framework may also lead to new conservation strategies and actions. To demonstrate its potential, we apply the framework to Kirtland’s warblers ('Setophaga kirtlandii' , a conservation-reliant migratory songbird. Results show accomplishments from long-term research and recovery efforts on the warbler in the context of the telecoupling framework. The results also show 24 research gaps even though the species has been relatively well-studied compared to many other species. An important gap is a lack of systematic studies on feedbacks among breeding, wintering, and stopover sites, as well as other “spillover” systems that may affect and be affected by migration (e.g., via tourism, land use, or climate change. The framework integrated scattered information and provided useful insights about new research topics and flow-centered management approaches that encapsulate the full annual cycle of migration. We also illustrate the similarities and differences between Kirtland’s warblers and several other migratory species, indicating the applicability of the telecoupling framework to

  1. Multiple gene genealogies and phenotypic characters differentiate several novel species of Mycosphaerella and related anamorphs on banana.

    Science.gov (United States)

    Arzanlou, M; Groenewald, J Z; Fullerton, R A; Abeln, E C A; Carlier, J; Zapater, M-F; Buddenhagen, I W; Viljoen, A; Crous, P W

    2008-06-01

    Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is known about these taxa, and for the majority of these species no culture or DNA is available for study. In the present study, we collected a global set of Mycosphaerella strains from banana, and compared them by means of morphology and a multi-gene nucleotide sequence data set. The phylogeny inferred from the ITS region and the combined data set containing partial gene sequences of the actin gene, the small subunit mitochondrial ribosomal DNA and the histone H3 gene revealed a rich diversity of Mycosphaerella species on Musa. Integration of morphological and molecular data sets confirmed more than 20 species of Mycosphaerella (incl. anamorphs) to occur on banana. This study reconfirmed the previously described presence of Cercospora apii, M. citri and M. thailandica, and also identified Mycosphaerella communis, M. lateralis and Passalora loranthi on this host. Moreover, eight new species identified from Musa are described, namely Dissoconium musae, Mycosphaerella mozambica, Pseudocercospora assamensis, P. indonesiana, P. longispora, Stenella musae, S. musicola, and S. queenslandica.

  2. Generalized fractional supersymmetry associated to different species of anyons

    International Nuclear Information System (INIS)

    Douari, Jamila; Abdus Salam International Centre for Theoretical Physics, Trieste; Hassouni, Yassine

    2001-01-01

    We consider multiple species of anyons characterized by different statistical parameters. First, we redefine the anyonic algebra and then generalize this definition by constructing the anyonic superalgebra. Finally, we use these tools to generalize the fractional supersymmetry already discussed. (author)

  3. The Effects of Urban Sprawl on Birds at Multiple Levels of Biological Organization

    Directory of Open Access Journals (Sweden)

    Robert Blair

    2004-12-01

    Full Text Available Urban sprawl affects the environment in myriad ways and at multiple levels of biological organization. In this paper I explore the effects of sprawl on native bird communities by comparing the occurrence of birds along gradients of urban land use in southwestern Ohio and northern California and by examining patterns at the individual, species, community, landscape, and continental levels. I do this by assessing the distribution and abundance of all bird species occupying sites of differing land-use intensity in Ohio and California. Additionally, I conducted predation experiments using artificial nests, tracked the nest fate of American Robins and Northern Cardinals, and assessed land cover in these sites. At the individual level, predation on artificial nests decreased with urbanization; however, this trend was not reflected in the nesting success of robins and cardinals, which did not increase with urbanization. At the species level, sprawl affected local patterns of extinction and invasion; the density of different species peaked at different levels of urbanization. At the community level, species richness and diversity peaked at moderate levels of urbanization, and the number of low-nesting species and of species with multiple broods increased with urbanization. The community-level results may reflect both the species-level patterns of local extinction and invasion as well as broader landscape-level patterns. At the landscape level, a linear combination of spatial heterogeneity and density of woody patches accurately predicted both species richness and Shannon Diversity. At the continental level, local extinction of endemic species, followed by the invasion of ubiquitous weedy species, leads to faunal homogenization between ecoregions.

  4. Multiple sclerosis: general features and pharmacologic approach; Esclerosis multiple: aspectos generales y abordaje farmacologico

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen Lagumersindez, Denis; Martinez Sanchez, Gregorio [Instituto de Farmacia y Alimentos, Universidad de La Habana, La Habana (Cuba)

    2009-07-01

    Multiple sclerosis is an autoimmune, inflammatory and desmyelinization disease central nervous system (CNS) of unknown etiology and critical evolution. There different etiological hypotheses talking of a close interrelation among predisposing genetic factors and dissimilar environmental factors, able to give raise to autoimmune response at central nervous system level. Hypothesis of autoimmune pathogeny is based on study of experimental models, and findings in biopsies of affected patients by disease. Accumulative data report that the oxidative stress plays a main role in pathogenesis of multiple sclerosis. Oxygen reactive species generated by macrophages has been involved as mediators of demyelinization and of axon damage, in experimental autoimmune encephalomyelitis and strictly in multiple sclerosis. Disease diagnosis is difficult because of there is not a confirmatory unique test. Management of it covers the treatment of acute relapses, disease modification, and symptoms management. These features require an individualized approach, base on evolution of this affection, and tolerability of treatments. In addition to diet, among non-pharmacologic treatments for multiple sclerosis it is recommended physical therapy. Besides, some clinical assays have been performed in which we used natural extracts, nutrition supplements, and other agents with promising results. Pharmacology allowed neurologists with a broad array of proved effectiveness drugs; however, results of research laboratories in past years make probable that therapeutical possibilities increase notably in future. (Author)

  5. Towards Arctic Resource Governance of Marine Invasive Species

    DEFF Research Database (Denmark)

    Kourantidou, Melina; Kaiser, Brooks; Fernandez, Linda

    2015-01-01

    Scientific and policy-oriented publications highlighting the magnitude of uncertainty in the changing Arctic and the possibilities for effective regional governance are proliferating, yet it remains a challenging task to examine Arctic marine biodiversity. Limited scientific data are currently...... available. Through analysis of marine invasions in the Arctic, we work to identify and assess patterns in the knowledge gaps regarding invasive species in the Arctic that affect the ability to generate improved governance outcomes. These patterns are expected to depend on multiple aspects of scientific...... research into invasive species threats in the Arctic, including the ways in which known marine invasions are related to different stakeholder groups and existing disparate national and international experiences with invasive species. Stakeholdergroups include dominant industries (fishing, shipping, tourism...

  6. Predicting the presence and cover of management relevant invasive plant species on protected areas.

    Science.gov (United States)

    Iacona, Gwenllian; Price, Franklin D; Armsworth, Paul R

    2016-01-15

    Invasive species are a management concern on protected areas worldwide. Conservation managers need to predict infestations of invasive plants they aim to treat if they want to plan for long term management. Many studies predict the presence of invasive species, but predictions of cover are more relevant for management. Here we examined how predictors of invasive plant presence and cover differ across species that vary in their management priority. To do so, we used data on management effort and cover of invasive plant species on central Florida protected areas. Using a zero-inflated multiple regression framework, we showed that protected area features can predict the presence and cover of the focal species but the same features rarely explain both. There were several predictors of either presence or cover that were important across multiple species. Protected areas with three days of frost per year or fewer were more likely to have occurrences of four of the six focal species. When invasive plants were present, their proportional cover was greater on small preserves for all species, and varied with surrounding household density for three species. None of the predictive features were clearly related to whether species were prioritized for management or not. Our results suggest that predictors of cover and presence can differ both within and across species but do not covary with management priority. We conclude that conservation managers need to select predictors of invasion with care as species identity can determine the relationship between predictors of presence and the more management relevant predictors of cover. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Looking beyond rare species as umbrella species: Northern Bobwhites (Colinus virginianus) and conservation of grassland and shrubland birds

    Science.gov (United States)

    Crosby, Andrew D.; Elmore, R.D.; Leslie,, David M.; Will, Rodney E.

    2015-01-01

    Changes in land use and land cover throughout the eastern half of North America have caused substantial declines in populations of birds that rely on grassland and shrubland vegetation types, including socially and economically important game birds such as the Northern Bobwhite (Colinus virginianus; hereafter bobwhites). As much attention is focused on habitat management and restoration for bobwhites, they may act as an umbrella species for other bird species with similar habitat requirements. We quantified the relationship of bobwhites to the overall bird community and evaluated the potential for bobwhites to act as an umbrella species for grassland and shrubland birds. We monitored bobwhite presence and bird community composition within 31 sample units on selected private lands in the south-central United States from 2009 to 2011. Bobwhites were strongly associated with other grassland and shrubland birds and were a significant positive predictor for 9 species. Seven of these, including Bell's Vireo (Vireo bell), Dicksissel (Spiza americana), and Grasshopper Sparrow (Ammodramus savannarum), are listed as species of conservation concern. Species richness and occupancy probability of grassland and shrubland birds were higher relative to the overall bird community in sample units occupied by bobwhites. Our results show that bobwhites can act as an umbrella species for grassland and shrubland birds, although the specific species in any given situation will depend on region and management objectives. These results suggest that efficiency in conservation funding can be increased by using public interest in popular game species to leverage resources to meet multiple conservation objectives.

  8. Sarmentine, a natural herbicide from Piper species with multiple herbicide mechanisms of action

    Science.gov (United States)

    Sarmentine, 1-(1-pyrrolidinyl)-(2E,4E)-2,4-decadien-1-one, is a natural amide isolated from the fruits of Piper species. The compound has a number of interesting biological properties, including its broad-spectrum activity on weeds as a contact herbicide. Initial studies highlighted a similarity in ...

  9. Dynamics of two competing species in the presence of Lévy noise sources

    Science.gov (United States)

    La Cognata, A.; Valenti, D.; Dubkov, A. A.; Spagnolo, B.

    2010-07-01

    We consider a Lotka-Volterra system of two competing species subject to multiplicative α -stable Lévy noise. The interaction parameter between the species is a random process which obeys a stochastic differential equation with a generalized bistable potential in the presence both of a periodic driving term and an additive α -stable Lévy noise. We study the species dynamics, which is characterized by two different regimes, exclusion of one species and coexistence of both. We find quasiperiodic oscillations and stochastic resonance phenomenon in the dynamics of the competing species, analyzing the role of the Lévy noise sources.

  10. Revised species definitions and nomenclature of the rose colored Cithaerias butterflies (Lepidoptera, Nymphalidae, Satyrinae).

    Science.gov (United States)

    Penz, Carla M; Alexander, Laura G; Devries, Philip J

    2014-10-20

    This study provides updated species definitions for five rose-colored Cithaerias butterflies, starting with a historical overview of their taxonomy. Given their mostly transparent wings, genitalia morphology yielded the most reliable characters for species definition and identification. Genitalic divergence is more pronounced when multiple species occur in sympatry than between parapatric taxa. Cithaerias aurorina is granted full species status, C. cliftoni is reinstated as a full species, and one new combination is proposed, i.e. C. aurora tambopata. Two new synonyms are proposed, Callitaera phantoma and Callitaera aura = Cithaerias aurora. 

  11. Bracken: estimating species abundance in metagenomics data

    Directory of Open Access Journals (Sweden)

    Jennifer Lu

    2017-01-01

    Full Text Available Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.

  12. Busy Bees: Variation in Insect Flower-Visiting Rates across Multiple Plant Species

    Directory of Open Access Journals (Sweden)

    Margaret J. Couvillon

    2015-01-01

    Full Text Available We quantified insect visitation rates by counting how many flowers/inflorescences were probed per unit time for five plant species (four native and one garden: California lilac, bramble, ragwort, wild marjoram, and ivy growing in Sussex, United Kingdom, by following individual insects (n=2987 from nine functional groups (honey bees (Apis mellifera, bumble bees (Bombus spp., hoverflies, flies, butterflies, beetles, wasps, non-Apidae bees, and moths. Additionally, we made a census of the insect diversity on the studied plant species. Overall we found that insect groups differed greatly in their rate of flower visits (P<2.2e-16, with bumble bees and honey bees visiting significantly more flowers per time (11.5 and 9.2 flowers/minute, resp. than the other insect groups. Additionally, we report on a within-group difference in the non-Apidae bees, where the genus Osmia, which is often suggested as an alternative to honey bees as a managed pollinator, was very speedy (13.4 flowers/minute compared to the other non-Apidae bees (4.3 flowers/minute. Our census showed that the plants attracted a range of insects, with the honey bee as the most abundant visitor (34%. Therefore, rate differences cannot be explained by particular specializations. Lastly, we discuss potential implications of our conclusions for pollination.

  13. Ecological impacts of non-native species

    Science.gov (United States)

    Wilkinson, John W.

    2012-01-01

    Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and

  14. Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species

    KAUST Repository

    Arrigoni, Roberto

    2016-09-09

    Scleractinian corals are affected by environment-induced phenotypic plasticity and intraspecific morphological variation caused by genotype. In an effort to identify new strategies for resolving this taxonomic issue, we applied a molecular approach for species evaluation to two closely related genera, Echinophyllia and Oxypora, for which few molecular data are available. A robust multi-locus phylogeny using DNA sequence data across four loci of both mitochondrial (COI, ATP6-NAD4) and nuclear (histone H3, ITS region) origin from 109 coral colonies was coupled with three independent putative species delimitation methods based on barcoding threshold (ABGD) and coalescence theory (PTP, GMYC). Observed overall congruence across multiple genetic analyses distinguished two traditional species (E. echinoporoides and O. convoluta), a species complex composed of E. aspera, E. orpheensis, E. tarae, and O. glabra, whereas O. lacera and E. echinata were indistinguishable with the sequenced loci. The combination of molecular species delimitation approaches and skeletal character observations allowed the description of two new reef coral species, E. bulbosa sp. n. from the Red Sea and E. gallii sp. n. from the Maldives and Mayotte. This work demonstrated the efficiency of multi-locus phylogenetic analyses and recently developed molecular species delimitation approaches as valuable tools to disentangle taxonomic issues caused by morphological ambiguities and to re-assess the diversity of scleractinian corals. (C) 2016 Elsevier Inc. All rights reserved.

  15. Fungal species and multiple mycotoxin contamination of cultivated forage crops

    Directory of Open Access Journals (Sweden)

    Galina Kononenko

    2015-12-01

    Full Text Available The quality of grass samples used for animal feed by combining mycotoxin measures and mycological determination of mycobiota were explored. The samples of the plant material were collected in 2014 in two stages: before the first mowing (May–June and before the second one (July–August from the fields of stock-farms located in northwestern part of the Russia. All samples were divided into three types: grasses, mixture of different grasses and clover, alfalfa mixed with timothy. The occurrence of aflatoxin B1, alternariol, citrinin, cyclopiazonic acid, deoxynivalenol, diacetoxyscirpenol, emodin, ergot alkaloids, fumonisins, mycophenolic acid, ochratoxin A, PR-toxin, roridin A, sterigmatocystin, T-2 toxin, and zearalenone were determined using ELISA. The multiple fungal and mycotoxin contaminations are already formed in plant tissues by the moment of first mowing. The complexes of mycotoxins including up to 14–16 components and the combined character of plant contamination quite correspond to the taxonomic variety of mycobiota.

  16. Multiple ovulation and embryo transfer (MOET in camels: An overview

    Directory of Open Access Journals (Sweden)

    Binoy S. Vettical

    2016-04-01

    Full Text Available Unlike in other domestic animal species like cattle, reproductive biotechnologies like Artificial Insemination (AI and Embryo Transfer (ET are not well developed and thus are not being used as routine breeding procedures in camels. One of the important objectives of this manuscript is to focus on analyzing the present status of Multiple Ovulation and Embryo Transfer (MOET in camels and its future perspectives. Camels are induced ovulators, thus require hormonal treatment to induce ovulation and control the follicular cycles, which is the main reason why protocols used in other domestic animal species cannot be directly used in this species. The review suggests that the best method for super stimulation of ovaries in camels is use of a combination of Equine Chorionic Gonadotropin (eCG and Follicle Stimulating Hormone (FSH at any stage after elimination of dominant follicle if any or at the early stage of the follicular wave and ovulation of the developed multiple follicles can be achieved by mating donors. The review highlights that a better pregnancy rate is achieved with recipients who ovulate 24 h after the donor.

  17. Irrigation requirements for seed production of five Lomatium species in a semiarid environment

    Science.gov (United States)

    Clinton C. Shock; Erik B. G. Feibert; Alicia Rivera; Lamont D. Saunders; Nancy Shaw; Francis F. Kilkenny

    2016-01-01

    Seeds of native plants are needed for rangeland restoration in the Intermountain West. Many of these plants are rarely cultivated and relatively little is known about the cultural practices required for their seed production. Irrigation trials were conducted for five perennial Lomatium species over multiple years. Lomatium species grown at the Oregon State University...

  18. Multiple gene genealogies and phenotypic characters differentiate several novel species of Mycosphaerella and related anamorphs on banana

    NARCIS (Netherlands)

    Arzanlou, M.; Groenewald, J.Z.; Fullerton, R.A.; Abeln, E.C.A.; Carlier, J.; Zapater, M.-F.; Buddenhagen, I.W.; Viljoen, A.; Crous, P.W.

    2008-01-01

    Three species of Mycosphaerella, namely M. eumusae, M. fijiensis, and M. musicola are involved in the Sigatoka disease complex of bananas. Besides these three primary pathogens, several additional species of Mycosphaerella or their anamorphs have been described from Musa. However, very little is

  19. Above- and below-ground effects of plant diversity depend on species origin

    DEFF Research Database (Denmark)

    Kuebbing, Sara E.; Classen, Aimee Taylor; Sanders, Nate

    2015-01-01

    -interaction models to describe how species' interactions influenced diversity-productivity relationships. Communities with more species had higher total biomass than did monoculture communities, but native and nonnative communities diverged in root : shoot ratios and the mechanism responsible for increased......Although many plant communities are invaded by multiple nonnative species, we have limited information on how a species' origin affects ecosystem function. We tested how differences in species richness and origin affect productivity and seedling establishment. We created phylogenetically paired...... native and nonnative plant communities in a glasshouse experiment to test diversity-productivity relationships and responsible mechanisms (i.e. selection or complementarity effects). Additionally, we tested how productivity and associated mechanisms influenced seedling establishment. We used diversity...

  20. Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases.

    Directory of Open Access Journals (Sweden)

    Kai Wang

    2009-12-01

    Full Text Available Co-expression networks are routinely used to study human diseases like obesity and diabetes. Systematic comparison of these networks between species has the potential to elucidate common mechanisms that are conserved between human and rodent species, as well as those that are species-specific characterizing evolutionary plasticity. We developed a semi-parametric meta-analysis approach for combining gene-gene co-expression relationships across expression profile datasets from multiple species. The simulation results showed that the semi-parametric method is robust against noise. When applied to human, mouse, and rat liver co-expression networks, our method out-performed existing methods in identifying gene pairs with coherent biological functions. We identified a network conserved across species that highlighted cell-cell signaling, cell-adhesion and sterol biosynthesis as main biological processes represented in genome-wide association study candidate gene sets for blood lipid levels. We further developed a heterogeneity statistic to test for network differences among multiple datasets, and demonstrated that genes with species-specific interactions tend to be under positive selection throughout evolution. Finally, we identified a human-specific sub-network regulated by RXRG, which has been validated to play a different role in hyperlipidemia and Type 2 diabetes between human and mouse. Taken together, our approach represents a novel step forward in integrating gene co-expression networks from multiple large scale datasets to leverage not only common information but also differences that are dataset-specific.

  1. Multiple paternity in reptiles: patterns and processes.

    Science.gov (United States)

    Uller, Tobias; Olsson, Mats

    2008-06-01

    The evolution of female promiscuity poses an intriguing problem as benefits of mating with multiple males often have to arise via indirect, genetic, effects. Studies on birds have documented that multiple paternity is common in natural populations but strong evidence for selection via female benefits is lacking. In an attempt to evaluate the evidence more broadly, we review studies of multiple paternity in natural populations of all major groups of nonavian reptiles. Multiple paternity has been documented in all species investigated so far and commonly exists in over 50% of clutches, with particularly high levels in snakes and lizards. Marine turtles and lizards with prolonged pair-bonding have relatively low levels of multiple paternity but levels are nevertheless higher than in many vertebrates with parental care. There is no evidence that high levels of polyandry are driven by direct benefits to females and the evidence that multiple paternity arises from indirect genetic benefits is weak. Instead, we argue that the most parsimonious explanation for patterns of multiple paternity is that it represents the combined effect of mate-encounter frequency and conflict over mating rates between males and females driven by large male benefits and relatively small female costs, with only weak selection via indirect benefits. A crucial step for researchers is to move from correlative approaches to experimental tests of assumptions and predictions of theory under natural settings, using a combination of molecular techniques and behavioural observations.

  2. Algal bioremediation of waste waters from land-based aquaculture using ulva: selecting target species and strains.

    Directory of Open Access Journals (Sweden)

    Rebecca J Lawton

    Full Text Available The optimised reduction of dissolved nutrient loads in aquaculture effluents through bioremediation requires selection of appropriate algal species and strains. The objective of the current study was to identify target species and strains from the macroalgal genus Ulva for bioremediation of land-based aquaculture facilities in Eastern Australia. We surveyed land-based aquaculture facilities and natural coastal environments across three geographic locations in Eastern Australia to determine which species of Ulva occur naturally in this region and conducted growth trials at three temperature treatments on a subset of samples from each location to determine whether local strains had superior performance under local environmental conditions. DNA barcoding using the markers ITS and tufA identified six species of Ulva, with U. ohnoi being the most common blade species and U. sp. 3 the most common filamentous species. Both species occurred at multiple land-based aquaculture facilities in Townsville and Brisbane and multiple strains of each species grew well in culture. Specific growth rates of U. ohnoi and U. sp. 3 were high (over 9% and 15% day(-1 respectively across temperature treatments. Within species, strains of U. ohnoi had higher growth in temperatures corresponding to local conditions, suggesting that strains may be locally adapted. However, across all temperature treatments Townsville strains had the highest growth rates (11.2-20.4% day(-1 and Sydney strains had the lowest growth rates (2.5-8.3% day(-1. We also found significant differences in growth between strains of U. ohnoi collected from the same geographic location, highlighting the potential to isolate and cultivate fast growing strains. In contrast, there was no clearly identifiable competitive strain of filamentous Ulva, with multiple species and strains having variable performance. The fast growth rates and broad geographical distribution of U. ohnoi make this an ideal species to

  3. An experimental test of fitness variation across a hydrologic gradient predicts willow and poplar species distributions.

    Science.gov (United States)

    Wei, Xiaojing; Savage, Jessica A; Riggs, Charlotte E; Cavender-Bares, Jeannine

    2017-05-01

    Environmental filtering is an important community assembly process influencing species distributions. Contrasting species abundance patterns along environmental gradients are commonly used to provide evidence for environmental filtering. However, the same abundance patterns may result from alternative or concurrent assembly processes. Experimental tests are an important means to decipher whether species fitness varies with environment, in the absence of dispersal constraints and biotic interactions, and to draw conclusions about the importance of environmental filtering in community assembly. We performed an experimental test of environmental filtering in 14 closely related willow and poplar species (family Salicaceae) by transplanting cuttings of each species into 40 common gardens established along a natural hydrologic gradient in the field, where competition was minimized and herbivory was controlled. We analyzed species fitness responses to the hydrologic environment based on cumulative growth and survival over two years using aster fitness models. We also examined variation in nine drought and flooding tolerance traits expected to contribute to performance based on a priori understanding of plant function in relation to water availability and stress. We found substantial evidence that environmental filtering along the hydrologic gradient played a critical role in determining species distributions. Fitness variation of each species in the field experiment was used to model their water table depth optima. These optima predicted 68% of the variation in species realized hydrologic niches based on peak abundance in naturally assembled communities in the surrounding region. Multiple traits associated with water transport efficiency and water stress tolerance were correlated with species hydrologic niches, but they did not necessarily covary with each other. As a consequence, species occupying similar hydrologic niches had different combinations of trait values

  4. Chapter Four : Towards an Integration of Biodiversity–Ecosystem Functioning and Food Web Theory to Evaluate Relationships between Multiple Ecosystem Services

    NARCIS (Netherlands)

    Hines, J.; Putten, van der W.H.; Deyn, de G.B.; Wagg, C.; Voigt, W.; Mulder, C.; Weisser, W.W.; Engel, J.; Melian, C.; Scheu, S.; Birkhofer, K.; Ebeling, A.; Scherber, C.; Eisenhauer, N.

    2015-01-01

    Ecosystem responses to changes in species diversity are often studied individually. However, changes in species diversity can simultaneously influence multiple interdependent ecosystem functions. Therefore, an important challenge is to determine when and how changes in species diversity that

  5. Measuring management success for protected species: Looking beyond biological outcomes

    Directory of Open Access Journals (Sweden)

    Kathryn D Bisack

    2016-05-01

    Full Text Available The complexity of the ocean ecosystem, including the human component, is such that a single fishery may require multiple policy instruments to support recovery and conservation of protected species, in addition to those for fisheries management. As regulations multiply, the need for retrospective analysis and evaluation grows in order to inform future policy. To accurately evaluate policy instruments, clear objectives and their link to outcomes are necessary, as well as identifying criteria to evaluate outcomes. The Northeast United States sink gillnet groundfish fishery provides a case study of the complexity of regulations and policy instruments implemented under the Marine Mammal Protection Act and the Endangered Species Act to address bycatch of marine mammals. The case study illustrates a range of possible objectives for the policy instruments including biological, economic, social-normative and longevity factors. We highlight links between possible objectives, outcomes and criteria for the four factors, as well as areas for consideration when undertaking ex-post analyses. To support learning from past actions, we call for a coordinated effort involving multiple disciplines and jurisdictions to undertake retrospective analyses and evaluations of key groups of policy instruments used for protected species.

  6. DLRS: gene tree evolution in light of a species tree.

    Science.gov (United States)

    Sjöstrand, Joel; Sennblad, Bengt; Arvestad, Lars; Lagergren, Jens

    2012-11-15

    PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).

  7. 77 FR 58405 - Endangered Species; Marine Mammals; Receipt of Applications for Permit

    Science.gov (United States)

    2012-09-20

    ... decisions are: (1) Those supported by quantitative information or studies; and (2) Those that include... species. Multiple Applicants The following applicants each request a permit to import the sport- hunted...

  8. The evolution of female preferences for multiple indicators of quality.

    NARCIS (Netherlands)

    Van Doorn, G.S.; Weissing, F.J.

    In a variety of species, females exhibit preferences for multiple male ornaments. Several hypotheses have been proposed to explain this phenomenon. Which, if any, of these hypotheses is the most plausible in general remains largely unresolved based on the available empirical data. Yet theoretical

  9. Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi.

    Science.gov (United States)

    Ropars, Jeanne; Rodríguez de la Vega, Ricardo C; López-Villavicencio, Manuela; Gouzy, Jérôme; Sallet, Erika; Dumas, Émilie; Lacoste, Sandrine; Debuchy, Robert; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana

    2015-10-05

    Domestication is an excellent model for studies of adaptation because it involves recent and strong selection on a few, identified traits [1-5]. Few studies have focused on the domestication of fungi, with notable exceptions [6-11], despite their importance to bioindustry [12] and to a general understanding of adaptation in eukaryotes [5]. Penicillium fungi are ubiquitous molds among which two distantly related species have been independently selected for cheese making-P. roqueforti for blue cheeses like Roquefort and P. camemberti for soft cheeses like Camembert. The selected traits include morphology, aromatic profile, lipolytic and proteolytic activities, and ability to grow at low temperatures, in a matrix containing bacterial and fungal competitors [13-15]. By comparing the genomes of ten Penicillium species, we show that adaptation to cheese was associated with multiple recent horizontal transfers of large genomic regions carrying crucial metabolic genes. We identified seven horizontally transferred regions (HTRs) spanning more than 10 kb each, flanked by specific transposable elements, and displaying nearly 100% identity between distant Penicillium species. Two HTRs carried genes with functions involved in the utilization of cheese nutrients or competition and were found nearly identical in multiple strains and species of cheese-associated Penicillium fungi, indicating recent selective sweeps; they were experimentally associated with faster growth and greater competitiveness on cheese and contained genes highly expressed in the early stage of cheese maturation. These findings have industrial and food safety implications and improve our understanding of the processes of adaptation to rapid environmental changes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  10. Isolation and identification of oedogonium species and strains for biomass applications.

    Directory of Open Access Journals (Sweden)

    Rebecca J Lawton

    Full Text Available Freshwater macroalgae from the genus Oedogonium have recently been targeted for biomass applications; however, strains of Oedogonium for domestication have not yet been identified. Therefore, the objective of this study was to compare the performance of isolates of Oedogonium collected from multiple geographic locations under varying environmental conditions. We collected and identified wild-type isolates of Oedogonium from three geographic locations in Eastern Australia, then measured the growth of these isolates under a range of temperature treatments corresponding to ambient conditions in each geographic location. Our sampling identified 11 isolates of Oedogonium that could be successfully maintained under culture conditions. It was not possible to identify most isolates to species level using DNA barcoding techniques or taxonomic keys. However, there were considerable genetic and morphological differences between isolates, strongly supporting each being an identifiable species. Specific growth rates of species were high (>26% day-1 under 7 of the 9 temperature treatments (average tested temperature range: 20.9-27.7°C. However, the variable growth rates of species under lower temperature treatments demonstrated that some were better able to tolerate lower temperatures. There was evidence for local adaptation under lower temperature treatments (winter conditions, but not under higher temperature treatments (summer conditions. The high growth rates we recorded across multiple temperature treatments for the majority of species confirm the suitability of this diverse genus for biomass applications and the domestication of Oedogonium.

  11. Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes.

    Science.gov (United States)

    Gaynor, Kaitlyn M; Solomon, Joseph W; Siller, Stefanie; Jessell, Linnet; Duffy, J Emmett; Rubenstein, Dustin R

    2017-11-01

    Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes. © 2017 John Wiley & Sons Ltd.

  12. The contrasting nature of woody plant species in different neotropical forest biomes reflects differences in ecological stability.

    Science.gov (United States)

    Pennington, R Toby; Lavin, Matt

    2016-04-01

    A fundamental premise of this review is that distinctive phylogenetic and biogeographic patterns in clades endemic to different major biomes illuminate the evolutionary process. In seasonally dry tropical forests (SDTFs), phylogenies are geographically structured and multiple individuals representing single species coalesce. This pattern of monophyletic species, coupled with their old species stem ages, is indicative of maintenance of small effective population sizes over evolutionary timescales, which suggests that SDTF is difficult to immigrate into because of persistent resident lineages adapted to a stable, seasonally dry ecology. By contrast, lack of coalescence in conspecific accessions of abundant and often widespread species is more frequent in rain forests and is likely to reflect large effective population sizes maintained over huge areas by effective seed and pollen flow. Species nonmonophyly, young species stem ages and lack of geographical structure in rain forest phylogenies may reflect more widespread disturbance by drought and landscape evolution causing resident mortality that opens up greater opportunities for immigration and speciation. We recommend full species sampling and inclusion of multiple accessions representing individual species in phylogenies to highlight nonmonophyletic species, which we predict will be frequent in rain forest and savanna, and which represent excellent case studies of incipient speciation. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  13. Species or Genotypes? Reassessment of Four Recently Described Species of the Ceratocystis Wilt Pathogen, Ceratocystis fimbriata, on Mangifera indica.

    Science.gov (United States)

    Oliveira, Leonardo S S; Harrington, Thomas C; Ferreira, Maria A; Damacena, Michelle B; Al-Sadi, Abdullah M; Al-Mahmooli, Issa H S; Alfenas, Acelino C

    2015-09-01

    Ceratocystis wilt is among the most important diseases on mango (Mangifera indica) in Brazil, Oman, and Pakistan. The causal agent was originally identified in Brazil as Ceratocystis fimbriata, which is considered by some as a complex of many cryptic species, and four new species on mango trees were distinguished from C. fimbriata based on variation in internal transcribed spacer sequences. In the present study, phylogenetic analyses using DNA sequences of mating type genes, TEF-1α, and β-tubulin failed to identify lineages corresponding to the four new species names. Further, mating experiments found that the mango isolates representing the new species were interfertile with each other and a tester strain from sweet potato (Ipomoea batatas), on which the name C. fimbriata is based, and there was little morphological variation among the mango isolates. Microsatellite markers found substantial differentiation among mango isolates at the regional and population levels, but certain microsatellite genotypes were commonly found in multiple populations, suggesting that these genotypes had been disseminated in infected nursery stock. The most common microsatellite genotypes corresponded to the four recently named species (C. manginecans, C. acaciivora, C. mangicola, and C. mangivora), which are considered synonyms of C. fimbriata. This study points to the potential problems of naming new species based on introduced genotypes of a pathogen, the value of an understanding of natural variation within and among populations, and the importance of phenotype in delimiting species.

  14. Genome-wide comparative analysis of four Indian Drosophila species.

    Science.gov (United States)

    Mohanty, Sujata; Khanna, Radhika

    2017-12-01

    Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

  15. Automated identification and quantification of glycerophospholipid molecular species by multiple precursor ion scanning

    DEFF Research Database (Denmark)

    Ejsing, Christer S.; Duchoslav, Eva; Sampaio, Julio

    2006-01-01

    We report a method for the identification and quantification of glycerophospholipid molecular species that is based on the simultaneous automated acquisition and processing of 41 precursor ion spectra, specific for acyl anions of common fatty acids moieties and several lipid class-specific fragment...... of glycerophospholipids. The automated analysis of total lipid extracts was powered by a robotic nanoflow ion source and produced currently the most detailed description of the glycerophospholipidome....

  16. Trophic structure and metal bioaccumulation differences in multiple fish species exposed to coal ash-associated metals

    Energy Technology Data Exchange (ETDEWEB)

    Otter, Ryan [Middle Tennessee State University; Bailey, Frank [Middle Tennessee State University; Fortner, Allison M [ORNL; Adams, Marshall [ORNL

    2012-01-01

    On December 22, 2008 a dike containing coal fly ash from the Tennessee Valley Authority Kingston Fossil Plant near Kingston Tennessee USA failed and resulted in the largest coal ash spill in U.S. history. Coal ash, the by-product of coal combustion, is known to contain multiple contaminants of concern, including arsenic and selenium. The purpose of this study was to investigate the bioaccumulation of arsenic and selenium and to identify possible differences in trophic dynamics in feral fish at various sites in the vicinity of the Kingston coal ash spill. Elevated levels of arsenic and selenium were observed in various tissues of largemouth bass, white crappie, bluegill and redear sunfish from sites associated with the Kingston coal ash spill. Highest concentrations of selenium were found in redear sunfish with liver concentrations as high as 24.83 mg/kg dry weight and ovary concentrations up to 10.40 mg/kg dry weight at coal ash-associated sites. To help explain the elevated selenium levels observed in redear sunfish, investigations into the gut pH and trophic dynamics of redear sunfish and bluegill were conducted which demonstrated a large difference in the gut physiology between these two species. Redear sunfish stomach and intestinal pH was found to be 1.1 and 0.16 pH units higher than in bluegill, respectively. In addition, fish from coal ash-associated sites showed enrichment of 15N & 13C compared to no ash sites, indicating differences in food web dynamics between sites. These results imply the incorporation of coal ash-associated compounds into local food webs and/or a shift in diet at ash sites compared to the no ash reference sites. Based on these results, further investigation into a broader food web at ash-associated sites is warranted.

  17. Stochastic resonance and noise delayed extinction in a model of two competing species

    Science.gov (United States)

    Valenti, D.; Fiasconaro, A.; Spagnolo, B.

    2004-01-01

    We study the role of the noise in the dynamics of two competing species. We consider generalized Lotka-Volterra equations in the presence of a multiplicative noise, which models the interaction between the species and the environment. The interaction parameter between the species is a random process which obeys a stochastic differential equation with a generalized bistable potential in the presence of a periodic driving term, which accounts for the environment temperature variation. We find noise-induced periodic oscillations of the species concentrations and stochastic resonance phenomenon. We find also a nonmonotonic behavior of the mean extinction time of one of the two competing species as a function of the additive noise intensity.

  18. Species specificity in major urinary proteins by parallel evolution.

    Directory of Open Access Journals (Sweden)

    Darren W Logan

    Full Text Available Species-specific chemosignals, pheromones, regulate social behaviors such as aggression, mating, pup-suckling, territory establishment, and dominance. The identity of these cues remains mostly undetermined and few mammalian pheromones have been identified. Genetically-encoded pheromones are expected to exhibit several different mechanisms for coding 1 diversity, to enable the signaling of multiple behaviors, 2 dynamic regulation, to indicate age and dominance, and 3 species-specificity. Recently, the major urinary proteins (Mups have been shown to function themselves as genetically-encoded pheromones to regulate species-specific behavior. Mups are multiple highly related proteins expressed in combinatorial patterns that differ between individuals, gender, and age; which are sufficient to fulfill the first two criteria. We have now characterized and fully annotated the mouse Mup gene content in detail. This has enabled us to further analyze the extent of Mup coding diversity and determine their potential to encode species-specific cues.Our results show that the mouse Mup gene cluster is composed of two subgroups: an older, more divergent class of genes and pseudogenes, and a second class with high sequence identity formed by recent sequential duplications of a single gene/pseudogene pair. Previous work suggests that truncated Mup pseudogenes may encode a family of functional hexapeptides with the potential for pheromone activity. Sequence comparison, however, reveals that they have limited coding potential. Similar analyses of nine other completed genomes find Mup gene expansions in divergent lineages, including those of rat, horse and grey mouse lemur, occurring independently from a single ancestral Mup present in other placental mammals. Our findings illustrate that increasing genomic complexity of the Mup gene family is not evolutionarily isolated, but is instead a recurring mechanism of generating coding diversity consistent with a species

  19. Phylogenetically diverse macrophyte community promotes species diversity of mobile epi-benthic invertebrates

    Science.gov (United States)

    Nakamoto, Kenta; Hayakawa, Jun; Kawamura, Tomohiko; Kodama, Masafumi; Yamada, Hideaki; Kitagawa, Takashi; Watanabe, Yoshiro

    2018-07-01

    Various aspects of plant diversity such as species diversity and phylogenetic diversity enhance the species diversity of associated animals in terrestrial systems. In marine systems, however, the effects of macrophyte diversity on the species diversity of associated animals have received little attention. Here, we sampled in a subtropical seagrass-seaweed mixed bed to elucidate the effect of the macrophyte phylogenetic diversity based on the taxonomic relatedness as well as the macrophyte species diversity on species diversity of mobile epi-benthic invertebrates. Using regression analyses for each macrophyte parameter as well as multiple regression analyses, we found that the macrophyte phylogenetic diversity (taxonomic diversity index: Delta) positively influenced the invertebrate species richness and diversity index (H‧). Although the macrophyte species richness and H‧ also positively influenced the invertebrate species richness, the best fit model for invertebrate species richness did not include them, suggesting that the macrophyte species diversity indirectly influenced invertebrate species diversity. Possible explanations of the effects of macrophyte Delta on the invertebrate species diversity were the niche complementarity effect and the selection effect. This is the first study which demonstrates that macrophyte phylogenetic diversity has a strong effect on the species diversity of mobile epi-benthic invertebrates.

  20. Citizen science contributes to our knowledge of invasive plant species distributions

    Science.gov (United States)

    Crall, Alycia W.; Jarnevich, Catherine S.; Young, Nicholas E.; Panke, Brendon; Renz, Mark; Stohlgren, Thomas

    2015-01-01

    Citizen science is commonly cited as an effective approach to expand the scale of invasive species data collection and monitoring. However, researchers often hesitate to use these data due to concerns over data quality. In light of recent research on the quality of data collected by volunteers, we aimed to demonstrate the extent to which citizen science data can increase sampling coverage, fill gaps in species distributions, and improve habitat suitability models compared to professionally generated data sets used in isolation. We combined data sets from professionals and volunteers for five invasive plant species (Alliaria petiolata, Berberis thunbergii, Cirsium palustre, Pastinaca sativa, Polygonum cuspidatum) in portions of Wisconsin. Volunteers sampled counties not sampled by professionals for three of the five species. Volunteers also added presence locations within counties not included in professional data sets, especially in southern portions of the state where professional monitoring activities had been minimal. Volunteers made a significant contribution to the known distribution, environmental gradients sampled, and the habitat suitability of P. cuspidatum. Models generated with professional data sets for the other four species performed reasonably well according to AUC values (>0.76). The addition of volunteer data did not greatly change model performance (AUC > 0.79) but did change the suitability surface generated by the models, making them more realistic. Our findings underscore the need to merge data from multiple sources to improve knowledge of current species distributions, and to predict their movement under present and future environmental conditions. The efficiency and success of these approaches require that monitoring efforts involve multiple stakeholders in continuous collaboration via established monitoring networks.

  1. Prevalence and Antimicrobial Resistance of Enterococcus Species: A Hospital-Based Study in China

    Directory of Open Access Journals (Sweden)

    Wei Jia

    2014-03-01

    Full Text Available Objective: to investigate the prevalence and antimicrobial resistance of Enterococcus species isolated from a university hospital, and explore the mechanisms underlying the antimicrobial resistance, so as to provide clinical evidence for the inappropriate clinical use of antimicrobial agents and the control and prevention of enterococcal infections. Methods: a total of 1,157 enterococcal strains isolated from various clinical specimens from January 2010 to December 2012 in the General Hospital of Ningxia Medical University were identified to species level with a VITEK-2 COMPACT fully automated microbiological system, and the antimicrobial susceptibility of Enterococcus species was determined using the Kirby-Bauer disc diffusion method. The multiple-drug resistant enterococcal isolates were screened from the clinical isolates of Enterococcus species from the burns department. The minimal inhibitory concentration (MIC of Enterococcus species to the three fluoroquinolones, including ciprofloxacin, gatifloxacin and levofloxacin was determined with the agar dilution method, and the changes in the MIC of Enterococcus species to the three fluoroquinolones following reserpine treatment were evaluated. The β-lactam, aminoglycoside, tetracycline, macrolide, glycopeptide resistance genes and the efflux pump emeA genes were detected in the enterococcal isolates using a polymerase chain reaction (PCR assay. Results: the 1,157 clinical isolates of Enterococcus species included 679 E. faecium isolates (58.7%, 382 E. faecalis isolates (33%, 26 E. casseliflavus isolates (2.2%, 24 E. avium isolates (2.1%, and 46 isolates of other Enterococcus species (4%. The prevalence of antimicrobial resistance varied significantly between E. faecium and E. faecalis, and ≤1.1% of these two Enterococcus species were found to be resistant to vancomycin, teicoplanin or linezolid. In addition, the Enterococcus species isolated from different departments of the hospital

  2. Minimizing species extinctions through strategic planning for conservation fencing.

    Science.gov (United States)

    Ringma, Jeremy L; Wintle, Brendan; Fuller, Richard A; Fisher, Diana; Bode, Michael

    2017-10-01

    Conservation fences are an increasingly common management action, particularly for species threatened by invasive predators. However, unlike many conservation actions, fence networks are expanding in an unsystematic manner, generally as a reaction to local funding opportunities or threats. We conducted a gap analysis of Australia's large predator-exclusion fence network by examining translocation of Australian mammals relative to their extinction risk. To address gaps identified in species representation, we devised a systematic prioritization method for expanding the conservation fence network that explicitly incorporated population viability analysis and minimized expected species' extinctions. The approach was applied to New South Wales, Australia, where the state government intends to expand the existing conservation fence network. Existing protection of species in fenced areas was highly uneven; 67% of predator-sensitive species were unrepresented in the fence network. Our systematic prioritization yielded substantial efficiencies in that it reduced expected number of species extinctions up to 17 times more effectively than ad hoc approaches. The outcome illustrates the importance of governance in coordinating management action when multiple projects have similar objectives and rely on systematic methods rather than expanding networks opportunistically. © 2017 Society for Conservation Biology.

  3. Does enemy damage vary across the range of exotic plant species? Evidence from two coastal dune plant species in eastern Australia.

    Science.gov (United States)

    Tabassum, Samiya; Leishman, Michelle R

    2018-02-01

    Release from natural enemies is often cited as a key factor for understanding the success of invasive plant species in novel environments. However, with time invasive species will accumulate native enemies in their invaded range, with factors such as spread distance from the site of introduction, climate and leaf-level traits potentially affecting enemy acquisition rates. However, the influence of such factors is difficult to assess without examining enemy attack across the entire species' range. We tested the significance of factors associated with range expansion (distance from source population and maximum population density), climatic variables (annual temperature and rainfall) and leaf-level traits [specific leaf area (SLA) and foliar nitrogen concentration] in explaining variation in enemy damage across multiple populations of two coastal invasive plants (Gladiolus gueinzii Kunze and Hydrocotyle bonariensis Lam.) along their entire introduced distribution in eastern Australia. We found that for H. bonariensis, amount of foliar damage increased with distance from source population. In contrast, for G. gueinzii, probability and amount of foliar damage decreased with decreasing temperature and increasing rainfall, respectively. Our results show that patterns of enemy attack across species' ranges are complex and cannot be generalised between species or even range edges.

  4. Marine species in ambient low-oxygen regions subject to double jeopardy impacts of climate change.

    Science.gov (United States)

    Stortini, Christine H; Chabot, Denis; Shackell, Nancy L

    2017-06-01

    We have learned much about the impacts of warming on the productivity and distribution of marine organisms, but less about the impact of warming combined with other environmental stressors, including oxygen depletion. Also, the combined impact of multiple environmental stressors requires evaluation at the scales most relevant to resource managers. We use the Gulf of St. Lawrence, Canada, characterized by a large permanently hypoxic zone, as a case study. Species distribution models were used to predict the impact of multiple scenarios of warming and oxygen depletion on the local density of three commercially and ecologically important species. Substantial changes are projected within 20-40 years. A eurythermal depleted species already limited to shallow, oxygen-rich refuge habitat (Atlantic cod) may be relatively uninfluenced by oxygen depletion but increase in density within refuge areas with warming. A more stenothermal, deep-dwelling species (Greenland halibut) is projected to lose ~55% of its high-density areas under the combined impacts of warming and oxygen depletion. Another deep-dwelling, more eurythermal species (Northern shrimp) would lose ~4% of its high-density areas due to oxygen depletion alone, but these impacts may be buffered by warming, which may increase density by 8% in less hypoxic areas, but decrease density by ~20% in the warmest parts of the region. Due to local climate variability and extreme events, and that our models cannot project changes in species sensitivity to hypoxia with warming, our results should be considered conservative. We present an approach to effectively evaluate the individual and cumulative impacts of multiple environmental stressors on a species-by-species basis at the scales most relevant to managers. Our study may provide a basis for work in other low-oxygen regions and should contribute to a growing literature base in climate science, which will continue to be of support for resource managers as climate change

  5. Number of endemic and native plant species in the Galapagos Archipelago in relation to geographical parameters

    DEFF Research Database (Denmark)

    Willerslev, Eske; Hansen, Anders J.; Nielsen, Kirstine Klitgaard

    2002-01-01

    By simple and multiple regression analyses we investigate updated species numbers of endemic and native vascular plants and seed plants in the Galapagos Archipelago in relation to geographical parameters. We find that the best models to describe species numbers are regression models with log......-transformed species numbers as dependent and log-transformed modified area (i.e. area not covered with barren lava) as an independent variable. This holds both for total species number, for native species number, for endemic species number and for total number of seed plants as well as number of endemic seed plants...

  6. Oxidative responsiveness to multiple stressors in the key Antarctic species, Adamussium colbecki: Interactions between temperature, acidification and cadmium exposure.

    Science.gov (United States)

    Benedetti, Maura; Lanzoni, Ilaria; Nardi, Alessandro; d'Errico, Giuseppe; Di Carlo, Marta; Fattorini, Daniele; Nigro, Marco; Regoli, Francesco

    2016-10-01

    High-latitude marine ecosystems are ranked to be among the most sensitive regions to climate change since highly stenothermal and specially adapted organisms might be seriously affected by global warming and ocean acidification. The present investigation was aimed to provide new insights on the sensitivity to such environmental stressors in the key Antarctic species, Adamussium colbecki, focussing also on their synergistic effects with cadmium exposure, naturally abundant in this area for upwelling phenomena. Scallops were exposed for 2 weeks to various combinations of Cd (0 and 40 μgL-1), pH (8.05 and 7.60) and temperature (-1 and +1 °C). Beside Cd bioaccumulation, a wide panel of early warning biomarkers were analysed in digestive glands and gills including levels of metallothioneins, individual antioxidants and total oxyradical scavenging capacity, onset of oxidative cell damage like lipid peroxidation, lysosomal stability, DNA integrity and peroxisomal proliferation. Results indicated reciprocal interactions between multiple stressors and their elaboration by a quantitative hazard model based on the relevance and magnitude of effects, highlighted a different sensitivity of analysed tissues. Due to cellular adaptations to high basal Cd content, digestive gland appeared more tolerant toward other prooxidant stressors, but sensitive to variations of the metal. On the other hand, gills were more affected by various combinations of stressors occurring at higher temperature. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Genomic characterisation of Arachis porphyrocalyx (Valls & C.E. Simpson, 2005) (Leguminosae): multiple origin of Arachis species with x = 9

    Science.gov (United States)

    Celeste, Silvestri María; Ortiz, Alejandra Marcela; Robledo, Germán Ariel; Valls, José Francisco Montenegro; Lavia, Graciela Inés

    2017-01-01

    Abstract The genus Arachis Linnaeus, 1753 comprises four species with x = 9, three belong to the section Arachis: Arachis praecox (Krapov. W.C. Greg. & Valls, 1994), Arachis palustris (Krapov. W.C. Greg. & Valls, 1994) and Arachis decora (Krapov. W.C. Greg. & Valls, 1994) and only one belongs to the section Erectoides: Arachis porphyrocalyx (Valls & C.E. Simpson, 2005). Recently, the x = 9 species of section Arachis have been assigned to G genome, the latest described so far. The genomic relationship of Arachis porphyrocalyx with these species is controversial. In the present work, we carried out a karyotypic characterisation of Arachis porphyrocalyx to evaluate its genomic structure and analyse the origin of all x = 9 Arachis species. Arachis porphyrocalyx showed a karyotype formula of 14m+4st, one pair of A chromosomes, satellited chromosomes type 8, one pair of 45S rDNA sites in the SAT chromosomes, one pair of 5S rDNA sites and pericentromeric C-DAPI+ bands in all chromosomes. Karyotype structure indicates that Arachis porphyrocalyx does not share the same genome type with the other three x = 9 species and neither with the remaining Erectoides species. Taking into account the geographic distribution, morphological and cytogenetic features, the origin of species with x = 9 of the genus Arachis cannot be unique; instead, they originated at least twice in the evolutionary history of the genus. PMID:28919947

  8. Multiple scales in metapopulations of public goods producers

    Science.gov (United States)

    Bauer, Marianne; Frey, Erwin

    2018-04-01

    Multiple scales in metapopulations can give rise to paradoxical behavior: in a conceptual model for a public goods game, the species associated with a fitness cost due to the public good production can be stabilized in the well-mixed limit due to the mere existence of these scales. The scales in this model involve a length scale corresponding to separate patches, coupled by mobility, and separate time scales for reproduction and interaction with a local environment. Contrary to the well-mixed high mobility limit, we find that for low mobilities, the interaction rate progressively stabilizes this species due to stochastic effects, and that the formation of spatial patterns is not crucial for this stabilization.

  9. Assessment of ecological risks to wide-ranging wildlife species on the Oak Ridge Reservation

    International Nuclear Information System (INIS)

    Sample, B.

    1995-01-01

    Ecological risk assessment at CERCLA sites generally focuses on species that may be definitively associated with a contaminated area. While appropriate for sites with single, discrete areas of contamination, this approach is not adequate for sites with multiple, spatially separated contaminated areas such as the Oak Ridge Reservation (ORR). Wide-ranging wildlife species may travel between and use multiple contaminated sites. These species may therefore be exposed to and be at risk from contaminants from multiple locations. Use of a site (and therefore exposure and risk) by wildlife is dependent upon the availability of habitat. Availability and distribution of habitat on the ORR was determined using satellite imagery. The proportion of habitat within contaminated areas was then determined by overlaying boundaries of contaminated areas (Operable Units or OUs) on the ORR habitat map. The likelihood of contaminant exposure was estimated by comparing the habitat requirements for wildlife species to the proportion of suitable habitat within OUs. OU-specific contaminant concentrations in surface water, soil, or biota were used to estimate the magnitude of risk presented by each DU. The proportion of ORR-wide population likely to be exposed was estimated using literature-derived population density data for each endpoint. At present, due to major data gaps (i.e., lack of data for all OUs, site-specific population density or habitat use data, etc.) uncertainty associated with conclusions is high. Results of this assessment must therefore be considered to be preliminary

  10. Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada.

    Science.gov (United States)

    Jeffery, Nicholas W; Elías-Gutiérrez, Manuel; Adamowicz, Sarah J

    2011-01-01

    The region of Churchill, Manitoba, contains a wide variety of habitats representative of both the boreal forest and arctic tundra and has been used as a model site for biodiversity studies for nearly seven decades within Canada. Much previous work has been done in Churchill to study the Daphnia pulex species complex in particular, but no study has completed a wide-scale survey on the crustacean species that inhabit Churchill's aquatic ecosystems using molecular markers. We have employed DNA barcoding to study the diversity of the Branchiopoda (Crustacea) in a wide variety of freshwater habitats and to determine the likely origins of the Churchill fauna following the last glaciation. The standard animal barcode marker (COI) was sequenced for 327 specimens, and a 3% divergence threshold was used to delineate potential species. We found 42 provisional and valid branchiopod species from this survey alone, including several cryptic lineages, in comparison with the 25 previously recorded from previous ecological works. Using published sequence data, we explored the phylogeographic affinities of Churchill's branchiopods, finding that the Churchill fauna apparently originated from all directions from multiple glacial refugia (including southern, Beringian, and high arctic regions). Overall, these microcrustaceans are very diverse in Churchill and contain multiple species complexes. The present study introduces among the first sequences for some understudied genera, for which further work is required to delineate species boundaries and develop a more complete understanding of branchiopod diversity over a larger spatial scale.

  11. The status of Botryosphaeriaceae species infecting grapevines

    Directory of Open Access Journals (Sweden)

    Jose Ramón URBEZ-TORRES

    2011-12-01

    Full Text Available Normal 0 MicrosoftInternetExplorer4 Normal 0 MicrosoftInternetExplorer4 Species in the Botryosphaeriaceae have a cosmopolitan distribution, and occur on a wide range of annual and perennial hosts including grapevines. To date, morphological and taxonomic studies, as well as analyses of nucleotide sequences of multiple genes, have allowed the identification of at least 21 different species in the Botryosphaeriaceae occurring in grapevines worldwide. Grapevine disease symptoms caused by members of this family include leaf spots, fruit rots, shoot dieback, bud necrosis, vascular discoloration of the wood, and perennial cankers, and their current status as pathogens is reviewed. Additionally, the disease name Botryosphaeria dieback is proposed here to describe the different grapevine trunk disease symptoms caused by species of Botryosphaeriaceae. Much has been written during the last decade about the association between species in the Botryosphaeriaceae and grapevine trunk diseases, which has contributed to a better understanding of the role that these fungal taxa play in grapevine diseases. Although virulence has been shown to vary between species and isolates of the same species in different countries, these fungi have become well-recognized as important grapevine pathogens worldwide. Latest and novel findings from studies conducted in different countries, on disease etiology and species distribution, epidemiology and biology are discussed. Much progress has been achieved in the development and implementation of novel diagnostic and detection techniques.Vineyard sanitation techniques, as well as chemical, biological, and cultural control strategies available at the present time to reduce the infection caused by botryosphaeriaceous fungi, are presented in this review. 

  12. Plant species richness and ecosystem multifunctionality in global drylands

    Science.gov (United States)

    Maestre, Fernando T.; Quero, Jose L.; Gotelli, Nicholas J.; Escudero, Adrian; Ochoa, Victoria; Delgado-Baquerizo, Manuel; Garcia-Gomez, Miguel; Bowker, Matthew A.; Soliveres, Santiago; Escolar, Cristina; Garcia-Palacios, Pablo; Berdugo, Miguel; Valencia, Enrique; Gozalo, Beatriz; Gallardo, Antonio; Aguilera, Lorgio; Arredondo, Tulio; Blones, Julio; Boeken, Bertrand; Bran, Donaldo; Conceicao, Abel A.; Cabrera, Omar; Chaieb, Mohamed; Derak, Mchich; Eldridge, David J.; Espinosa, Carlos I.; Florentino, Adriana; Gaitan, Juan; Gatica, M. Gabriel; Ghiloufi, Wahida; Gomez-Gonzalez, Susana; Gutie, Julio R.; Hernandez, Rosa M.; Huang, Xuewen; Huber-Sannwald, Elisabeth; Jankju, Mohammad; Miriti, Maria; Monerris, Jorge; Mau, Rebecca L.; Morici, Ernesto; Naseri, Kamal; Ospina, Abelardo; Polo, Vicente; Prina, Anibal; Pucheta, Eduardo; Ramirez-Collantes, David A.; Romao, Roberto; Tighe, Matthew; Torres-Diaz, Cristian; Val, James; Veiga, Jose P.; Wang, Deli; Zaady, Eli

    2012-01-01

    Experiments suggest that biodiversity enhances the ability of ecosystems to maintain multiple functions, such as carbon storage, productivity, and the buildup of nutrient pools (multifunctionality). However, the relationship between biodiversity and multifunctionality has never been assessed globally in natural ecosystems. We report here on a global empirical study relating plant species richness and abiotic factors to multifunctionality in drylands, which collectively cover 41% of Earth's land surface and support over 38% of the human population. Multifunctionality was positively and significantly related to species richness. The best-fitting models accounted for over 55% of the variation in multifunctionality and always included species richness as a predictor variable. Our results suggest that the preservation of plant biodiversity is crucial to buffer negative effects of climate change and desertification in drylands.

  13. Covalent Immobilization of Enoxacin onto Titanium Implant Surfaces for Inhibiting Multiple Bacterial Species Infection and In Vivo Methicillin-Resistant Staphylococcus aureus Infection Prophylaxis.

    Science.gov (United States)

    Nie, Bin'en; Long, Teng; Ao, Haiyong; Zhou, Jianliang; Tang, Tingting; Yue, Bing

    2017-01-01

    Infection is one of the most important causes of titanium implant failure in vivo A developing prophylactic method involves the immobilization of antibiotics, especially vancomycin, onto the surface of the titanium implant. However, these methods have a limited effect in curbing multiple bacterial infections due to antibiotic specificity. In the current study, enoxacin was covalently bound to an amine-functionalized Ti surface by use of a polyethylene glycol (PEG) spacer, and the bactericidal effectiveness was investigated in vitro and in vivo The titanium surface was amine functionalized with 3-aminopropyltriethoxysilane (APTES), through which PEG spacer molecules were covalently immobilized onto the titanium, and then the enoxacin was covalently bound to the PEG, which was confirmed by X-ray photoelectron spectrometry (XPS). A spread plate assay, confocal laser scanning microscopy (CLSM), and scanning electron microscopy (SEM) were used to characterize the antimicrobial activity. For the in vivo study, Ti implants were inoculated with methicillin-resistant Staphylococcus aureus (MRSA) and implanted into the femoral medullary cavity of rats. The degree of infection was assessed by radiography, micro-computed tomography, and determination of the counts of adherent bacteria 3 weeks after surgery. Our data demonstrate that the enoxacin-modified PEGylated Ti surface effectively prevented bacterial colonization without compromising cell viability, adhesion, or proliferation in vitro Furthermore, it prevented MRSA infection of the Ti implants in vivo Taken together, our results demonstrate that the use of enoxacin-modified Ti is a potential approach to the alleviation of infections of Ti implants by multiple bacterial species. Copyright © 2016 American Society for Microbiology.

  14. Multiple free-radical scavenging capacity in serum

    Science.gov (United States)

    Oowada, Shigeru; Endo, Nobuyuki; Kameya, Hiromi; Shimmei, Masashi; Kotake, Yashige

    2012-01-01

    We have developed a method to determine serum scavenging-capacity profile against multiple free radical species, namely hydroxyl radical, superoxide radical, alkoxyl radical, alkylperoxyl radical, alkyl radical, and singlet oxygen. This method was applied to a cohort of chronic kidney disease patients. Each free radical species was produced with a common experimental procedure; i.e., uv/visible-light photolysis of free-radical precursor/sensitizer. The decrease in free-radical concentration by the presence of serum was quantified with electron spin resonance spin trapping method, from which the scavenging capacity was calculated. There was a significant capacity change in the disease group (n = 45) as compared with the healthy control group (n = 30). The percent values of disease’s scavenging capacity with respect to control group indicated statistically significant differences in all free-radical species except alkylperoxyl radical, i.e., hydroxyl radical, 73 ± 12% (p = 0.001); superoxide radical, 158 ± 50% (p = 0.001); alkoxyl radical, 121 ± 30% (p = 0.005); alkylperoxyl radical, 123 ± 32% (p>0.1); alkyl radical, 26 ± 14% (p = 0.001); and singlet oxygen, 57 ± 18% (p = 0.001). The scavenging capacity profile was illustrated using a radar chart, clearly demonstrating the characteristic change in the disease group. Although the cause of the scavenging capacity change by the disease state is not completely understood, the profile of multiple radical scavenging capacities may become a useful diagnostic tool. PMID:22962529

  15. Strategies to reduce the apical necrosis in vitro multiplication and rooting of Pistachio

    Directory of Open Access Journals (Sweden)

    Mariela Cid

    2016-07-01

    Full Text Available The pistachio (Pistacia sp. is one of the least exploited fruit among the main causes is the high cost of plant material by the difficulties of propagation of the species. The propagation in vitro offers great potential for the industry of this species by multiplication scale of selected clones. The aim of this study was to control the apical necrosis of outbreaks in the in vitro propagation Pistachio. From young shoots of plants of this species kept in growing houses, proceeded to disinfection with sodium hypochlorite 1% for different times. The apical and axillary buds were established in the culture medium Murashige and Skoog (1962 modified and supplemented with 1 mg/L Metatopolina. Different types of bottles, number and type of explants and culture media formulations for two subcultures multiplication and rooting were evaluated. Glass flask of 200 ml capacity, and line proliferates DKW medium achieved the lowest values apical necrosis. In the multiplication phase values were low in all treatments tested no statistical difference between them compared to rooting where apical necrosis reached higher values. The average DKW and prolific lines obtained lower values. MS medium modified crop, favored the number of segments rooted and DKW (Driver and Kuniyuki, 1984 the number of segments that sprouted, the latter having lower incidence of apical necrosis.

  16. Links between plant litter chemistry, species diversity, and below-ground ecosystem function

    OpenAIRE

    Meier, Courtney L.; Bowman, William D.

    2008-01-01

    Decomposition is a critical source of plant nutrients, and drives the largest flux of terrestrial C to the atmosphere. Decomposing soil organic matter typically contains litter from multiple plant species, yet we lack a mechanistic understanding of how species diversity influences decomposition processes. Here, we show that soil C and N cycling during decomposition are controlled by the composition and diversity of chemical compounds within plant litter mixtures, rather than by simple metrics...

  17. Deciphering chemotaxis pathways using cross species comparisons

    Directory of Open Access Journals (Sweden)

    Armitage Judith P

    2010-01-01

    Full Text Available Abstract Background Chemotaxis is the process by which motile bacteria sense their chemical environment and move towards more favourable conditions. Escherichia coli utilises a single sensory pathway, but little is known about signalling pathways in species with more complex systems. Results To investigate whether chemotaxis pathways in other bacteria follow the E. coli paradigm, we analysed 206 species encoding at least 1 homologue of each of the 5 core chemotaxis proteins (CheA, CheB, CheR, CheW and CheY. 61 species encode more than one of all of these 5 proteins, suggesting they have multiple chemotaxis pathways. Operon information is not available for most bacteria, so we developed a novel statistical approach to cluster che genes into putative operons. Using operon-based models, we reconstructed putative chemotaxis pathways for all 206 species. We show that cheA-cheW and cheR-cheB have strong preferences to occur in the same operon as two-gene blocks, which may reflect a functional requirement for co-transcription. However, other che genes, most notably cheY, are more dispersed on the genome. Comparison of our operons with shuffled equivalents demonstrates that specific patterns of genomic location may be a determining factor for the observed in vivo chemotaxis pathways. We then examined the chemotaxis pathways of Rhodobacter sphaeroides. Here, the PpfA protein is known to be critical for correct partitioning of proteins in the cytoplasmically-localised pathway. We found ppfA in che operons of many species, suggesting that partitioning of cytoplasmic Che protein clusters is common. We also examined the apparently non-typical chemotaxis components, CheA3, CheA4 and CheY6. We found that though variants of CheA proteins are rare, the CheY6 variant may be a common type of CheY, with a significantly disordered C-terminal region which may be functionally significant. Conclusions We find that many bacterial species potentially have multiple

  18. Assessing future suitability of tree species under climate change by multiple methods: a case study in southern Germany

    Directory of Open Access Journals (Sweden)

    Helge Walentowski

    2017-07-01

    Full Text Available We compared results derived using three different approaches to assess the suitability of common tree species on the Franconian Plateau in southern Germany under projected warmer and drier climate conditions in the period 2061-2080. The study area is currently a relatively warm and dry region of Germany. We calculated species distribution models (SDMs using information on species’ climate envelopes to predict regional species spectra under 63 different climate change scenarios. We complemented this with fine-scale ecological niche analysis using data from 51 vegetation surveys in seven forest reserves in the study area, and tree-ring analysis (TRA from local populations of five tree species to quantify their sensitivity to climatic extreme years. The SDMs showed that predicted future climate change in the region remains within the climate envelope of certain species (e.g. Quercus petraea, whilst for e.g. Fagus sylvatica, future climate conditions in one third of the scenarios are too warm and dry. This was confirmed by the TRA: sensitivity to drought periods is lower for Q. petraea than for F. sylvatica. The niche analysis shows that the local ecological niches of Quercus robur and Fraxinus excelsior are mainly characterized by soils providing favorable water supply than by climate, and Pinus sylvestris (planted is strongly influenced by light availability. The best adapted species for a warmer and potentially drier climate in the study region are Acer campestre, Sorbus torminalis, S. aria, Ulmus minor, and Tilia platyphyllos, which should therefore play a more prominent role in future climate-resilient mixed forest ecosystems.

  19. Scopulariopsis and scopulariopsis-like species from indoor environments

    Directory of Open Access Journals (Sweden)

    J.H.C. Woudenberg

    2017-09-01

    Full Text Available Scopulariopsis-like species are often reported from the indoor environment, as well as from clinical samples. The lack of type isolates and thorough phylogenetic studies in the Microascaceae hampered the correct identification of these isolates. Based on recent phylogenetic studies, which resulted in multiple name changes, the aim is to molecularly identify the Scopulariopsis and scopulariopsis-like species which occur in the indoor environment and give an overview of the current species in these genera and their habitats. Strains from the CBS culture collection were supplemented with almost 80 indoor strains of which the internal transcribed spacer 1 and 2 and intervening 5.8S nrDNA (ITS, beta-tubulin (tub2 and translation elongation factor 1-alpha (tef1 gene regions were sequenced for phylogenetic inference. The multi-gene phylogenies recognise 33 Microascus species and 12 Scopulariopsis species and showed that the recently established genus Fuscoannellis, typified by Scopulariopsis carbonaria, should be synonymized with the genus Yunnania. Seven new Microascus species, four new Scopulariopsis species, and one new Yunnania species, are described, and a new name in Microascus and two new name combinations (one in Microascus, and one in Yunnania are proposed. In the indoor environment 14 Microascus species and three Scopulariopsis species were found. Scopulariopsis brevicaulis (22 indoor isolates and Microascus melanosporus (19 indoor isolates are the most common indoor species, in number of isolates, followed by M. paisii (8 indoor isolates and S. candida (7 indoor isolates. A genus phylogeny based on the ITS, tef1 and the large subunit 28S nrDNA (LSU of the type or representative isolates of all here recognised species is provided depicting all species habitats. No correlation between phylogenetic relationship and habitat preference could be observed. Ten species which are found indoor are also found in relation with human-derived samples. A

  20. Impact of multiple stressors on juvenile fish in estuaries of the northeast Pacific.

    Science.gov (United States)

    Toft, Jason D; Munsch, Stuart H; Cordell, Jeffery R; Siitari, Kiira; Hare, Van C; Holycross, Brett M; DeBruyckere, Lisa A; Greene, Correigh M; Hughes, Brent B

    2018-05-01

    A key step in identifying global change impacts on species and ecosystems is to quantify effects of multiple stressors. To date, the science of global change has been dominated by regional field studies, experimental manipulation, meta-analyses, conceptual models, reviews, and studies focusing on a single stressor or species over broad spatial and temporal scales. Here, we provide one of the first studies for coastal systems examining multiple stressor effects across broad scales, focused on the nursery function of 20 estuaries spanning 1,600 km of coastline, 25 years of monitoring, and seven fish and invertebrate species along the northeast Pacific coast. We hypothesized those species most estuarine dependent and negatively impacted by human activities would have lower presence and abundances in estuaries with greater anthropogenic land cover, pollution, and water flow stress. We found significant negative relationships between juveniles of two of seven species (Chinook salmon and English sole) and estuarine stressors. Chinook salmon were less likely to occur and were less abundant in estuaries with greater pollution stress. They were also less abundant in estuaries with greater flow stress, although this relationship was marginally insignificant. English sole were less abundant in estuaries with greater land cover stress. Together, we provide new empirical evidence that effects of stressors on two fish species culminate in detectable trends along the northeast Pacific coast, elevating the need for protection from pollution, land cover, and flow stressors to their habitats. Lack of response among the other five species could be related to differing resistance to specific stressors, type and precision of the stressor metrics, and limitations in catch data across estuaries and habitats. Acquiring improved measurements of impacts to species will guide future management actions, and help predict how estuarine nursery functions can be optimized given anthropogenic

  1. Trends in extinction risk for imperiled species in Canada.

    Directory of Open Access Journals (Sweden)

    Brett Favaro

    Full Text Available Protecting and promoting recovery of species at risk of extinction is a critical component of biodiversity conservation. In Canada, the Committee on the Status of Endangered Wildlife in Canada (COSEWIC determines whether species are at risk of extinction or extirpation, and has conducted these assessments since 1977. We examined trends in COSEWIC assessments to identify whether at-risk species that have been assessed more than once tended to improve, remain constant, or deteriorate in status, as a way of assessing the effectiveness of biodiversity conservation in Canada. Of 369 species that met our criteria for examination, 115 deteriorated, 202 remained unchanged, and 52 improved in status. Only 20 species (5.4% improved to the point where they were 'not at risk', and five of those were due to increased sampling efforts rather than an increase in population size. Species outcomes were also dependent on the severity of their initial assessment; for example, 47% of species that were initially listed as special concern deteriorated between assessments. After receiving an at-risk assessment by COSEWIC, a species is considered for listing under the federal Species at Risk Act (SARA, which is the primary national tool that mandates protection for at-risk species. We examined whether SARA-listing was associated with improved COSEWIC assessment outcomes relative to unlisted species. Of 305 species that had multiple assessments and were SARA-listed, 221 were listed at a level that required identification and protection of critical habitat; however, critical habitat was fully identified for only 56 of these species. We suggest that the Canadian government should formally identify and protect critical habitat, as is required by existing legislation. In addition, our finding that at-risk species in Canada rarely recover leads us to recommend that every effort be made to actively prevent species from becoming at-risk in the first place.

  2. Patterns of specificity and diversity in species of Paraorygmatobothrium Ruhnke, 1994 (Cestoda: Phyllobothriidae) in Moreton Bay, Queensland, Australia, with the description of four new species.

    Science.gov (United States)

    Cutmore, Scott C; Bennett, Michael B; Miller, Terrence L; Cribb, Thomas H

    2017-11-01

    A survey of tapeworms of galeomorph sharks from Moreton Bay (Queensland, Australia) identified a complex of species of Paraorygmatobothrium Ruhnke, 1994 infecting 11 carcharhiniform and two orectolobiform species. Combined morphological and multi-locus molecular analyses (based on the 28S nuclear ribosomal RNA and partial mitochondrial NADH dehydrogenase subunit 1 genes) revealed the presence of 12 species of Paraorygmatobothrium; four species (Paraorygmatobothrium christopheri n. sp., P. harti n. sp., P. sinclairtaylori n. sp. and P. ullmanni n. sp.) are considered to be new to science and are formally described, four represent known species, and four lack sufficient morphological data to allow definitive identification. In contrast to previous records for the genus, four of the species found in this study exhibited low host specificity [P. orectolobi (Butler, 1987) Ruhnke, 2011, P. sinclairtaylori, P. ullmanni and Paraorygmatobothrium sp. 3], three stenoxenic species were each found in two closely-related sharks (P. orectolobi, P. ullmanni and Paraorygmatobothrium sp. 3) and one euryxenic species was found in five species from two shark families (P. sinclairtaylori). One species was found to exhibit mild morphologically plasticity (P. orectolobi), with size range being associated with different shark species. Conversely, collections of almost morphologically indistinguishable specimens from single shark species were found to represent multiple species of Paraorygmatobothrium. The findings of this study indicate that the description of species of this genus on the basis of morphological data alone is problematic and that the inclusion of multi-locus molecular data is essential for future work on Paraorygmatobothrium. Host specificity, morphology and phylogenetic relatedness of species of Paraorygmatobothrium are explored.

  3. Species Composition at the Sub-Meter Level in Discontinuous Permafrost in Subarctic Sweden

    Science.gov (United States)

    Anderson, S. M.; Palace, M. W.; Layne, M.; Varner, R. K.; Crill, P. M.

    2013-12-01

    Northern latitudes are experiencing rapid warming. Wetlands underlain by permafrost are particularly vulnerable to warming which results in changes in vegetative cover. Specific species have been associated with greenhouse gas emissions therefore knowledge of species compositional shift allows for the systematic change and quantification of emissions and changes in such emissions. Species composition varies on the sub-meter scale based on topography and other microsite environmental parameters. This complexity and the need to scale vegetation to the landscape level proves vital in our estimation of carbon dioxide (CO2) and methane (CH4) emissions and dynamics. Stordalen Mire (68°21'N, 18°49'E) in Abisko and is located at the edge of discontinuous permafrost zone. This provides a unique opportunity to analyze multiple vegetation communities in a close proximity. To do this, we randomly selected 25 1x1 meter plots that were representative of five major cover types: Semi-wet, wet, hummock, tall graminoid, and tall shrub. We used a quadrat with 64 sub plots and measured areal percent cover for 24 species. We collected ground based remote sensing (RS) at each plot to determine species composition using an ADC-lite (near infrared, red, green) and GoPro (red, blue, green). We normalized each image based on a Teflon white chip placed in each image. Textural analysis was conducted on each image for entropy, angular second momentum, and lacunarity. A logistic regression was developed to examine vegetation cover types and remote sensing parameters. We used a multiple linear regression using forwards stepwise variable selection. We found statistical difference in species composition and diversity indices between vegetation cover types. In addition, we were able to build regression model to significantly estimate vegetation cover type as well as percent cover for specific key vegetative species. This ground-based remote sensing allows for quick quantification of vegetation

  4. SPECIES DIVERSITY AND STABILITY OF BIRD COMMUNITIES

    Directory of Open Access Journals (Sweden)

    Matsyura M.V.

    2011-12-01

    Full Text Available When comparing the suggested stability indicators, we obtained statistically significant correlations for indicators of annual stability of species and total number and standard deviation of the logarithm of the number. Annual Stability Index can be applied with a high degree of reliability as a characteristic of the averaged structure of the community and its pyramid of abundances. The results of correlation analysis confirm our assumptions about the correlation between stability over the years and indices of species diversity and relative uniformity.The final task of the study was to create a mathematical model of stability, where the independent variables are the indices of species diversity. The calculation of these indices allows forecasting birds’ community stability. According to the result of multiple regression for the indicators of diversity and stability of the breeding birds’ community highest correlation coefficients were obtained fro Shannon index and Simpson's dominance Index.Community stability could be determined by its overall species diversity. When considering the stability of community its diversity should be considered as a combination of uniformity of their total number and number of species. The most suitable predictors for the community stability were the nonparametric index of dominance and information-statistical indices, since they considered simultaneously evenness and richness. The community stability is subject of the complexity of its internal communications pattern.

  5. Intra-species sequence comparisons for annotating genomes

    Energy Technology Data Exchange (ETDEWEB)

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  6. Global variation in woodpecker species richness shaped by tree availability

    DEFF Research Database (Denmark)

    Ilsoe, Sigrid Kistrup; Kissling, W. Daniel; Fjeldsa, Jon

    2017-01-01

    . Location: Global. Methods: We used spatial and non-spatial regressions to test for relationships between broad-scale woodpecker species richness and predictor variables describing current and deep-time availability of trees, current climate, Quaternary climate change, human impact, topographical...... a negative indirect effect on woodpecker species richness. Main conclusions: Global species richness of woodpeckers is primarily shaped by current tree cover and precipitation, reflecting a strong biotic association between woodpeckers and trees. Human influence can have a negative effect on woodpecker....... As an example, woodpeckers (Picidae) are closely associated with trees and woody habitats because of multiple morphological and ecological specializations. In this study, we test whether this strong biotic association causes woodpecker diversity to be closely linked to tree availability at a global scale...

  7. Process-based species pools reveal the hidden signature of biotic interactions amid the influence of temperature filtering

    DEFF Research Database (Denmark)

    Lessard, Jean-Philippe; Weinstein, Ben G.; Borregaard, Michael Krabbe

    2016-01-01

    A persistent challenge in ecology is to tease apart the in-fluence of multiple processes acting simultaneously and interacting in complex ways to shape the structure of species assemblages. We implement a heuristic approach that relies on explicitly defining spe-cies pools and permits assessment ...

  8. Barcoding and Phylogenetic Inferences in Nine Mugilid Species (Pisces, Mugiliformes

    Directory of Open Access Journals (Sweden)

    Neonila Polyakova

    2013-10-01

    Full Text Available Accurate identification of fish and fish products, from eggs to adults, is important in many areas. Grey mullets of the family Mugilidae are distributed worldwide and inhabit marine, estuarine, and freshwater environments in all tropical and temperate regions. Various Mugilid species are commercially important species in fishery and aquaculture of many countries. For the present study we have chosen two Mugilid genes with different phylogenetic signals: relatively variable mitochondrial cytochrome oxidase subunit I (COI and conservative nuclear rhodopsin (RHO. We examined their diversity within and among 9 Mugilid species belonging to 4 genera, many of which have been examined from multiple specimens, with the goal of determining whether DNA barcoding can achieve unambiguous species recognition of Mugilid species. The data obtained showed that information based on COI sequences was diagnostic not only for species-level identification but also for recognition of intraspecific units, e.g., allopatric populations of circumtropical Mugil cephalus, or even native and acclimatized specimens of Chelon haematocheila. All RHO sequences appeared strictly species specific. Based on the data obtained, we conclude that COI, as well as RHO sequencing can be used to unambiguously identify fish species. Topologies of phylogeny based on RHO and COI sequences coincided with each other, while together they had a good phylogenetic signal.

  9. An improved null model for assessing the net effects of multiple stressors on communities.

    Science.gov (United States)

    Thompson, Patrick L; MacLennan, Megan M; Vinebrooke, Rolf D

    2018-01-01

    Ecological stressors (i.e., environmental factors outside their normal range of variation) can mediate each other through their interactions, leading to unexpected combined effects on communities. Determining whether the net effect of stressors is ecologically surprising requires comparing their cumulative impact to a null model that represents the linear combination of their individual effects (i.e., an additive expectation). However, we show that standard additive and multiplicative null models that base their predictions on the effects of single stressors on community properties (e.g., species richness or biomass) do not provide this linear expectation, leading to incorrect interpretations of antagonistic and synergistic responses by communities. We present an alternative, the compositional null model, which instead bases its predictions on the effects of stressors on individual species, and then aggregates them to the community level. Simulations demonstrate the improved ability of the compositional null model to accurately provide a linear expectation of the net effect of stressors. We simulate the response of communities to paired stressors that affect species in a purely additive fashion and compare the relative abilities of the compositional null model and two standard community property null models (additive and multiplicative) to predict these linear changes in species richness and community biomass across different combinations (both positive, negative, or opposite) and intensities of stressors. The compositional model predicts the linear effects of multiple stressors under almost all scenarios, allowing for proper classification of net effects, whereas the standard null models do not. Our findings suggest that current estimates of the prevalence of ecological surprises on communities based on community property null models are unreliable, and should be improved by integrating the responses of individual species to the community level as does our

  10. INFLUENCES OF 50HZ ELECTRIC FIELDS ON GROWTH AND MULTIPLICATION OF SOME MICROORGANISMS

    Directory of Open Access Journals (Sweden)

    VOINA A.

    2016-07-01

    Full Text Available By dielectric spectroscopy and specific microbiological techniques have been studied the development (cell multiplication of Saccharomyces cerevisiae and Aspergillus niger growing and multiplication - both on culture media with sucrose and on those with starch. The experimental results have been revealed that the biochemical processes of the studied biomasses have significant changes in certain frequencies in the range 1 - 160Hz, characteristic of the different species/metabolized carbon source, respectively species/ metabolized carbon source/ development phase. It has also been found that in the case of Saccharomyces cerevisiae, the electric field of 50 Hz up to 20V/cm reduces the length of the LAG time and increases the growth rate of intensive increasing phase. Cultures of Aspergillus niger on culture medium with sucrose are stimulated (increasing the spores production by approx. 50% and reducing the maturity time of 50Hz signals up to 15V/cm. Electric fields higher than 30 V/cm in all media and investigated cultures carry on to the growth reduction / multiplication - up to a complete inhibition of growth at approx. 50V/cm

  11. Integrated presentation of ecological risk from multiple stressors

    OpenAIRE

    Goussen, Benoit Regis Marc; Price, Oliver R.; Rendal, Cecilie; Ashauer, Roman

    2016-01-01

    Current environmental risk assessments (ERA) do not account explicitly for ecological factors (e.g. species composition, temperature or food availability) and multiple stressors. Assessing mixtures of chemical and ecological stressors is needed as well as accounting for variability in environmental conditions and uncertainty of data and models. Here we propose a novel probabilistic ERA framework to overcome these limitations, which focusses on visualising assessment outcomes by construct-ing ...

  12. Animal species endangerment: The role of environmental pollution

    Science.gov (United States)

    Pattee, Oliver H.; Fellows, Valerie L.; Bounds, Dixie L.; Hoffman, David J.; Rattner, Barnett A.; Burton, G. Allen; Cairns, John

    2003-01-01

    Multiple factors contribute to the decline of species. Habitat destruction is the primary factor that threatens species. affecting 73 % of endangered species. The second major factor causing species decline is the introduction of nonnative species. affecting 68% of endangered species. Pollution and overharvesting were identified as impacting, respectively, 38 and 15% of endangered species. Other factors affecting species decline include hybridization, competition, disease, and other interspecific interactions. Once a species is reduced to a remnant of its former population size and distribution, its vulnerability to catastrophic pollution events increases, frequently exceeding or replacing the factors responsible for the initial decline. Small, isolated populations are particularly vulnerable to catastrophic loss by an acute event. such as a chemical spill or pesticide application. However, when it comes to surviving a single disaster, widespread subpopulations of a species are far more resilient and ensure genetic survival. Hypothesizing theoretical concerns of potential factors that could affect an endangered species could predispose the scientific and political communities to jeopardizing threats. The user of recovery plans as a data source must be aware of the bias within the data set. These data should be used with the caveat that the source of information in recovery plans is not always based on scientific research and rigorous data collection. Over 58% of the information identifying species threats is based on estimates or personal communication. while only 42% is based on peer reviewed literature, academic research. or government reports. Many recovery plans were written when a species was initially listed in the 1970s or 1980s. Politics, human disturbance, and habitat demand issues evolve over a 20- to 30-year period. leaving much of the threats facing endangered species outdated and inadequate. These data are most valuable when used to facilitate reviews

  13. SENSITIVITY OF NEST SUCCESS, YOUNG FLEDGED, AND PROBABILITY OF RENESTING TO SEASONAL FECUNDITY IN MULTI-BROODED SPECIES

    Science.gov (United States)

    A considerable number of avian species can produce multiple broods within a season. Seasonal fecundity in these species can vary by changes in the number of young fledged per nest, the probability of a successful nest, and the probability of initiating additional nests (e.g., re...

  14. Gastric volvulus in guinea pigs: comparison with other species.

    Science.gov (United States)

    Dudley, Emily S; Boivin, Gregory P

    2011-07-01

    Gastric volvulus has been documented in several species of animals and is associated with high morbidity and mortality. We report 2 cases of gastric volvulus in guinea pigs that died without detection of prior clinical signs. Both guinea pigs were adult female guinea pigs in a breeding colony and had given birth to multiple litters; one was pregnant at the time of death. Gastric rotations of 540° and 360° were identified at necropsy examination. These cases include the first known report of gastric rotation greater than 360° in any species. Although gastric volvulus has been reported to occur in guinea pigs, little is known about its risk factors, etiology, and pathogenesis. We conducted a literature review to compare gastric volvulus between guinea pigs and other species. Copyright 2011 by the American Association for Laboratory Animal Science

  15. Scaling local species-habitat relations to the larger landscape with a hierarchical spatial count model

    Science.gov (United States)

    Thogmartin, W.E.; Knutson, M.G.

    2007-01-01

    Much of what is known about avian species-habitat relations has been derived from studies of birds at local scales. It is entirely unclear whether the relations observed at these scales translate to the larger landscape in a predictable linear fashion. We derived habitat models and mapped predicted abundances for three forest bird species of eastern North America using bird counts, environmental variables, and hierarchical models applied at three spatial scales. Our purpose was to understand habitat associations at multiple spatial scales and create predictive abundance maps for purposes of conservation planning at a landscape scale given the constraint that the variables used in this exercise were derived from local-level studies. Our models indicated a substantial influence of landscape context for all species, many of which were counter to reported associations at finer spatial extents. We found land cover composition provided the greatest contribution to the relative explained variance in counts for all three species; spatial structure was second in importance. No single spatial scale dominated any model, indicating that these species are responding to factors at multiple spatial scales. For purposes of conservation planning, areas of predicted high abundance should be investigated to evaluate the conservation potential of the landscape in their general vicinity. In addition, the models and spatial patterns of abundance among species suggest locations where conservation actions may benefit more than one species. ?? 2006 Springer Science+Business Media B.V.

  16. A Source Area Approach Demonstrates Moderate Predictive Ability but Pronounced Variability of Invasive Species Traits.

    Directory of Open Access Journals (Sweden)

    Günther Klonner

    Full Text Available The search for traits that make alien species invasive has mostly concentrated on comparing successful invaders and different comparison groups with respect to average trait values. By contrast, little attention has been paid to trait variability among invaders. Here, we combine an analysis of trait differences between invasive and non-invasive species with a comparison of multidimensional trait variability within these two species groups. We collected data on biological and distributional traits for 1402 species of the native, non-woody vascular plant flora of Austria. We then compared the subsets of species recorded and not recorded as invasive aliens anywhere in the world, respectively, first, with respect to the sampled traits using univariate and multiple regression models; and, second, with respect to their multidimensional trait diversity by calculating functional richness and dispersion metrics. Attributes related to competitiveness (strategy type, nitrogen indicator value, habitat use (agricultural and ruderal habitats, occurrence under the montane belt, and propagule pressure (frequency were most closely associated with invasiveness. However, even the best multiple model, including interactions, only explained a moderate fraction of the differences in invasive success. In addition, multidimensional variability in trait space was even larger among invasive than among non-invasive species. This pronounced variability suggests that invasive success has a considerable idiosyncratic component and is probably highly context specific. We conclude that basing risk assessment protocols on species trait profiles will probably face hardly reducible uncertainties.

  17. Genetic data and the listing of species under the U.S. Endangered Species Act.

    Science.gov (United States)

    Fallon, Sylvia M

    2007-10-01

    Genetic information is becoming an influential factor in determining whether species, subspecies, and distinct population segments qualify for protection under the U.S. Endangered Species Act. Nevertheless, there are currently no standards or guidelines that define how genetic information should be used by the federal agencies that administer the act. I examined listing decisions made over a 10-year period (February 1996-February 2006) that relied on genetic information. There was wide variation in the genetic data used to inform listing decisions in terms of which genomes (mitochondrial vs. nuclear) were sampled and the number of markers (or genetic techniques) and loci evaluated. In general, whether the federal agencies identified genetic distinctions between putative taxonomic units or populations depended on the type and amount of genetic data. Studies that relied on multiple genetic markers were more likely to detect distinctions, and those organisms were more likely to receive protection than studies that relied on a single genetic marker. Although the results may, in part, reflect the corresponding availability of genetic techniques over the given time frame, the variable use of genetic information for listing decisions has the potential to misguide conservation actions. Future management policy would benefit from guidelines for the critical evaluation of genetic information to list or delist organisms under the Endangered Species Act.

  18. Global hotspots and correlates of alien species richness across taxonomic groups

    Science.gov (United States)

    Dawson, Wayne; Moser, Dietmar; van Kleunen, Mark; Kreft, Holger; Pergl, Jan; Pysek, Petr; Weigelt, Patrick; Winter, Marten; Lenzner, Bernd; Blackburn, Tim M.; Dyer, Ellie; Cassey, Phillip; Scrivens, Sally-Louise; Economo, Evan P.; Guenard, Benoit; Capinha, Cesar; Seebens, Hanno; Garcia-Diaz, Pablo; Nentwig, Wolfgang; Garcia-Berthou, Emili; Casal, Christine; Mandrak, Nicholas E.; Fuller, Pam; Meyer, Carsten; Essl, Franz

    2017-01-01

    Human-mediated transport beyond biogeographic barriers has led to the introduction and establishment of alien species in new regions worldwide. However, we lack a global picture of established alien species richness for multiple taxonomic groups. Here, we assess global patterns and potential drivers of established alien species richness across eight taxonomic groups (amphibians, ants, birds, freshwater fishes, mammals, vascular plants, reptiles and spiders) for 186 islands and 423 mainland regions. Hotspots of established alien species richness are predominantly island and coastal mainland regions. Regions with greater gross domestic product per capita, human population density, and area have higher established alien richness, with strongest effects emerging for islands. Ants and reptiles, birds and mammals, and vascular plants and spiders form pairs of taxonomic groups with the highest spatial congruence in established alien richness, but drivers explaining richness differ between the taxa in each pair. Across all taxonomic groups, our results highlight the need to prioritize prevention of further alien species introductions to island and coastal mainland regions globally.

  19. Adaptive training diminishes distractibility in aging across species.

    Science.gov (United States)

    Mishra, Jyoti; de Villers-Sidani, Etienne; Merzenich, Michael; Gazzaley, Adam

    2014-12-03

    Aging is associated with deficits in the ability to ignore distractions, which has not yet been remediated by any neurotherapeutic approach. Here, in parallel auditory experiments with older rats and humans, we evaluated a targeted cognitive training approach that adaptively manipulated distractor challenge. Training resulted in enhanced discrimination abilities in the setting of irrelevant information in both species that was driven by selectively diminished distraction-related errors. Neural responses to distractors in auditory cortex were selectively reduced in both species, mimicking the behavioral effects. Sensory receptive fields in trained rats exhibited improved spectral and spatial selectivity. Frontal theta measures of top-down engagement with distractors were selectively restrained in trained humans. Finally, training gains generalized to group and individual level benefits in aspects of working memory and sustained attention. Thus, we demonstrate converging cross-species evidence for training-induced selective plasticity of distractor processing at multiple neural scales, benefitting distractor suppression and cognitive control. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. Endangered Species Day | Endangered Species Coalition

    Science.gov (United States)

    Annual Top 10 Report Protecting the Endangered Species Act Wildlife Voices Stand for Wolves Endangered Campaigns Wildlife Voices Protecting the Endangered Species Act Annual Top 10 Report Endangered Species Day Stand for Wolves Vanishing BOOK: A Wild Success The Endangered Species Act at 40 Endangered Species The

  1. Chromosome mapping of repetitive sequences in four Serrasalmidae species (Characiformes

    Directory of Open Access Journals (Sweden)

    Leila Braga Ribeiro

    2014-01-01

    Full Text Available The Serrasalmidae family is composed of a number of commercially interesting species, mainly in the Amazon region where most of these fishes occur. In the present study, we investigated the genomic organization of the 18S and 5S rDNA and telomeric sequences in mitotic chromosomes of four species from the basal clade of the Serrasalmidae family: Colossoma macropomum, Mylossoma aureum, M. duriventre, and Piaractus mesopotamicus, in order to understand the chromosomal evolution in the family. All the species studied had diploid numbers 2n = 54 and exclusively biarmed chromosomes, but variations of the karyotypic formulas were observed. C-banding resulted in similar patterns among the analyzed species, with heterochromatic blocks mainly present in centromeric regions. The 18S rDNA mapping of C. macropomum and P. mesopotamicus revealed multiple sites of this gene; 5S rDNA sites were detected in two chromosome pairs in all species, although not all of them were homeologs. Hybridization with a telomeric probe revealed signals in the terminal portions of chromosomes in all the species and an interstitial signal was observed in one pair of C. macropomum.

  2. Optimal conservation of migratory species.

    Directory of Open Access Journals (Sweden)

    Tara G Martin

    Full Text Available BACKGROUND: Migratory animals comprise a significant portion of biodiversity worldwide with annual investment for their conservation exceeding several billion dollars. Designing effective conservation plans presents enormous challenges. Migratory species are influenced by multiple events across land and sea-regions that are often separated by thousands of kilometres and span international borders. To date, conservation strategies for migratory species fail to take into account how migratory animals are spatially connected between different periods of the annual cycle (i.e. migratory connectivity bringing into question the utility and efficiency of current conservation efforts. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report the first framework for determining an optimal conservation strategy for a migratory species. Employing a decision theoretic approach using dynamic optimization, we address the problem of how to allocate resources for habitat conservation for a Neotropical-Nearctic migratory bird, the American redstart Setophaga ruticilla, whose winter habitat is under threat. Our first conservation strategy used the acquisition of winter habitat based on land cost, relative bird density, and the rate of habitat loss to maximize the abundance of birds on the wintering grounds. Our second strategy maximized bird abundance across the entire range of the species by adding the constraint of maintaining a minimum percentage of birds within each breeding region in North America using information on migratory connectivity as estimated from stable-hydrogen isotopes in feathers. We show that failure to take into account migratory connectivity may doom some regional populations to extinction, whereas including information on migratory connectivity results in the protection of the species across its entire range. CONCLUSIONS/SIGNIFICANCE: We demonstrate that conservation strategies for migratory animals depend critically upon two factors: knowledge of

  3. Ecological niche transferability using invasive species as a case study.

    Directory of Open Access Journals (Sweden)

    Miguel Fernández

    Full Text Available Species distribution modeling is widely applied to predict invasive species distributions and species range shifts under climate change. Accurate predictions depend upon meeting the assumption that ecological niches are conserved, i.e., spatially or temporally transferable. Here we present a multi-taxon comparative analysis of niche conservatism using biological invasion events well documented in natural history museum collections. Our goal is to assess spatial transferability of the climatic niche of a range of noxious terrestrial invasive species using two complementary approaches. First we compare species' native versus invasive ranges in environmental space using two distinct methods, Principal Components Analysis and Mahalanobis distance. Second we compare species' native versus invaded ranges in geographic space as estimated using the species distribution modeling technique Maxent and the comparative index Hellinger's I. We find that species exhibit a range of responses, from almost complete transferability, in which the invaded niches completely overlap with the native niches, to a complete dissociation between native and invaded ranges. Intermediate responses included expansion of dimension attributable to either temperature or precipitation derived variables, as well as niche expansion in multiple dimensions. We conclude that the ecological niche in the native range is generally a poor predictor of invaded range and, by analogy, the ecological niche may be a poor predictor of range shifts under climate change. We suggest that assessing dimensions of niche transferability prior to standard species distribution modeling may improve the understanding of species' dynamics in the invaded range.

  4. Introduction of wild MAP species into the field culture

    Directory of Open Access Journals (Sweden)

    Dušková, Elena

    2016-07-01

    Full Text Available Althea officinalis L., Dracocephalum moldavica L., Gentiana lutea L., Rhodiola rosea L., and Valeriana officinalis L. are the species of wild medicinal plants which are not very commonly grown in field culture. The methods and practical experiences of their multiplication and growing in a field nursery in Olomouc (the Czech Republic are explained and shown in the manuscript.

  5. Novel multiplex PCR reveals multiple trypanosomatid species infecting North American bumble bees (Hymenoptera: Apidae: Bombus)

    Science.gov (United States)

    Crithidia bombi and Crithidia expoeki (Trypanosomatidae) are common parasites of bumble bees (Bombus spp.). Crithidia bombi was described in the 1980s, and C. expoeki was recently discovered using molecular tools. Both species have cosmopolitan distributions among their bumble bee hosts, but there h...

  6. Liquid chromatographic determination of oxytetracycline in edible fish fillets from six species of fish

    Science.gov (United States)

    Meinertz, J.R.; Stehly, G.R.; Gingerich, W.H.

    1998-01-01

    The approved use of oxytetracycline (OTC) in U.S. Aquaculture is limited to specific diseases in salmonids and channel catfish. OTC may also be effective in controlling diseases in other fish species important to public aquaculture, but before approved use of OTC can be augmented, an analytical method for determining OTC in fillet tissue from multiple species of fish will be required to support residue depletion studies. The objective of this study was to develop and validate a liquid chromatographic (LC) method that is accurate, precise, and sensitive for OTC in edible fillets from multiple species of fish. Homogenized fillet tissues from walleye, Atlantic salmon, striped bass, white sturgeon, rainbow trout, and channel catfish were fortified with OTC at nominal concentrations of 10, 20, 100, 1000, and 5000 ng/g. In tissues fortified with OTC at 100, 1000, and 5000 ng/g, mean recoveries ranged from 83 to 90%, and relative standard deviations (RSDs) ranged from 0.9 to 5.8%. In all other tissues, mean recoveries ranged from 59 to 98%, and RSDs ranged from 3.3 to 20%. Method quantitation limits ranged from 6 to 22 ng/g for the 6 species. The LC parameters produced easily integratable OTC peaks without coelution of endogenous compounds. The method is accurate, precise, and sensitive for OTC in fillet tissue from 6 species of fish from 5 phylogenetically diverse groups.

  7. Evaluating ecosystem services provided by non-native species: an experimental test in California grasslands.

    Science.gov (United States)

    Stein, Claudia; Hallett, Lauren M; Harpole, W Stanley; Suding, Katharine N

    2014-01-01

    The concept of ecosystem services--the benefits that nature provides to human's society--has gained increasing attention over the past decade. Increasing global abiotic and biotic change, including species invasions, is threatening the secure delivery of these ecosystem services. Efficient evaluation methods of ecosystem services are urgently needed to improve our ability to determine management strategies and restoration goals in face of these new emerging ecosystems. Considering a range of multiple ecosystem functions may be a useful way to determine such strategies. We tested this framework experimentally in California grasslands, where large shifts in species composition have occurred since the late 1700's. We compared a suite of ecosystem functions within one historic native and two non-native species assemblages under different grazing intensities to address how different species assemblages vary in provisioning, regulatory and supporting ecosystem services. Forage production was reduced in one non-native assemblage (medusahead). Cultural ecosystem services, such as native species diversity, were inherently lower in both non-native assemblages, whereas most other services were maintained across grazing intensities. All systems provided similar ecosystem services under the highest grazing intensity treatment, which simulated unsustainable grazing intensity. We suggest that applying a more comprehensive ecosystem framework that considers multiple ecosystem services to evaluate new emerging ecosystems is a valuable tool to determine management goals and how to intervene in a changing ecosystem.

  8. Species-specific challenges in dog cloning.

    Science.gov (United States)

    Kim, G A; Oh, H J; Park, J E; Kim, M J; Park, E J; Jo, Y K; Jang, G; Kim, M K; Kim, H J; Lee, B C

    2012-12-01

    Somatic cell nuclear transfer (SCNT) is now an established procedure used in cloning of several species. SCNT in dogs involves multiple steps including the removal of the nuclear material, injection of a donor cell, fusion, activation of the reconstructed oocytes and finally transfer to a synchronized female recipient. There are therefore many factors that contribute to cloning efficiency. By performing a retrospective analysis of 2005-2012 published papers regarding dog cloning, we define the optimum procedure and summarize the specific feature for dog cloning. © 2012 Blackwell Verlag GmbH.

  9. Ecological impacts of non-native species: Chapter 2

    Science.gov (United States)

    Pilliod, David S.; Griffiths, R.A.; Kuzmin, S.L.; Heatwole, Harold; Wilkinson, John W.

    2012-01-01

    Non-native species are considered one of the greatest threats to freshwater biodiversity worldwide (Drake et al. 1989; Allen and Flecker 1993; Dudgeon et al. 2005). Some of the first hypotheses proposed to explain global patterns of amphibian declines included the effects of non-native species (Barinaga 1990; Blaustein and Wake 1990; Wake and Morowitz 1991). Evidence for the impact of non-native species on amphibians stems (1) from correlative research that relates the distribution or abundance of a species to that of a putative non-native species, and (2) from experimental tests of the effects of a non-native species on survival, growth, development or behaviour of a target species (Kats and Ferrer 2003). Over the past two decades, research on the effects of non-native species on amphibians has mostly focused on introduced aquatic predators, particularly fish. Recent research has shifted to more complex ecological relationships such as influences of sub-lethal stressors (e.g. contaminants) on the effects of non-native species (Linder et al. 2003; Sih et al. 2004), non-native species as vectors of disease (Daszak et al. 2004; Garner et al. 2006), hybridization between non-natives and native congeners (Riley et al. 2003; Storfer et al. 2004), and the alteration of food-webs by non-native species (Nystrom et al. 2001). Other research has examined the interaction of non-native species in terms of facilitation (i.e. one non-native enabling another to become established or spread) or the synergistic effects of multiple non-native species on native amphibians, the so-called invasional meltdown hypothesis (Simerloff and Von Holle 1999). Although there is evidence that some non-native species may interact (Ricciardi 2001), there has yet to be convincing evidence that such interactions have led to an accelerated increase in the number of non-native species and cumulative impacts are still uncertain (Simberloff 2006). Applied research on the control, eradication, and

  10. EPANET Multi-Species Extension Software and User's Manual ...

    Science.gov (United States)

    Software and User's Manual EPANET is used in homeland security research to model contamination threats to water systems. Historically, EPANET has been limited to tracking the dynamics of a single chemical transported through a network of pipes and storage tanks, such as a fluoride used in a tracer study or free chlorine used in a disinfection decay study. Recently, the NHSRC released a new extension to EPANET called EPANET-MSX (Multi-Species eXtension) that allows for the consideration of multiple interacting species in the bulk flow and on the pipe walls. This capability has been incorporated into both a stand-alone executable program as well as a toolkit library of functions that programmers can use to build customized applications.

  11. [Informative predation: Towards a new species concept].

    Science.gov (United States)

    Lherminier, Philippe

    2018-04-01

    We distinguish two types of predations: the predation of matter-energy equals the food chain, and the informative predation is the capture of the information brought by the sexual partners. The cell or parent consumes energy and matter to grow, multiply and produce offspring. A fixed amount of resources is divided by the number of organisms, so individual growth and numerical multiplication are limited by depletion resources of the environment. Inversely, fertilization does not destroy information, but instead produces news. The information is multiplied by the number of partners and children, since each fertilization gives rise to a new genome following a combinatorial process that continues without exhaustion. The egg does not swallow the sperm to feed, but exchange good food for quality information. With the discovery of sex, that is, 1.5 Ga ago, life added soft predation to hard predation, i.e. information production within each species to matter-energy flow between species. Replicative and informative structures are subject to two competing biological constraints: replicative fidelity promotes proliferation, but limits adaptive evolution. On the contrary, the offspring of a couple obviously cannot be a copy of both partners, they are a new production, a re-production. Sexual recombination allows the exponential enrichment of the genetic diversity, thus promoting indefinite adaptive and evolutionary capacities. Evolutionary history illustrates this: the bacteria proliferate but have remained at the first purely nutritive stage in which most of the sensory functions, mobility, defense, and feeding have experienced almost no significant novelty in three billion years. Another world appeared with the sexual management of information. Sexual reproduction actually combines two functions: multiplicative by "vertical transfer" and informative by "horizontal transfer". This distinction is very common: polypus - medusa alternations, parasite multiplication cycles, the

  12. Dancing multiplicity states supported by a carboxylated group in dicopper structures bonded to O2

    KAUST Repository

    Poater, Albert

    2013-01-29

    The present study pretends to assign the correct multiplicity state to dinuclear copper complexes when interacting with free molecular oxygen. Recently, the formation of a bridge butterfly μ-η2: η2-peroxo dicopper core structure stabilized by the direct interaction of the counterion, a carboxylate group that allows the double bridge linking both metal-centre atoms, was characterized by crystallography. This system was assigned as a diradical singlet with Ms = 0. However, after new calculations it has turned out to be triplet (Ms = 1) despite the stabilization for this latter multiplicity state is not high. Here, the factors that contribute to make this structure display a multiplicity different with respect to the previously expected diradical singlet are described. In the present theoretical study, the roles of the αSp ligand constraints and the counterion are unravelled. On the other hand, the relative stability between the butterfly μ-η2: η2-peroxo structure and the isomeric bis(μ-oxo) species is also on discussion. Despite the relative stabilities of all these either structural or electronic isomeric species are supposed to depend on the computational method, which is a difficulty to reach a definite conclusion about the nature of the active species, all DFT methods using either pure or not pure DFT functionals here reach the same conclusion, favoring the triplet as the ground state for the butterfly μ-η2: η2-peroxo dicopper core structure, and the bis(μ-oxo) species when removing the benzoate counterion. © Springer-Verlag Berlin Heidelberg 2013.

  13. Bovine digital dermatitis: Possible pathogenic consortium consisting of Dichelobacter nodosus and multiple Treponema species

    DEFF Research Database (Denmark)

    Rasmussen, Marianne; Capion, Nynne; Schou, Kirstine Klitgaard

    2012-01-01

    not colonized by bacteria while only four samples were found normal. We hypothesise that external noxious stimuli allow D. nodosus to break down the epidermal barrier creating a suitable environment for the secondary invaders, Treponema species, which gradually take over the infection site. The variety...... and different distribution of treponemes in the DD lesions observed in this study, suggests that most of the Treponema phylotypes have the potential to be pathogenic....

  14. Species richness alone does not predict cultural ecosystem service value

    Science.gov (United States)

    Graves, Rose A.; Pearson, Scott M.; Turner, Monica G.

    2017-01-01

    Many biodiversity-ecosystem services studies omit cultural ecosystem services (CES) or use species richness as a proxy and assume that more species confer greater CES value. We studied wildflower viewing, a key biodiversity-based CES in amenity-based landscapes, in Southern Appalachian Mountain forests and asked (i) How do aesthetic preferences for wildflower communities vary with components of biodiversity, including species richness?; (ii) How do aesthetic preferences for wildflower communities vary across psychographic groups?; and (iii) How well does species richness perform as an indicator of CES value compared with revealed social preferences for wildflower communities? Public forest visitors (n = 293) were surveyed during the summer of 2015 and asked to choose among images of wildflower communities in which flower species richness, flower abundance, species evenness, color diversity, and presence of charismatic species had been digitally manipulated. Aesthetic preferences among images were unrelated to species richness but increased with more abundant flowers, greater species evenness, and greater color diversity. Aesthetic preferences were consistent across psychographic groups and unaffected by knowledge of local flora or value placed on wildflower viewing. When actual wildflower communities (n = 54) were ranked based on empirically measured flower species richness or wildflower viewing utility based on multinomial logit models of revealed preferences, rankings were broadly similar. However, designation of hotspots (CES values above the median) based on species richness alone missed 27% of wildflower viewing utility hotspots. Thus, conservation priorities for sustaining CES should incorporate social preferences and consider multiple dimensions of biodiversity that underpin CES supply. PMID:28320953

  15. Role of the noise on the transient dynamics of an ecosystem of interacting species

    Science.gov (United States)

    Spagnolo, B.; La Barbera, A.

    2002-11-01

    We analyze the transient dynamics of an ecosystem described by generalized Lotka-Volterra equations in the presence of a multiplicative noise and a random interaction parameter between the species. We consider specifically three cases: (i) two competing species, (ii) three interacting species (one predator-two preys), (iii) n-interacting species. The interaction parameter in case (i) is a stochastic process which obeys a stochastic differential equation. We find noise delayed extinction of one of two species, which is akin to the noise-enhanced stability phenomenon. Other two noise-induced effects found are temporal oscillations and spatial patterns of the two competing species. In case (ii) the noise induces correlated spatial patterns of the predator and of the two preys concentrations. Finally, in case (iii) we find the asymptotic behavior of the time average of the ith population when the ecosystem is composed of a great number of interacting species.

  16. Anharmonic Rovibrational Partition Functions for Fluxional Species at High Temperatures via Monte Carlo Phase Space Integrals

    Energy Technology Data Exchange (ETDEWEB)

    Jasper, Ahren W. [Chemical Sciences and Engineering; Gruey, Zackery B. [Chemical Sciences and Engineering; Harding, Lawrence B. [Chemical Sciences and Engineering; Georgievskii, Yuri [Chemical Sciences and Engineering; Klippenstein, Stephen J. [Chemical Sciences and Engineering; Wagner, Albert F. [Chemical Sciences and Engineering

    2018-02-03

    Monte Carlo phase space integration (MCPSI) is used to compute full dimensional and fully anharmonic, but classical, rovibrational partition functions for 22 small- and medium-sized molecules and radicals. Several of the species considered here feature multiple minima and low-frequency nonlocal motions, and efficiently sampling these systems is facilitated using curvilinear (stretch, bend, and torsion) coordinates. The curvilinear coordinate MCPSI method is demonstrated to be applicable to the treatment of fluxional species with complex rovibrational structures and as many as 21 fully coupled rovibrational degrees of freedom. Trends in the computed anharmonicity corrections are discussed. For many systems, rovibrational anharmonicities at elevated temperatures are shown to vary consistently with the number of degrees of freedom and with temperature once rovibrational coupling and torsional anharmonicity are accounted for. Larger corrections are found for systems with complex vibrational structures, such as systems with multiple large-amplitude modes and/or multiple minima.

  17. Biofluorescence as a survey tool for cryptic marine species.

    Science.gov (United States)

    De Brauwer, Maarten; Hobbs, Jean-Paul A; Ambo-Rappe, Rohani; Jompa, Jamaluddin; Harvey, Euan S; McIlwain, Jennifer L

    2017-10-06

    As ecosystems come under increasing anthropogenic pressure, rare species face the highest risk of extinction. Paradoxically, data necessary to evaluate the conservation status of rare species are often lacking because of the challenges of detecting species with low abundance. One group of fishes subject to this undersampling bias are those with cryptic body patterns. Twenty-one percent of cryptic fish species assessed for their extinction risk (International Union for Conservation of Nature [IUCN]) are data deficient. We developed a nondestructive method for surveying cryptically patterned marine fishes based on the presence of biofluorescence (underwater biofluorescence census, UBC). Blue LED torches were used to investigate how widespread biofluorescence was in cryptic reef fishes in the Coral Triangle region. The effectiveness of UBC to generate abundance data was tested on a data-deficient pygmy seahorse species (Hippocampus bargibanti) and compared with data obtained from standard underwater visual census (UVC) surveys. We recorded 95 reef fish species displaying biofluorescence, 73 of which had not been previously described as biofluorescent. Of those fish with cryptic patterns, 87% were biofluorescent compared with 9% for noncryptic fishes. The probability of species displaying biofluorescence was 70.9 times greater for cryptic species than for noncryptic species. Almost twice the number of H. bargibanti was counted using the UBC compared with UVC. For 2 triplefin species (Ucla xenogrammus, Enneapterygius tutuilae), the abundance detected with UBC was triple that detected with UVC. The UBC method was effective at finding cryptic species that would otherwise be difficult to detect and thus will reduce interobserver variability inherent to UVC surveys. Biofluorescence is ubiquitous in cryptic fishes, making this method applicable across a wide range of species. Data collected using UBC could be used with multiple IUCN criteria to assess the extinction risk of

  18. Standardization of a two-step real-time polymerase chain reaction based method for species-specific detection of medically important Aspergillus species.

    Science.gov (United States)

    Das, P; Pandey, P; Harishankar, A; Chandy, M; Bhattacharya, S; Chakrabarti, A

    2017-01-01

    Standardization of Aspergillus polymerase chain reaction (PCR) poses two technical challenges (a) standardization of DNA extraction, (b) optimization of PCR against various medically important Aspergillus species. Many cases of aspergillosis go undiagnosed because of relative insensitivity of conventional diagnostic methods such as microscopy, culture or antigen detection. The present study is an attempt to standardize real-time PCR assay for rapid sensitive and specific detection of Aspergillus DNA in EDTA whole blood. Three nucleic acid extraction protocols were compared and a two-step real-time PCR assay was developed and validated following the recommendations of the European Aspergillus PCR Initiative in our setup. In the first PCR step (pan-Aspergillus PCR), the target was 28S rDNA gene, whereas in the second step, species specific PCR the targets were beta-tubulin (for Aspergillus fumigatus, Aspergillus flavus, Aspergillus terreus), gene and calmodulin gene (for Aspergillus niger). Species specific identification of four medically important Aspergillus species, namely, A. fumigatus, A. flavus, A. niger and A. terreus were achieved by this PCR. Specificity of the PCR was tested against 34 different DNA source including bacteria, virus, yeast, other Aspergillus sp., other fungal species and for human DNA and had no false-positive reactions. The analytical sensitivity of the PCR was found to be 102 CFU/ml. The present protocol of two-step real-time PCR assays for genus- and species-specific identification for commonly isolated species in whole blood for diagnosis of invasive Aspergillus infections offers a rapid, sensitive and specific assay option and requires clinical validation at multiple centers.

  19. High-resolution pattern of mangrove species distribution is controlled by surface elevation

    Science.gov (United States)

    Leong, Rick C.; Friess, Daniel A.; Crase, Beth; Lee, Wei Kit; Webb, Edward L.

    2018-03-01

    Mangrove vegetation species respond to multiple environmental gradients, and an enhanced understanding of how mangrove species are distributed across these gradients will facilitate conservation and management. Many environmental gradients correlate with tidal inundation; however small-scale inundation patterns resulting from microtopographical changes are difficult to capture empirically. In contrast, surface elevation is often a suitable, measurable and cost-effective proxy for inundation. This study investigated the relationships between species distribution and surface elevation in a mangrove forest in northwest Singapore. Through high-resolution land surveying, we developed a digital elevation model (DEM) and conducted a comprehensive survey of 4380 trees with a stem diameter ≥ 5 cm. A total of 15 species were encountered, and elevation envelopes were generated for 12. Species envelopes were distributed along an elevation continuum, with most species overlapping within the continuum. Spatial autocorrelation (SAC) was present for nine of the 15 species, and when taken into account, species ordering was modified across the elevation continuum. The presence of SAC strongly reinforces the need for research to control for SAC: classical spatial description of mangrove species distribution should be revised to account for ecological factors. This study suggests that (1) surface elevation applies strong controls on species distribution and (2) most mangroves at our study site have similar physiological tolerances.

  20. Taxonomic status of maskrays of the Neotrygon kuhlii species complex (Myliobatoidei: Dasyatidae) with the description of three new species from the Indo-West Pacific.

    Science.gov (United States)

    Last, Peter R; White, William T; Séret, Bernard

    2016-02-23

    The bluespotted maskray, Neotrygon kuhlii (Müller & Henle, 1841), once thought to be widely distributed in the Indo-West Pacific, consists of a complex of several species and the type series consists of multiple species; its nomenclature is discussed. A lectotype and paralectotype are designated and the species rediagnosed based on the types and a fresh specimen from Honiara (Solomon Islands), near to the collection locality of the lectotype (Vanikoro, Solomon Islands). Molecular and morphological data provide confirmatory evidence that this maskray is distinct from some other regional forms. Three members of the complex from the Western Pacific identified in earlier studies are confirmed to be new species; Neotrygon australiae sp. nov. (Australia, New Guinea and eastern Indonesia), N. caeruleopunctata sp. nov. (Indian Ocean), and N. orientale sp. nov. (North-West Pacific). These species differ from each other and N. kuhlii in their adult size, anterior angle of the disc, number and distribution of blue spots on the dorsal disc, and other more subtle morphometric and meristic characters. Another largely plain-coloured Neotrygon, also currently misidentified as N. kuhlii, is sympatric with N. orientale sp. nov. in the South China Sea and off Taiwan. Neotrygon varidens (Garman) is resurrected as the valid name for this ray. A key is provided to species of the genus.

  1. Keeping All the PIECES: Phylogenetically Informed Ex Situ Conservation of Endangered Species.

    Science.gov (United States)

    Larkin, Daniel J; Jacobi, Sarah K; Hipp, Andrew L; Kramer, Andrea T

    2016-01-01

    Ex situ conservation in germplasm and living collections is a major focus of global plant conservation strategies. Prioritizing species for ex situ collection is a necessary component of this effort for which sound strategies are needed. Phylogenetic considerations can play an important role in prioritization. Collections that are more phylogenetically diverse are likely to encompass more ecological and trait variation, and thus provide stronger conservation insurance and richer resources for future restoration efforts. However, phylogenetic criteria need to be weighed against other, potentially competing objectives. We used ex situ collection and threat rank data for North American angiosperms to investigate gaps in ex situ coverage and phylogenetic diversity of collections and to develop a flexible framework for prioritizing species across multiple objectives. We found that ex situ coverage of 18,766 North American angiosperm taxa was low with respect to the most vulnerable taxa: just 43% of vulnerable to critically imperiled taxa were in ex situ collections, far short of a year-2020 goal of 75%. In addition, species held in ex situ collections were phylogenetically clustered (P species been drawn at random. These patterns support incorporating phylogenetic considerations into ex situ prioritization in a manner balanced with other criteria, such as vulnerability. To meet this need, we present the 'PIECES' index (Phylogenetically Informed Ex situ Conservation of Endangered Species). PIECES integrates phylogenetic considerations into a flexible framework for prioritizing species across competing objectives using multi-criteria decision analysis. Applying PIECES to prioritizing ex situ conservation of North American angiosperms, we show strong return on investment across multiple objectives, some of which are negatively correlated with each other. A spreadsheet-based decision support tool for North American angiosperms is provided; this tool can be customized to

  2. Multiple sclerosis: general features and pharmacologic approach

    International Nuclear Information System (INIS)

    Nielsen Lagumersindez, Denis; Martinez Sanchez, Gregorio

    2009-01-01

    Multiple sclerosis is an autoimmune, inflammatory and desmyelinization disease central nervous system (CNS) of unknown etiology and critical evolution. There different etiological hypotheses talking of a close interrelation among predisposing genetic factors and dissimilar environmental factors, able to give raise to autoimmune response at central nervous system level. Hypothesis of autoimmune pathogeny is based on study of experimental models, and findings in biopsies of affected patients by disease. Accumulative data report that the oxidative stress plays a main role in pathogenesis of multiple sclerosis. Oxygen reactive species generated by macrophages has been involved as mediators of demyelinization and of axon damage, in experimental autoimmune encephalomyelitis and strictly in multiple sclerosis. Disease diagnosis is difficult because of there is not a confirmatory unique test. Management of it covers the treatment of acute relapses, disease modification, and symptoms management. These features require an individualized approach, base on evolution of this affection, and tolerability of treatments. In addition to diet, among non-pharmacologic treatments for multiple sclerosis it is recommended physical therapy. Besides, some clinical assays have been performed in which we used natural extracts, nutrition supplements, and other agents with promising results. Pharmacology allowed neurologists with a broad array of proved effectiveness drugs; however, results of research laboratories in past years make probable that therapeutical possibilities increase notably in future. (Author)

  3. Symplectin evolved from multiple duplications in bioluminescent squid

    DEFF Research Database (Denmark)

    Francis, Warren R.; Christianson, Lynne M.; Haddock, Steven H.D.

    2017-01-01

    The squid Sthenoteuthis oualaniensis, formerly Symplectoteuthis oualaniensis, generates light using the luciferin coelenterazine and a unique enzyme, symplectin. Genetic information is limited for bioluminescent cephalopod species, so many proteins, including symplectin, occur in public databases...... functioning is conserved across essentially all members of the protein family, even those unlikely to be used for bioluminescence. Conversely, active site residues involved in pantetheinase catalysis are also conserved across essentially all of these proteins, suggesting that symplectin may have multiple...

  4. Species from within the Phytophthora cryptogea complex and related species, P. erythroseptica and P. sansomeana, readily hybridize.

    Science.gov (United States)

    Safaiefarahani, Banafsheh; Mostowfizadeh-Ghalamfarsa, Reza; Hardy, Giles E St J; Burgess, Treena I

    2016-08-01

    During a study on the phylogenetic relationships between species in the Phytophthora cryptogea complex and related species, Phytophthora erythroseptica and Phytophthora sansomeana, 19 hybrid isolates with multiple polymorphisms in the nuclear sequences were observed. Molecular characterization of hybrids was achieved by sequencing three nuclear (internal transcribed spacers, β-tubulin (TUB), heat shock protein 90) and two mitochondrial (cytochrome c oxidase subunit I (coxI), NADH dehydrogenase subunit I (NADH)) gene regions and cloning of the single-copy nuclear gene, TUB. Based on the molecular studies the hybrid isolates belonged to six distinct groups between P. cryptogea, P. erythroseptica, Phytophthora pseudocryptogea, P. sansomeana, and Phytophthora sp. kelmania. In all cases, only a single coxI and NADH allele was detected and nuclear genes were biparentally inherited, suggesting that the hybrids arose from sexual recombination events. Colony morphology, growth rate, cardinal temperatures, breeding system, and morphology of sporangia, oogonia, oospores, and antheridia were also determined. Some morphological differences between the hybrids and the parental species were noted; however, they were not sufficient to reliably distinguish the taxa and DNA markers from nuclear and mitochondrial genes will to be necessary for their identification. The parental species are all important pathogens of agricultural fields that have been transported globally. With the apparent ease of hybridization within this group there is ample opportunity for virulent hybrids to form, perhaps with extended host ranges. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  5. Screening Study of Leaf Terpene Concentration of 75 Borneo Rainforest Plant Species: Relationships with Leaf Elemental Concentrations and Morphology

    Directory of Open Access Journals (Sweden)

    Jordi Sardans

    2015-01-01

    Full Text Available Terpenes confer advantage in plant protection against abiotic stresses such as heat and drought and biotic stresses such as herbivore and pathogen attack. We conducted a screening of leaf mono- and sesquiterpene concentrations in 75 common woody plant species in the rainforest of Danum Valley (Borneo. Terpene compounds were found in 73 out of the 75 analysed species. Similar or lower proportions have been reported in other parts of the world. To our knowledge, this study reports for the first time the foliar concentration of mono- and/or sesquiterpene for 71 species and 39 genera not previously analyzed. Altogether 80 terpene compounds were determined across the species, and out of these only linalool oxide and (E- g -bisabolene had phylogenetic signal. A significant negative relationship between leaf monoterpene concentration and leaf length was observed, but leaf mono- and sesquitepene concentration were not related to any other leaf morphological trait nor to leaf elemental composition. Functions such as temperature protection, radiation protection or signaling and communication could underlie the high frequency of terpene-containing species of this tropical ecosystem which has multiple and very diverse interactions among multiple species.

  6. HAL: a hierarchical format for storing and analyzing multiple genome alignments.

    Science.gov (United States)

    Hickey, Glenn; Paten, Benedict; Earl, Dent; Zerbino, Daniel; Haussler, David

    2013-05-15

    Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance. We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover). All documentation and source code for the HAL API and tools are freely available at http://github.com/glennhickey/hal. hickey@soe.ucsc.edu or haussler@soe.ucsc.edu Supplementary data are available at Bioinformatics online.

  7. Scleractinian species richness for Florida Keys National Marine Sanctuary from 1996-2012 (NODC Accession 0123059)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains records of scleractinian species richness compiled from multiple sources. These are: CREMP, SCREAM, AGRRA, and FRRP CREMP: Coral Reef...

  8. Molecular interrogation of the feeding behaviour of field captured individual insects for interpretation of multiple host plant use.

    Directory of Open Access Journals (Sweden)

    James P Hereward

    Full Text Available The way in which herbivorous insect individuals use multiple host species is difficult to quantify under field conditions, but critical to understanding the evolutionary processes underpinning insect-host plant relationships. In this study we developed a novel approach to understanding the host plant interactions of the green mirid, Creontiades dilutus, a highly motile heteropteran bug that has been associated with many plant species. We combine quantified sampling of the insect across its various host plant species within particular sites and a molecular comparison between the insects' gut contents and available host plants. This approach allows inferences to be made as to the plants fed upon by individual insects in the field. Quantified sampling shows that this "generalist" species is consistently more abundant on two species in the genus Cullen (Fabaceae, its primary host species, than on any other of its numerous listed hosts. The chloroplast intergenic sequences reveal that C. dilutus frequently feeds on plants additional to the one from which it was collected, even when individuals were sampled from the primary host species. These data may be reconciled by viewing multiple host use in this species as an adaptation to survive spatiotemporally ephemeral habitats. The methodological framework developed here provides a basis from which new insights into the feeding behaviour and host plant relationships of herbivorous insects can be derived, which will benefit not only ecological interpretation but also our understanding of the evolution of these relationships.

  9. PCR-RFLP Method to Identify Salmonid Species of Economic Importance

    Directory of Open Access Journals (Sweden)

    Andreea Dudu

    2011-05-01

    Full Text Available The identification of different fish species by molecular methods has become necessary to avoid both the incorrect labelling of individuals involved in repopulation programmes and the commercial frauds on the fish market. Different fish species of great economical importance, like the salmonids, which are very much requested for their meat, can be identified using molecular techniques such as PCR-RFLP. The method is based on the amplification of a target region from the genome by PCR reaction followed by endonucleases digestion to detect the polymorphism of restriction fragments. In our study we analysed the following salmonid species from Romania: Salmo trutta fario, Salmo labrax, Salvelinus fontinalis, Onchorhynchus mykiss, Thymallus thymallus and Hucho hucho. In order to discriminate between the analysed species we amplified a fragment of mitochondrial genome comprising tRNAGlu/ cytochrome b/ tRNAThr/ tRNAPro/ D-loop/ tRNAPhe, followed by digestion with a specific restriction enzyme. The direct digestion of unpurified PCR products generated species-specific restriction patterns and proved to be a simple, reliable, inexpensive and fast method. Thus, it may be successfully utilized in specialized laboratories for the correct identification of the fish species for multiple purposes, including the traceability of fish food products.

  10. Simultaneous gene finding in multiple genomes.

    Science.gov (United States)

    König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

    2016-11-15

    As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. Wide-band tracheids are present in almost all species of Cactaceae.

    Science.gov (United States)

    Mauseth, James D

    2004-02-01

    Wide-band tracheids (WBTs) have been found in seedlings of most species of cacti that have fibrous wood in their adult bodies. Consequently, this cell type is now known to be present in almost all cacti. Earlier studies of adult plants revealed WBTs to be present only in cacti with globose or short, broad bodies, whereas all species with large columnar or long slender bodies had fibrous wood without WBTs. However, even these species produce WBTs during the first several months after germination. In species with fibrous wood in their adult bodies (species with large or slender bodies), seedlings undergo a phase transition in wood morphogenesis after a few months and stop producing the juvenile (WBT) wood and begin producing adult (fibrous) wood. If adult plants have an intermediate size, the phase transition is delayed and the plant produces WBT wood for several years. Species with globose bodies repress the phase transition completely and never switch to producing adult (fibrous) wood. Because WBTs are so widespread, they probably originated only once in Cactaceae, not multiple times as suggested earlier, or there may have been just a single origin in the Cactaceae/Portulacaceae clade.

  12. Multiple Trypanosoma infections are common amongst Glossina species in the new farming areas of Rufiji district, Tanzania

    Directory of Open Access Journals (Sweden)

    Malele Imna I

    2011-11-01

    Full Text Available Abstract Background Tsetse flies and trypanosomiasis are among several factors that constrain livestock development in Tanzania. Over the years Rufiji District was excluded from livestock production owing to tsetse fly infestation, however, a few years ago there was an influx of livestock following evictions aimed at conserving the Usangu wetlands. Methods A study was conducted to determine the efficiency of available traps for catching tsetse flies, Glossina species infesting the area, their infection rates and Trypanosoma species circulating in the area. Trapping was conducted during the semi dry season for a total of 30 days (ten days each month during the onset of the dry season of May - July 2009. Harvested flies after every 24 hours were dissected and examined under a light microscope for trypanosome infections and whole fly DNA was extracted from 82 flies and analyzed for trypanosomes by polymerase chain reaction (PCR using different sets of primers. Results The proportions of total tsetse catches per trap were in the following decreasing order S3 (33%, H-Trap (27%, Pyramidal (19%, sticky panel (11% and biconical trap (10%. Of the 1200 trapped flies, 75.6% were identified as Glossina pallidipes, 11.7% as G. brevipalpis, 9.6% as G. austeni and 3.0% G. morsitans morsitans. Dissections revealed the overall infection rate of 6.6% (13/197. Whole DNA was extracted from 82 tsetse flies and the prevalence of trypanosomes circulating in the area in descending order was 92.7% (76/82 for T. simiae; 70.7% (58/82 for T. brucei types; 48.8% (40/82 for the T. vivax types and 32.9% (27/82 for the T. congolense types as determined by PCR. All trypanosome types were found in all tsetse species analysed except for the T. congolense types, which were absent in G. m. morsitans. None of the T. brucei positive samples contained human infective trypanosomes by SRA - PCR test Conclusion All tsetse species found in Rufiji are biologically important in the

  13. Environmental heterogeneity–species richness relationships from a global perspective

    Directory of Open Access Journals (Sweden)

    Anke Stein

    2016-01-01

    Full Text Available Spatial environmental heterogeneity (EH is considered one of the most important factors promoting species richness, but no general consent about the EH–richness relationship exists so far. This is because research methods and study settings vary widely, and because non-significant and negative associations have also been reported. My thesis provides a comprehensive review of the different measurements and terminologies of EH used in the literature, and presents strong quantitative evidence of a generally positive relationship between biotic and abiotic EH and species richness of terrestrial plants and animals from landscape to global extents. In a meta-analysis and a subsequent case study comparing multiple EH measures and their association with mammal species richness worldwide, I furthermore reveal that the outcome of EH–richness studies depends strongly on study design, including both the EH measure chosen and spatial scale. My research contributes to a better understanding of the EH–richness relationship, while identifying future research needs.

  14. Replication of honey bee-associated RNA viruses across multiple bee species in apple orchards of Georgia, Germany and Kyrgyzstan.

    Science.gov (United States)

    Radzevičiūtė, Rita; Theodorou, Panagiotis; Husemann, Martin; Japoshvili, George; Kirkitadze, Giorgi; Zhusupbaeva, Aigul; Paxton, Robert J

    2017-06-01

    The essential ecosystem service of pollination is provided largely by insects, which are considered threatened by diverse biotic and abiotic global change pressures. RNA viruses are one such pressure, and have risen in prominence as a major threat for honey bees (Apis mellifera) and global apiculture, as well as a risk factor for other bee species through pathogen spill-over between managed honey bees and sympatric wild pollinator communities. Yet despite their potential role in global bee decline, the prevalence of honey bee-associated RNA viruses in wild bees is poorly known from both geographic and taxonomic perspectives. We screened members of pollinator communities (honey bees, bumble bees and other wild bees belonging to four families) collected from apple orchards in Georgia, Germany and Kyrgyzstan for six common honey bee-associated RNA virus complexes encompassing nine virus targets. The Deformed wing virus complex (DWV genotypes A and B) had the highest prevalence across all localities and host species and was the only virus complex found in wild bee species belonging to all four studied families. Based on amplification of negative-strand viral RNA, we found evidence for viral replication in wild bee species of DWV-A/DWV-B (hosts: Andrena haemorrhoa and several Bombus spp.) and Black queen cell virus (hosts: Anthophora plumipes, several Bombus spp., Osmia bicornis and Xylocopa spp.). Viral amplicon sequences revealed that DWV-A and DWV-B are regionally distinct but identical in two or more bee species at any one site, suggesting virus is shared amongst sympatric bee taxa. This study demonstrates that honey bee associated RNA viruses are geographically and taxonomically widespread, likely infective in wild bee species, and shared across bee taxa. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Cytogenetic analysis of five Hypostomus species (Siluriformes, Loricariidae)

    Science.gov (United States)

    Martinez, Emanuel Ricardo Monteiro; Zawadzki, Claudio Henrique; Foresti, Fausto; Oliveira, Claudio

    2011-01-01

    In this work, we analyzed the karyotypes of five Hypostomus species. Hypostomus cf. heraldoi, from the Mogi-Guaçu River, had 2n = 72 chromosomes, with a nucleolar organizer region (NOR) in one chromosomal pair. Hypostomus regani, from the Mogi-Guaçu River had 2n = 72 chromosomes with NORs in two chromosomal pairs. Hypostomus sp., from the Mogi-Guaçu River basin, had 2n = 68 chromosomes, with NORs in two chromosomal pairs. Hypostomus aff. agna, from Cavalo Stream, had 2n = 74 chromosomes with NORs in two chromosomal pairs. Hypostomus cf. topavae, from Carrapato Stream, had 2n = 80 chromosomes, with NORs in two chromosomal pairs. Hypostomus species showed marked diversity in the karyotypic formula, which suggested the occurrence of several Robertsonian rearrangements and pericentric inversions during the evolutionary history of this genus. This hypothesis was supported by the occurrence of a large number of uniarmed chromosomes and multiple NORs in a terminal position in most species and may be a derived condition in the Loricariidae. PMID:22215958

  16. Cytogenetic analysis of five Hypostomus species (Siluriformes, Loricariidae

    Directory of Open Access Journals (Sweden)

    Emanuel Ricardo Monteiro Martinez

    2011-01-01

    Full Text Available In this work, we analyzed the karyotypes of five species. Hypostomus cf. heraldoi, from the Mogi-Guaçu River, had 2n = 72 chromosomes, with a nucleolar organizer region (NOR in one chromosomal pair. Hypostomus regani, from the Mogi-Guaçu River had 2n = 72 chromosomes with NORs in two chromosomal pairs. Hypostomus sp., from the Mogi-Guaçu River basin, had 2n = 68 chromosomes, with NORs in two chromosomal pairs. Hypostomus aff. agna, from Cavalo Stream, had 2n = 74 chromosomes with NORs in two chromosomal pairs. Hypostomus cf. topavae, from Carrapato Stream, had 2n = 80 chromosomes, with NORs in two chromosomal pairs. Hypostomus species showed marked diversity in the karyotypic formula, which suggested the occurrence of several Robertsonian rearrangements and pericentric inversions during the evolutionary history of this genus. This hypothesis was supported by the occurrence of a large number of uniarmed chromosomes and multiple NORs in a terminal position in most species and may be a derived condition in the Loricariidae.

  17. Near infra-red spectroscopy quantitative modelling of bivalve protein, lipid and glycogen composition using single-species versus multi-species calibration and validation sets

    Science.gov (United States)

    Bartlett, Jill K.; Maher, William A.; Purss, Matthew B. J.

    2018-03-01

    Near infrared spectroscopy (NIRS) quantitative modelling was used to measure the protein, lipid and glycogen composition of five marine bivalve species (Saccostrea glomerata, Ostrea angasi, Crassostrea gigas, Mytilus galloprovincialis and Anadara trapezia) from multiple locations and seasons. Predictive models were produced for each component using individual species and aggregated sample populations for the three oyster species (S. glomerata, O. angasi and C. gigas) and for all five bivalve species. Whole animal tissues were freeze dried, ground to > 20 μm and scanned by NIRS. Protein, lipid and glycogen composition were determined by traditional chemical analyses and calibration models developed to allow rapid NIRS-measurement of these components in the five bivalve species. Calibration modelling was performed using wavelet selection, genetic algorithms and partial least squares analysis. Model quality was assessed using RPIQ and RMESP. For protein composition, single species model results had RPIQ values between 2.4 and 3.5 and RMSEP between 8.6 and 18%, the three oyster model had an RPIQ of 2.6 and an RMSEP of 10.8% and the five bivalve species had an RPIQ of 3.6 and RMSEP of 8.7% respectively. For lipid composition, single species models achieved RPIQ values between 2.9 and 5.3 with RMSEP between 9.1 and 11.2%, the oyster model had an RPIQ of 3.6 and RMSEP of 6.8 and the five bivalve model had an RPIQ of 5.2 and RMSEP of 6.8% respectively. For glycogen composition, the single species models had RPIQs between 3.8 and 18.9 with RMSEP between 3.5 and 9.2%, the oyster model had an RPIQ of 5.5 and RMSEP of 7.1% and the five bivalve model had an RPIQ of 4 and RMSEP of 7.6% respectively. Comparison between individual species models and aggregated models for three oyster species and five bivalve species for each component indicate that aggregating data from like species produces high quality models with robust and reliable quantitative application. The benefit of

  18. Geochemical Cycling of Iodine Species in Soils

    International Nuclear Information System (INIS)

    Hu, Q.; Moran, J.E.; Blackwood, V.

    2007-01-01

    Iodine is an important element in studies of environmental protection and human health, global-scale hydrologic processes and nuclear nonproliferation. Biogeochemical cycling of iodine in soils is complex, because iodine occurs in multiple oxidation states and as inorganic and organic species that may be hydrophilic, atmophilic, and biophilic. In this study, we applied new analytical techniques to study the content and speciation of stable iodine in representative surface soils, and sorption and transport behavior of iodine species (iodide, iodate, and 4-iodoaniline) in sediments collected at numerous nuclear facilities in the United States, where anthropogenic 129 I from prior nuclear fuel processing activities poses an environmental risk. The surface soil samples were chosen for their geographic locations (e.g., near the ocean or nuclear facilities) and for their differing physico-chemical characteristics (organic matter, texture, etc). Extracted solutions were analyzed by IC and ICP-MS methods to determine iodine concentrations and to examine iodine speciation (iodide, iodate, and organic iodine). In natural soils, iodine is mostly (nearly 90% of total iodine) present as organic species, while inorganic iodine becomes important (up to 50%) only in sediments with low organic matter. Results from laboratory column studies, aimed at examining transport of different iodine species, showed much greater retardation of 4-iodoaniline than iodide or iodate. Careful attention must be given to potential interconversion among species when interpreting the biogeochemical behavior of iodine in the environment. In addition to speciation, input concentration and residence time effects will influence the biogeochemical cycling of anthropogenic 129I deposited on surface soils

  19. Mycobacterium malmesburyense sp. nov., a non-tuberculous species of the genus Mycobacterium revealed by multiple gene sequence characterization.

    Science.gov (United States)

    Gcebe, Nomakorinte; Rutten, Victor; Pittius, Nicolaas Gey van; Naicker, Brendon; Michel, Anita

    2017-04-01

    Non-tuberculous mycobacteria (NTM) are ubiquitous in the environment, and an increasing number of NTM species have been isolated and characterized from both humans and animals, highlighting the zoonotic potential of these bacteria. Host exposure to NTM may impact on cross-reactive immune responsiveness, which may affect diagnosis of bovine tuberculosis and may also play a role in the variability of the efficacy of Mycobacterium bovis BCG vaccination against tuberculosis. In this study we characterized 10 NTM isolates originating from water, soil, nasal swabs of cattle and African buffalo as well as bovine tissue samples. These isolates were previously identified during an NTM survey and were all found, using 16S rRNA gene sequence analysis to be closely related to Mycobacterium moriokaense. A polyphasic approach that included phenotypic characterization, antibiotic susceptibility profiling, mycolic acid profiling and phylogenetic analysis of four gene loci, 16S rRNA, hsp65, sodA and rpoB, was employed to characterize these isolates. Sequence data analysis of the four gene loci revealed that these isolates belong to a unique species of the genus Mycobacterium. This evidence was further supported by several differences in phenotypic characteristics between the isolates and the closely related species. We propose the name Mycobacterium malmesburyense sp. nov. for this novel species. The type strain is WCM 7299T (=ATCC BAA-2759T=CIP 110822T).

  20. Within-species patterns challenge our understanding of the leaf economics spectrum.

    Science.gov (United States)

    Anderegg, Leander D L; Berner, Logan T; Badgley, Grayson; Sethi, Meera L; Law, Beverly E; HilleRisLambers, Janneke

    2018-05-01

    The utility of plant functional traits for predictive ecology relies on our ability to interpret trait variation across multiple taxonomic and ecological scales. Using extensive data sets of trait variation within species, across species and across communities, we analysed whether and at what scales leaf economics spectrum (LES) traits show predicted trait-trait covariation. We found that most variation in LES traits is often, but not universally, at high taxonomic levels (between families or genera in a family). However, we found that trait covariation shows distinct taxonomic scale dependence, with some trait correlations showing opposite signs within vs. across species. LES traits responded independently to environmental gradients within species, with few shared environmental responses across traits or across scales. We conclude that, at small taxonomic scales, plasticity may obscure or reverse the broad evolutionary linkages between leaf traits, meaning that variation in LES traits cannot always be interpreted as differences in resource use strategy. © 2018 John Wiley & Sons Ltd/CNRS.

  1. Fit-for-purpose: species distribution model performance depends on evaluation criteria - Dutch Hoverflies as a case study.

    Science.gov (United States)

    Aguirre-Gutiérrez, Jesús; Carvalheiro, Luísa G; Polce, Chiara; van Loon, E Emiel; Raes, Niels; Reemer, Menno; Biesmeijer, Jacobus C

    2013-01-01

    Understanding species distributions and the factors limiting them is an important topic in ecology and conservation, including in nature reserve selection and predicting climate change impacts. While Species Distribution Models (SDM) are the main tool used for these purposes, choosing the best SDM algorithm is not straightforward as these are plentiful and can be applied in many different ways. SDM are used mainly to gain insight in 1) overall species distributions, 2) their past-present-future probability of occurrence and/or 3) to understand their ecological niche limits (also referred to as ecological niche modelling). The fact that these three aims may require different models and outputs is, however, rarely considered and has not been evaluated consistently. Here we use data from a systematically sampled set of species occurrences to specifically test the performance of Species Distribution Models across several commonly used algorithms. Species range in distribution patterns from rare to common and from local to widespread. We compare overall model fit (representing species distribution), the accuracy of the predictions at multiple spatial scales, and the consistency in selection of environmental correlations all across multiple modelling runs. As expected, the choice of modelling algorithm determines model outcome. However, model quality depends not only on the algorithm, but also on the measure of model fit used and the scale at which it is used. Although model fit was higher for the consensus approach and Maxent, Maxent and GAM models were more consistent in estimating local occurrence, while RF and GBM showed higher consistency in environmental variables selection. Model outcomes diverged more for narrowly distributed species than for widespread species. We suggest that matching study aims with modelling approach is essential in Species Distribution Models, and provide suggestions how to do this for different modelling aims and species' data

  2. Umbrellas can work under water: Using threatened species as indicator and management surrogates can improve coastal conservation

    Science.gov (United States)

    Gilby, Ben L.; Olds, Andrew D.; Connolly, Rod M.; Yabsley, Nicholas A.; Maxwell, Paul S.; Tibbetts, Ian R.; Schoeman, David S.; Schlacher, Thomas A.

    2017-12-01

    Species surrogates, the use of particular species to index habitat condition or to represent ecological assemblages are commonly identified in many ecosystems, but are less tested, and therefore less employed in estuaries. Estuaries provide important ecosystem goods (e.g. harvestable species) and services (e.g. carbon processing, coastal armouring), but require protection from multiple human activities, meaning that finding surrogates for estuarine condition or faunal assemblages is a significant knowledge gap. In this study, we test the efficacy of the threatened estuary ray Hemitrygon fluviorum, as a suitable indicator of ecosystem condition and management umbrella surrogate species for conservation prioritisation and monitoring purposes within estuaries. We surveyed fish assemblages and ray presence at ten sites within each of 22 estuaries in southeast Queensland, Australia, using one hour deployments of baited video arrays. We then tested for correlations between ray presence, a series of environmental variables considered important to ecosystem management within estuaries (i.e. testing rays as indicator species), and the co-occurring fish species (i.e. testing rays as umbrella species). Estuary rays function as both umbrella species and ecological indicators of habitat status in subtropical Australian estuaries. As umbrellas, ray occurrence concords with elevated species richness. As ecological indicators, ray distribution concords with habitats of good water quality (especially low turbidity) and more natural vegetation remaining in the catchment. These results highlight the potential for other threatened aquatic vertebrates that are both readily detectable and that are reliable proxies for ecosystems status to be become useful management tools in estuaries. The protection of such large, threatened species in coastal seascapes allows managers to address multiple targets for conservation, especially; (1) protecting species of conservation concern; (2

  3. Poisson-Nernst-Planck equations with steric effects - non-convexity and multiple stationary solutions

    Science.gov (United States)

    Gavish, Nir

    2018-04-01

    We study the existence and stability of stationary solutions of Poisson-Nernst-Planck equations with steric effects (PNP-steric equations) with two counter-charged species. We show that within a range of parameters, steric effects give rise to multiple solutions of the corresponding stationary equation that are smooth. The PNP-steric equation, however, is found to be ill-posed at the parameter regime where multiple solutions arise. Following these findings, we introduce a novel PNP-Cahn-Hilliard model, show that it is well-posed and that it admits multiple stationary solutions that are smooth and stable. The various branches of stationary solutions and their stability are mapped utilizing bifurcation analysis and numerical continuation methods.

  4. Evaluation of semiarid grassland degradation in North China from multiple perspectives

    Science.gov (United States)

    Han, D.; Wang, G.; Xue, B. L.; Xu, X.

    2017-12-01

    There has been increasing interest in grassland ecosystem degradation resulting from intensive human activity and climate change, especially in arid and semiarid regions. Species composition, grassland desertification, and aboveground biomass (AGB) are used as indicators of grassland degradation in this study. We comprehensively analyzed variations in these three indicators in semiarid grassland in North China, on multiple time scales, based on MODIS products and field sampling datasets. Since 1984, species composition has become simpler and species indicative of grassland degradation, such as Potentilla acaulis and Artemisia frigida, have become dominant. These changes indicate that serious grassland degradation has occurred since 1984. Grassland degradation was also analyzed on shorter time scales. Analyses of interannual variations during 2005-2015 showed that desertification decreased and average AGB in the growth season increased over the study area, indicating that grassland was recovering. Analyses of spatial variations showed that the position of slightly desertified grassland shifted and formed a band in the west, where the lowest AGB in the growth season was recorded but tendency ratio of AGB increased from 2005 to 2015. Climatic factors had critical effects on grassland degradation, as identified by the three indicators on different time scales. The simpler species composition resulted from the increase in average temperature and decrease in average precipitation over the past 30 years. For nearly a decade, an increase in precipitation and decreases in temperature and potential evapotranspiration reduced desertification and increased AGB in the growth season overall. Consequently, there has distinct difference in grassland degradation between analysis results on above two time scales, indicating multiple perspectives should be considered to accurately assess the state and characteristics of grassland degradation.

  5. STRIDE: Species Tree Root Inference from Gene Duplication Events.

    Science.gov (United States)

    Emms, David M; Kelly, Steven

    2017-12-01

    The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of well-supported in-group gene duplication events from a set of unrooted gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of its root. We show that STRIDE correctly identifies the root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of timescales and taxonomic groups. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for data sets where information is limited. Furthermore, application of STRIDE to outgroup-free inference of the origin of the eukaryotic tree resulted in a root probability distribution that provides additional support for leading hypotheses for the origin of the eukaryotes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Agroforestry parkland species diversity : uses and management in semi-arid West-Africa (Burkina Faso)

    OpenAIRE

    Nikiema, A.

    2005-01-01

    Agroforestry parkland in semi-arid West Africa is a rural land use system, which allows farmers to grow annual crops in combination with useful trees. In addition to cereals, tree products such as vegetables, fruits, vegetable oil, firewood, fodder, and medicines are obtained from the parklands. However the multiple function of the parkland system can only be fulfilled if parkland species diversity is adequately managed.This thesis is focused on assessing the woody species diversity in the pa...

  7. Multiple losses of flight and recent speciation in steamer ducks

    Science.gov (United States)

    Fulton, Tara L.; Letts, Brandon; Shapiro, Beth

    2012-01-01

    Steamer ducks (Tachyeres) comprise four species, three of which are flightless. The flightless species are believed to have diverged from a flying common ancestor during the Late Pleistocene; however, their taxonomy remains contentious. Of particular interest is the previously unstudied population of flying steamer ducks in the Falkland Islands. We present the first genetic data from this insular population, and illustrate that the flying and flightless steamer ducks on the Falkland Islands are genetically indistinguishable, in contrast to their traditional classification as separate species. The three species that reside in continental South America form a genetically distinct lineage from the Falkland Island ducks. The Falkland steamer ducks diverged from their continental relatives 2.2–0.6 million years ago, coincident with a probable land bridge connecting the Falkland Islands to the mainland. The three continental species share a common ancestor approximately 15 000 years ago, possibly owing to isolation during a recent glacial advance. The continental steamer duck species are not reciprocally monophyletic, but show some amount of genetic differentiation between them. Each lineage of Tachyeres represents a different stage between flight and flightlessness. Their phylogenetic relationships suggest multiple losses of flight and/or long-term persistence of mixed-flight capability. As such, steamer ducks may provide a model system to study the evolution of flightlessness. PMID:22319122

  8. Plasma mass density, species mix and fluctuation diagnostics using fast Alfven wave

    International Nuclear Information System (INIS)

    Ikezi, H.; deGrassie, J.S.; Pinsker, R.I.; Snider, R.T.

    1996-06-01

    The authors propose to employ a fast Alfven wave interferometer and reflectometer as a tokamak diagnostic to measure the plasma mass density, D-T species mix profile, and density fluctuations. Utilize the property that the phase velocity of the fast wave propagating across the magnetic field is the Alfven speed with thermal correction, this fast wave interferometer on the DIII-D tokamak was successfully used to obtain the line integrated density. Since the position of the ion-ion hybrid cut-off in tokamaks is uniquely determined by the species mix ratio and the wave frequency, the reflectometer arrangement finds the species mix profile. The inversion method of reflectometry is discussed. The multiple chord interferometer also measures the mass density fluctuation profile

  9. Plasma mass density, species mix and fluctuation diagnostics using fast Alfven wave

    Energy Technology Data Exchange (ETDEWEB)

    Ikezi, H.; deGrassie, J.S.; Pinsker, R.I.; Snider, R.T.

    1996-06-01

    The authors propose to employ a fast Alfven wave interferometer and reflectometer as a tokamak diagnostic to measure the plasma mass density, D-T species mix profile, and density fluctuations. Utilize the property that the phase velocity of the fast wave propagating across the magnetic field is the Alfven speed with thermal correction, this fast wave interferometer on the DIII-D tokamak was successfully used to obtain the line integrated density. Since the position of the ion-ion hybrid cut-off in tokamaks is uniquely determined by the species mix ratio and the wave frequency, the reflectometer arrangement finds the species mix profile. The inversion method of reflectometry is discussed. The multiple chord interferometer also measures the mass density fluctuation profile.

  10. Northeastern conifer research: Multiple species and multiple values

    Science.gov (United States)

    Laura S. Kenefic; John C. Brissette; Richard W. Judd

    2014-01-01

    The northern conifer, or spruce-fir, forest of the northeastern USA and adjacent Canada has had a defining influence on the economy and culture of the region. The same can be said of the USDA Forest Service’s research in this forest, which began more than 100 years ago. Forest Service research has evolved since that time in response to changes in the needs and...

  11. Proactive conservation management of an island-endemic bird species in the face of global change

    Science.gov (United States)

    Morrison, S.A.; Sillett, T. Scott; Ghalambor, Cameron K.; Fitzpatrick, J.W.; Graber, D.M.; Bakker, V.J.; Bowman, R.; Collins, C.T.; Collins, P.W.; Delaney, K.S.; Doak, D.F.; Koenig, Walter D.; Laughrin, L.; Lieberman, A.A.; Marzluff, J.M.; Reynolds, M.D.; Scott, J.M.; Stallcup, J.A.; Vickers, W.; Boyce, W.M.

    2011-01-01

    Biodiversity conservation in an era of global change and scarce funding benefits from approaches that simultaneously solve multiple problems. Here, we discuss conservation management of the island scrub-jay (Aphelocoma insularis), the only island-endemic passerine species in the continental United States, which is currently restricted to 250-square-kilometer Santa Cruz Island, California. Although the species is not listed as threatened by state or federal agencies, its viability is nonetheless threatened on multiple fronts. We discuss management actions that could reduce extinction risk, including vaccination, captive propagation, biosecurity measures, and establishing a second free-living population on a neighboring island. Establishing a second population on Santa Rosa Island may have the added benefit of accelerating the restoration and enhancing the resilience of that island's currently highly degraded ecosystem. The proactive management framework for island scrub-jays presented here illustrates how strategies for species protection, ecosystem restoration, and adaptation to and mitigation of climate change can converge into an integrated solution. ?? 2011 by American Institute of Biological Sciences. All rights reserved.

  12. Quantitative degenerate four-wave mixing spectroscopy: Probes for molecular species

    Energy Technology Data Exchange (ETDEWEB)

    Farrow, R.; Rakestraw, D.; Paul, P.; Lucht, R.; Danehy, P.; Friedman-Hill, E.; Germann, G. [Sandia National Laboratories, Livermore, CA (United States)

    1993-12-01

    Resonant degenerate four-wave mixing (DFWM) is currently the subject of intensive investigation as a sensitive diagnostic tool for molecular species. DFWM has the advantage of generating a coherent (beam-like) signal which results in null-background detection and provides excellent immunity to background-light interference. Since multiple one-photon resonances are involved in the signal generation process, the DFWM technique can allow sensitive detection of molecules via electronic, vibrational or rotational transitions. These properties combine to make DFWM a widely applicable diagnostic technique for the probing of molecular species. The authors are conducting fundamental and applied investigations of DFWM for quantitative measurements of trace species in reacting gases. During the past year, efforts have been focussed in two areas: (1) understanding the effects of collisional processes on the DFWM signal generation process, and (2) exploring the applicability of infrared DFWM to detect polyatomic molecules via rovibrational transitions.

  13. Seasonal patterns of mixed species groups in large East African mammals.

    Science.gov (United States)

    Kiffner, Christian; Kioko, John; Leweri, Cecilia; Krause, Stefan

    2014-01-01

    Mixed mammal species groups are common in East African savannah ecosystems. Yet, it is largely unknown if co-occurrences of large mammals result from random processes or social preferences and if interspecific associations are consistent across ecosystems and seasons. Because species may exchange important information and services, understanding patterns and drivers of heterospecific interactions is crucial for advancing animal and community ecology. We recorded 5403 single and multi-species clusters in the Serengeti-Ngorongoro and Tarangire-Manyara ecosystems during dry and wet seasons and used social network analyses to detect patterns of species associations. We found statistically significant associations between multiple species and association patterns differed spatially and seasonally. Consistently, wildebeest and zebras preferred being associated with other species, whereas carnivores, African elephants, Maasai giraffes and Kirk's dik-diks avoided being in mixed groups. During the dry season, we found that the betweenness (a measure of importance in the flow of information or disease) of species did not differ from a random expectation based on species abundance. In contrast, in the wet season, we found that these patterns were not simply explained by variations in abundances, suggesting that heterospecific associations were actively formed. These seasonal differences in observed patterns suggest that interspecific associations may be driven by resource overlap when resources are limited and by resource partitioning or anti-predator advantages when resources are abundant. We discuss potential mechanisms that could drive seasonal variation in the cost-benefit tradeoffs that underpin the formation of mixed-species groups.

  14. Multiple infections of rodents with zoonotic pathogens in Austria.

    Science.gov (United States)

    Schmidt, Sabrina; Essbauer, Sandra S; Mayer-Scholl, Anne; Poppert, Sven; Schmidt-Chanasit, Jonas; Klempa, Boris; Henning, Klaus; Schares, Gereon; Groschup, Martin H; Spitzenberger, Friederike; Richter, Dania; Heckel, Gerald; Ulrich, Rainer G

    2014-07-01

    Rodents are important reservoirs for a large number of zoonotic pathogens. We examined the occurrence of 11 viral, bacterial, and parasitic agents in rodent populations in Austria, including three different hantaviruses, lymphocytic choriomeningitis virus, orthopox virus, Leptospira spp., Borrelia spp., Rickettsia spp., Bartonella spp., Coxiella burnetii, and Toxoplasma gondii. In 2008, 110 rodents of four species (40 Clethrionomys glareolus, 29 Apodemus flavicollis, 26 Apodemus sylvaticus, and 15 Microtus arvalis) were trapped at two rural sites in Lower Austria. Chest cavity fluid and samples of lung, spleen, kidney, liver, brain, and ear pinna skin were collected. We screened selected tissue samples for hantaviruses, lymphocytic choriomeningitis virus, orthopox viruses, Leptospira, Borrelia, Rickettsia, Bartonella spp., C. burnetii, and T. gondii by RT-PCR/PCR and detected nucleic acids of Tula hantavirus, Leptospira spp., Borrelia afzelii, Rickettsia spp., and different Bartonella species. Serological investigations were performed for hantaviruses, lymphocytic choriomeningitis virus, orthopox viruses, and Rickettsia spp. Here, Dobrava-Belgrade hantavirus-, Tula hantavirus-, lymphocytic choriomeningitis virus-, orthopox virus-, and rickettsia-specific antibodies were demonstrated. Puumala hantavirus, C. burnetii, and T. gondii were neither detected by RT-PCR/PCR nor by serological methods. In addition, multiple infections with up to three pathogens were shown in nine animals of three rodent species from different trapping sites. In conclusion, these results show that rodents in Austria may host multiple zoonotic pathogens. Our observation raises important questions regarding the interactions of different pathogens in the host, the countermeasures of the host's immune system, the impact of the host-pathogen interaction on the fitness of the host, and the spread of infectious agents among wild rodents and from those to other animals or humans.

  15. Ensemble forecasting of species distributions.

    Science.gov (United States)

    Araújo, Miguel B; New, Mark

    2007-01-01

    Concern over implications of climate change for biodiversity has led to the use of bioclimatic models to forecast the range shifts of species under future climate-change scenarios. Recent studies have demonstrated that projections by alternative models can be so variable as to compromise their usefulness for guiding policy decisions. Here, we advocate the use of multiple models within an ensemble forecasting framework and describe alternative approaches to the analysis of bioclimatic ensembles, including bounding box, consensus and probabilistic techniques. We argue that, although improved accuracy can be delivered through the traditional tasks of trying to build better models with improved data, more robust forecasts can also be achieved if ensemble forecasts are produced and analysed appropriately.

  16. Multiple cues for winged morph production in an aphid metacommunity.

    Directory of Open Access Journals (Sweden)

    Mohsen Mehrparvar

    Full Text Available Environmental factors can lead individuals down different developmental pathways giving rise to distinct phenotypes (phenotypic plasticity. The production of winged or unwinged morphs in aphids is an example of two alternative developmental pathways. Dispersal is paramount in aphids that often have a metapopulation structure, where local subpopulations frequently go extinct, such as the specialized aphids on tansy (Tanacetum vulgare. We conducted various experiments to further understand the cues involved in the production of winged dispersal morphs by the two dominant species of the tansy aphid metacommunity, Metopeurum fuscoviride and Macrosiphoniella tanacetaria. We found that the ant-tended M. fuscoviride produced winged individuals predominantly at the beginning of the season while the untended M. tanacetaria produced winged individuals throughout the season. Winged mothers of both species produced winged offspring, although in both species winged offspring were mainly produced by unwinged females. Crowding and the presence of predators, effects already known to influence wing production in other aphid species, increased the percentage of winged offspring in M. tanacetaria, but not in M. fuscoviride. We find there are also other factors (i.e. temporal effects inducing the production of winged offspring for natural aphid populations. Our results show that the responses of each aphid species are due to multiple wing induction cues.

  17. The intertidal fish fauna of the west coast of South Africa - species ...

    African Journals Online (AJOL)

    1991-11-05

    Nov 5, 1991 ... elucidated by means of stepwise multiple regression, both at the whole community and individual species levels. ... and were selected to represent the full range of pool parame- ... fish and the total mass of fish caught as dependent variables .... 'bi- and tri-modal' vertical zonation patterns at Groenrivier.

  18. Succulent species differ substantially in their tolerance and phytoextraction potential when grown in the presence of Cd, Cr, Cu, Mn, Ni, Pb, and Zn.

    Science.gov (United States)

    Zhang, Chengjun; Sale, Peter W G; Clark, Gary J; Liu, Wuxing; Doronila, Augustine I; Kolev, Spas D; Tang, Caixian

    2015-12-01

    Plants for the phytoextraction of heavy metals should have the ability to accumulate high concentrations of such metals and exhibit multiple tolerance traits to cope with adverse conditions such as coexistence of multiple heavy metals, high salinity, and drought which are the characteristics of many contaminated soils. This study compared 14 succulent species for their phytoextraction potential of Cd, Cr, Cu, Mn, Ni, Pb, and Zn. There were species variations in metal tolerance and accumulation. Among the 14 succulent species, an Australian native halophyte Carpobrotus rossii exhibited the highest relative growth rate (20.6-26.6 mg plant(-1) day(-1)) and highest tolerance index (78-93%), whilst Sedum "Autumn Joy" had the lowest relative growth rate (8.3-13.6 mg plant(-1) day(-1)), and Crassula multicava showed the lowest tolerance indices (phytoextraction of these heavy metals than other species. These findings suggest that Carpobrotus rossii is a promising candidate for phytoextraction of multiple heavy metals, and the aquatic or semiterrestrial Crassula helmsii is suitable for phytoextraction of Cd and Zn from polluted waters or wetlands.

  19. Regional management units for marine turtles: a novel framework for prioritizing conservation and research across multiple scales.

    Science.gov (United States)

    Wallace, Bryan P; DiMatteo, Andrew D; Hurley, Brendan J; Finkbeiner, Elena M; Bolten, Alan B; Chaloupka, Milani Y; Hutchinson, Brian J; Abreu-Grobois, F Alberto; Amorocho, Diego; Bjorndal, Karen A; Bourjea, Jerome; Bowen, Brian W; Dueñas, Raquel Briseño; Casale, Paolo; Choudhury, B C; Costa, Alice; Dutton, Peter H; Fallabrino, Alejandro; Girard, Alexandre; Girondot, Marc; Godfrey, Matthew H; Hamann, Mark; López-Mendilaharsu, Milagros; Marcovaldi, Maria Angela; Mortimer, Jeanne A; Musick, John A; Nel, Ronel; Pilcher, Nicolas J; Seminoff, Jeffrey A; Troëng, Sebastian; Witherington, Blair; Mast, Roderic B

    2010-12-17

    Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques--including site-based monitoring, genetic analyses, mark-recapture studies and telemetry--can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine- to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition, the RMU framework--including maps and supporting metadata--will be an

  20. Regional Management Units for Marine Turtles: A Novel Framework for Prioritizing Conservation and Research across Multiple Scales

    Science.gov (United States)

    Wallace, Bryan P.; DiMatteo, Andrew D.; Hurley, Brendan J.; Finkbeiner, Elena M.; Bolten, Alan B.; Chaloupka, Milani Y.; Hutchinson, Brian J.; Abreu-Grobois, F. Alberto; Amorocho, Diego; Bjorndal, Karen A.; Bourjea, Jerome; Bowen, Brian W.; Dueñas, Raquel Briseño; Casale, Paolo; Choudhury, B. C.; Costa, Alice; Dutton, Peter H.; Fallabrino, Alejandro; Girard, Alexandre; Girondot, Marc; Godfrey, Matthew H.; Hamann, Mark; López-Mendilaharsu, Milagros; Marcovaldi, Maria Angela; Mortimer, Jeanne A.; Musick, John A.; Nel, Ronel; Pilcher, Nicolas J.; Seminoff, Jeffrey A.; Troëng, Sebastian; Witherington, Blair; Mast, Roderic B.

    2010-01-01

    Background Resolving threats to widely distributed marine megafauna requires definition of the geographic distributions of both the threats as well as the population unit(s) of interest. In turn, because individual threats can operate on varying spatial scales, their impacts can affect different segments of a population of the same species. Therefore, integration of multiple tools and techniques — including site-based monitoring, genetic analyses, mark-recapture studies and telemetry — can facilitate robust definitions of population segments at multiple biological and spatial scales to address different management and research challenges. Methodology/Principal Findings To address these issues for marine turtles, we collated all available studies on marine turtle biogeography, including nesting sites, population abundances and trends, population genetics, and satellite telemetry. We georeferenced this information to generate separate layers for nesting sites, genetic stocks, and core distributions of population segments of all marine turtle species. We then spatially integrated this information from fine- to coarse-spatial scales to develop nested envelope models, or Regional Management Units (RMUs), for marine turtles globally. Conclusions/Significance The RMU framework is a solution to the challenge of how to organize marine turtles into units of protection above the level of nesting populations, but below the level of species, within regional entities that might be on independent evolutionary trajectories. Among many potential applications, RMUs provide a framework for identifying data gaps, assessing high diversity areas for multiple species and genetic stocks, and evaluating conservation status of marine turtles. Furthermore, RMUs allow for identification of geographic barriers to gene flow, and can provide valuable guidance to marine spatial planning initiatives that integrate spatial distributions of protected species and human activities. In addition

  1. Termites amplify effects of wood traits on decomposition rates among multiple bamboo and dicot woody species

    NARCIS (Netherlands)

    Liu, Guofang; Cornwell, W.K.; Cao, Kunfang; Hu, Yukun; van Logtestijn, R.S.P; Yang, Shijian; Xie, Xiufang; Zhang, Yalin; Ye, Duo; Pan, Xu; Ye, Xuehua; Huang, Zhenying; Dong, Ming; Cornelissen, J.H.C.

    2015-01-01

    Wood decomposition is a key process in the terrestrial carbon cycle, controlling carbon storage with feedback to climate. In (sub) tropical forest, termites are major players in wood decomposition, but their role relative to that of microbial decomposers and wood traits of different tree species is

  2. Octocoral Species Richness for the Florida Keys National Marine Sanctuary from 1999-2009 (NODC Accession 0123059)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dataset includes species richness of benthic branching and encrusting gorgonians collected from multiple habitat types across the south Florida shelf, inside and...

  3. Phylogenetic analysis and DNA-based species confirmation in Anopheles (Nyssorhynchus.

    Directory of Open Access Journals (Sweden)

    Peter G Foster

    Full Text Available Specimens of neotropical Anopheles (Nyssorhynchus were collected and identified morphologically. We amplified three genes for phylogenetic analysis-the single copy nuclear white and CAD genes, and the COI barcode region. Since we had multiple specimens for most species we were able to test how well the single or combined genes were able to corroborate morphologically defined species by placing the species into exclusive groups. We found that single genes, including the COI barcode region, were poor at confirming species, but that the three genes combined were able to do so much better. This has implications for species identification, species delimitation, and species discovery, and we caution that single genes are not enough. Higher level groupings were partially resolved with some well-supported groupings, whereas others were found to be either polyphyletic or paraphyletic. There were examples of known groups, such as the Myzorhynchella Section, which were poorly supported with single genes but were well supported with combined genes. From this we can infer that more sequence data will be needed in order to show more higher-level groupings with good support. We got unambiguously good support (0.94-1.0 Bayesian posterior probability from all DNA-based analyses for a grouping of An. dunhami with An. nuneztovari and An. goeldii, and because of this and because of morphological similarities we propose that An. dunhami be included in the Nuneztovari Complex. We obtained phylogenetic corroboration for new species which had been recognised by morphological differences; these will need to be formally described and named.

  4. Algorithmic approaches to aid species' delimitation in multidimensional morphospace

    Directory of Open Access Journals (Sweden)

    Pearson Paul N

    2010-06-01

    Full Text Available Abstract Background The species is a fundamental unit of biological pattern and process, but its delimitation has proven a ready source of argument and disagreement. Here, we discuss four key steps that utilize statistical thresholds to describe the morphological variability within a sample and hence assess whether there is evidence for one or multiple species. Once the initial set of biologically relevant traits on comparable individuals has been identified, there is no need for the investigator to hypothesise how specimens might be divided among groups, nor the traits on which groups might be separated. Results Principal components are obtained using robust covariance estimates and retained only if they exceed threshold amounts of explanatory power, before model-based clustering is performed on the dimension-reduced space. We apply these steps in an attempt to resolve ongoing debates among taxonomists working on the extinct Eocene planktonic foraminifera Turborotalia, providing statistical evidence for two species shortly before the lineage's extinction near the Eocene/Oligocene boundary. Conclusion By estimating variance robustly (samples containing incipient species are unlikely to be scaled optimally by means and standard deviations and identifying thresholds relevant to a particular system rather than universal standards, the steps of the framework aim to optimize the chances of delineation without imposing pre-conceived patterns onto estimates of species limits.

  5. Characterization of multiple antibiotic resistant clinical strains of Staphylococcus isolated from pregnant women vagina.

    Science.gov (United States)

    Hetsa, Bakwena Ashton; Kumar, Ajay; Ateba, Collins Njie

    2018-03-29

    Vagina which is one of the important reservoirs for Staphylococcus and in pregnant women pathogenic strains may infect the child during the birth or by vertical transmission. A total of 68 presumptive Staphylococcus strains isolated from human vagina were found to be gram-positive cocci, and only 32 (47%) isolates were found beta-hemolytic. Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) results confirmed 33 isolates belonged to Staphylococcus which consisting of 6 species, i.e., S. aureus (14), S. vitulinus (7), S. epidermidis (4), S cohnii (3), S. equorum (3), and S. succinus (2). Further, the result of antibiotic susceptibility tests showed that large proportions (76%-100%) of the isolates were resistant to multiple antibiotics and more often resistant to penicillin (100%), ampicillin (100%), oxacillin (97%), oxytetracycline (97%), vancomycin (97%), rifampin (85%), erythromycin (82%), and streptomycin (76%). In the present study, only the sec enterotoxin gene was detected in four S. aureus strains. DNA fingerprints of the 33 isolates that were generated using random amplified polymorphic DNA (RAPD) and enterobacterial repetitive intergenic consensus (ERIC) PCR analysis revealed great genetic relatedness of isolates. High prevalence of vaginal colonization with multiple antibiotic-resistant staphylococci among pregnant women was observed which were emerged from the single respective species clones that underwent evolution. The vertical transmission of these multiple antibiotic-resistant Staphylococcus species to the infant is possible; therefore, the findings of this study emphasize the need for regular surveillance of antibiotic-resistant bacterial strains in pregnant women in this area.

  6. Multiplicities of $\\pi^{0}$, $\\eta$, $K^{0}$ and of charged particles in quark and gluon jets

    CERN Document Server

    Abbiendi, G.; Ainsley, C.; Akesson, P.F.; Alexander, G.; Allison, John; Anderson, K.J.; Arcelli, S.; Asai, S.; Ashby, S.F.; Axen, D.; Azuelos, G.; Bailey, I.; Ball, A.H.; Barberio, E.; Barlow, Roger J.; Batley, J.R.; Baumann, S.; Behnke, T.; Bell, Kenneth Watson; Bella, G.; Bellerive, A.; Bentvelsen, S.; Bethke, S.; Biebel, O.; Bloodworth, I.J.; Bock, P.; Bohme, J.; Boeriu, O.; Bonacorsi, D.; Boutemeur, M.; Braibant, S.; Bright-Thomas, P.; Brigliadori, L.; Brown, Robert M.; Burckhart, H.J.; Cammin, J.; Capiluppi, P.; Carnegie, R.K.; Carter, A.A.; Carter, J.R.; Chang, C.Y.; Charlton, David G.; Ciocca, C.; Clarke, P.E.L.; Clay, E.; Cohen, I.; Cooke, O.C.; Couchman, J.; Couyoumtzelis, C.; Coxe, R.L.; Cuffiani, M.; Dado, S.; Dallavalle, G.Marco; Dallison, S.; de Roeck, A.; Dervan, P.; Desch, K.; Dienes, B.; Dixit, M.S.; Donkers, M.; Dubbert, J.; Duchovni, E.; Duckeck, G.; Duerdoth, I.P.; Estabrooks, P.G.; Etzion, E.; Fabbri, F.; Fanti, M.; Feld, L.; Ferrari, P.; Fiedler, F.; Fleck, I.; Ford, M.; Frey, A.; Furtjes, A.; Futyan, D.I.; Gagnon, P.; Gary, J.W.; Gaycken, G.; Geich-Gimbel, C.; Giacomelli, G.; Giacomelli, P.; Glenzinski, D.; Goldberg, J.; Grandi, C.; Graham, K.; Gross, E.; Grunhaus, J.; Gruwe, M.; Gunther, P.O.; Hajdu, C.; Hanson, G.G.; Hansroul, M.; Hapke, M.; Harder, K.; Harel, A.; Hargrove, C.K.; Harin-Dirac, M.; Hauke, A.; Hauschild, M.; Hawkes, C.M.; Hawkings, R.; Hemingway, R.J.; Hensel, C.; Herten, G.; Heuer, R.D.; Hildreth, M.D.; Hill, J.C.; Hocker, James Andrew; Hoffman, Kara Dion; Homer, R.J.; Honma, A.K.; Horvath, D.; Hossain, K.R.; Howard, R.; Huntemeyer, P.; Igo-Kemenes, P.; Ishii, K.; Jacob, F.R.; Jawahery, A.; Jeremie, H.; Jones, C.R.; Jovanovic, P.; Junk, T.R.; Kanaya, N.; Kanzaki, J.; Karapetian, G.; Karlen, D.; Kartvelishvili, V.; Kawagoe, K.; Kawamoto, T.; Keeler, R.K.; Kellogg, R.G.; Kennedy, B.W.; Kim, D.H.; Klein, K.; Klier, A.; Kobayashi, T.; Kobel, M.; Kokott, T.P.; Komamiya, S.; Kowalewski, Robert V.; Kress, T.; Krieger, P.; von Krogh, J.; Kuhl, T.; Kupper, M.; Kyberd, P.; Lafferty, G.D.; Landsman, H.; Lanske, D.; Lawson, I.; Layter, J.G.; Leins, A.; Lellouch, D.; Letts, J.; Levinson, L.; Liebisch, R.; Lillich, J.; List, B.; Littlewood, C.; Lloyd, A.W.; Lloyd, S.L.; Loebinger, F.K.; Long, G.D.; Losty, M.J.; Lu, J.; Ludwig, J.; Macchiolo, A.; Macpherson, A.; Mader, W.; Mannelli, M.; Marcellini, S.; Marchant, T.E.; Martin, A.J.; Martin, J.P.; Martinez, G.; Mashimo, T.; Mattig, Peter; McDonald, W.John; McKenna, J.; McMahon, T.J.; McPherson, R.A.; Meijers, F.; Mendez-Lorenzo, P.; Merritt, F.S.; Mes, H.; Michelini, A.; Mihara, S.; Mikenberg, G.; Miller, D.J.; Mohr, W.; Montanari, A.; Mori, T.; Nagai, K.; Nakamura, I.; Neal, H.A.; Nisius, R.; O'Neale, S.W.; Oakham, F.G.; Odorici, F.; Ogren, H.O.; Oh, A.; Okpara, A.; Oreglia, M.J.; Orito, S.; Pasztor, G.; Pater, J.R.; Patrick, G.N.; Patt, J.; Pfeifenschneider, P.; Pilcher, J.E.; Pinfold, J.; Plane, David E.; Poli, B.; Polok, J.; Pooth, O.; Przybycien, M.; Quadt, A.; Rembser, C.; Rick, H.; Robins, S.A.; Rodning, N.; Roney, J.M.; Rosati, S.; Roscoe, K.; Rossi, A.M.; Rozen, Y.; Runge, K.; Runolfsson, O.; Rust, D.R.; Sachs, K.; Saeki, T.; Sahr, O.; Sarkisyan, E.K.G.; Sbarra, C.; Schaile, A.D.; Schaile, O.; Scharff-Hansen, P.; Schmitt, S.; Schroder, Matthias; Schumacher, M.; Schwick, C.; Scott, W.G.; Seuster, R.; Shears, T.G.; Shen, B.C.; Shepherd-Themistocleous, C.H.; Sherwood, P.; Siroli, G.P.; Skuja, A.; Smith, A.M.; Snow, G.A.; Sobie, R.; Soldner-Rembold, S.; Spagnolo, S.; Sproston, M.; Stahl, A.; Stephens, K.; Stoll, K.; Strom, David M.; Strohmer, R.; Surrow, B.; Talbot, S.D.; Tarem, S.; Taylor, R.J.; Teuscher, R.; Thiergen, M.; Thomas, J.; Thomson, M.A.; Torrence, E.; Towers, S.; Trefzger, T.; Trigger, I.; Trocsanyi, Z.; Tsur, E.; Turner-Watson, M.F.; Ueda, I.; Vannerem, P.; Verzocchi, M.; Voss, H.; Vossebeld, J.; Waller, D.; Ward, C.P.; Ward, D.R.; Watkins, P.M.; Watson, A.T.; Watson, N.K.; Wells, P.S.; Wengler, T.; Wermes, N.; Wetterling, D.; White, J.S.; Wilson, G.W.; Wilson, J.A.; Wyatt, T.R.; Yamashita, S.; Zacek, V.; Zer-Zion, D.

    2000-01-01

    We compared the multiplicities of pizero, eta, Kzero and of charged particles in quark and gluon jets in 3-jet events, as measured by the OPAL experiment at LEP. The comparisons were performed for distributions unfolded to 100% pure quark and gluon jets, at an effective scale Qjet which took into account topological dependences of the 3-jet environment. The ratio of particle multiplicity in gluon jets to that in quark jets as a function of Qjet for pizero, eta and Kzero was found to be independent of the particle species. This is consistent with the QCD prediction that the observed enhancement in the mean particle rate in gluon jets with respect to quark jets should be independent of particle species. In contrast to some theoretical predictions and previous observations, we observed no evidence for an enhancement of eta meson production in gluon jets with respect to quark jets, beyond that observed for charged particles. We measured the ratio of the slope of the average charged particle multiplicity in gluon ...

  7. Unravelling Darwin's entangled bank: architecture and robustness of mutualistic networks with multiple interaction types.

    Science.gov (United States)

    Dáttilo, Wesley; Lara-Rodríguez, Nubia; Jordano, Pedro; Guimarães, Paulo R; Thompson, John N; Marquis, Robert J; Medeiros, Lucas P; Ortiz-Pulido, Raul; Marcos-García, Maria A; Rico-Gray, Victor

    2016-11-30

    Trying to unravel Darwin's entangled bank further, we describe the architecture of a network involving multiple forms of mutualism (pollination by animals, seed dispersal by birds and plant protection by ants) and evaluate whether this multi-network shows evidence of a structure that promotes robustness. We found that species differed strongly in their contributions to the organization of the multi-interaction network, and that only a few species contributed to the structuring of these patterns. Moreover, we observed that the multi-interaction networks did not enhance community robustness compared with each of the three independent mutualistic networks when analysed across a range of simulated scenarios of species extinction. By simulating the removal of highly interacting species, we observed that, overall, these species enhance network nestedness and robustness, but decrease modularity. We discuss how the organization of interlinked mutualistic networks may be essential for the maintenance of ecological communities, and therefore the long-term ecological and evolutionary dynamics of interactive, species-rich communities. We suggest that conserving these keystone mutualists and their interactions is crucial to the persistence of species-rich mutualistic assemblages, mainly because they support other species and shape the network organization. © 2016 The Author(s).

  8. The coontie’s new clothes: asymmetric genetic diversification within Zamia (Cycadales: Zamiaceae) on Puerto Rico, and an hypothesis of multiple introductions

    Science.gov (United States)

    Three distinctive Zamia species occur on Puerto Rico: Z. erosa on the north coast, and Z. portoricensis and Z. pumila, both in the south. Their relationships are largely unknown. We tested an hypothesis of multiple introductions and explored whether the three species show divergent patterns of ge...

  9. Mapping Habitat Connectivity for Multiple Rare, Threatened, and Endangered Species on and Around Military Installations

    Science.gov (United States)

    2011-05-01

    population sizes, reduced flow of individuals and genes between populations, and greater risk of extinction of native species (Fisher and Lindenmayer 2007...allow recolonization of both original and restored breeding sites where the local population has gone extinct , or simply to increase the chance that...movement for pollen dispersal by honey bees . Ecology 74:493-500. Müller, J., J. Stadler, R. Brandl., 2009. Composition versus physiognomy of vegetation

  10. Analysis of the RNA species isolated from defective particles of vesicular stomatitis virus.

    Science.gov (United States)

    Adler, R; Banerjee, A K

    1976-10-01

    Serial high multiplicity passage of a cloned stock of vesicular stomatitis virus was found to generate defective interfering particles containing three size classes of RNA, with sedimentaiton coefficients of 31 S, 23 S and 19 S. The 31 S and 23 S RNA species were found to be complementary to both the 12 to 18 S and 31 S size classes of VSV mRNAs. The 19 S class of RNA was found to be partially base-paired. All three RNA species were found to contain ppAp at their 5' termini.

  11. Helminths from an introduced species (Tupinambis merianae), and two endemic species (Trachylepis atlantica and Amphisbaena ridley) from Fernando de Noronha Archipelago, Brazil.

    Science.gov (United States)

    Ramalho, A C O; da Silva, R J; Schwartz, H O; Péres, A K

    2009-08-01

    The present study reports the occurrence of helminths in the introduced species Tupinambis merianae (tegu lizard), and in two endemic species Trachylepis atlantica (small lizard) and Amphisbaena ridleyi (two-head-snake lizard ), from Fernando de Noronha Archipelago, State of Pernambuco, Brazil. Nine species of helminths were found, mainly in the digestive tract and accessory organs, with the following prevalence (P) and mean infection intensity (MII). Tupinambis merianae: Diaphanocephalus galeatus (P = 96%, MII = 20.5), Spinicauda spinicauda (P = 100%, MII = 197.8), and Oochoristica sp.l (P = 20%, MII = 4.4). Trachylepis atlantica: Moaciria alvarengai (P = 20%, MII = 1.4), S. spinicauda (P = 92%, MII = 22.1), Mesocoelium monas (P = 4%, MII = 3.0), Platynosomum sp. (P = 8%, MII = 7.0), and Oochoristica sp.2 (P = 16%, MII = 1.25). Amphisbaena ridleyi: Aplectana albae (P = 96%, MII = 143.4), Thelandros alvarengai (P = 4%, MII = 1.0), Me. monas (P = 44%, MII = 2.8), Platynosomum sp. (P = 36%; MII = 13.8), and Oochoristica sp.2 (P = 48%; MII = 2.17). More than 80% of T. merianae were infected with 2, or more, helminth species. In Tr. atlantica, single-species infections were present in 50% of the specimens, but co-occurrence of 2 parasites was also high (41.7%). In A. ridleyi, multiple infections were more common, with up to 5 parasite species present. The helminth fauna observed allowed us to conclude that helminths can be carried together with their host when they colonize new geographic localities and that these introduced helminths can, in turn, colonize endemic, or native, hosts.

  12. Mitochondrial genomes of Australian chicken Eimeria support the presence of ten species with low genetic diversity among strains.

    Science.gov (United States)

    Morgan, Jess A T; Godwin, Rosamond M

    2017-08-30

    Modern molecular approaches have vastly improved diagnostic capabilities for differentiating among species of chicken infecting Eimeria. Consolidating information from multiple genetic markers, adding additional poultry Eimeria species and increasing the size of available data-sets is improving the resolving power of the DNA, and consequently our understanding of the genus. This study adds information from 25 complete mitochondrial DNA genomes from Australian chicken Eimeria isolates representing all 10 species known to occur in Australia, including OTU-X, -Y and -Z. The resulting phylogeny provides a comprehensive view of species relatedness highlighting where the OTUs align with respect to others members of the genus. All three OTUs fall within the Eimeria clade that contains only chicken-infecting species with close affinities to E. maxima, E. brunetti and E. mitis. Mitochondrial genetic diversity was low among Australian isolates likely reflecting their recent introduction to the country post-European settlement. The lack of observed genetic diversity is a promising outcome as it suggests that the currently used live vaccines should continue to offer widespread protection against Eimeria outbreaks in all states and territories. Flocks were frequently found to host multiple strains of the same species, a factor that should be considered when studying disease epidemiology in the field. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  13. Genetically based differentiation in growth of multiple non-native plant species along a steep environmental gradient.

    Science.gov (United States)

    Haider, Sylvia; Kueffer, Christoph; Edwards, Peter J; Alexander, Jake M

    2012-09-01

    A non-native plant species spreading along an environmental gradient may need to adjust its growth to the prevailing conditions that it encounters by a combination of phenotypic plasticity and genetic adaptation. There have been several studies of how non-native species respond to changing environmental conditions along latitudinal gradients, but much less is known about elevational gradients. We conducted a climate chamber experiment to investigate plastic and genetically based growth responses of 13 herbaceous non-native plants along an elevational gradient from 100 to 2,000 m a.s.l. in Tenerife. Conditions in the field ranged from high anthropogenic disturbance but generally favourable temperatures for plant growth in the lower half of the gradient, to low disturbance but much cooler conditions in the upper half. We collected seed from low, mid and high elevations and grew them in climate chambers under the characteristic temperatures at these three elevations. Growth of all species was reduced under lower temperatures along both halves of the gradient. We found consistent genetically based differences in growth over the upper elevational gradient, with plants from high-elevation sites growing more slowly than those from mid-elevation ones, while the pattern in the lower part of the gradient was more mixed. Our data suggest that many non-native plants might respond to climate along elevational gradients by genetically based changes in key traits, especially at higher elevations where low temperatures probably impose a stronger selection pressure. At lower elevations, where anthropogenic influences are greater, higher gene flow and frequent disturbance might favour genotypes with broad ecological amplitudes. Thus the importance of evolutionary processes for invasion success is likely to be context-dependent.

  14. Oral microbiota species in acute apical endodontic abscesses

    Directory of Open Access Journals (Sweden)

    Noelle George

    2016-03-01

    Full Text Available Background and objectives: Acute apical abscesses are serious endodontic diseases resulting from pulpal infection with opportunistic oral microorganisms. The objective of this study was to identify and compare the oral microbiota in patients (N=18 exhibiting acute apical abscesses, originating from the demographic region in Portland, Oregon. The study hypothesis is that abscesses obtained from this demographic region may contain unique microorganisms not identified in specimens from other regions. Design: Endodontic abscesses were sampled from patients at the Oregon Health & Science University (OHSU School of Dentistry. DNA from abscess specimens was subjected to polymerase chain reaction amplification using 16S rRNA gene-specific primers and Cy3-dCTP labeling. Labeled DNA was then applied to microbial microarrays (280 species generated by the Human Oral Microbial Identification Microarray Laboratory (Forsyth Institute, Cambridge, MA. Results: The most prevalent microorganisms, found across multiple abscess specimens, include Fusobacterium nucleatum, Parvimonas micra, Megasphaera species clone CS025, Prevotella multisaccharivorax, Atopobium rimae, and Porphyromonas endodontalis. The most abundant microorganisms, found in highest numbers within individual abscesses, include F. nucleatum, P. micra, Streptococcus Cluster III, Solobacterium moorei, Streptococcus constellatus, and Porphyromonas endodontalis. Strong bacterial associations were identified between Prevotella multisaccharivorax, Acidaminococcaceae species clone DM071, Megasphaera species clone CS025, Actinomyces species clone EP053, and Streptococcus cristatus (all with Spearman coefficients >0.9. Conclusions: Cultivable and uncultivable bacterial species have been identified in endodontic abscesses obtained from the Portland, Oregon demographic region, and taxa identifications correlated well with other published studies, with the exception of Treponema and Streptococcus cristae, which

  15. Oral microbiota species in acute apical endodontic abscesses.

    Science.gov (United States)

    George, Noelle; Flamiatos, Erin; Kawasaki, Kellie; Kim, Namgu; Carriere, Charles; Phan, Brian; Joseph, Raphael; Strauss, Shay; Kohli, Richie; Choi, Dongseok; Baumgartner, J Craig; Sedgley, Christine; Maier, Tom; Machida, Curtis A

    2016-01-01

    Acute apical abscesses are serious endodontic diseases resulting from pulpal infection with opportunistic oral microorganisms. The objective of this study was to identify and compare the oral microbiota in patients (N=18) exhibiting acute apical abscesses, originating from the demographic region in Portland, Oregon. The study hypothesis is that abscesses obtained from this demographic region may contain unique microorganisms not identified in specimens from other regions. Endodontic abscesses were sampled from patients at the Oregon Health & Science University (OHSU) School of Dentistry. DNA from abscess specimens was subjected to polymerase chain reaction amplification using 16S rRNA gene-specific primers and Cy3-dCTP labeling. Labeled DNA was then applied to microbial microarrays (280 species) generated by the Human Oral Microbial Identification Microarray Laboratory (Forsyth Institute, Cambridge, MA). The most prevalent microorganisms, found across multiple abscess specimens, include Fusobacterium nucleatum, Parvimonas micra, Megasphaera species clone CS025, Prevotella multisaccharivorax, Atopobium rimae, and Porphyromonas endodontalis. The most abundant microorganisms, found in highest numbers within individual abscesses, include F. nucleatum, P. micra, Streptococcus Cluster III, Solobacterium moorei, Streptococcus constellatus, and Porphyromonas endodontalis. Strong bacterial associations were identified between Prevotella multisaccharivorax, Acidaminococcaceae species clone DM071, Megasphaera species clone CS025, Actinomyces species clone EP053, and Streptococcus cristatus (all with Spearman coefficients >0.9). Cultivable and uncultivable bacterial species have been identified in endodontic abscesses obtained from the Portland, Oregon demographic region, and taxa identifications correlated well with other published studies, with the exception of Treponema and Streptococcus cristae, which were not commonly identified in endodontic abscesses between the

  16. Intraspecific variation of cuticular hydrocarbon profiles in the Anastrepha fraterculus (Diptera: Tephritidae) species complex

    Czech Academy of Sciences Publication Activity Database

    Vaníčková, Lucie; Břízová, Radka; Mendonca, A. L.; Pompeiano, A.; do Nascimento, R. R.

    2015-01-01

    Roč. 139, č. 9 (2015), s. 679-689 ISSN 0931-2048 Institutional support: RVO:61388963 Keywords : chemotaxonomy * GCxGC/TOFMS * multiple factorial analyses * putative species * South American fruit fly Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 1.517, year: 2015

  17. On the nature of species: insights from Paramecium and other ciliates

    Science.gov (United States)

    Hall, Meaghan S.; Katz, Laura A.

    2011-01-01

    The multiple species concepts currently in use by the scientific community (e.g. Morphological, Biological, Phylogenetic) are united in that they all aim to capture the process of divergence between populations. For example, the Biological Species Concept (BSC) defines a species as a natural group of organisms that is reproductively isolated from other such groups. Here we synthesize nearly a century of research on the ciliate genus Paramecium that highlights the shortcomings of our prevailing notions on the nature of species. In this lineage, there is discordance between morphology, mating behavior, and genetics, features assumed to be correlated, at least after sufficient time has passed, under all species concepts. Intriguingly, epigenetic phenomena are well documented in ciliates where they influence features such as germline/soma differentiation and mating type determination. Consequently, we hypothesize that divergence within ciliate populations is due to a dynamic interaction between genetic and epigenetic factors. The growing list of examples of epigenetic phenomena that potentially impact speciation (i.e. by influencing the dynamics of sex chromosomes, fate of hybrids, zygotic drive and genomic conflicts) suggests that interactions between genetics and epigenetics may also drive divergence in other eukaryotic lineages. PMID:21505762

  18. Multiple origins of subsociality in crab spiders (Thomisidae).

    Science.gov (United States)

    Ruch, Jasmin; Riehl, Torben; May-Collado, Laura J; Agnarsson, Ingi

    2015-01-01

    Determining factors that facilitate the transition from a solitary to a social lifestyle is a major challenge in evolutionary biology, especially in taxa that are usually aggressive towards conspecifics. Most spiders live solitarily and few species are known to be social. Nevertheless, sociality has evolved multiple times across several families and nearly all studied social lineages have originated from a periodically social (subsocial) ancestor. Group-living crab spiders (Thomisidae) are exclusively found in Australia and differ from most other social spiders because they lack a communal capture web. Three of the group-living species were placed in the genus Diaea and another in the genus Xysticus. Most Australian thomisids are, however, difficult to identify as most descriptions are old and of poor quality, and the genera Diaea and Xysticus may not correspond to monophyletic groups. Here, we clarify the phylogenetic relationships of the four group-living Australian thomisids and conclude that amongst these subsociality has evolved two to three times independently. The subsocial Xysticus bimaculatus is not closely related to any of the social Diaea and an independent origin of subsociality is likely in this case. The presented data indicates that within Diaea two origins of subsociality are possible. Our results help to understand the evolution of sociality in thomisids and support the hypothesis that permanent sociality in spiders has evolved multiple times relatively recently from subsocial ancestors. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Patterns and causes of species richness: a general simulation model for macroecology

    DEFF Research Database (Denmark)

    Gotelli, Nicholas J; Anderson, Marti J; Arita, Hector T

    2009-01-01

    to a mechanistic understanding of the patterns. During the past two decades, macroecologists have successfully addressed technical problems posed by spatial autocorrelation, intercorrelation of predictor variables and non-linearity. However, curve-fitting approaches are problematic because most theoretical models...... in macroecology do not make quantitative predictions, and they do not incorporate interactions among multiple forces. As an alternative, we propose a mechanistic modelling approach. We describe computer simulation models of the stochastic origin, spread, and extinction of species' geographical ranges...... in an environmentally heterogeneous, gridded domain and describe progress to date regarding their implementation. The output from such a general simulation model (GSM) would, at a minimum, consist of the simulated distribution of species ranges on a map, yielding the predicted number of species in each grid cell...

  20. Considerations on the biochemical composition of some freshwater zooplankton species.

    Directory of Open Access Journals (Sweden)

    Nicoletta RICCARDI

    1999-02-01

    Full Text Available The mean elemental (C, H, N and biochemical composition (lipids, carbohydrates and proteins of some abundant crustacean zooplankton species of Italian insubric lakes has been estimated by the analysis of samples collected at different seasons from various environments (Lake Maggiore, Lake Varese, Lake Comabbio, Lake Monate. From each sample an adequate number of specimens of each abundant species was sorted and analyzed by a CHN elemental analyzer. The percentage of lipids, carbohydrates and proteins and the calorific content were calculated from the elemental composition according to Gnaiger & Bitterlich (1984. Inter- and intraspecific variability of biochemical composition was quite high, while elemental composition and calorific content were less variable. An estimate of the mean elemental and biochemical composition of each species was obtained by pooling the data. These mean values have been used to estimate the pools of elements and compounds in the crustacean zooplankton of Lake Comabbio to provide an example of the importance of a multiple approach in zooplankton studies.

  1. The role of advection in a two-species competition model

    CERN Document Server

    Averill, Isabel; Lou, Yuan

    2017-01-01

    The effects of weak and strong advection on the dynamics of reaction-diffusion models have long been studied. In contrast, the role of intermediate advection remains poorly understood. For example, concentration phenomena can occur when advection is strong, providing a mechanism for the coexistence of multiple populations, in contrast with the situation of weak advection where coexistence may not be possible. The transition of the dynamics from weak to strong advection is generally difficult to determine. In this work the authors consider a mathematical model of two competing populations in a spatially varying but temporally constant environment, where both species have the same population dynamics but different dispersal strategies: one species adopts random dispersal, while the dispersal strategy for the other species is a combination of random dispersal and advection upward along the resource gradient. For any given diffusion rates the authors consider the bifurcation diagram of positive steady states by u...

  2. Mapping Indigenous land management for threatened species conservation: An Australian case-study.

    Science.gov (United States)

    Renwick, Anna R; Robinson, Catherine J; Garnett, Stephen T; Leiper, Ian; Possingham, Hugh P; Carwardine, Josie

    2017-01-01

    Much biodiversity lives on lands to which Indigenous people retain strong legal and management rights. However this is rarely quantified. Here we provide the first quantitative overview of the importance of Indigenous land for a critical and vulnerable part of biodiversity, threatened species, using the continent of Australia as a case study. We find that three quarters of Australia's 272 terrestrial or freshwater vertebrate species listed as threatened under national legislation have projected ranges that overlap Indigenous lands. On average this overlap represents 45% of the range of each threatened species while Indigenous land is 52% of the country. Hotspots where multiple threatened species ranges overlap occur predominantly in coastal Northern Australia. Our analysis quantifies the vast potential of Indigenous land in Australia for contributing to national level conservation goals, and identifies the main land management arrangements available to Indigenous people which may enable them to deliver those goals should they choose to do so.

  3. Disease and community structure: white-nose syndrome alters spatial and temporal niche partitioning in sympatric bat species

    Science.gov (United States)

    Jachowski, David S.; Dobony, Christopher A.; Coleman, Laci S.; Ford, W. Mark; Britzke, Eric R.; Rodrigue, Jane L.

    2014-01-01

    AimEmerging infectious diseases present a major perturbation with apparent direct effects such as reduced population density, extirpation and/or extinction. Comparatively less is known about the potential indirect effects of disease that likely alter community structure and larger ecosystem function. Since 2006, white-nose syndrome (WNS) has resulted in the loss of over 6 million hibernating bats in eastern North America. Considerable evidence exists concerning niche partitioning in sympatric bat species in this region, and the unprecedented, rapid decline in multiple species following WNS may provide an opportunity to observe a dramatic restructuring of the bat community.LocationWe conducted our study at Fort Drum Army Installation in Jefferson and Lewis counties, New York, USA, where WNS first impacted extant bat species in winter 2007–2008.MethodsAcoustical monitoring during 2003–2011 allowed us to test the hypothesis that spatial and temporal niche partitioning by bats was relaxed post-WNS.ResultsWe detected nine bat species pre- and post-WNS. Activity for most bat species declined post-WNS. Dramatic post-WNS declines in activity of little brown bat (Myotis lucifugus, MYLU), formerly the most abundant bat species in the region, were associated with complex, often species-specific responses by other species that generally favoured increased spatial and temporal overlap with MYLU.Main conclusionsIn addition to the obvious direct effects of disease on bat populations and activity levels, our results provide evidence that disease can have cascading indirect effects on community structure. Recent occurrence of WNS in North America, combined with multiple existing stressors, is resulting in dramatic shifts in temporal and spatial niche partitioning within bat communities. These changes might influence long-term population viability of some bat species as well as broader scale ecosystem structure and function.

  4. A Paleocene penguin from New Zealand substantiates multiple origins of gigantism in fossil Sphenisciformes.

    Science.gov (United States)

    Mayr, Gerald; Scofield, R Paul; De Pietri, Vanesa L; Tennyson, Alan J D

    2017-12-12

    One of the notable features of penguin evolution is the occurrence of very large species in the early Cenozoic, whose body size greatly exceeded that of the largest extant penguins. Here we describe a new giant species from the late Paleocene of New Zealand that documents the very early evolution of large body size in penguins. Kumimanu biceae, n. gen. et sp. is larger than all other fossil penguins that have substantial skeletal portions preserved. Several plesiomorphic features place the new species outside a clade including all post-Paleocene giant penguins. It is phylogenetically separated from giant Eocene and Oligocene penguin species by various smaller taxa, which indicates multiple origins of giant size in penguin evolution. That a penguin rivaling the largest previously known species existed in the Paleocene suggests that gigantism in penguins arose shortly after these birds became flightless divers. Our study therefore strengthens previous suggestions that the absence of very large penguins today is likely due to the Oligo-Miocene radiation of marine mammals.

  5. Validation of a PCR Assay for Chlamydophila abortus rRNA gene detection in a murine model

    Directory of Open Access Journals (Sweden)

    Francielle Gibson da Silva-Zacarias

    2009-11-01

    Full Text Available Chlamydophila abortus (C. abortus is associated with reproductive problems in cattle, sheep, and goats. Diagnosis of C. abortus using embryonated chicken eggs or immortalized cell lines has a very low sensitivity. Polymerase chain reaction (PCR assays have been used to detect C. abortus infection in clinical specimens and organ fragments, such as placenta, fetal organs, vaginal secretions, and semen. The aim of this study was to develop a PCR assay for the amplification of an 856-bp fragment of the rRNA gene of the Chlamydiaceae family. The PCR assay was evaluated using organs from 15 mice experimentally infected with the S26/3 reference strain of C. abortus. The results of the rRNA PCR were compared to the results from another PCR system (Omp2 PCR that has been previously described for the Omp2 (outer major protein gene from the Chlamydiaceae family. From the 15 C. abortus-inoculated mice, 13 (K=0.84, standard error =0.20 tested positive using the rRNA PCR assay and 9 (K=0.55, standard error=0.18 tested positive using the Omp2 PCR assay. The detection limit, measured using inclusion-forming units (IFU, for C. abortus with the rRNA PCR (1.05 IFU was 100-fold lower than for the Omp2 PCR (105 IFU. The higher sensitivity of the rRNA PCR, as compared to the previously described PCR assay, and the specificity of the assay, demonstrated using different pathogenic microorganisms of the bovine reproductive system, suggest that the new PCR assay developed in this study can be used for the molecular diagnosis of C. abortus in abortion and other reproductive failures in bovines, caprines, and ovines.Chlamydophila abortus (C. abortus é frequentemente associada a distúrbios reprodutivos em bovinos, ovinos e caprinos. Para o diagnóstico, os métodos de cultivo em ovo embrionado de galinha e em células de linhagem contínua apresentam baixa sensibilidade. A reação em cadeia da polimerase (PCR tem sido utilizada em placenta, órgãos fetais, secre

  6. Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

    DEFF Research Database (Denmark)

    Morin, Phillip A; Archer, Frederick I.; Foote, Andrew David

    2010-01-01

    Killer whales (Orcinus orca) currently comprise a single, cosmopolitan species with a diverse diet. However, studies over the last 30 yr have revealed populations of sympatric "ecotypes" with discrete prey preferences, morphology, and behaviors. Although these ecotypes avoid social interactions...... and are not known to interbreed, genetic studies to date have found extremely low levels of diversity in the mitochondrial control region, and few clear phylogeographic patterns worldwide. This low level of diversity is likely due to low mitochondrial mutation rates that are common to cetaceans. Using killer whales...... as a case study, we have developed a method to readily sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples to more accurately assess phylogeography and estimate divergence times. This represents an important tool for wildlife management, not only for killer whales...

  7. Computing all hybridization networks for multiple binary phylogenetic input trees.

    Science.gov (United States)

    Albrecht, Benjamin

    2015-07-30

    The computation of phylogenetic trees on the same set of species that are based on different orthologous genes can lead to incongruent trees. One possible explanation for this behavior are interspecific hybridization events recombining genes of different species. An important approach to analyze such events is the computation of hybridization networks. This work presents the first algorithm computing the hybridization number as well as a set of representative hybridization networks for multiple binary phylogenetic input trees on the same set of taxa. To improve its practical runtime, we show how this algorithm can be parallelized. Moreover, we demonstrate the efficiency of the software Hybroscale, containing an implementation of our algorithm, by comparing it to PIRNv2.0, which is so far the best available software computing the exact hybridization number for multiple binary phylogenetic trees on the same set of taxa. The algorithm is part of the software Hybroscale, which was developed specifically for the investigation of hybridization networks including their computation and visualization. Hybroscale is freely available(1) and runs on all three major operating systems. Our simulation study indicates that our approach is on average 100 times faster than PIRNv2.0. Moreover, we show how Hybroscale improves the interpretation of the reported hybridization networks by adding certain features to its graphical representation.

  8. Characterizing fish responses to a river restoration over 21 years based on species' traits.

    Science.gov (United States)

    Höckendorff, Stefanie; Tonkin, Jonathan D; Haase, Peter; Bunzel-Drüke, Margret; Zimball, Olaf; Scharf, Matthias; Stoll, Stefan

    2017-10-01

    Understanding restoration effectiveness is often impaired by a lack of high-quality, long-term monitoring data and, to date, few researchers have used species' trait information to gain insight into the processes that drive the reaction of fish communities to restoration. We examined fish-community responses with a highly resolved data set from 21 consecutive years of electrofishing (4 years prerestoration and 17 years postrestoration) at multiple restored and unrestored reaches from a river restoration project on the Lippe River, Germany. Fish abundance peaked in the third year after the restoration; abundance was 6 times higher than before the restoration. After 5-7 years, species richness and abundance stabilized at 2 and 3.5 times higher levels relative to the prerestoration level, respectively. However, interannual variability of species richness and abundance remained considerable, illustrating the challenge of reliably assessing restoration outcomes based on data from individual samplings, especially in the first years following restoration. Life-history and reproduction-related traits best explained differences in species' responses to restoration. Opportunistic short-lived species with early female maturity and multiple spawning runs per year exhibited the strongest increase in abundance, which reflected their ability to rapidly colonize new habitats. These often small-bodied and fusiform fishes typically live in dynamic and ephemeral instream and floodplain areas that river-habitat restorations often aim to create, and in this case their increases in abundance indicated successful restoration. Our results suggest that a greater consideration of species' traits may enhance the causal understanding of community processes and the coupling of restoration to functional ecology. Trait-based assessments of restoration outcomes would furthermore allow for easier transfer of knowledge across biogeographic borders than studies based on taxonomy. © 2017 Society for

  9. Seasonal patterns of mixed species groups in large East African mammals.

    Directory of Open Access Journals (Sweden)

    Christian Kiffner

    Full Text Available Mixed mammal species groups are common in East African savannah ecosystems. Yet, it is largely unknown if co-occurrences of large mammals result from random processes or social preferences and if interspecific associations are consistent across ecosystems and seasons. Because species may exchange important information and services, understanding patterns and drivers of heterospecific interactions is crucial for advancing animal and community ecology. We recorded 5403 single and multi-species clusters in the Serengeti-Ngorongoro and Tarangire-Manyara ecosystems during dry and wet seasons and used social network analyses to detect patterns of species associations. We found statistically significant associations between multiple species and association patterns differed spatially and seasonally. Consistently, wildebeest and zebras preferred being associated with other species, whereas carnivores, African elephants, Maasai giraffes and Kirk's dik-diks avoided being in mixed groups. During the dry season, we found that the betweenness (a measure of importance in the flow of information or disease of species did not differ from a random expectation based on species abundance. In contrast, in the wet season, we found that these patterns were not simply explained by variations in abundances, suggesting that heterospecific associations were actively formed. These seasonal differences in observed patterns suggest that interspecific associations may be driven by resource overlap when resources are limited and by resource partitioning or anti-predator advantages when resources are abundant. We discuss potential mechanisms that could drive seasonal variation in the cost-benefit tradeoffs that underpin the formation of mixed-species groups.

  10. Evolutionary transition from single to multiple mating in fungus-growing ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Gertsch, P J; Frydenberg, Jane

    1999-01-01

    Queens of leafcutter ants exhibit the highest known levels of multiple mating (up to 10 mates per queen) among ants. Multiple mating may have been selected to increase genetic diversity among nestmate workers, which is hypothesized to be critical in social systems with large, long-lived colonies...... under severe pressure of pathogens. Advanced fungus-growing (leafcutter) ants have large numbers (104-106 workers) and long-lived colonies, whereas basal genera in the attine tribe have small (... to have lower queen mating frequencies, similar to those found in most other ants. We tested this prediction by analysing queen mating frequency and colony kin structure in three basal attine species: Myrmicocrypta ednaella, Apterostigma collare and Cyphomyrmex longiscapus. Microsatellite marker analyses...

  11. Ontogenetic specialism in predators with multiple niche shifts prevents predator population recovery and establishment

    NARCIS (Netherlands)

    van Leeuwen, A.; Huss, M.; Gårdmark, A.; de Roos, A.M.

    2014-01-01

    The effects of ontogenetic niche shifts on community structure and dynamics are underexplored, despite the occurrence of such shifts in the majority of animal species. We studied the form of niche shifts in a predator that exhibits multiple ontogenetic niche shifts, and analyzed how this life

  12. Species identification by conservation practitioners using online images: accuracy and agreement between experts

    Directory of Open Access Journals (Sweden)

    Gail E. Austen

    2018-01-01

    Full Text Available Emerging technologies have led to an increase in species observations being recorded via digital images. Such visual records are easily shared, and are often uploaded to online communities when help is required to identify or validate species. Although this is common practice, little is known about the accuracy of species identification from such images. Using online images of newts that are native and non-native to the UK, this study asked holders of great crested newt (Triturus cristatus licences (issued by UK authorities to permit surveying for this species to sort these images into groups, and to assign species names to those groups. All of these experts identified the native species, but agreement among these participants was low, with some being cautious in committing to definitive identifications. Individuals’ accuracy was also independent of both their experience and self-assessed ability. Furthermore, mean accuracy was not uniform across species (69–96%. These findings demonstrate the difficulty of accurate identification of newts from a single image, and that expert judgements are variable, even within the same knowledgeable community. We suggest that identification decisions should be made on multiple images and verified by more than one expert, which could improve the reliability of species data.

  13. Evolutionary Genetic Analysis Uncovers Multiple Species with Distinct Habitat Preferences and Antibiotic Resistance Phenotypes in the Stenotrophomonas maltophilia Complex

    Directory of Open Access Journals (Sweden)

    Luz E. Ochoa-Sánchez

    2017-08-01

    Full Text Available The genus Stenotrophomonas (Gammaproteobacteria has a broad environmental distribution. Stenotrophomonas maltophilia is its best known species because it is a globally emerging, multidrug-resistant (MDR, opportunistic pathogen. Members of this species are known to display high genetic, ecological and phenotypic diversity, forming the so-called S. maltophilia complex (Smc. Heterogeneous resistance and virulence phenotypes have been reported for environmental Smc isolates of diverse ecological origin. We hypothesized that this heterogeneity could be in part due to the potential lumping of several cryptic species in the Smc. Here we used state-of-the-art phylogenetic and population genetics methods to test this hypothesis based on the multilocus dataset available for the genus at pubmlst.org. It was extended with sequences from complete and draft genome sequences to assemble a comprehensive set of reference sequences. This framework was used to analyze 108 environmental isolates obtained in this study from the sediment and water column of four rivers and streams in Central Mexico, affected by contrasting levels of anthropogenic pollution. The aim of the study was to identify species in this collection, defined as genetically cohesive sequence clusters, and to determine the extent of their genetic, ecological and phenotypic differentiation. The multispecies coalescent, coupled with Bayes factor analysis was used to delimit species borders, together with population genetic structure analyses, recombination and gene flow estimates between sequence clusters. These analyses consistently revealed that the Smc contains at least 5 significantly differentiated lineages: S. maltophilia and Smc1 to Smc4. Only S. maltophilia was found to be intrinsically MDR, all its members expressing metallo-β-lactamases (MBLs. The other Smc lineages were not MDR and did not express MBLs. We also obtained isolates related to S. acidaminiphila, S. humi and S. terrae. They

  14. Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria and mycorrhizal fungi.

    Science.gov (United States)

    Afkhami, Michelle E; Stinchcombe, John R

    2016-10-01

    While all species interact with multiple mutualists, the fitness consequences and molecular mechanisms underlying these interactions remain largely unknown. We combined factorial ecological experiments with genomewide expression analyses to examine the phenotypic and transcriptomic responses of model legume Medicago truncatula to rhizobia and mycorrhizal fungi. We found synergistic effects of these mutualists on plant performance and examined unique features of plant gene expression responses to multiple mutualists. There were genomewide signatures of mutualists and multiple mutualists on expression, with partners often affecting unique sets of genes. Mycorrhizal fungi had stronger effects on plant expression than rhizobia, with 70% of differentially expressed genes affected by fungi. Fungal and bacterial mutualists had joint effects on 10% of differentially expressed genes, including unexpected, nonadditive effects on some genes with important functions such as nutrient metabolism. For a subset of genes, interacting with multiple mutualists even led to reversals in the direction of expression (shifts from up to downregulation) compared to interacting with single mutualists. Rhizobia also affected the expression of several mycorrhizal genes, including those involved in nutrient transfer to host plants, indicating that partner species can also impact each other's molecular phenotypes. Collectively, these data illustrate the diverse molecular mechanisms and transcriptional responses associated with the synergistic benefits of multiple mutualists. © 2016 John Wiley & Sons Ltd.

  15. Modeling species’ realized climatic niche space and predicting their response to global warming for several western forest species with small geographic distributions

    Science.gov (United States)

    Marcus V. Warwell; Gerald E. Rehfeldt; Nicholas L. Crookston

    2010-01-01

    The Random Forests multiple regression tree was used to develop an empirically based bioclimatic model of the presence-absence of species occupying small geographic distributions in western North America. The species assessed were subalpine larch (Larix lyallii), smooth Arizona cypress (Cupressus arizonica ssp. glabra...

  16. Multiple-Ring Digital Communication Network

    Science.gov (United States)

    Kirkham, Harold

    1992-01-01

    Optical-fiber digital communication network to support data-acquisition and control functions of electric-power-distribution networks. Optical-fiber links of communication network follow power-distribution routes. Since fiber crosses open power switches, communication network includes multiple interconnected loops with occasional spurs. At each intersection node is needed. Nodes of communication network include power-distribution substations and power-controlling units. In addition to serving data acquisition and control functions, each node acts as repeater, passing on messages to next node(s). Multiple-ring communication network operates on new AbNET protocol and features fiber-optic communication.

  17. The Arabidopsis thaliana mobilome and its impact at the species level.

    Science.gov (United States)

    Quadrana, Leandro; Bortolini Silveira, Amanda; Mayhew, George F; LeBlanc, Chantal; Martienssen, Robert A; Jeddeloh, Jeffrey A; Colot, Vincent

    2016-06-03

    Transposable elements (TEs) are powerful motors of genome evolution yet a comprehensive assessment of recent transposition activity at the species level is lacking for most organisms. Here, using genome sequencing data for 211 Arabidopsis thaliana accessions taken from across the globe, we identify thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We further show that the composition and activity of the 'mobilome' vary extensively between accessions in relation to climate and genetic factors. Moreover, TEs insert equally throughout the genome and are rapidly purged by natural selection from gene-rich regions because they frequently affect genes, in multiple ways. Remarkably, loci controlling adaptive responses to the environment are the most frequent transposition targets observed. These findings demonstrate the pervasive, species-wide impact that a rich mobilome can have and the importance of transposition as a recurrent generator of large-effect alleles.

  18. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction

    Science.gov (United States)

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-01-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. PMID:25281847

  19. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction.

    Science.gov (United States)

    De Oliveira Martins, Leonardo; Mallo, Diego; Posada, David

    2016-05-01

    Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

  20. Measuring β-diversity with species abundance data.

    Science.gov (United States)

    Barwell, Louise J; Isaac, Nick J B; Kunin, William E

    2015-07-01

    In 2003, 24 presence-absence β-diversity metrics were reviewed and a number of trade-offs and redundancies identified. We present a parallel investigation into the performance of abundance-based metrics of β-diversity. β-diversity is a multi-faceted concept, central to spatial ecology. There are multiple metrics available to quantify it: the choice of metric is an important decision. We test 16 conceptual properties and two sampling properties of a β-diversity metric: metrics should be 1) independent of α-diversity and 2) cumulative along a gradient of species turnover. Similarity should be 3) probabilistic when assemblages are independently and identically distributed. Metrics should have 4) a minimum of zero and increase monotonically with the degree of 5) species turnover, 6) decoupling of species ranks and 7) evenness differences. However, complete species turnover should always generate greater values of β than extreme 8) rank shifts or 9) evenness differences. Metrics should 10) have a fixed upper limit, 11) symmetry (βA,B  = βB,A ), 12) double-zero asymmetry for double absences and double presences and 13) not decrease in a series of nested assemblages. Additionally, metrics should be independent of 14) species replication 15) the units of abundance and 16) differences in total abundance between sampling units. When samples are used to infer β-diversity, metrics should be 1) independent of sample sizes and 2) independent of unequal sample sizes. We test 29 metrics for these properties and five 'personality' properties. Thirteen metrics were outperformed or equalled across all conceptual and sampling properties. Differences in sensitivity to species' abundance lead to a performance trade-off between sample size bias and the ability to detect turnover among rare species. In general, abundance-based metrics are substantially less biased in the face of undersampling, although the presence-absence metric, βsim , performed well overall. Only

  1. Similar local and landscape processes affect both a common and a rare newt species.

    Science.gov (United States)

    Denoël, Mathieu; Perez, Amélie; Cornet, Yves; Ficetola, Gentile Francesco

    2013-01-01

    Although rare species are often the focus of conservation measures, more common species may experience similar decline and suffer from the same threatening processes. We tested this hypothesis by examining, through an information-theoretic approach, the importance of ecological processes at multiple scales in the great crested newt Triturus cristatus, regionally endangered and protected in Europe, and the more common smooth newt, Lissotriton vulgaris. Both species were similarly affected by the same processes, i.e. suitability of aquatic and terrestrial components of their habitat at different scales, connectivity among breeding sites, and the presence of introduced fish. T. cristatus depended more on water depth and aquatic vegetation than L. vulgaris. The results show that environmental pressures threaten both common and rare species, and therefore the more widespread species should not be neglected in conservation programs. Because environmental trends are leading to a deterioration of aquatic and terrestrial habitat features required by newt populations, populations of the common species may follow the fate of the rarest species. This could have substantial conservation implications because of the numerical importance of common species in ecosystems and because commonness could be a transient state moving towards rarity. On the other hand, in agreement with the umbrella species concept, targeting conservation efforts on the most demanding species would also protect part of the populations of the most common species.

  2. Post-fledging care, multiple breeding and the costs of reproduction in the great tit

    NARCIS (Netherlands)

    Verhulst, S; Hut, RA

    In species that initiate multiple broods in a single season there is usually a trade-off between the number of young in the first brood, and the timing and occurrence of subsequent broods in the same season. The hypothesis that experimental reduction of clutch size reduces the duration of

  3. Post-fledging care, multiple breeding and the cost of reproduction in the great tit

    NARCIS (Netherlands)

    Verhulst, S.; Hut, R.A.

    1996-01-01

    In species that initiate multiple broods in a single season there is usually a trade-off between the number of young in the first brood, and the timing and occurrence of subsequent broods in the same season. The hypothesis that experimental reduction of clutch size reduces the duration of

  4. Ion Acceleration by Double Layers with Multi-Component Ion Species

    Science.gov (United States)

    Good, Timothy; Aguirre, Evan; Scime, Earl; West Virginia University Team

    2017-10-01

    Current-free double layers (CFDL) models have been proposed to explain observations of magnetic field-aligned ion acceleration in plasmas expanding into divergent magnetic field regions. More recently, experimental studies of the Bohm sheath criterion in multiple ion species plasma reveal an equilibration of Bohm speeds at the sheath-presheath boundary for a grounded plate in a multipole-confined filament discharge. We aim to test this ion velocity effect for CFDL acceleration. We report high resolution ion velocity distribution function (IVDF) measurements using laser induced fluorescence downstream of a CFDL in a helicon plasma. Combinations of argon-helium, argon-krypton, and argon-xenon gases are ionized and measurements of argon or xenon IVDFs are investigated to determine whether ion acceleration is enhanced (or diminished) by the presence of lighter (or heavier) ions in the mix. We find that the predominant effect is a reduction of ion acceleration consistent with increased drag arising from increased gas pressure under all conditions, including constant total gas pressure, equal plasma densities of different ions, and very different plasma densities of different ions. These results suggest that the physics responsible for acceleration of multiple ion species in simple sheaths is not responsible for the ion acceleration observed in these expanding plasmas. Department of Physics, Gettysburg College.

  5. Multiple nuclear and mitochondrial genotyping identifies emperors and large-eye breams (Teleostei : Lethrinidae) from New Caledonia and reveals new large-eye bream species

    OpenAIRE

    Borsa, Philippe; Collet, Adeline; Carassou, Laure; Ponton, Dominique; Chen, W. J.

    2010-01-01

    International audience; Species identification is fundamental to address questions about community ecology, biodiversity, conservation and resource management, at any life history stage. Current studies on fish larval ecology of tropical species are hampered by the lack of reliable and effective tools for identifying larvae at the species level. Emperors and large-eye breams comprise fish species from the perciform fish family Lethrinidae. They inhabit coastal and coral-reef habitats of the t...

  6. Canopy and knowledge gaps when invasive alien insects remove foundation species.

    Science.gov (United States)

    Marler, Thomas E; Lawrence, John H

    2013-01-01

    The armored scale Aulacaspis yasumatsui invaded the northern range of the cycad Cycas micronesica in 2003, and epidemic tree mortality ensued due to a lack of natural enemies of the insect. We quantified cycad demographic responses to the invasion, but the ecological responses to the selective removal of this foundation species have not been addressed. We use this case to highlight information gaps in our understanding of how alien invasive phytophagous insects force cascading adverse ecosystem changes. The mechanistic role of unique canopy gaps, oceanic island examples and threatened foundation species with distinctive traits are three issues that deserve research efforts in a quest to understand this facet of ecosystem change occurring across multiple settings globally.

  7. Multiple Input - Multiple Output (MIMO) SAR

    Data.gov (United States)

    National Aeronautics and Space Administration — This effort will research and implement advanced Multiple-Input Multiple-Output (MIMO) Synthetic Aperture Radar (SAR) techniques which have the potential to improve...

  8. Detecting the limits of regulatory element conservation anddivergence estimation using pairwise and multiple alignments

    Energy Technology Data Exchange (ETDEWEB)

    Pollard, Daniel A.; Moses, Alan M.; Iyer, Venky N.; Eisen,Michael B.

    2006-08-14

    Background: Molecular evolutionary studies of noncodingsequences rely on multiple alignments. Yet how multiple alignmentaccuracy varies across sequence types, tree topologies, divergences andtools, and further how this variation impacts specific inferences,remains unclear. Results: Here we develop a molecular evolutionsimulation platform, CisEvolver, with models of background noncoding andtranscription factor binding site evolution, and use simulated alignmentsto systematically examine multiple alignment accuracy and its impact ontwo key molecular evolutionary inferences: transcription factor bindingsite conservation and divergence estimation. We find that the accuracy ofmultiple alignments is determined almost exclusively by the pairwisedivergence distance of the two most diverged species and that additionalspecies have a negligible influence on alignment accuracy. Conservedtranscription factor binding sites align better than surroundingnoncoding DNA yet are often found to be misaligned at relatively shortdivergence distances, such that studies of binding site gain and losscould easily be confounded by alignment error. Divergence estimates frommultiple alignments tend to be overestimated at short divergencedistances but reach a tool specific divergence at which they cease toincrease, leading to underestimation at long divergences. Our moststriking finding was that overall alignment accuracy, binding sitealignment accuracy and divergence estimation accuracy vary greatly acrossbranches in a tree and are most accurate for terminal branches connectingsister taxa and least accurate for internal branches connectingsub-alignments. Conclusions: Our results suggest that variation inalignment accuracy can lead to errors in molecular evolutionaryinferences that could be construed as biological variation. Thesefindings have implications for which species to choose for analyses, whatkind of errors would be expected for a given set of species and howmultiple alignment tools and

  9. Assessments at multiple levels of biological organization allow for an integrative determination of physiological tolerances to turbidity in an endangered fish species

    OpenAIRE

    Hasenbein, Matthias; Fangue, Nann A.; Geist, Juergen; Komoroske, Lisa M.; Truong, Jennifer; McPherson, Rina; Connon, Richard E.

    2016-01-01

    Turbidity can influence trophic levels by altering species composition and can potentially affect fish feeding strategies and predator?prey interactions. The estuarine turbidity maximum, described as an area of increased suspended particles, phytoplankton and zooplankton, generally represents a zone with higher turbidity and enhanced food sources important for successful feeding and growth in many fish species. The delta smelt (Hypomesus transpacificus) is an endangered, pelagic fish species ...

  10. Strains of bacterial species induce a greatly varied acute adaptive immune response: The contribution of the accessory genome.

    Directory of Open Access Journals (Sweden)

    Uri Sela

    2018-01-01

    Full Text Available A fundamental question in human susceptibility to bacterial infections is to what extent variability is a function of differences in the pathogen species or in individual humans. To focus on the pathogen species, we compared in the same individual the human adaptive T and B cell immune response to multiple strains of two major human pathogens, Staphylococcus aureus and Streptococcus pyogenes. We found wide variability in the acute adaptive immune response induced by various strains of a species, with a unique combination of activation within the two arms of the adaptive response. Further, this was also accompanied by a dramatic difference in the intensity of the specific protective T helper (Th response. Importantly, the same immune response differences induced by the individual strains were maintained across multiple healthy human donors. A comparison of isogenic phage KO strains, demonstrated that of the pangenome, prophages were the major contributor to inter-strain immune heterogeneity, as the T cell response to the remaining "core genome" was noticeably blunted. Therefore, these findings extend and modify the notion of an adaptive response to a pathogenic bacterium, by implying that the adaptive immune response signature of a bacterial species should be defined either per strain or alternatively to the species' 'core genome', common to all of its strains. Further, our results demonstrate that the acquired immune response variation is as wide among different strains within a single pathogenic species as it is among different humans, and therefore may explain in part the clinical heterogeneity observed in patients infected with the same species.

  11. MULTIPLE OBJECTS

    Directory of Open Access Journals (Sweden)

    A. A. Bosov

    2015-04-01

    Full Text Available Purpose. The development of complicated techniques of production and management processes, information systems, computer science, applied objects of systems theory and others requires improvement of mathematical methods, new approaches for researches of application systems. And the variety and diversity of subject systems makes necessary the development of a model that generalizes the classical sets and their development – sets of sets. Multiple objects unlike sets are constructed by multiple structures and represented by the structure and content. The aim of the work is the analysis of multiple structures, generating multiple objects, the further development of operations on these objects in application systems. Methodology. To achieve the objectives of the researches, the structure of multiple objects represents as constructive trio, consisting of media, signatures and axiomatic. Multiple object is determined by the structure and content, as well as represented by hybrid superposition, composed of sets, multi-sets, ordered sets (lists and heterogeneous sets (sequences, corteges. Findings. In this paper we study the properties and characteristics of the components of hybrid multiple objects of complex systems, proposed assessments of their complexity, shown the rules of internal and external operations on objects of implementation. We introduce the relation of arbitrary order over multiple objects, we define the description of functions and display on objects of multiple structures. Originality.In this paper we consider the development of multiple structures, generating multiple objects.Practical value. The transition from the abstract to the subject of multiple structures requires the transformation of the system and multiple objects. Transformation involves three successive stages: specification (binding to the domain, interpretation (multiple sites and particularization (goals. The proposed describe systems approach based on hybrid sets

  12. A vulnerability assessment of 300 species in Florida: threats from sea level rise, land use, and climate change.

    Directory of Open Access Journals (Sweden)

    Joshua Steven Reece

    Full Text Available Species face many threats, including accelerated climate change, sea level rise, and conversion and degradation of habitat from human land uses. Vulnerability assessments and prioritization protocols have been proposed to assess these threats, often in combination with information such as species rarity; ecological, evolutionary or economic value; and likelihood of success. Nevertheless, few vulnerability assessments or prioritization protocols simultaneously account for multiple threats or conservation values. We applied a novel vulnerability assessment tool, the Standardized Index of Vulnerability and Value, to assess the conservation priority of 300 species of plants and animals in Florida given projections of climate change, human land-use patterns, and sea level rise by the year 2100. We account for multiple sources of uncertainty and prioritize species under five different systems of value, ranging from a primary emphasis on vulnerability to threats to an emphasis on metrics of conservation value such as phylogenetic distinctiveness. Our results reveal remarkable consistency in the prioritization of species across different conservation value systems. Species of high priority include the Miami blue butterfly (Cyclargus thomasi bethunebakeri, Key tree cactus (Pilosocereus robinii, Florida duskywing butterfly (Ephyriades brunnea floridensis, and Key deer (Odocoileus virginianus clavium. We also identify sources of uncertainty and the types of life history information consistently missing across taxonomic groups. This study characterizes the vulnerabilities to major threats of a broad swath of Florida's biodiversity and provides a system for prioritizing conservation efforts that is quantitative, flexible, and free from hidden value judgments.

  13. The evolution of microbial species - a view through the genomic lens

    Energy Technology Data Exchange (ETDEWEB)

    Varghese, Neha; Mukherjee, Supratim; ivanova, Natalia; Mavromatis, Konstantinos; Konstantinidis, Konstantinos; Kyrpides, Nikos; Pati, Amrita

    2014-03-17

    For a long time prokaryotic species definition has been under debate and a constant source of turmoil in microbiology. This has recently prompted the ASM to call for a scalable and reproducible technique, which uses meaningful commonalities to cluster microorganisms into groups corresponding to prokaryotic species. Whole-genome Average Nucleotide Identity (gANI) was previously suggested as a measure of genetic distance that generally agrees with prokaryotic species assignments based on the accepted best practices (DNA-DNA hybridization and 16S rDNA similarity). In this work, we prove that gANI is indeed the meaningful commonality based on which microorganisms can be grouped into the aforementioned clusters. By analyzing 1.76 million pairs of genomes we find that identification of the closest relatives of an organism via gANI is precise, scalable, reproducible, and reflects the evolutionary dynamics of microbes. We model the previously unexplored statistical properties of gANI using 6,000 microbial genomes and apply species-specific gANI cutoffs to reveal anomalies in the current taxonomic species definitions for almost 50percent of the species with multiple genome sequences. We also provide evidence of speciation events and genetic continuums in 17.8percent of those species. We consider disagreements between gANI-based groupings and named species and demonstrate that the former have all the desired features to serve as the much-needed natural groups for moving forward with taxonomy. Further, the groupings identified are presented in detail at http://ani.jgi-psf.org to facilitate comprehensive downstream analysis for researchers across different disciplines

  14. Combining landscape variables and species traits can improve the utility of climate change vulnerability assessments

    Science.gov (United States)

    Nadeau, Christopher P.; Fuller, Angela K.

    2016-01-01

    Conservation organizations worldwide are investing in climate change vulnerability assessments. Most vulnerability assessment methods focus on either landscape features or species traits that can affect a species vulnerability to climate change. However, landscape features and species traits likely interact to affect vulnerability. We compare a landscape-based assessment, a trait-based assessment, and an assessment that combines landscape variables and species traits for 113 species of birds, herpetofauna, and mammals in the northeastern United States. Our aim is to better understand which species traits and landscape variables have the largest influence on assessment results and which types of vulnerability assessments are most useful for different objectives. Species traits were most important for determining which species will be most vulnerable to climate change. The sensitivity of species to dispersal barriers and the species average natal dispersal distance were the most important traits. Landscape features were most important for determining where species will be most vulnerable because species were most vulnerable in areas where multiple landscape features combined to increase vulnerability, regardless of species traits. The interaction between landscape variables and species traits was important when determining how to reduce climate change vulnerability. For example, an assessment that combines information on landscape connectivity, climate change velocity, and natal dispersal distance suggests that increasing landscape connectivity may not reduce the vulnerability of many species. Assessments that include landscape features and species traits will likely be most useful in guiding conservation under climate change.

  15. A spatially and temporally explicit, individual-based, life-history and productivity modeling approach for aquatic species

    Science.gov (United States)

    Realized life history expression and productivity in aquatic species, and salmonid fishes in particular, is the result of multiple interacting factors including genetics, habitat, growth potential and condition, and the thermal regime individuals experience, both at critical stag...

  16. Species boundaries and phylogenetic relationships in the critically endangered Asian box turtle genus Cuora.

    Science.gov (United States)

    Spinks, Phillip Q; Thomson, Robert C; Zhang, YaPing; Che, Jing; Wu, Yonghua; Shaffer, H Bradley

    2012-06-01

    Turtles are currently the most endangered major clade of vertebrates on earth, and Asian box turtles (Cuora) are in catastrophic decline. Effective management of this diverse turtle clade has been hampered by human-mediated, and perhaps natural hybridization, resulting in discordance between mitochondrial and nuclear markers and confusion regarding species boundaries and phylogenetic relationships among hypothesized species of Cuora. Here, we present analyses of mitochondrial and nuclear DNA data for all 12 currently hypothesized species to resolve both species boundaries and phylogenetic relationships. Our 15-gene, 40-individual nuclear data set was frequently in conflict with our mitochondrial data set; based on its general concordance with published morphological analyses and the strength of 15 independent estimates of evolutionary history, we interpret the nuclear data as representing the most reliable estimate of species boundaries and phylogeny of Cuora. Our results strongly reiterate the necessity of using multiple nuclear markers for phylogeny and species delimitation in these animals, including any form of DNA "barcoding", and point to Cuora as an important case study where reliance on mitochondrial DNA can lead to incorrect species identification. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Phenology of selected herbaceous species of northern Wisconsin deciduous forests and forest roads

    International Nuclear Information System (INIS)

    Zavitkovski, J.

    1977-01-01

    Vegetative and reproductive phenophases were observed from 1970 to 1974 on 30 native and 8 introduced herbaceous species growing under deciduous forests and on an abandoned logging road in the Enterprise Radiation Forest in northern Wisconsin. Forest herbs started growing in the same order each year, but logging-road herbs varied. Growth initiation was more variable in the early-starting than in the late-starting species. In most years logging-road herbs started growth a few days earlier than forest herbs. Initiation of flowering of the 38 species was bimodal, culminating around mid-May for forest species and around mid-July for logging-road species. In general, the annual start of flowering varied less than the start of vegetative growth. Duration of flowering of most species was variable, however. Seed ripening times varied strikingly among species, ranging from 11 days for Taraxacum officinale to 101 days for Iris versicolor. Seeds of forest herbs took longer to ripen than those of logging-road species. On the basis of growth initiation of the 6 earliest species, spring arrival in 1970 to 1974 differed by 26 days and appeared to be related to snow disappearance. The growing season of most species paralleled cumulative current-year (May--July) and last-year (August--September) precipitation. Multiple regression analyses between precipitation and average length of growing season explained 87 percent of the total variation for forest herbs and 69 percent of that for logging-road herbs

  18. Global warming and extinctions of endemic species from biodiversity hotspots.

    Science.gov (United States)

    Malcolm, Jay R; Liu, Canran; Neilson, Ronald P; Hansen, Lara; Hannah, Lee

    2006-04-01

    Global warming is a key threat to biodiversity, but few researchers have assessed the magnitude of this threat at the global scale. We used major vegetation types (biomes) as proxies for natural habitats and, based on projected future biome distributions under doubled-CO2 climates, calculated changes in habitat areas and associated extinctions of endemic plant and vertebrate species in biodiversity hotspots. Because of numerous uncertainties in this approach, we undertook a sensitivity analysis of multiple factors that included (1) two global vegetation models, (2) different numbers of biome classes in our biome classification schemes, (3) different assumptions about whether species distributions were biome specific or not, and (4) different migration capabilities. Extinctions were calculated using both species-area and endemic-area relationships. In addition, average required migration rates were calculated for each hotspot assuming a doubled-CO2 climate in 100 years. Projected percent extinctions ranged from hotspots were the Cape Floristic Region, Caribbean, Indo-Burma, Mediterranean Basin, Southwest Australia, and Tropical Andes, where plant extinctions per hotspot sometimes exceeded 2000 species. Under the assumption that projected habitat changes were attained in 100 years, estimated global-warming-induced rates of species extinctions in tropical hotspots in some cases exceeded those due to deforestation, supporting suggestions that global warming is one of the most serious threats to the planet's biodiversity.

  19. Marine alien species as an aspect of global change

    Directory of Open Access Journals (Sweden)

    Anna Occhipinti-Ambrogi

    2010-06-01

    Full Text Available The transport of organisms across oceans is an anthropogenic agent of global change that has profoundly affected the natural distribution of littoral biota and altered the makeup of biogeographic regions. The homogenization of marine biotas is a phenomenon especially affecting coastal regions and is spearheaded by a suite of opportunistic species at the expense of native species. Climate change may exacerbate the trend: sea surface temperatures, hydrodynamics, pH and carbonate cycles, already show marked fluctuations compared to the past. Alien invasive species are impacted by the change of marine climate in a variety of ways, which are we have just begun to notice, observe and interpret. A conceptual framework has yet to be conceived that links theories on biological introductions and invasions with the physical aspects of global change. Therefore predicting the scale of invasions or their impact on biodiversity is a daunting task. Integration of biological and environmental information systems, niche models, and climate projections would improve management of aquatic ecosystems under the dual threats of biotic invasions and climate change. The recorded spread of alien species and analysis of patterns of invasions may serve as the starting point for searching connections with climate change descriptors. The Mediterranean Sea is home to an exceptionally large number of alien species, resulting from its exceptional history and multiple vectors. For much of the twentieth century alien thermophilic species, which had entered the Mediterranean through the Suez Canal, have been confined to the Levantine Basin. In recent years climate driven hydrographic changes have coincided with a pronounced expansion of alien thermophilic biota to the central and western basins of the Mediterranean. We discuss some changes in emergent functions and services in Mediterranean ecosystems under the combined effect of invasive species and climate changes.

  20. Albumin and multiple sclerosis.

    Science.gov (United States)

    LeVine, Steven M

    2016-04-12

    Leakage of the blood-brain barrier (BBB) is a common pathological feature in multiple sclerosis (MS). Following a breach of the BBB, albumin, the most abundant protein in plasma, gains access to CNS tissue where it is exposed to an inflammatory milieu and tissue damage, e.g., demyelination. Once in the CNS, albumin can participate in protective mechanisms. For example, due to its high concentration and molecular properties, albumin becomes a target for oxidation and nitration reactions. Furthermore, albumin binds metals and heme thereby limiting their ability to produce reactive oxygen and reactive nitrogen species. Albumin also has the potential to worsen disease. Similar to pathogenic processes that occur during epilepsy, extravasated albumin could induce the expression of proinflammatory cytokines and affect the ability of astrocytes to maintain potassium homeostasis thereby possibly making neurons more vulnerable to glutamate exicitotoxicity, which is thought to be a pathogenic mechanism in MS. The albumin quotient, albumin in cerebrospinal fluid (CSF)/albumin in serum, is used as a measure of blood-CSF barrier dysfunction in MS, but it may be inaccurate since albumin levels in the CSF can be influenced by multiple factors including: 1) albumin becomes proteolytically cleaved during disease, 2) extravasated albumin is taken up by macrophages, microglia, and astrocytes, and 3) the location of BBB damage affects the entry of extravasated albumin into ventricular CSF. A discussion of the roles that albumin performs during MS is put forth.

  1. Soil chemical factors and grassland species density in Emas National Park (central Brazil).

    Science.gov (United States)

    Amorim, P K; Batalha, M A

    2008-05-01

    Studies of grasslands on specific soil types suggest that different nutrients can limit biomass production and, hence, species composition and number. The Brazilian cerrado is the major savanna region in America and once covered about 2 million km(2), mainly in the Brazilian Central Plateau, under seasonal climate, with wet summer and dry winter. In view of the importance of soil chemical factors in the distribution of the vegetation forms within the Cerrado domain and which may influence the number of species, we analyzed some soil characteristics in three herbaceous vegetation forms -- hyperseasonal cerrado, seasonal cerrado, and wet grassland -- in Emas National Park, a core cerrado site, to investigate the relationship between number of species and soil characteristics. We collected vegetation and soil samples in these three vegetation forms and submitted the obtained data to multiple linear regression. We found out that aluminum and pH were the best predictors of species density, the former positively related to species density and the latter negatively related. Since the predictable variation in species density is important in determining areas of conservation, we can postulate that these two soil factors are indicators of high species density areas in tropical grasslands, which could be used in selecting priority sites for conservation.

  2. Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds (Pachyramphus).

    Science.gov (United States)

    Musher, Lukas J; Cracraft, Joel

    2018-01-01

    Phylogeographic studies within the Neotropics continue to uncover hidden diversity, the extent of which remains poorly known. In birds, molecular studies are producing evidence that species-level diversity is substantially underestimated. Many avian taxa comprise large complexes of subspecies that often represent species-level taxa by various criteria. One such group of Neotropical suboscine birds, the becards (Pachyramphus), ranges from Argentina through northern Mexico. Their taxonomic limits have been complex and controversial as the genus has bounced around a number of suboscine families. Additionally, the phylogenetic relationships within Pachyramphus are unresolved due to insufficient sampling of taxa and populations across species' ranges. We used target capture of ultraconserved elements for 62 individuals representing 42 taxa, and sequenced two mitochondrial genes and two nuclear introns covering 265 individuals of 51 taxa, including all recognized species, resulting in the most densely and completely sampled phylogenetic hypothesis for Pachyramphus to date. We delimited species using a traditional taxonomic approach and then tested them under a Bayesian multi-species coalescent framework. In doing so, we provide evidence for multiple young, previously undetected evolutionary lineages within Pachyramphus. Deep, well-supported branches and a high number of intraspecific lineages across the tree suggest that at least 50% of species diversity may be unrecognized. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Comparison of lipid peroxidation and catalase response in invasive dreissenid mussels exposed to single and multiple stressors.

    Science.gov (United States)

    Nowicki, Carly J; Kashian, Donna R

    2018-02-14

    Dreissenid mussels Dreissena bugensis (quagga mussel) and Dreissena polymorpha (zebra mussel) are prolific invasive species to the freshwaters of the United States and Western Europe. In the Great Lakes, D. polymorpha has initially dominated the system since its invasion in the mid-1980s; however, recently D. bugensis has displaced D. polymorpha as the dominant species. Dreissena bugensis has several competitive advantages over D. polymorpha, including greater tolerances to deeper and colder waters and lower respiration rates. Nevertheless, physiological differences between the species remain largely unknown. The oxidative stress response is a mechanism used by all organisms to mitigate environmental stress by reducing oxygen radicals in the body, and comparing this mechanism between similar species can be useful for understanding how different species compete in aquatic environments. We compared oxidative stress biomarkers (lipid peroxidation [LPO] and catalase [CAT] activity) in mussels after exposure to 4 stressors (i.e., high densities, temperature, hypoxia, and polychlorinated biphenyls [PCBs]) independently and in combinations of 2 stressors. Overall, D. bugensis had lower LPO and CAT activity than D. polymorpha when exposed to single stressors; however, in multiple stressor treatments D. bugensis had increased LPO, especially with high temperatures and PCBs. The lower lipid damage in D. bugensis compared with D. polymorpha under single stressor conditions may come at the cost of the ability to respond to multiple stressors. Environ Toxicol Chem 2018;9999:1-12. © 2018 SETAC. © 2018 SETAC.

  4. Links between plant litter chemistry, species diversity, and below-ground ecosystem function.

    Science.gov (United States)

    Meier, Courtney L; Bowman, William D

    2008-12-16

    Decomposition is a critical source of plant nutrients, and drives the largest flux of terrestrial C to the atmosphere. Decomposing soil organic matter typically contains litter from multiple plant species, yet we lack a mechanistic understanding of how species diversity influences decomposition processes. Here, we show that soil C and N cycling during decomposition are controlled by the composition and diversity of chemical compounds within plant litter mixtures, rather than by simple metrics of plant species diversity. We amended native soils with litter mixtures containing up to 4 alpine plant species, and we used 9 litter chemical traits to evaluate the chemical composition (i.e., the identity and quantity of compounds) and chemical diversity of the litter mixtures. The chemical composition of the litter mixtures was the strongest predictor of soil respiration, net N mineralization, and microbial biomass N. Soil respiration and net N mineralization rates were also significantly correlated with the chemical diversity of the litter mixtures. In contrast, soil C and N cycling rates were poorly correlated with plant species richness, and there was no relationship between species richness and the chemical diversity of the litter mixtures. These results indicate that the composition and diversity of chemical compounds in litter are potentially important functional traits affecting decomposition, and simple metrics like plant species richness may fail to capture variation in these traits. Litter chemical traits therefore provide a mechanistic link between organisms, species diversity, and key components of below-ground ecosystem function.

  5. Multiple constant multiplication optimizations for field programmable gate arrays

    CERN Document Server

    Kumm, Martin

    2016-01-01

    This work covers field programmable gate array (FPGA)-specific optimizations of circuits computing the multiplication of a variable by several constants, commonly denoted as multiple constant multiplication (MCM). These optimizations focus on low resource usage but high performance. They comprise the use of fast carry-chains in adder-based constant multiplications including ternary (3-input) adders as well as the integration of look-up table-based constant multipliers and embedded multipliers to get the optimal mapping to modern FPGAs. The proposed methods can be used for the efficient implementation of digital filters, discrete transforms and many other circuits in the domain of digital signal processing, communication and image processing. Contents Heuristic and ILP-Based Optimal Solutions for the Pipelined Multiple Constant Multiplication Problem Methods to Integrate Embedded Multipliers, LUT-Based Constant Multipliers and Ternary (3-Input) Adders An Optimized Multiple Constant Multiplication Architecture ...

  6. Functional traits drive the contribution of solar radiation to leaf litter decomposition among multiple arid-zone species

    NARCIS (Netherlands)

    Pan, Xu; Song, Yao-Bin; Liu, Guo-Fang; Hu, Yu-Kun; Ye, Xue-Hua; Cornwell, W.K.; Prinzing, A.; Dong, Ming; Cornelissen, J.H.C.

    2015-01-01

    In arid zones, strong solar radiation has important consequences for ecosystem processes. To better understand carbon and nutrient dynamics, it is important to know the contribution of solar radiation to leaf litter decomposition of different arid-zone species. Here we investigated: (1) whether such

  7. Tree diversity and species identity effects on soil fungi, protists and animals are context dependent.

    Science.gov (United States)

    Tedersoo, Leho; Bahram, Mohammad; Cajthaml, Tomáš; Põlme, Sergei; Hiiesalu, Indrek; Anslan, Sten; Harend, Helery; Buegger, Franz; Pritsch, Karin; Koricheva, Julia; Abarenkov, Kessy

    2016-02-01

    Plant species richness and the presence of certain influential species (sampling effect) drive the stability and functionality of ecosystems as well as primary production and biomass of consumers. However, little is known about these floristic effects on richness and community composition of soil biota in forest habitats owing to methodological constraints. We developed a DNA metabarcoding approach to identify the major eukaryote groups directly from soil with roughly species-level resolution. Using this method, we examined the effects of tree diversity and individual tree species on soil microbial biomass and taxonomic richness of soil biota in two experimental study systems in Finland and Estonia and accounted for edaphic variables and spatial autocorrelation. Our analyses revealed that the effects of tree diversity and individual species on soil biota are largely context dependent. Multiple regression and structural equation modelling suggested that biomass, soil pH, nutrients and tree species directly affect richness of different taxonomic groups. The community composition of most soil organisms was strongly correlated due to similar response to environmental predictors rather than causal relationships. On a local scale, soil resources and tree species have stronger effect on diversity of soil biota than tree species richness per se.

  8. Multiple blood feeding and host-seeking behavior in Aedes aegypti and Aedes albopictus (Diptera: Culicidae).

    Science.gov (United States)

    Farjana, Thahsin; Tuno, Nobuko

    2013-07-01

    The body size of mosquitoes can influence a number of bionomic factors, such as their blood-feeding ability, host attack rate, and fecundity. All of these traits are important determinants of their potential to transmit diseases. Among abiotic and biotic factors, high temperature and low nutrition in the developing stages of mosquitoes generally result in small adults. We studied the relationship between body size and multiple feeding in a gonotrophic cycle and some fecundity attributes by using three strains of two competent vector species, Aedes aegypti (L.) and Aedes albopictus (Skuse). We raised small and large mosquitoes under low and high food conditions in the laboratory to measure parameters of fecundity and blood-feeding behavior. Fecundity was positively correlated with body size in both species, whereas the number of bloodmeals, the frequency of host-seeking behavior, and egg retention were negatively correlated with body size in the Ae. albopictus Nagasaki strain. We found that multiple feeding and host-seeking behavior were negatively correlated with body size, i.e., small mosquitoes tended to have more contact with hosts. We found that two mechanisms that inhibit engorged mosquitoes from seeking out hosts, distension-induced and oocyte-induced inhibition, were not strong enough to limit host-seeking behavior, and multiple feeding increased fecundity. Size-dependent multiple feeding and host-seeking behavior affect contact frequency with hosts and should be considered when predicting how changes in mosquito body size affect disease transmission.

  9. Stime della biomassa marina attraverso il metodo acustico: discernimento delle specie e gestione delle risorse ittiche - Acoustical estimation of fish biomass: species identification and stocks management

    Directory of Open Access Journals (Sweden)

    Víctor Espinosa

    2015-09-01

    Full Text Available L’acustica è alla base delle più importanti tecnologie nelle telecomunicazioni subacquee, nonché nel rilevamento e nella determinazione dei target acustici nei mezzi acquatici. Le misure a multi-frequenza sono lo strumento principale per l’identificazione selettiva delle specie marine e per la pesca sostenibile. Lo sviluppo di sistemi a larga banda larga e le tecniche basate su sonar multi-beam costituiscono l'attuale sfida per gli scienziati e gli sviluppatori. Al contempo, sistemi più semplici ed economicamente efficienti, come boe satellitari, sono in grado di offrire informazioni per il monitoraggio degli ecosistemi o l’individuazione di specie bersaglio nella pesca marittima. ------ Acoustics is the basics of the most important technologies for underwater telecommunication, as well as for target detection and identification in the aquatic media. Multiple frequency measurements are the key for species discrimination and open the door for sustainable fisheries. The development of wider broadband systems and quantitative multi-beam sonars and processing techniques constitute the present challenge for scientists and developers. In parallel, simpler and cost-efficient systems like satellite buoys can offer clue information for marine ecosystem monitoring or target species fisheries.

  10. Physiological differentiation within a single-species biofilm fueled by serpentinization.

    Science.gov (United States)

    Brazelton, William J; Mehta, Mausmi P; Kelley, Deborah S; Baross, John A

    2011-01-01

    Carbonate chimneys at the Lost City hydrothermal field are coated in biofilms dominated by a single phylotype of archaea known as Lost City Methanosarcinales. In this study, we have detected surprising physiological complexity in single-species biofilms, which is typically indicative of multispecies biofilm communities. Multiple cell morphologies were visible within the biofilms by transmission electron microscopy, and some cells contained intracellular membranes that may facilitate methane oxidation. Both methane production and oxidation were detected at 70 to 80°C and pH 9 to 10 in samples containing the single-species biofilms. Both processes were stimulated by the presence of hydrogen (H(2)), indicating that methane production and oxidation are part of a syntrophic interaction. Metagenomic data included a sequence encoding AMP-forming acetyl coenzyme A synthetase, indicating that acetate may play a role in the methane-cycling syntrophy. A wide range of nitrogen fixation genes were also identified, many of which were likely acquired via lateral gene transfer (LGT). Our results indicate that cells within these single-species biofilms may have differentiated into multiple physiological roles to form multicellular communities linked by metabolic interactions and LGT. Communities similar to these Lost City biofilms are likely to have existed early in the evolution of life, and we discuss how the multicellular characteristics of ancient hydrogen-fueled biofilm communities could have stimulated ecological diversification, as well as unity of biochemistry, during the earliest stages of cellular evolution. Our previous work at the Lost City hydrothermal field has shown that its carbonate chimneys host microbial biofilms dominated by a single uncultivated "species" of archaea. In this paper, we integrate evidence from these previous studies with new data on the metabolic activity and cellular morphology of these archaeal biofilms. We conclude that the archaeal biofilm

  11. The multiple Dirichlet product and the multiple Dirichlet series

    OpenAIRE

    Onozuka, Tomokazu

    2016-01-01

    First, we define the multiple Dirichlet product and study the properties of it. From those properties, we obtain a zero-free region of a multiple Dirichlet series and a multiple Dirichlet series expression of the reciprocal of a multiple Dirichlet series.

  12. DNA Barcoding the Canadian Arctic Flora: Core Plastid Barcodes (rbcL + matK) for 490 Vascular Plant Species

    Science.gov (United States)

    Saarela, Jeffery M.; Sokoloff, Paul C.; Gillespie, Lynn J.; Consaul, Laurie L.; Bull, Roger D.

    2013-01-01

    Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA–trnH, psbK–psbI, atpF–atpH) collected for a subset of Poa and Puccinellia species, only atpF–atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species. PMID

  13. Mechanical branch constraints contribute to life-history variation across tree species in a Bolivian forest.

    NARCIS (Netherlands)

    Sterck, F.J.; Gelder, van H.A.; Poorter, L.

    2006-01-01

    1 Trade-offs among plant traits may contribute to specialization for different environments and coexistence of plant species. This may be the first study that shows how trade-offs among branch traits contribute to variation in crown size, light requirements and maximum height across multiple

  14. Real-time detection and quantification of Rhizoctonia and Pythium species on the Cook Agronomy Farm.

    Science.gov (United States)

    Populations of Rhizoctonia and Pythium are diverse in eastern Washington, with multiple species/anastomosis groups present throughout the region and within individual fields. The process of identifying the pathogen present in a sample is laborious and the high diversity increases the difficulty in a...

  15. Mitochondrial phylogeny of grey mullets (Acanthopterygii: Mugilidae) suggests high proportion of cryptic species.

    Science.gov (United States)

    Durand, Jean-Dominique; Borsa, Philippe

    2015-04-01

    The low level of morphometric variability and the poor phylogenetic information borne by the morpho-anatomical characters used thus far in the systematics of grey mullets (Mugilidae) emphasize the utility of molecular systematics in this family. A recent mitochondrial phylogeny of grey mullets has uncovered multiple deep lineages within several species, flagging putative cryptic species. Here, we considered that several of the deeply divergent lineages represent separate species based on either the tree topology, independent data from nuclear markers, geographic distributions, or a combination of the foregoing. By analogy with these well-documented cases, we considered other deep lineages in seven genera we focused on to represent putative cryptic species. Up to two cryptic species were thus potentially detected in the genus Chelon, three in Crenimugil (including two within the single Crenimugil seheli), two in Dajaus, one in Ellochelon, 16 in Mugil (including 13 within the single M. cephalus), two in Osteomugil, and 10 in Planiliza. Wherever possible, we kept the current species epithets to designate those lineages that unambiguously correspond to the type material, based on type locality, and we assigned arbitrary letters (sp. A, B, etc.) to the other lineages. We present a molecular diagnosis for 24 of the species analysed in this work, as well as for 25 putative cryptic species. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  16. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    Energy Technology Data Exchange (ETDEWEB)

    Ovacik, Meric A. [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Androulakis, Ioannis P., E-mail: yannis@rci.rutgers.edu [Chemical and Biochemical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States); Biomedical Engineering Department, Rutgers University, Piscataway, NJ 08854 (United States)

    2013-09-15

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.

  17. Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

    International Nuclear Information System (INIS)

    Ovacik, Meric A.; Androulakis, Ioannis P.

    2013-01-01

    Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy

  18. The Arabidopsis thaliana mobilome and its impact at the species level

    Science.gov (United States)

    Quadrana, Leandro; Bortolini Silveira, Amanda; Mayhew, George F; LeBlanc, Chantal; Martienssen, Robert A; Jeddeloh, Jeffrey A; Colot, Vincent

    2016-01-01

    Transposable elements (TEs) are powerful motors of genome evolution yet a comprehensive assessment of recent transposition activity at the species level is lacking for most organisms. Here, using genome sequencing data for 211 Arabidopsis thaliana accessions taken from across the globe, we identify thousands of recent transposition events involving half of the 326 TE families annotated in this plant species. We further show that the composition and activity of the 'mobilome' vary extensively between accessions in relation to climate and genetic factors. Moreover, TEs insert equally throughout the genome and are rapidly purged by natural selection from gene-rich regions because they frequently affect genes, in multiple ways. Remarkably, loci controlling adaptive responses to the environment are the most frequent transposition targets observed. These findings demonstrate the pervasive, species-wide impact that a rich mobilome can have and the importance of transposition as a recurrent generator of large-effect alleles. DOI: http://dx.doi.org/10.7554/eLife.15716.001 PMID:27258693

  19. Tubulin-isotype analysis of two grass species-resistant to dinitroaniline herbicides.

    Science.gov (United States)

    Waldin, T R; Ellis, J R; Hussey, P J

    1992-09-01

    Trifluralin-resistant biotypes of Eleusine indica (L.) Gaertn. (goosegrass) and Setaria viridis (L.) Beauv. (green foxtail) exhibit cross-resistance to other dinitroaniline herbicides. Since microtubules are considered the primary target site for dinitroaniline herbicides we investigated whether the differential sensitivity of resistant and susceptible biotypes of these species results from modified tubulin polypeptides. One-dimensional and two-dimensional polyacrylamide gel electrophoresis combined with immunoblotting using well-characterised anti-tubulin monoclonal antibodies were used to display the family of tubulin isotypes in each species. Seedlings of E. indica exhibited four β-tubulin isotypes and one α-tubulin isotype, whereas those of S. viridis exhibited two β-tubulin and two α-tubulin isotypes. Comparison of the susceptible and resistant biotypes within each species revealed no differences in electrophoretic properties of the multiple tubulin isotypes. These results provide no evidence that resistance to dinitroaniline herbicides is associated with a modified tubulin polypeptide in these biotypes of E. indica or S. viridis.

  20. Trophodynamics of the Hanna Shoal Ecosystem (Chukchi Sea, Alaska): Connecting multiple end-members to a rich food web

    Science.gov (United States)

    McTigue, N. D.; Dunton, K. H.

    2017-10-01

    Predicting how alterations in sea ice-mediated primary production will impact Arctic food webs remains a challenge in forecasting ecological responses to climate change. One top-down approach to this challenge is to elucidate trophic roles of consumers as either specialists (i.e., consumers of predominantly one food resource) or generalists (i.e., consumers of multiple food resources) to categorize the dependence of consumers on each primary producer. At Hanna Shoal in the Chukchi Sea, Alaska, we used stable carbon and nitrogen isotope data to quantify trophic redundancy with standard ellipse areas at both the species and trophic guild levels. We also investigated species-level trophic plasticity by analyzing the varying extents that three end-members were assimilated by the food web using the mixing model simmr (Stable Isotope Mixing Model in R). Our results showed that ice algae, a combined phytoplankton and sediment organic matter composite (PSOM), and a hypothesized microphytobenthos (MPB) component were incorporated by consumers in the benthic food web, but their importance varied by species. Some primary consumers relied heavily on PSOM (e.g, the amphipods Ampelisca sp. and Byblis sp.; the copepod Calanus sp.), while others exhibited generalist feeding and obtained nutrition from multiple sources (e.g., the holothuroidean Ocnus glacialis, the gastropod Tachyrhynchus sp., the sipunculid Golfingia margaritacea, and the bivalves Ennucula tenuis, Nuculana pernula, Macoma sp., and Yoldia hyperborea). Most higher trophic level benthic predators, including the gastropods Buccinum sp., Cryptonatica affinis, and Neptunea sp, the seastar Leptasterias groenlandica, and the amphipod Anonyx sp. also exhibited trophic plasticity by coupling energy pathways from multiple primary producers including PSOM, ice algae, and MPB. Our stable isotope data indicate that consumers in the Hanna Shoal food web exhibit considerable trophic redundancy, while few species were specialists

  1. Multiple Reversals of Bill Length over 1.7 Million Years in a Hawaiian Bird Lineage.

    Science.gov (United States)

    Freed, Leonard A; Medeiros, Matthew C I; Cann, Rebecca L

    2016-03-01

    Evolutionary change has been documented over geological time, but reversals in morphology, from an ancestral state to a derived state and back again, tend to be rare. Multiple reversals along the same lineage are even rarer. We use the chronology of the Hawaiian Islands and an avian example, the Hawaiian honeycreeper 'amakihi (Hemignathus spp.) lineage, which originated on the oldest main island of Kaua'i 1.7 million years ago, to examine the process of sequential reversals in bill length. We document three single and two multiple reversals of bill length on six main islands from oldest to youngest, consistent with the phylogeny of the lineage. Longer bills occur on islands with endemic species, including phylogenetically relevant outgroups, that may compete with or dominate the 'amakihi. On islands without those species, the 'amakihi had shorter bills of similar length. Both types of reversals in morphology in this lineage integrate microevolutionary processes with macroevolution in the adaptive radiation of Hawaiian honeycreepers.

  2. Endangered Species

    Science.gov (United States)

    EPA's Endangered Species Protection Program helps promote recovery of listed species. The ESPP determines if pesticide use in a geographic area may affect any listed species. Find needed limits on pesticide use in Endangered Species Protection Bulletins.

  3. At a global scale, do climate change threatened species also face a greater number of non-climatic threats?

    Science.gov (United States)

    Fortini, Lucas B.; Dye, Kaipo

    2017-01-01

    For many species the threats of climate change occur in a context of multiple existing threats. Given the current focus of global change ecology in identifying and understanding species vulnerable to climate change, we performed a global analysis to characterize the multi-threat context for species threatened by climate change. Utilizing 30,053 species from the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species, we sought to evaluate if species threatened by climate change are more likely threatened by a greater number of non-climatic threats than species not threatened by climate change. Our results show that species threatened by climate change are generally impacted by 21% more non-climatic threats than species not threatened by climate change. Across all species, this pattern is related to IUCN risk status, where endangered species threatened by climate change face 33% more non-climatic threats than endangered species not threatened by climate change. With the clear challenges of assessing current and projected impacts of climate change on species and ecosystems, research often requires reductionist approaches that result in downplaying this multi-threat context. This cautionary note bears relevance beyond climate change threatened species as we also

  4. Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation

    Science.gov (United States)

    Freeman, Mary C.; Hagler, Megan M.; Bumpers, Phillip M.; Wheeler, Kit; Wengerd, Seth J.; Freeman, Byron J.

    2017-01-01

    Free-flowing river segments provide refuges for many imperiled aquatic biota that have been extirpated elsewhere in their native ranges. These biodiversity refuges are also foci of conservation concerns because species persisting within isolated habitat fragments may be particularly vulnerable to local environmental change. We have analyzed long-term (14- and 20-y) survey data to assess evidence of fish species declines in two southeastern U.S. rivers where managers and stakeholders have identified potentially detrimental impacts of current and future land uses. The Conasauga River (Georgia and Tennessee) and the Etowah River (Georgia) form free-flowing headwaters of the extensively dammed Coosa River system. These rivers are valued in part because they harbor multiple species of conservation concern, including three federally endangered and two federally threatened fishes. We used data sets comprising annual surveys for fish species at multiple, fixed sites located at river shoals to analyze occupancy dynamics and temporal changes in species richness. Our analyses incorporated repeated site-specific surveys in some years to estimate and account for incomplete species detection, and test for species-specific (rarity, mainstem-restriction) and year-specific (elevated frequencies of low- or high-flow days) covariates on occupancy dynamics. In the Conasauga River, analysis of 26 species at 13 sites showed evidence of temporal declines in colonization rates for nearly all taxa, accompanied by declining species richness. Four taxa (including one federally endangered species) had reduced occupancy across the Conasauga study sites, with three of these taxa apparently absent for at least the last 5 y of the study. In contrast, a similar fauna of 28 taxa at 10 sites in the Etowah River showed no trends in species persistence, colonization, or occupancy. None of the tested covariates showed strong effects on persistence or colonization rates in either river. Previous studies

  5. Uncertainty of future projections of species distributions in mountainous regions.

    Directory of Open Access Journals (Sweden)

    Ying Tang

    Full Text Available Multiple factors introduce uncertainty into projections of species distributions under climate change. The uncertainty introduced by the choice of baseline climate information used to calibrate a species distribution model and to downscale global climate model (GCM simulations to a finer spatial resolution is a particular concern for mountainous regions, as the spatial resolution of climate observing networks is often insufficient to detect the steep climatic gradients in these areas. Using the maximum entropy (MaxEnt modeling framework together with occurrence data on 21 understory bamboo species distributed across the mountainous geographic range of the Giant Panda, we examined the differences in projected species distributions obtained from two contrasting sources of baseline climate information, one derived from spatial interpolation of coarse-scale station observations and the other derived from fine-spatial resolution satellite measurements. For each bamboo species, the MaxEnt model was calibrated separately for the two datasets and applied to 17 GCM simulations downscaled using the delta method. Greater differences in the projected spatial distributions of the bamboo species were observed for the models calibrated using the different baseline datasets than between the different downscaled GCM simulations for the same calibration. In terms of the projected future climatically-suitable area by species, quantification using a multi-factor analysis of variance suggested that the sum of the variance explained by the baseline climate dataset used for model calibration and the interaction between the baseline climate data and the GCM simulation via downscaling accounted for, on average, 40% of the total variation among the future projections. Our analyses illustrate that the combined use of gridded datasets developed from station observations and satellite measurements can help estimate the uncertainty introduced by the choice of baseline

  6. mEBT: multiple-matching Evidence-based Translator of Murine Genomic Responses for Human Immunity Studies.

    Science.gov (United States)

    Tae, Donghyun; Seok, Junhee

    2018-05-29

    In this paper, we introduce multiple-matching Evidence-based Translator (mEBT) to discover genomic responses from murine expression data for human immune studies, which are significant in the given condition of mice and likely have similar responses in the corresponding condition of human. mEBT is evaluated over multiple data sets and shows improved inter-species agreement. mEBT is expected to be useful for research groups who use murine models to study human immunity. http://cdal.korea.ac.kr/mebt/. jseok14@korea.ac.kr. Supplementary data are available at Bioinformatics online.

  7. Unraveling the drivers of community dissimilarity and species extinction in fragmented landscapes.

    Science.gov (United States)

    Banks-Leite, Cristina; Ewers, Robert M; Metzger, Jean Paul

    2012-12-01

    Communities in fragmented landscapes are often assumed to be structured by species extinction due to habitat loss, which has led to extensive use of the species-area relationship (SAR) in fragmentation studies. However, the use of the SAR presupposes that habitat loss leads species to extinction but does not allow for extinction to be offset by colonization of disturbed-habitat specialists. Moreover, the use of SAR assumes that species richness is a good proxy of community changes in fragmented landscapes. Here, we assessed how communities dwelling in fragmented landscapes are influenced by habitat loss at multiple scales; then we estimated the ability of models ruled by SAR and by species turnover in successfully predicting changes in community composition, and asked whether species richness is indeed an informative community metric. To address these issues, we used a data set consisting of 140 bird species sampled in 65 patches, from six landscapes with different proportions of forest cover in the Atlantic Forest of Brazil. We compared empirical patterns against simulations of over 8 million communities structured by different magnitudes of the power-law SAR and with species-specific rules to assign species to sites. Empirical results showed that, while bird community composition was strongly influenced by habitat loss at the patch and landscape scale, species richness remained largely unaffected. Modeling results revealed that the compositional changes observed in the Atlantic Forest bird metacommunity were only matched by models with either unrealistic magnitudes of the SAR or by models ruled by species turnover, akin to what would be observed along natural gradients. We show that, in the presence of such compositional turnover, species richness is poorly correlated with species extinction, and z values of the SAR strongly underestimate the effects of habitat loss. We suggest that the observed compositional changes are driven by each species reaching its

  8. GeMprospector--online design of cross-species genetic marker candidates in legumes and grasses.

    Science.gov (United States)

    Fredslund, Jakob; Madsen, Lene H; Hougaard, Birgit K; Sandal, Niels; Stougaard, Jens; Bertioli, David; Schauser, Leif

    2006-07-01

    The web program GeMprospector (URL: http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main) allows users to automatically design large sets of cross-species genetic marker candidates targeting either legumes or grasses. The user uploads a collection of ESTs from one or more legume or grass species, and they are compared with a database of clusters of homologous EST and genomic sequences from other legumes or grasses, respectively. Multiple sequence alignments between submitted ESTs and their homologues in the appropriate database form the basis of automated PCR primer design in conserved exons such that each primer set amplifies an intron. The only user input is a collection of ESTs, not necessarily from more than one species, and GeMprospector can boost the potential of such an EST collection by combining it with a large database to produce cross-species genetic marker candidates for legumes or grasses.

  9. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

    Science.gov (United States)

    Allman, Elizabeth S; Degnan, James H; Rhodes, John A

    2011-06-01

    Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

  10. Identification of Ganglioside GM3 Molecular Species in Human Serum Associated with Risk Factors of Metabolic Syndrome.

    Directory of Open Access Journals (Sweden)

    Lucas Veillon

    Full Text Available Serum GM3 molecular species were quantified in 125 Japanese residents using tandem mass spectrometry multiple reaction monitoring. Individuals were categorized by the presence or absence of metabolic disease risk factors including visceral fat accumulation, hyperglycemia and dyslipidemia. A total of 23 GM3 molecular species were measured, of these, eight were found to be significantly elevated in individuals with visceral fat accumulation and metabolic disease, defined as the presence of hyperglycemia and dyslipidemia. All of the GM3 molecular species were composed of the sphingoid base sphingosine (d18:1 (Δ4 and, interestingly, six of the eight elevated GM3 molecular species contained a hydroxylated ceramide moiety. The hydroxylated GM3 species were, in order of decreasing abundance, d18:1-h24:0 ≈ d18:1-h24:1 > d18:1-h22:0 » d18:1-h20:0 > d18:1-h21:0 > d18:1-h18:1. Univariate and multiple linear regression analyses were conducted using a number of clinical health variables associated with obesity, type 2 diabetes, metabolic disease, atherosclerosis and hypertension. GM3(d18:1-h24:1 was identified as the best candidate for metabolic screening, proving to be significantly correlated with intima-media thickness, used for the detection of atherosclerotic disease in humans, and a number of metabolic disease risk factors including autotaxin, LDL-c and homeostatic model assessment insulin resistance (HOMA-IR.

  11. Functional interaction between type III-secreted protein IncA of Chlamydophila psittaci and human G3BP1.

    Science.gov (United States)

    Borth, Nicole; Litsche, Katrin; Franke, Claudia; Sachse, Konrad; Saluz, Hans Peter; Hänel, Frank

    2011-01-31

    Chlamydophila (Cp.) psittaci, the causative agent of psittacosis in birds and humans, is the most important zoonotic pathogen of the family Chlamydiaceae. These obligate intracellular bacteria are distinguished by a unique biphasic developmental cycle, which includes proliferation in a membrane-bound compartment termed inclusion. All Chlamydiaceae spp. possess a coding capacity for core components of a Type III secretion apparatus, which mediates specific delivery of anti-host effector proteins either into the chlamydial inclusion membrane or into the cytoplasm of target eukaryotic cells. Here we describe the interaction between Type III-secreted protein IncA of Cp. psittaci and host protein G3BP1 in a yeast two-hybrid system. In GST-pull down and co-immunoprecipitation experiments both in vitro and in vivo interaction between full-length IncA and G3BP1 were shown. Using fluorescence microscopy, the localization of G3BP1 near the inclusion membrane of Cp. psittaci-infected Hep-2 cells was demonstrated. Notably, infection of Hep-2 cells with Cp. psittaci and overexpression of IncA in HEK293 cells led to a decrease in c-Myc protein concentration. This effect could be ascribed to the interaction between IncA and G3BP1 since overexpression of an IncA mutant construct disabled to interact with G3BP1 failed to reduce c-Myc concentration. We hypothesize that lowering the host cell c-Myc protein concentration may be part of a strategy employed by Cp. psittaci to avoid apoptosis and scale down host cell proliferation.

  12. The Evolutionary History Of The White-Rayed Species Of Melampodium (Asteraceae) Involved Multiple Cycles Of Hybridization And Polyploidization1

    Science.gov (United States)

    Rebernig, Carolin A.; Weiss-Schneeweiss, Hanna; Blöch, Cordula; Turner, Barbara; Stuessy, Tod F.; Obermayer, Renate; Villaseñor, Jose L.; Schneeweiss, Gerald M.

    2014-01-01

    Premise of the study Polyploidy plays an important role in race differentiation and eventually speciation. Underlying mechanisms include chromosomal and genomic changes facilitating reproductive isolation and/or stabilization of hybrids. A prerequisite for studying these processes is a sound knowledge on the origin of polyploids. A well-suited group for studying polyploid evolution consists of the three species of Melampodium ser. Leucantha (Asteraceae): M. argophyllum, M. cinereum, and M. leucanthum. Methods The origin of polyploids was inferred using network and tree-based phylogenetic analyses of several plastid and nuclear DNA sequences and of fingerprint data (AFLP). Genome evolution was assessed via genome size measurements, karyotype analysis, and in situ hybridization of ribosomal DNA. Key results Tetraploid cytotypes of the phylogenetically distinct M. cinereum and M. leucanthum had, compared to the diploid cytotypes, doubled genome sizes and no evidence of gross chromosomal rearrangements. Hexaploid M. argophyllum constituted a separate lineage with limited intermixing with the other species, except in analyses from nuclear ITS. Its genome size was lower than expected if M. cinereum and/or M. leucanthum were involved in its origin, and no chromosomal rearrangements were evident. Conclusions Polyploids in M. cinereum and M. leucanthum are of recent autopolyploid origin in line with the lack of significant genomic changes. Hexaploid M. argophyllum also appears to be of autopolyploid origin against the previous hypothesis of an allopolyploid origin involving the other two species, but some gene flow with the other species in early phases of differentiation cannot be excluded. PMID:22645096

  13. Personal Moral Norms and Attitudes Toward Endangered Species Policies on Private Land

    Directory of Open Access Journals (Sweden)

    Leigh Raymond

    2014-01-01

    Full Text Available Research across multiple disciplines has shown that personal moral norms can play an important role in shaping individuals′ attitudes and behaviour. Despite this, we know relatively little about patterns of support among landowners for either a personal moral norm favouring a strong, ′intrinsic′ right of private ownership, or a moral duty to prevent extinction. In addition, we know even less about the ability of such norms to predict attitudes toward species protection on private lands, especially for non-charismatic species with few qualities that typically generate positive attitudes for conservation. Results from a mail survey of central Indiana landowners suggest broad support for a personal moral norm favouring a strong, ′intrinsic′ right of ownership as well as a personal moral norm to prevent extinction, and that these norms are better predictors of attitudes toward endangered species policies than partisan identification, identification as an environmentalist, strong religious beliefs, or several other demographic factors. The results suggest that those seeking to influence landowner attitudes toward species protection policies should pay closer attention to the influence of these personal moral norms.

  14. Multilocus sequence typing (MLST methods for the emerging Campylobacter species C. hyointestinalis, C. lanienae, C. sputorum, C. concisus and C. curvus

    Directory of Open Access Journals (Sweden)

    William G Miller

    2012-04-01

    Full Text Available Multilocus sequence typing (MLST systems have been reported previously for multiple food- and food animal-associated Campylobacter species (e.g. C. jejuni, C. coli, C. lari and C. fetus to both differentiate strains and identify clonal lineages. These MLST methods focused primarily on campylobacters of human clinical (e.g. C. jejuni or veterinary (e.g. C. fetus relevance. However, other, emerging, Campylobacter species have been isolated increasingly from environmental, food animal or human clinical samples. We describe herein MLST methods for five emerging Campylobacter species: C. hyointestinalis, C. lanienae, C. sputorum, C. concisus and C. curvus. The concisus/curvus method uses the loci aspA, atpA, glnA, gltA, glyA, ilvD and pgm, whereas the other methods use the seven loci defined for C. jejuni (i.e., aspA, atpA, glnA, gltA, glyA, pgm, and tkt. Multiple food animal and human clinical C. hyointestinalis (n=48, C. lanienae (n=34 and C. sputorum (n=24 isolates were typed, along with 86 human clinical C. concisus and C. curvus isolates. A large number of sequence types (STs were identified using all four MLST methods. Similar to Campylobacter MLST methods described previously, these novel MLST methods identified mixed isolates containing two or more strains of the same species. Additionally, these methods speciated unequivocally isolates that had been typed ambiguously using other molecular-based speciation methods, such as 16S rDNA sequencing. Finally, the design of degenerate primer pairs for some methods permitted the typing of related species; for example, the C. hyointestinalis primer pairs could be used to type C. fetus strains. Therefore, these novel Campylobacter MLST methods will prove useful in speciating and differentiating strains of multiple, emerging Campylobacter species.

  15. High congruence of isotope sewage signals in multiple marine taxa

    International Nuclear Information System (INIS)

    Connolly, Rod M.; Gorman, Daniel; Hindell, Jeremy S.; Kildea, Timothy N.; Schlacher, Thomas A.

    2013-01-01

    Highlights: • Sewage inputs are routinely mapped with stable isotopes ( 15 N) in organisms. • We tested whether choice of species influences spatial 15 N distributions. • Spatial gradients were consistent between algae, seagrasses, crabs, and fish. • A match of sewage-N signals in multiple marine taxa has not been reported before. • Spatially-coupled transfers in the food web produce the congruence of N imprints. -- Abstract: Assessments of sewage pollution routinely employ stable nitrogen isotope analysis (δ 15 N) in biota, but multiple taxa are rarely used. This single species focus leads to underreporting of whether derived spatial N patterns are consistent. Here we test the question of ‘reproducibility’, incorporating ‘taxonomic replication’ in the measurement of δ 15 N gradients in algae, seagrasses, crabs and fish with distance from a sewage outfall on the Adelaide coast (southern Australia). Isotopic sewage signals were equally strong in all taxa and declined at the same rate. This congruence amongst taxa has not been reported previously. It implies that sewage-N propagates to fish via a tight spatial coupling between production and consumption processes, resulting from limited animal movement that closely preserves the spatial pollution imprint. In situations such as this where consumers mirror pollution signals of primary producers, analyses of higher trophic levels will capture a broader ambit of ecological effects

  16. The NASA Ames PAH IR Spectroscopic Database: Computational Version 3.00 with Updated Content and the Introduction of Multiple Scaling Factors

    Science.gov (United States)

    Bauschlicher, Charles W., Jr.; Ricca, A.; Boersma, C.; Allamandola, L. J.

    2018-02-01

    Version 3.00 of the library of computed spectra in the NASA Ames PAH IR Spectroscopic Database (PAHdb) is described. Version 3.00 introduces the use of multiple scale factors, instead of the single scaling factor used previously, to align the theoretical harmonic frequencies with the experimental fundamentals. The use of multiple scale factors permits the use of a variety of basis sets; this allows new PAH species to be included in the database, such as those containing oxygen, and yields an improved treatment of strained species and those containing nitrogen. In addition, the computed spectra of 2439 new PAH species have been added. The impact of these changes on the analysis of an astronomical spectrum through database-fitting is considered and compared with a fit using Version 2.00 of the library of computed spectra. Finally, astronomical constraints are defined for the PAH spectral libraries in PAHdb.

  17. Phylogenetic disassembly of species boundaries in a widespread group of Australian skinks (Scincidae: Ctenotus).

    Science.gov (United States)

    Rabosky, Daniel L; Hutchinson, Mark N; Donnellan, Stephen C; Talaba, Amanda L; Lovette, Irby J

    2014-08-01

    Scincid lizards in the genus Ctenotus represent one of Australia's most species-rich vertebrate clades, with more than 100 recognized species. Formal diagnoses of many species have relied on qualitative assessments of adult color pattern, but the validity of many such species has not been tested in a phylogenetic framework. We used mitochondrial and nuclear DNA to perform the first phylogenetic analysis of species in the Ctenotus inornatus group, a complex of at least 11 nominal forms that are distributed widely across the Australian continent. Mitochondrial and nuclear gene phylogenies support the presence of multiple species in the group, but these clades largely fail to match species boundaries as currently defined. Multivariate analyses of color pattern indicate that extreme intraspecific morphological variation in this character has created a significant impediment to understanding taxonomic diversity in the group. Our results suggest that nearly all species in the C. inornatus group require substantial taxonomic revision, and several geographically widespread forms ("C. saxatilis" and "C. robustus") appear to be polyphyletic taxa drawn from phenotypically similar but genetically distinct lineages. We describe one new species and provide redescriptions for three additional species. We synonymize names applied to a number of genetically incoherent or otherwise poorly-defined forms. The results of our study highlight an acute need for population genetic studies of species boundaries in Australian skinks, many of which are recognized by morphological traits that vary greatly within and between populations. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Effects of urbanization on carnivore species distribution and richness

    Science.gov (United States)

    Ordenana, Miguel A.; Crooks, Kevin R.; Boydston, Erin E.; Fisher, Robert N.; Lyren, Lisa M.; Siudyla, Shalene; Haas, Christopher D.; Harris, Sierra; Hathaway, Stacie A.; Turschak, Greta M.; Miles, A. Keith; Van Vuren, Dirk H.

    2010-01-01

    Urban development can have multiple effects on mammalian carnivore communities. We conducted a meta-analysis of 7,929 photographs from 217 localities in 11 camera-trap studies across coastal southern California to describe habitat use and determine the effects of urban proximity (distance to urban edge) and intensity (percentage of area urbanized) on carnivore occurrence and species richness in natural habitats close to the urban boundary. Coyotes (Canis latrans) and bobcats (Lynx rufus) were distributed widely across the region. Domestic dogs (Canis lupus familiaris), striped skunks (Mephitis mephitis), raccoons (Procyon lotor), gray foxes (Urocyon cinereoargenteus), mountain lions (Puma concolor), and Virginia opossums (Didelphis virginiana) were detected less frequently, and long-tailed weasels (Mustela frenata), American badgers (Taxidea taxus), western spotted skunks (Spilogale gracilis), and domestic cats (Felis catus) were detected rarely. Habitat use generally reflected availability for most species. Coyote and raccoon occurrence increased with both proximity to and intensity of urbanization, whereas bobcat, gray fox, and mountain lion occurrence decreased with urban proximity and intensity. Domestic dogs and Virginia opossums exhibited positive and weak negative relationships, respectively, with urban intensity but were unaffected by urban proximity. Striped skunk occurrence increased with urban proximity but decreased with urban intensity. Native species richness was negatively associated with urban intensity but not urban proximity, probably because of the stronger negative response of individual species to urban intensity.

  19. Intra-specific downsizing of frugivores affects seed germination of fleshy-fruited plant species

    Science.gov (United States)

    Pérez-Méndez, Néstor; Rodríguez, Airam; Nogales, Manuel

    2018-01-01

    The loss of largest-bodied individuals within species of frugivorous animals is one of the major consequences of defaunation. The gradual disappearance of large-bodied frugivores is expected to entail a parallel deterioration in seed dispersal functionality if the remaining smaller-sized individuals are not so effective as seed dispersers. While the multiple impacts of the extinction of large bodied species have been relatively well studied, the impact of intraspecific downsizing (i.e. the extinction of large individuals within species) on seed dispersal has rarely been evaluated. Here we experimentally assessed the impact of body-size reduction in the frugivorous lizard Gallotia galloti (Lacertidae), an endemic species of the Canary Islands, on the seed germination patterns of two fleshy-fruited plant species (Rubia fruticosa and Withania aristata). Seed germination curves and the proportions of germinated seeds were compared for both plant species after being defecated by large-sized individuals and small-sized individuals. The data show that seeds of W. aristata defecated by larger-sized lizards germinated faster and in a higher percentage than those defecated by small-sized lizards, while no differences were found for R. fruticosa seeds. Our results suggest that disappearance of the largest individuals of frugivorous species may impair recruitment of some plant species by worsening seed germination. They also warn us of a potential cryptic loss of seed dispersal functionality on defaunated ecosystems, even when frugivorous species remain abundant.

  20. Gastric Volvulus in Guinea Pigs: Comparison with Other Species

    OpenAIRE

    Dudley, Emily S; Boivin, Gregory P

    2011-01-01

    Gastric volvulus has been documented in several species of animals and is associated with high morbidity and mortality. We report 2 cases of gastric volvulus in guinea pigs that died without detection of prior clinical signs. Both guinea pigs were adult female guinea pigs in a breeding colony and had given birth to multiple litters; one was pregnant at the time of death. Gastric rotations of 540° and 360° were identified at necropsy examination. These cases include the first known report of g...

  1. Species richness in soil bacterial communities: a proposed approach to overcome sample size bias.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2008-09-01

    Estimates of species richness based on 16S rRNA gene clone libraries are increasingly utilized to gauge the level of bacterial diversity within various ecosystems. However, previous studies have indicated that regardless of the utilized approach, species richness estimates obtained are dependent on the size of the analyzed clone libraries. We here propose an approach to overcome sample size bias in species richness estimates in complex microbial communities. Parametric (Maximum likelihood-based and rarefaction curve-based) and non-parametric approaches were used to estimate species richness in a library of 13,001 near full-length 16S rRNA clones derived from soil, as well as in multiple subsets of the original library. Species richness estimates obtained increased with the increase in library size. To obtain a sample size-unbiased estimate of species richness, we calculated the theoretical clone library sizes required to encounter the estimated species richness at various clone library sizes, used curve fitting to determine the theoretical clone library size required to encounter the "true" species richness, and subsequently determined the corresponding sample size-unbiased species richness value. Using this approach, sample size-unbiased estimates of 17,230, 15,571, and 33,912 were obtained for the ML-based, rarefaction curve-based, and ACE-1 estimators, respectively, compared to bias-uncorrected values of 15,009, 11,913, and 20,909.

  2. Multi-species genetic connectivity in a terrestrial habitat network.

    Science.gov (United States)

    Marrotte, Robby R; Bowman, Jeff; Brown, Michael G C; Cordes, Chad; Morris, Kimberley Y; Prentice, Melanie B; Wilson, Paul J

    2017-01-01

    Habitat fragmentation reduces genetic connectivity for multiple species, yet conservation efforts tend to rely heavily on single-species connectivity estimates to inform land-use planning. Such conservation activities may benefit from multi-species connectivity estimates, which provide a simple and practical means to mitigate the effects of habitat fragmentation for a larger number of species. To test the validity of a multi-species connectivity model, we used neutral microsatellite genetic datasets of Canada lynx ( Lynx canadensis ), American marten ( Martes americana ), fisher ( Pekania pennanti ), and southern flying squirrel ( Glaucomys volans ) to evaluate multi-species genetic connectivity across Ontario, Canada. We used linear models to compare node-based estimates of genetic connectivity for each species to point-based estimates of landscape connectivity (current density) derived from circuit theory. To our knowledge, we are the first to evaluate current density as a measure of genetic connectivity. Our results depended on landscape context: habitat amount was more important than current density in explaining multi-species genetic connectivity in the northern part of our study area, where habitat was abundant and fragmentation was low. In the south however, where fragmentation was prevalent, genetic connectivity was correlated with current density. Contrary to our expectations however, locations with a high probability of movement as reflected by high current density were negatively associated with gene flow. Subsequent analyses of circuit theory outputs showed that high current density was also associated with high effective resistance, underscoring that the presence of pinch points is not necessarily indicative of gene flow. Overall, our study appears to provide support for the hypothesis that landscape pattern is important when habitat amount is low. We also conclude that while current density is proportional to the probability of movement per unit area

  3. Antifungal Susceptibilities of Candida Species Causing Vulvovaginitis and Epidemiology of Recurrent Cases

    Science.gov (United States)

    Richter, Sandra S.; Galask, Rudolph P.; Messer, Shawn A.; Hollis, Richard J.; Diekema, Daniel J.; Pfaller, Michael A.

    2005-01-01

    There are limited data regarding the antifungal susceptibility of yeast causing vulvovaginal candidiasis, since cultures are rarely performed. Susceptibility testing was performed on vaginal yeast isolates collected from January 1998 to March 2001 from 429 patients with suspected vulvovaginal candidiasis. The charts of 84 patients with multiple positive cultures were reviewed. The 593 yeast isolates were Candida albicans (n = 420), Candida glabrata (n = 112), Candida parapsilosis (n = 30), Candida krusei (n = 12), Saccharomyces cerevisiae ( n = 9), Candida tropicalis (n = 8), Candida lusitaniae (n = 1), and Trichosporon sp. (n = 1). Multiple species suggesting mixed infection were isolated from 27 cultures. Resistance to fluconazole and flucytosine was observed infrequently (3.7% and 3.0%); 16.2% of isolates were resistant to itraconazole (MIC ≥ 1 μg/ml). The four imidazoles (econazole, clotrimazole, miconazole, and ketoconazole) were active: 94.3 to 98.5% were susceptible at ≤1 μg/ml. Among different species, elevated fluconazole MICs (≥16 μg/ml) were only observed in C. glabrata (15.2% resistant [R], 51.8% susceptible-dose dependent [S-DD]), C. parapsilosis (3.3% S-DD), S. cerevisiae (11.1% S-DD), and C. krusei (50% S-DD, 41.7% R, considered intrinsically fluconazole resistant). Resistance to itraconazole was observed among C. glabrata (74.1%), C. krusei (58.3%), S. cerevisiae (55.6%), and C. parapsilosis (3.4%). Among 84 patients with recurrent episodes, non-albicans species were more common (42% versus 20%). A ≥4-fold rise in fluconazole MIC was observed in only one patient with C. parapsilosis. These results support the use of azoles for empirical therapy of uncomplicated candidal vulvovaginitis. Recurrent episodes are more often caused by non-albicans species, for which azole agents are less likely to be effective. PMID:15872235

  4. Many Species, Many Threats: A Composite Risk Assessment of Climate Impacts for Salmonids in the Pacific Northwest

    Science.gov (United States)

    Graham, M. C.; Greene, C.; Beechie, T. J.; Raymond, C.

    2016-02-01

    The life cycles of salmonid species span freshwater, estuarine, and marine environments, exposing these economically, ecologically, and culturally important species to a wide variety of climate change threats. The diverse life histories of salmonids make them differentially vulnerable to climate change based on their use of different habitat types and the variability in climate change threats across these habitat types. Previous studies have focused mainly on assessing the vulnerability of particular life stages for a few species. Hence, we lack a broad perspective on how multiple climate threats are expected to impact the entire salmonid community, which spend much of their lives in marine waters. This lack of knowledge hampers our ability to prioritize various adaptation strategies for salmonid conservation. In order to conduct a more extensive vulnerability study of salmonids, we performed a life cycle-based risk assessment of climate change threats for nine species of salmonids (species within Oncorhynchus, Salvelinus, and Prosopium genera) inhabiting the Skagit River watershed, which is subject to an array of climate impacts. Our risk assessment integrated projections of impacts from various climate threats in freshwater, estuarine, and marine ecosystems with expert-based assessments of species-specific sensitivity and exposure. We found that projections (multiple global climate models under moderate emission scenarios) of both changes in magnitude and frequency of three flow-related freshwater impacts (flooding, low flows, and suspended sediment pulses) were more severe than threats in estuarine and marine habitats for which we could obtain projections. Combining projections with expert-based sensitivity and exposure scores revealed that these three threats exhibited the highest risk across all species. Of the nine species, the four most vulnerable were Chinook and coho salmon, steelhead, and bull trout. Even though these salmonids spend much of their lives

  5. Ureaplasma Species Multiple Banded Antigen (MBA) Variation Is Associated with the Severity of Inflammation In vivo and In vitro in Human Placentae.

    Science.gov (United States)

    Sweeney, Emma L; Kallapur, Suhas G; Meawad, Simone; Gisslen, Tate; Stephenson, Sally-Anne; Jobe, Alan H; Knox, Christine L

    2017-01-01

    Background: The multiple banded antigen (MBA), a surface-exposed lipoprotein, is a proposed virulence factor of Ureaplasma spp. We previously demonstrated that the number of Ureaplasma parvum MBA size variants in amniotic fluid was inversely proportional to the severity of chorioamnionitis in experimentally infected pregnant sheep. However, the effect of ureaplasma MBA size variation on inflammation in human pregnancies has not been reported. Methods: Ureaplasmas isolated from the chorioamnion of pregnant women from a previous study ( n = 42) were speciated/serotyped and MBA size variation was demonstrated by PCR and western blot. Results were correlated with the severity of chorioamnionitis and cord blood cytokines. In vitro , THP-1-derived macrophages were exposed to recombinant-MBA proteins of differing sizes and NF-κB activation and cytokine responses were determined. Results: MBA size variation was identified in 21/32 (65.6%) clinical isolates (in 10 clinical isolates MBA size variation was unable to be determined). Any size variation (increase/decrease) of the MBA (regardless of Ureaplasma species or serovar) was associated with mild or absent chorioamnionitis ( P = 0.023) and lower concentrations of cord blood cytokines IL-8 ( P = 0.04) and G-CSF ( P = 0.008). In vitro , recombinant-MBA variants elicited different cytokine responses and altered expression of NF-κB p65. Conclusion: This study demonstrates that size variation of the ureaplasma MBA protein modulates the host immune response in vivo and in vitro .

  6. Identification and characterization of multiple conserved nuclear localization signals within adenovirus E1A

    Energy Technology Data Exchange (ETDEWEB)

    Marshall, Kris S.; Cohen, Michael J.; Fonseca, Greg J.; Todorovic, Biljana; King, Cason R. [Department of Microbiology and Immunology, Western University, London Regional Cancer Program, London, ON, Canada N6A 4L6 (Canada); Yousef, Ahmed F. [Department of Chemical and Environmental Engineering, Masdar Institute, Abu Dhabi (United Arab Emirates); Zhang, Zhiying [College of Animal Science and Technologies, Northwest A and F University, Yangling, Shaanxi 712100 (China); Mymryk, Joe S., E-mail: jmymryk@uwo.ca [Department of Microbiology and Immunology, Western University, London Regional Cancer Program, London, ON, Canada N6A 4L6 (Canada); Department of Oncology, Western University, London Regional Cancer Program, London, ON, Canada N6A 4L6 (Canada)

    2014-04-15

    The human adenovirus 5 (HAdV-5) E1A protein has a well defined canonical nuclear localization signal (NLS) located at its C-terminus. We used a genetic assay in the yeast Saccharomyces cerevisiae to demonstrate that the canonical NLS is present and functional in the E1A proteins of each of the six HAdV species. This assay also detects a previously described non-canonical NLS within conserved region 3 and a novel active NLS within the N-terminal/conserved region 1 portion of HAdV-5 E1A. These activities were also present in the E1A proteins of each of the other five HAdV species. These results demonstrate that, despite substantial differences in primary sequence, HAdV E1A proteins are remarkably consistent in that they contain one canonical and two non-canonical NLSs. By utilizing independent mechanisms, these multiple NLSs ensure nuclear localization of E1A in the infected cell. - Highlights: • HAdV E1A uses multiple mechanisms for nuclear import. • We identified an additional non-canonical NLS in the N-terminal/CR1 portion of E1A. • The new NLS does not contact importin-alpha directly. • All NLSs are functionally conserved in the E1A proteins of all 6 HAdV species.

  7. The nuclear question: rethinking species importance in multi-species animal groups.

    Science.gov (United States)

    Srinivasan, Umesh; Raza, Rashid Hasnain; Quader, Suhel

    2010-09-01

    1. Animals group for various benefits, and may form either simple single-species groups, or more complex multi-species associations. Multi-species groups are thought to provide anti-predator and foraging benefits to participant individuals. 2. Despite detailed studies on multi-species animal groups, the importance of species in group initiation and maintenance is still rated qualitatively as 'nuclear' (maintaining groups) or 'attendant' (species following nuclear species) based on species-specific traits. This overly simplifies and limits understanding of inherently complex associations, and is biologically unrealistic, because species roles in multi-species groups are: (i) likely to be context-specific and not simply a fixed species property, and (ii) much more variable than this dichotomy indicates. 3. We propose a new view of species importance (measured as number of inter-species associations), along a continuum from 'most nuclear' to 'least nuclear'. Using mixed-species bird flocks from a tropical rainforest in India as an example, we derive inter-species association measures from randomizations on bird species abundance data (which takes into account species 'availability') and data on 86 mixed-species flocks from two different flock types. Our results show that the number and average strength of inter-species associations covary positively, and we argue that species with many, strong associations are the most nuclear. 4. From our data, group size and foraging method are ecological and behavioural traits of species that best explain nuclearity in mixed-species bird flocks. Parallels have been observed in multi-species fish shoals, in which group size and foraging method, as well as diet, have been shown to correlate with nuclearity. Further, the context in which multi-species groups occur, in conjunction with species-specific traits, influences the role played by a species in a multi-species group, and this highlights the importance of extrinsic factors in

  8. Who's My Daddy? Considerations for the influence of sexual selection on multiple paternity in elasmobranch mating systems.

    Science.gov (United States)

    Lyons, Kady; Chabot, Chris L; Mull, Christopher G; Paterson Holder, Corinne N; Lowe, Christopher G

    2017-08-01

    Polyandry resulting in multiply-sired litters has been documented in the majority of elasmobranch species examined to date. Although commonly observed, reasons for this mating system remain relatively obscure, especially in batoids. The round stingray ( Urobatis halleri ) is an abundant, well-studied elasmobranch distributed throughout the northeastern Pacific that we used to explore hypotheses regarding multiple paternity in elasmobranchs. Twenty mid- to late-term pregnant females were sampled off the coast of southern California and their litters analyzed for the occurrence of multiple paternity using five nuclear microsatellite loci. In addition, embryo sizes and their position within the female reproductive system (i.e., right or left uterus) were recorded and used to make inferences for patterns of ovulation. Multiple paternity was observed in 90% of litters and male reproductive success within litters was relatively even among sires. High variability in testes mass was observed suggesting that sperm competition is high in this species, although male reproductive success per litter appeared to be relatively even. Using embryo size as a proxy for fertilization, females were found to exhibit a variety of ovulation patterns that could function to limit a male's access to eggs and possibly promote high rates of multiple paternity. Our study highlights that elasmobranch mating systems may be more varied and complex than presumed and further investigation is warranted.

  9. Reexamination of the species assignment of Diacavolinia pteropods using DNA barcoding.

    Directory of Open Access Journals (Sweden)

    Amy E Maas

    Full Text Available Thecosome pteropods (Mollusca, Gastropoda are an ecologically important, diverse, and ubiquitous group of holoplanktonic animals that are the focus of intense research interest due to their external aragonite shell and vulnerability to ocean acidification. Characterizing the response of these animals to low pH and other environmental stressors has been hampered by continued uncertainty in their taxonomic identification. An example of this confusion in species assignment is found in the genus Diacavolinia. All members of this genus were originally indentified as a single species, Cavolinia longirostris, but over the past fifty years the taxonomy has been revisited multiple times; currently the genus comprises 22 different species. This study examines five species of Diacavolinia, including four sampled in the Northeast Atlantic (78 individuals and one from the Eastern tropical North Pacific (15 individuals. Diacavolina were identified to species based on morphological characteristics according to the current taxonomy, photographed, and then used to determine the sequence of the "DNA barcoding" region of the cytochrome c oxidase subunit I (COI. Specimens from the Atlantic, despite distinct differences in shell morphology, showed polyphyly and a genetic divergence of <3% (K2P distance whereas the Pacific and Atlantic samples were more distant (≈ 19%. Comparisons of Diacavolinia spp. with other Cavolinia spp. reveal larger distances (≈ 24%. These results indicate that specimens from the Atlantic comprise a single monophyletic species and suggest possible species-level divergence between Atlantic and Pacific populations. The findings support the maintenance of Diacavolinia as a separate genus, yet emphasize the inadequacy of our current taxonomic understanding of pteropods. They highlight the need for accurate species identifications to support estimates of biodiversity, range extent and natural exposure of these planktonic calcifiers to

  10. Invasions by two non-native insects alter regional forest species composition and successional trajectories

    Science.gov (United States)

    Randall S. Morin; Andrew M. Liebhold

    2015-01-01

    While invasions of individual non-native phytophagous insect species are known to affect growth and mortality of host trees, little is known about how multiple invasions combine to alter forest dynamics over large regions. In this study we integrate geographical data describing historical invasion spread of the hemlock woolly adelgid, Adelges tsugae...

  11. Characterization and multiplexing of EST-SSR primers in Cynodon (Poaceae) species1.

    Science.gov (United States)

    Jewell, Margaret C; Frere, Celine H; Prentis, Peter J; Lambrides, Christopher J; Godwin, Ian D

    2010-10-01

    Cynodon species are multiple-use grasses that display varying levels of adaptation to biotic and abiotic stress. Previously identified EST-SSR primers were characterized and multiplexed to assess the level of genetic diversity present within a collection of almost 1200 Cynodon accessions from across Australia. • Two multiplex reactions were developed comprising a total of 16 EST-SSR markers. All SSR markers amplified across different Cynodon species and different levels of ploidy. The number of alleles ranged from one to eight per locus and the total number of alleles for the germplasm collection was 79. • The 16 markers show sufficient variation for the characterization of Cynodon core collections and analysis of population genetic diversity in Cynodon grasses.

  12. Class 1 integrons and plasmid-mediated multiple resistance genes of the Campylobacter species from pediatric patient of a university hospital in Taiwan.

    Science.gov (United States)

    Chang, Yi-Chih; Tien, Ni; Yang, Jai-Sing; Lu, Chi-Cheng; Tsai, Fuu-Jen; Huang, Tsurng-Juhn; Wang, I-Kuan

    2017-01-01

    The Campylobacter species usually causes infection between humans and livestock interaction via livestock breeding. The studies of the Campylobacter species thus far in all clinical isolates were to show the many kinds of antibiotic phenomenon that were produced. Their integrons cause the induction of antibiotic resistance between bacterial species in the Campylobacter species. The bacterial strains from the diarrhea of pediatric patient which isolated by China Medical University Hospital storage bank. These isolates were identified by MALDI-TOF mass spectrometry. The anti-microbial susceptibility test showed that Campylobacter species resistant to cefepime, streptomycin, tobramycin and trimethoprim/sulfamethoxazole (all C. jejuni and C. coli isolates), ampicillin (89% of C. jejuni ; 75% of C. coli ), cefotaxime (78% of C. jejuni ; 100% of C. coli ), nalidixic acid (78% of C. jejuni ; 100% of C. coli ), tetracycline (89% of C. jejuni ; 25% C. coli ), ciprofloxacin (67% of C. jejuni ; 50% C. coli ), kanamycin (33% of C. jejuni ; 75% C. coli ) and the C. fetus isolate resisted to ampicillin, cefotaxime, nalidixic acid, tetracycline, ciprofloxacin, kanamycin by disc-diffusion method. The effect for ciprofloxacin and tetracycline of the Campylobacter species was tested using an E-test. The tet, erm , and integron genes were detected by PCR assay. According to the sequencing analysis (type I: dfr12 - gcuF - aadA2 genes and type II: dfrA7 gene), the cassette type was identified. The most common gene cassette type (type I: 9 C. jejuni and 2 C. coli isolates; type II: 1 C. coli isolates) was found in 12 class I integrase-positive isolates. Our results suggested an important information in the latency of Campylobacter species with resistance genes, and irrational antimicrobial use should be concerned.

  13. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers

    DEFF Research Database (Denmark)

    Friis-Nielsen, Jens; Kjartansdóttir, Kristín Rós; Mollerup, Sarah

    2016-01-01

    non-template controls, and 24 test samples. Recurrent sequences were statistically associated to biological, methodological or technical features with the aim to identify novel pathogens or plausible contaminants that may associate to a particular kit or method. We provide examples of identified......Virus discovery from high throughput sequencing data often follows a bottom-up approach where taxonomic annotation takes place prior to association to disease. Albeit effective in some cases, the approach fails to detect novel pathogens and remote variants not present in reference databases. We...... have developed a species independent pipeline that utilises sequence clustering for the identification of nucleotide sequences that co-occur across multiple sequencing data instances. We applied the workflow to 686 sequencing libraries from 252 cancer samples of different cancer and tissue types, 32...

  14. Native species that can replace exotic species in landscaping

    Directory of Open Access Journals (Sweden)

    Elisabeth Regina Tempel Stumpf

    2015-08-01

    Full Text Available Beyond aesthetics, the contemporary landscaping intends to provide other benefits for humans and environment, especially related to the environmental quality of urban spaces and conservation of the species. A trend in this direction is the reduction in the use of exotic plants in their designs, since, over time, they can become agents of replacement of native flora, as it has occurred in Rio Grande do Sul with many species introduced by settlers. However, the use of exotic species is unjustifiable, because the flora diversity of the Bioma Pampa offers many native species with appropriate features to the ornamental use. The commercial cultivation and the implantation of native species in landscaped areas constitute innovations for plant nurseries and landscapers and can provide a positive reduction in extractivism, contributing to dissemination, exploitation and preservation of native flora, and also decrease the impact of chemical products on environment. So, this work intends to identify native species of Bioma Pampa with features and uses similar to the most used exotic species at Brazilian landscaping. The species were selected from consulting books about native plants of Bioma Pampa and plants used at Brazilian landscaping, considering the similarity on habit and architecture, as well as characteristics of leafs, flowers and/or fruits and environmental conditions of occurrence and cultivation. There were identified 34 native species able to properly replace exotic species commonly used. The results show that many native species of Bioma Pampa have interesting ornamental features to landscape gardening, allowing them to replace exotic species that are traditionally cultivated.

  15. Inter and intra-guild interactions in egg parasitoid species of the soybean stink bug complex

    Directory of Open Access Journals (Sweden)

    Sujii Edison Ryoiti

    2002-01-01

    Full Text Available The objective of this research was to evaluate the parasitism behavior of Telenomus podisi Ashmead, Trissolcus basalis (Wollaston e Trissolcus urichi Crawford (Hymenoptera: Scelionidae on eggs of Nezara viridula L., Euschistus heros F., Piezodorus guildinii Westwood and Acrosternum aseadum Rolston (Heteroptera: Pentatomidae, in no choice and multiple choice experiments. For all parasitoid species, the results demonstrated the existence of a main host species that maximizes the reproductive success. The competitive interactions among the parasitoid species were investigated in experiments of sequential and simultaneous release of different combinations of parasitoid pairs on the hosts N. viridula, E. heros and A. aseadum. Exploitative competition was observed for egg batches at the genus level (Telenomus vs. Trissolcus and interference competition at the species level (T. basalis vs. T. urichi. Trissolcus urichi was the most aggressive species, interfering with the parasitism of T. basalis. Generally, T. basalis showed an opportunistic behavior trying to parasitise eggs after T. urichi had abandoned the egg batch. The selection of parasitoid species for use in augmentative biological control programs should take into account the diversity of pentatomids present in soybean in addition to the interactions among the different species of parasitoids.

  16. In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

    Directory of Open Access Journals (Sweden)

    Evandro Vagner Tambarussi

    2009-01-01

    Full Text Available The availability of chloroplast genome (cpDNA sequences of Atropa belladonna, Nicotiana sylvestris, N.tabacum, N. tomentosiformis, Solanum bulbocastanum, S. lycopersicum and S. tuberosum, which are Solanaceae species,allowed us to analyze the organization of cpSSRs in their genic and intergenic regions. In general, the number of cpSSRs incpDNA ranged from 161 in S. tuberosum to 226 in N. tabacum, and the number of intergenic cpSSRs was higher than geniccpSSRs. The mononucleotide repeats were the most frequent in studied species, but we also identified di-, tri-, tetra-, pentaandhexanucleotide repeats. Multiple alignments of all cpSSRs sequences from Solanaceae species made the identification ofnucleotide variability possible and the phylogeny was estimated by maximum parsimony. Our study showed that the plastomedatabase can be exploited for phylogenetic analysis and biotechnological approaches.

  17. Metabolic pathway alignment between species using a comprehensive and flexible similarity measure

    Directory of Open Access Journals (Sweden)

    de Ridder Dick

    2008-12-01

    Full Text Available Abstract Background Comparative analysis of metabolic networks in multiple species yields important information on their evolution, and has great practical value in metabolic engineering, human disease analysis, drug design etc. In this work, we aim to systematically search for conserved pathways in two species, quantify their similarities, and focus on the variations between them. Results We present an efficient framework, Metabolic Pathway Alignment and Scoring (M-PAS, for identifying and ranking conserved metabolic pathways. M-PAS aligns all reactions in entire metabolic networks of two species and assembles them into pathways, taking mismatches, gaps and crossovers into account. It uses a comprehensive scoring function, which quantifies pathway similarity such that we can focus on different pathways given different biological motivations. Using M-PAS, we detected 1198 length-four pathways fully conserved between Saccharomyces cerevisiae and Escherichia coli, and also revealed 1399 cases of a species using a unique route in otherwise highly conserved pathways. Conclusion Our method efficiently automates the process of exploring reaction arrangement possibilities, both between species and within species, to find conserved pathways. We not only reconstruct conventional pathways such as those found in KEGG, but also discover new pathway possibilities. Our results can help to generate hypotheses on missing reactions and manifest differences in highly conserved pathways, which is useful for biology and life science applications.

  18. Ribosomal DNA in diploid and polyploid Setaria (Poaceae) species: number and distribution

    Science.gov (United States)

    Nani, Thaís Furtado; Cenzi, Gisele; Pereira, Daniele Lais; Davide, Lisete Chamma; Techio, Vânia Helena

    2015-01-01

    Abstract Setaria Beauvois, 1812 is a genus of economically important forage species, including Setaria italica (Linnaeus, 1753) Beauvois, 1812 and Setaria viridis (Linnaeus, 1753) Beauvois, 1812, closely related species and considered as model systems for studies of C4 plants. However, complications and uncertainties related to taxonomy of other species of the genus are frequent due to the existence of numerous synonyms for the same species or multiple species with the same name, and overlapping of morphological characteristics. Cytogenetic studies in Setaria can be useful for taxonomic and evolutionary studies as well as for applications in breeding. Thus, this study is aimed at locating 45S and 5S rDNA sites through fluorescent in situ hybridization (FISH) in Setaria italica, Setaria viridis and Setaria sphacelata (Schumacher, 1827) Stapf, Hubbard, Moss, 1929 cultivars (cvs.) Narok and Nandi. Setaria italica and Setaria viridis have 18 chromosomes with karyotype formulas 6m + 3sm and 9m, respectively. The location of 45S and 5S rDNA for these species was in different chromosome pairs among the evaluated species. Setaria viridis presented a more symmetrical karyotype, strengthening the ancestral relationship with Setaria italica. Setaria sphacelata cvs. Narok and Nandi have 36 chromosomes, and karyotype formulas 11m+7sm and 16m+2sm, respectively. The 45S rDNA signals for both cultivars were also observed in distinct chromosome pairs; however chromosomes bearing 5S rDNA are conserved. Karyotypic variations found among the studied species are evidence of chromosomal rearrangements. PMID:26753080

  19. Using expert opinion surveys to rank threats to endangered species: a case study with sea turtles.

    Science.gov (United States)

    Donlan, C Josh; Wingfield, Dana K; Crowder, Larry B; Wilcox, Chris

    2010-12-01

    Little is known about how specific anthropogenic hazards affect the biology of organisms. Quantifying the effect of regional hazards is particularly challenging for species such as sea turtles because they are migratory, difficult to study, long lived, and face multiple anthropogenic threats. Expert elicitation, a technique used to synthesize opinions of experts while assessing uncertainty around those views, has been in use for several decades in the social science and risk assessment sectors. We conducted an internet-based survey to quantify expert opinion on the relative magnitude of anthropogenic hazards to sea turtle populations at the regional level. Fisheries bycatch and coastal development were most often ranked as the top hazards to sea turtle species in a geographic region. Nest predation and direct take followed as the second and third greatest threats, respectively. Survey results suggest most experts believe sea turtles are threatened by multiple factors, including substantial at-sea threats such as fisheries bycatch. Resources invested by the sea turtle community, however, appear biased toward terrestrial-based impacts. Results from the survey are useful for conservation planning because they provide estimates of relative impacts of hazards on sea turtles and a measure of consensus on the magnitude of those impacts among researchers and practitioners. Our survey results also revealed patterns of expert bias, which we controlled for in our analysis. Respondents with no experience with respect to a sea turtle species tended to rank hazards affecting that sea turtle species higher than respondents with experience. A more-striking pattern was with hazard-based expertise: the more experience a respondent had with a specific hazard, the higher the respondent scored the impact of that hazard on sea turtle populations. Bias-controlled expert opinion surveys focused on threatened species and their hazards can help guide and expedite species recovery plans.

  20. ConSpeciFix: Classifying prokaryotic species based on gene flow.

    Science.gov (United States)

    Bobay, Louis-Marie; Ellis, Brian Shin-Hua; Ochman, Howard

    2018-05-16

    Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life. ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML. ljbobay@uncg.edu.