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Sample records for species complex reveal

  1. Species delimitation in the Stenocereus griseus (Cactaceae species complex reveals a new species, S. huastecorum.

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    Hernán Alvarado-Sizzo

    Full Text Available The Stenocereus griseus species complex (SGSC has long been considered taxonomically challenging because the number of taxa belonging to the complex and their geographical boundaries remain poorly understood. Bayesian clustering and genetic distance-based methods were used based on nine microsatellite loci in 377 individuals of three main putative species of the complex. The resulting genetic clusters were assessed for ecological niche divergence and areolar morphology, particularly spination patterns. We based our species boundaries on concordance between genetic, ecological, and morphological data, and were able to resolve four species, three of them corresponding to S. pruinosus from central Mexico, S. laevigatus from southern Mexico, and S. griseus from northern South America. A fourth species, previously considered to be S. griseus and commonly misidentified as S. pruinosus in northern Mexico showed significant genetic, ecological, and morphological differentiation suggesting that it should be considered a new species, S. huastecorum, which we describe here. We show that population genetic analyses, ecological niche modeling, and morphological studies are complementary approaches for delimiting species in taxonomically challenging plant groups such as the SGSC.

  2. Cylindrocarpon root rot: multi-gene analysis reveals novel species within the Ilyonectria radicicola species complex

    NARCIS (Netherlands)

    Cabral, A.; Groenewald, J.Z.; Rego, C.; Oliveira, H.; Crous, P.W.

    2012-01-01

    Ilyonectria radicicola and its Cylindrocarpon-like anamorph represent a species complex that is commonly associated with root rot disease symptoms on a range of hosts. During the course of this study, several species could be distinguished from I. radicicola sensu stricto based on morphological and

  3. A spider species complex revealed high cryptic diversity in South China caves.

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    Zhang, Yuanyuan; Li, Shuqiang

    2014-10-01

    Cryptic species, which are an important component of biodiversity, have rarely been studied in South China karst. We investigated cryptic diversity in the cave species complex Telema cucurbitina, which has a narrow niche but widespread distribution among multiple caves. We sampled another 15 populations (caves) in addition to the population from the type locality. Phylogenetic results indicated that individuals from the same cave constituted well-supported clades. Species diversity within this species complex was assessed in a coalescent framework, first with a Bayesian extension of the general mixed Yule coalescent (bGMYC) model and a Bayesian species delimitation method (BPP). Both species delimitation methods identified each cave population as a separate species. We propose that each cave population within this species complex was a separate evolving lineage and therefore 16 OTUs were recovered based on our molecular data despite their high morphological similarities. We also propose that the unrecognized organism's diversity within South China caves might be extremely large considering our case. Furthermore, our work reveals that species discovery of cave organisms by morphological data has a high probability of underestimating hidden diversity. Our work also highlights the need for conservation strategies to protect this largely neglected diversity of cave organisms. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions.

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    Paul De Barro

    Full Text Available BACKGROUND: A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally. METHODOLOGY/PRINCIPAL FINDINGS: Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010. Only two species proposed in Dinsdale et al. (2010 departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED and Middle East - Asia Minor 1 (MEAM1, showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region. CONCLUSION/SIGNIFICANCE: The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of

  5. Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation.

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    Czaban, Adrian; Sharma, Sapna; Byrne, Stephen L; Spannagl, Manuel; Mayer, Klaus F X; Asp, Torben

    2015-03-28

    The Lolium-Festuca complex incorporates species from the Lolium genera and the broad leaf fescues, both belonging to the subfamily Pooideae. This subfamily also includes wheat, barley, oat and rye, making it extremely important to world agriculture. Species within the Lolium-Festuca complex show very diverse phenotypes, and many of them are related to agronomically important traits. Analysis of sequenced transcriptomes of these non-model species may shed light on the molecular mechanisms underlying this phenotypic diversity. We have generated de novo transcriptome assemblies for four species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family clusters for the four species using OrthoMCL and analyzed their inferred phylogenetic relationships. Our results indicate that VRN2 is a candidate gene for differentiating vernalization and non-vernalization types in the Lolium-Festuca complex. Grouping of the gene families based on their BLAST identity enabled us to divide ortholog groups into those that are very conserved and those that are more evolutionarily relaxed. The ratio of the non-synonumous to synonymous substitutions enabled us to pinpoint protein sequences evolving in response to positive selection. These proteins may explain some of the differences between the more stress tolerant Festuca, and the less stress tolerant Lolium species. Our data presents a comprehensive transcriptome sequence comparison between species from the Lolium-Festuca complex, with the identification of potential candidate genes underlying some important phenotypical differences within the complex (such as VRN2). The orthologous genes between the species have a very high %id (91,61%) and the majority of gene families were shared for all of them. It is

  6. Comparative transcriptome analysis within the Lolium/Festuca species complex reveals high sequence conservation

    DEFF Research Database (Denmark)

    Czaban, Adrian; Sharma, Sapna; Byrne, Stephen

    2015-01-01

    -Festuca complex show very diverse phenotypes, including for many agronomically important traits. Analysis of sequenced transcriptomes of these non-model species may shed light on the molecular mechanisms underlying this phenotypic diversity. Results We have generated de novo transcriptome assemblies for four......Background The Lolium-Festuca complex incorporates species from the Lolium genera and the broad leaf fescues, both belonging to the subfamily Pooideae. This subfamily also includes wheat, barley, oat and rye, making it extremely important to world agriculture. Species within the Lolium...... species from the Lolium-Festuca complex, ranging from 52,166 to 72,133 transcripts per assembly. We have also predicted a set of proteins and validated it with a high-confidence protein database from three closely related species (H. vulgare, B. distachyon and O. sativa). We have obtained gene family...

  7. Molecular data reveal a cryptic species within the Culex pipiens mosquito complex.

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    Dumas, E; Atyame, C M; Malcolm, C A; Le Goff, G; Unal, S; Makoundou, P; Pasteur, N; Weill, M; Duron, O

    2016-12-01

    The Culex pipiens mosquito complex is a group of evolutionarily closely related species including C. pipiens and Culex quinquefasciatus, both infected by the cytoplasmically inherited Wolbachia symbiont. A Wolbachia-uninfected population of C. pipiens was however described in South Africa and was recently proposed to represent a cryptic species. In this study, we reconsidered the existence of this species by undertaking an extensive screening for the presence of Wolbachia-uninfected C. pipiens specimens and by characterizing their genetic relatedness with known members of the complex. We first report on the presence of Wolbachia-uninfected specimens in several breeding sites. We next confirm that these uninfected specimens unambiguously belong to the C. pipiens complex. Remarkably, all uninfected specimens harbour mitochondrial haplotypes that are either novel or identical to those previously found in South Africa. In all cases, these mitochondrial haplotypes are closely related, but different, to those found in other C. pipiens complex members known to be infected by Wolbachia. Altogether, these results corroborate the presence of a widespread cryptic species within the C. pipiens species complex. The potential role of this cryptic C. pipiens species in the transmission of pathogens remains however to be determined. The designation 'Culex juppi nov. sp.' is proposed for this mosquito species. © 2016 The Royal Entomological Society.

  8. More species of the Agononida incerta complex revealed by molecules and morphology (Crustacea: Decapoda: Anomura: Munididae).

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    Poore, Gary C B; Andreakis, Nikos

    2014-09-05

    Squat lobsters from Madagascar, Vanuatu, Papua New Guinea, Fiji, eastern Australia and French Polynesia belonging to the Agononida incerta (Henderson, 1888) species complex are described as four new species: A. madagascerta, A. polycerta, A. tasmancerta and A. vanuacerta. This brings to ten the number of species in this complex. All species are morphologically distinguishable only on the basis of the shape of the anterolateral margin of the telson and setation of the dactyli of pereopods 2-4. The morphological delineation of nine of the species and their taxonomic status are robustly supported by phylogenetic analysis of the partial 16S rDNA gene and the partial mitochondrial cytochrome oxidase subunit 1 genes, and in some cases by colour. A phylogenetic analysis of the nine species for which molecular data are available grouped the species in two clades, one of four species with facial spines on the upper surface of pereopod 4 and the other of five species lacking facial spines. 

  9. Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species

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    Thompson, S.M.; Tan, Y.P.; Young, A.J.; Neate, S.M.; Aitken, E.A.B.; Shivas, R.G.

    2012-01-01

    The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are

  10. DNA Barcode Analysis of Thrips (Thysanoptera Diversity in Pakistan Reveals Cryptic Species Complexes.

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    Romana Iftikhar

    Full Text Available Although thrips are globally important crop pests and vectors of viral disease, species identifications are difficult because of their small size and inconspicuous morphological differences. Sequence variation in the mitochondrial COI-5' (DNA barcode region has proven effective for the identification of species in many groups of insect pests. We analyzed barcode sequence variation among 471 thrips from various plant hosts in north-central Pakistan. The Barcode Index Number (BIN system assigned these sequences to 55 BINs, while the Automatic Barcode Gap Discovery detected 56 partitions, a count that coincided with the number of monophyletic lineages recognized by Neighbor-Joining analysis and Bayesian inference. Congeneric species showed an average of 19% sequence divergence (range = 5.6% - 27% at COI, while intraspecific distances averaged 0.6% (range = 0.0% - 7.6%. BIN analysis suggested that all intraspecific divergence >3.0% actually involved a species complex. In fact, sequences for three major pest species (Haplothrips reuteri, Thrips palmi, Thrips tabaci, and one predatory thrips (Aeolothrips intermedius showed deep intraspecific divergences, providing evidence that each is a cryptic species complex. The study compiles the first barcode reference library for the thrips of Pakistan, and examines global haplotype diversity in four important pest thrips.

  11. Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories.

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    S Elfekih

    Full Text Available Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1 have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex. Here, we move beyond this by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that the two invasive members of the complex are closely related species with signatures of introgression with a third species (IO. Gene flow patterns were traced between contemporary invasive populations within MED and MEAM1 species and these were best explained by recent international trade. These findings have profound implications for delineating the B. tabaci species status and will impact quarantine measures and future management strategies of this global pest.

  12. Molecular phylogeny of Glossodoris (Ehrenberg, 1831) nudibranchs and related genera reveals cryptic and pseudocryptic species complexes

    KAUST Repository

    Matsuda, Shayle B.

    2017-03-01

    Chromodorid nudibranchs (Chromodorididae) are brightly coloured sea slugs that live in some of the most biodiverse and threatened coral reefs on the planet. However, the evolutionary relationships within this family have not been well understood, especially in the genus Glossodoris. Members of Glossodoris have experienced large-scale taxonomic instability over the last century and have been the subject of repeated taxonomic changes, in part due to morphological characters being the sole traditional taxonomic sources of data. Changing concepts of traditional generic boundaries based on morphology also have contributed to this instability. Despite recent advances in molecular systematics, many aspects of chromodorid taxonomy remain poorly understood, particularly at the traditional species and generic levels. In this study, 77 individuals comprising 32 previously defined species were used to build the most robust phylogenetic tree of Glossodoris and related genera using mitochondrial genes cytochrome c oxidase subunit I and 16S, and the nuclear gene 28S. Bayesian inference, maximum likelihood, and maximum parsimony analyses verify the most recent hypothesized evolutionary relationships within Glossodoris. Additionally, a pseudocryptic and cryptic species complex within Glossodoris cincta and a pseudocryptic complex within Glossodoris pallida emerged, and three new species of Doriprismatica are identified.

  13. DNA barcoding of Bemisia tabaci complex (Hemiptera: Aleyrodidae) reveals southerly expansion of the dominant whitefly species on cotton in Pakistan.

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    Ashfaq, Muhammad; Hebert, Paul D N; Mirza, M Sajjad; Khan, Arif M; Mansoor, Shahid; Shah, Ghulam S; Zafar, Yusuf

    2014-01-01

    Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan. Sequence diversity in the DNA barcode region (mtCOI-5') was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN) System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3' to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage "Pakistan". The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and "Pakistan" were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan. DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region.

  14. DNA barcoding of Bemisia tabaci complex (Hemiptera: Aleyrodidae reveals southerly expansion of the dominant whitefly species on cotton in Pakistan.

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    Muhammad Ashfaq

    Full Text Available Although whiteflies (Bemisia tabaci complex are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan.Sequence diversity in the DNA barcode region (mtCOI-5' was examined in 593 whiteflies from Pakistan to determine the number of whitefly species and their distributions in the cotton-growing areas of Punjab and Sindh provinces. These new records were integrated with another 173 barcode sequences for B. tabaci, most from India, to better understand regional whitefly diversity. The Barcode Index Number (BIN System assigned the 766 sequences to 15 BINs, including nine from Pakistan. Representative specimens of each Pakistan BIN were analyzed for mtCOI-3' to allow their assignment to one of the putative species in the B. tabaci complex recognized on the basis of sequence variation in this gene region. This analysis revealed the presence of Asia II 1, Middle East-Asia Minor 1, Asia 1, Asia II 5, Asia II 7, and a new lineage "Pakistan". The first two taxa were found in both Punjab and Sindh, but Asia 1 was only detected in Sindh, while Asia II 5, Asia II 7 and "Pakistan" were only present in Punjab. The haplotype networks showed that most haplotypes of Asia II 1, a species implicated in transmission of the cotton leaf curl virus, occurred in both India and Pakistan.DNA barcodes successfully discriminated cryptic species in B. tabaci complex. The dominant haplotypes in the B. tabaci complex were shared by India and Pakistan. Asia II 1 was previously restricted to Punjab, but is now the dominant lineage in southern Sindh; its southward spread may have serious implications for cotton plantations in this region.

  15. Simulated tri-trophic networks reveal complex relationships between species diversity and interaction diversity.

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    Pardikes, Nicholas A; Lumpkin, Will; Hurtado, Paul J; Dyer, Lee A

    2018-01-01

    Most of earth's biodiversity is comprised of interactions among species, yet it is unclear what causes variation in interaction diversity across space and time. We define interaction diversity as the richness and relative abundance of interactions linking species together at scales from localized, measurable webs to entire ecosystems. Large-scale patterns suggest that two basic components of interaction diversity differ substantially and predictably between different ecosystems: overall taxonomic diversity and host specificity of consumers. Understanding how these factors influence interaction diversity, and quantifying the causes and effects of variation in interaction diversity are important goals for community ecology. While previous studies have examined the effects of sampling bias and consumer specialization on determining patterns of ecological networks, these studies were restricted to two trophic levels and did not incorporate realistic variation in species diversity and consumer diet breadth. Here, we developed a food web model to generate tri-trophic ecological networks, and evaluated specific hypotheses about how the diversity of trophic interactions and species diversity are related under different scenarios of species richness, taxonomic abundance, and consumer diet breadth. We investigated the accumulation of species and interactions and found that interactions accumulate more quickly; thus, the accumulation of novel interactions may require less sampling effort than sampling species in order to get reliable estimates of either type of diversity. Mean consumer diet breadth influenced the correlation between species and interaction diversity significantly more than variation in both species richness and taxonomic abundance. However, this effect of diet breadth on interaction diversity is conditional on the number of observed interactions included in the models. The results presented here will help develop realistic predictions of the relationships

  16. Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast.

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    Vilaça, Sibelle T; Vargas, Sarah M; Lara-Ruiz, Paula; Molfetti, Érica; Reis, Estéfane C; Lôbo-Hajdu, Gisele; Soares, Luciano S; Santos, Fabrício R

    2012-09-01

    Surprisingly, a high frequency of interspecific sea turtle hybrids has been previously recorded in a nesting site along a short stretch of the Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of the females identified as Eretmochelys imbricata are hybrids in this area (Bahia State of Brazil). It is a remarkable find, because most of the nesting sites surveyed worldwide, including some in northern Brazil, presents no hybrids, and rare Caribbean sites present no more than 2% of hybrids. Thus, a detailed understanding of the hybridization process is needed to evaluate natural or anthropogenic causes of this regional phenomenon in Brazil, which could be an important factor affecting the conservation of this population. We analysed a set of 12 nuclear markers to investigate the pattern of hybridization involving three species of sea turtles: hawksbill (E. imbricata), loggerhead (Caretta caretta) and olive ridley (Lepidochelys olivacea). Our data indicate that most of the individuals in the crossings L. olivacea × E. imbricata and L. olivacea × C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings present F1 and backcrosses with both parental species. In addition, the C. caretta × E. imbricata hybridization seems to be gender and species biased, and we also found one individual with evidence of multispecies hybridization among C. caretta × E. imbricata × Chelonia mydas. The overall results also indicate that hybridization in this area is a recent phenomenon, spanning at least two generations or ~40 years. © 2012 Blackwell Publishing Ltd.

  17. Multilocus phylogeny of the avian family Alaudidae (larks) reveals complex morphological evolution, non-monophyletic genera and hidden species diversity.

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    Alström, Per; Barnes, Keith N; Olsson, Urban; Barker, F Keith; Bloomer, Paulette; Khan, Aleem Ahmed; Qureshi, Masood Ahmed; Guillaumet, Alban; Crochet, Pierre-André; Ryan, Peter G

    2013-12-01

    The Alaudidae (larks) is a large family of songbirds in the superfamily Sylvioidea. Larks are cosmopolitan, although species-level diversity is by far largest in Africa, followed by Eurasia, whereas Australasia and the New World have only one species each. The present study is the first comprehensive phylogeny of the Alaudidae. It includes 83.5% of all species and representatives from all recognised genera, and was based on two mitochondrial and three nuclear loci (in total 6.4 kbp, although not all loci were available for all species). In addition, a larger sample, comprising several subspecies of some polytypic species was analysed for one of the mitochondrial loci. There was generally good agreement in trees inferred from different loci, although some strongly supported incongruences were noted. The tree based on the concatenated multilocus data was overall well resolved and well supported by the data. We stress the importance of performing single gene as well as combined data analyses, as the latter may obscure significant incongruence behind strong nodal support values. The multilocus tree revealed many unpredicted relationships, including some non-monophyletic genera (Calandrella, Mirafra, Melanocorypha, Spizocorys). The tree based on the extended mitochondrial data set revealed several unexpected deep divergences between taxa presently treated as conspecific (e.g. within Ammomanes cinctura, Ammomanes deserti, Calandrella brachydactyla, Eremophila alpestris), as well as some shallow splits between currently recognised species (e.g. Certhilauda brevirostris-C. semitorquata-C. curvirostris; Calendulauda barlowi-C. erythrochlamys; Mirafra cantillans-M. javanica). Based on our results, we propose a revised generic classification, and comment on some species limits. We also comment on the extraordinary morphological adaptability in larks, which has resulted in numerous examples of parallel evolution (e.g. in Melanocorypha mongolica and Alauda leucoptera [both

  18. DNA Barcoding of Bemisia tabaci Complex (Hemiptera: Aleyrodidae) Reveals Southerly Expansion of the Dominant Whitefly Species on Cotton in Pakistan

    OpenAIRE

    Ashfaq, Muhammad; Hebert, Paul D. N.; Mirza, M. Sajjad; Khan, Arif M.; Mansoor, Shahid; Shah, Ghulam S.; Zafar, Yusuf

    2014-01-01

    Background Although whiteflies (Bemisia tabaci complex) are an important pest of cotton in Pakistan, its taxonomic diversity is poorly understood. As DNA barcoding is an effective tool for resolving species complexes and analyzing species distributions, we used this approach to analyze genetic diversity in the B. tabaci complex and map the distribution of B. tabaci lineages in cotton growing areas of Pakistan. Methods/Principal Findings Sequence diversity in the DNA barcode region (mtCOI-5′) ...

  19. Ecomorph or endangered coral? DNA and microstructure reveal hawaiian species complexes: Montipora dilatata/flabellata/turgescens & M. patula/verrilli.

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    Zac H Forsman

    2010-12-01

    Full Text Available M. dilatata, M. flabellata, and M. patula and 80 other scleractinian corals were petitioned to be listed under the US Endangered Species Act (ESA, which would have major conservation implications. One of the difficulties with this evaluation is that reproductive boundaries between morphologically defined coral species are often permeable, and morphology can be wildly variable. We examined genetic and morphological variation in Hawaiian Montipora with a suite of molecular markers (mitochondrial: COI, CR, Cyt-B, 16S, ATP6; nuclear: ATPsβ, ITS and microscopic skeletal measurements. Mitochondrial markers and the ITS region revealed four distinct clades: I M. patula/M. verrilli, II M. cf. incrassata, III M. capitata, IV M. dilatata/M. flabellata/M. cf. turgescens. These clades are likely to occur outside of Hawai'i according to mitochondrial control region haplotypes from previous studies. The ATPsβ intron data showed a pattern often interpreted as resulting from hybridization and introgression; however, incomplete lineage sorting may be more likely since the multicopy nuclear ITS region was consistent with the mitochondrial data. Furthermore, principal components analysis (PCA of skeletal microstructure was concordant with the mitochondrial clades, while nominal taxa overlapped. The size and shape of verrucae or papillae contributed most to identifying groups, while colony-level morphology was highly variable. It is not yet clear if these species complexes represent population-level variation or incipient speciation (CA<1MYA, two alternatives that have very different conservation implications. This study highlights the difficulty in understanding the scale of genetic and morphological variation that corresponds to species as opposed to population-level variation, information that is essential for conservation and for understanding coral biodiversity.

  20. Digitonthophagus Balthasar, 1959: taxonomy, systematics, and morphological phylogeny of the genus revealing an African species complex (Coleoptera: Scarabaeidae: Scarabaeinae).

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    Génier, François; Moretto, Philippe

    2017-03-31

    The taxonomy and systematics of the genus Digitonthophagus Balthasar (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini) is revised. A detailed study of the male genitalia combined with external morphology suggests that the variability, previously recognized, for D. gazella is hiding a species complex within the Afrotropical region and the Arabian Peninsula. The current study recognizes 16 species; 13 from the Afrotropical region and Arabian Peninsula and three from the eastern portion of the Saharo-Arabian region and the continental Indomalayan region. Species are organized into six species groups based on the results of the morphology-based phylogenetic analysis. The following 12 species are described as new: D. aksumensis Génier new species; D. biflagellatus Génier new species; D. dilatatus Génier new species; D. eucatta Génier new species; D. falciger Génier new species; D. fimator Génier new species; D. namaquensis Génier new species; D. petilus Génier new species; D. sahelicus Moretto new species; D. uks Génier new species; D. ulcerosus Génier new species; and D. viridicollis Génier new species. In order to stabilize nomenclature, lectotypes are designated for Scarabaeus bonasus Fabricius, 1775; Scarabaeus catta Fabricius, 1787, and Onthophagus gazella lusinganus d'Orbigny. A neotype is designated for Scarabaeus dorcas Olivier, 1789 whose status and synonymy need to be altered in order to clarify the status of Scarabaeus gazella auctorum, the widely introduced species with economic importance. A naming scheme is presented for the sclerites of the internal sac. External and male genitalia are illustrated and distribution maps are provided for each species.

  1. Is agriculture driving the diversification of the Bemisia tabaci species complex (Hemiptera: Sternorrhyncha: Aleyrodidae)?: Dating, diversification and biogeographic evidence revealed.

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    Boykin, Laura M; Bell, Charles D; Evans, Gregory; Small, Ian; De Barro, Paul J

    2013-10-18

    Humans and insect herbivores are competing for the same food crops and have been for thousands of years. Despite considerable advances in crop pest management, losses due to insects remain considerable. The global homogenisation of agriculture has supported the range expansion of numerous insect pests and has been driven in part by human-assisted dispersal supported through rapid global trade and low-cost air passenger transport. One of these pests, is the whitefly, Bemisia tabaci, a cryptic species complex that contains some of the world's most damaging pests of agriculture. The complex shows considerable genetic diversity and strong phylogeographic relationships. One consequence of the considerable impact that members of the B. tabaci complex have on agriculture, is the view that human activity, particularly in relation to agricultural practices, such as use of insecticides, has driven the diversification found within the species complex. This has been particularly so in the case of two members of the complex, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED), which have become globally distributed invasive species. An alternative hypothesis is that diversification is due to paleogeographic and paleoclimatological changes. The idea that human activity is driving speciation within the B. tabaci complex has never been tested, but the increased interest in fossil whiteflies and the growth in molecular data have enabled us to apply a relaxed molecular clock and so estimate divergence dates for the major lineages within the B. tabaci species complex. The divergence estimates do not support the view that human activity has been a major driver of diversification. Our analysis suggests that the major lineages within the complex arose approximately 60-30 mya and the highly invasive MED and MEAM1 split from the rest of the species complex around 12 mya well before the evolution of Homo sapiens and agriculture. Furthermore, the divergence dates coincide with a period

  2. Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex

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    Singh, Balwant; Singh, Nisha; Mishra, Shefali; Tripathi, Kabita; Singh, Bikram P.; Rai, Vandna; Singh, Ashok K.; Singh, Nagendra K.

    2018-01-01

    Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro-climatic zones

  3. Morphological and Molecular Data Reveal Three Distinct Populations of Indian Wild Rice Oryza rufipogon Griff. Species Complex

    Directory of Open Access Journals (Sweden)

    Balwant Singh

    2018-02-01

    Full Text Available Wild relatives of crops possess adaptive mutations for agronomically important traits, which could play significant role in crop improvement for sustainable agriculture. However, global climate change and human activities pose serious threats to the natural habitats leading to erosion of genetic diversity of wild rice populations. The purpose of this study was to explore and characterize India’s huge untapped wild rice diversity in Oryza rufipogon Griff. species complex from a wide range of ecological niches. We made strategic expeditions around diversity hot spots in 64 districts of nine different agro-climatic zones of the country and collected 418 wild rice accessions. Significant variation was observed among the accessions for 46 morphological descriptors, allowing classification into O. nivara, O. rufipogon, and O. sativa f. spontanea morpho-taxonomic groups. Genome-specific pSINE1 markers confirmed all the accessions having AA genome, which were further classified using ecotype-specific pSINE1 markers into annual, perennial, intermediate, and an unknown type. Principal component analysis revealed continuous variation for the morphological traits in each ecotype group. Genetic diversity analysis based on multi-allelic SSR markers clustered these accessions into three major groups and analysis of molecular variance for nine agro-climatic zones showed that 68% of the genetic variation was inherent amongst individuals while only 11% of the variation separated the zones, though there was significant correlation between genetic and spatial distances of the accessions. Model based population structure analysis using genome wide bi-allelic SNP markers revealed three sub-populations designated ‘Pro-Indica,’ ‘Pro-Aus,’ and ‘Mid-Gangetic,’ which showed poor correspondence with the morpho-taxonomic classification or pSINE1 ecotypes. There was Pan-India distribution of the ‘Pro-Indica’ and ‘Pro-Aus’ sub-populations across agro

  4. Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data.

    Science.gov (United States)

    Wood, Dustin A; Vandergast, A G; Lemos Espinal, J A; Fisher, R N; Holycross, A T

    2011-09-01

    Glacial-interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline. © 2011 Blackwell Publishing Ltd.

  5. Genome-wide single-nucleotide polymorphism data reveal cryptic species within cryptic freshwater snail species-The case of theAncylus fluviatilisspecies complex.

    Science.gov (United States)

    Weiss, Martina; Weigand, Hannah; Weigand, Alexander M; Leese, Florian

    2018-01-01

    DNA barcoding utilizes short standardized DNA sequences to identify species and is increasingly used in biodiversity assessments. The technique has unveiled an unforeseeably high number of morphologically cryptic species. However, if speciation has occurred relatively recently and rapidly, the use of single gene markers, and especially the exclusive use of mitochondrial markers, will presumably fail in delimitating species. Therefore, the true number of biological species might be even higher. One mechanism that can result in rapid speciation is hybridization of different species in combination with polyploidization, that is, allopolyploid speciation. In this study, we analyzed the population genetic structure of the polyploid freshwater snail Ancylus fluviatilis , for which allopolyploidization was postulated as a speciation mechanism. DNA barcoding has already revealed four cryptic species within A. fluviatilis (i.e., A. fluviatilis s. str., Ancylus sp. A-C), but early allozyme data even hint at the presence of additional cryptic lineages in Central Europe. We combined COI sequencing with high-resolution genome-wide SNP data (ddRAD data) to analyze the genetic structure of A. fluviatilis populations in a Central German low mountain range (Sauerland). The ddRAD data results indicate the presence of three cryptic species within A. fluviatilis s. str. occurring in sympatry and even syntopy, whereas mitochondrial sequence data only support the existence of one species, with shared haplotypes between species. Our study hence points to the limitations of DNA barcoding when dealing with organismal groups where speciation is assumed to have occurred rapidly, for example, through the process of allopolyploidization. We therefore emphasize that single marker DNA barcoding can underestimate the true species diversity and argue in strong favor of using genome-wide data for species delimitation in such groups.

  6. The rediscovery of a long described species reveals additional complexity in speciation patterns of poeciliid fishes in sulfide springs.

    Science.gov (United States)

    Palacios, Maura; Arias-Rodriguez, Lenin; Plath, Martin; Eifert, Constanze; Lerp, Hannes; Lamboj, Anton; Voelker, Gary; Tobler, Michael

    2013-01-01

    The process of ecological speciation drives the evolution of locally adapted and reproductively isolated populations in response to divergent natural selection. In Southern Mexico, several lineages of the freshwater fish species of the genus Poecilia have independently colonized toxic, hydrogen sulfide-rich springs. Even though ecological speciation processes are increasingly well understood in this system, aligning the taxonomy of these fish with evolutionary processes has lagged behind. While some sulfide spring populations are classified as ecotypes of Poecilia mexicana, others, like P. sulphuraria, have been described as highly endemic species. Our study particularly focused on elucidating the taxonomy of the long described sulfide spring endemic, Poecilia thermalis Steindachner 1863, and investigates if similar evolutionary patterns of phenotypic trait divergence and reproductive isolation are present as observed in other sulfidic species of Poecilia. We applied a geometric morphometric approach to assess body shape similarity to other sulfidic and non-sulfidic fish of the genus Poecilia. We also conducted phylogenetic and population genetic analyses to establish the phylogenetic relationships of P. thermalis and used a population genetic approach to determine levels of gene flow among Poecilia from sulfidic and non-sulfidic sites. Our results indicate that P. thermalis' body shape has evolved in convergence with other sulfide spring populations in the genus. Phylogenetic analyses placed P. thermalis as most closely related to one population of P. sulphuraria, and population genetic analyses demonstrated that P. thermalis is genetically isolated from both P. mexicana ecotypes and P. sulphuraria. Based on these findings, we make taxonomic recommendations for P. thermalis. Overall, our study verifies the role of hydrogen sulfide as a main factor shaping convergent, phenotypic evolution and the emergence of reproductive isolation between Poecilia populations

  7. Comparative genomic analysis reveals species-dependent complexities that explain difficulties with microsatellite marker development in molluscs.

    Science.gov (United States)

    McInerney, C E; Allcock, A L; Johnson, M P; Bailie, D A; Prodöhl, P A

    2011-01-01

    Reliable population DNA molecular markers are difficult to develop for molluscs, the reasons for which are largely unknown. Identical protocols for microsatellite marker development were implemented in three gastropods. Success rates were lower for Gibbula cineraria compared to Littorina littorea and L. saxatilis. Comparative genomic analysis of 47.2 kb of microsatellite containing sequences (MCS) revealed a high incidence of cryptic repetitive DNA in their flanking regions. The majority of these were novel, and could be grouped into DNA families based upon sequence similarities. Significant inter-specific variation in abundance of cryptic repetitive DNA and DNA families was observed. Repbase scans show that a large proportion of cryptic repetitive DNA was identified as transposable elements (TEs). We argue that a large number of TEs and their transpositional activity may be linked to differential rates of DNA multiplication and recombination. This is likely to be an important factor explaining inter-specific variation in genome stability and hence microsatellite marker development success rates. Gastropods also differed significantly in the type of TEs classes (autonomous vs non-autonomous) observed. We propose that dissimilar transpositional mechanisms differentiate the TE classes in terms of their propensity for transposition, fixation and/or silencing. Consequently, the phylogenetic conservation of non-autonomous TEs, such as CvA, suggests that dispersal of these elements may have behaved as microsatellite-inducing elements. Results seem to indicate that, compared to autonomous, non-autonomous TEs maybe have a more active role in genome rearrangement processes. The implications of the findings for genomic rearrangement, stability and marker development are discussed.

  8. Comparative population genomics of the Borrelia burgdorferi species complex reveals high degree of genetic isolation among species and underscores benefits and constraints to studying intra-specific epidemiological processes.

    Directory of Open Access Journals (Sweden)

    Maude Jacquot

    Full Text Available Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France, a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a ∼50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s.s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used

  9. Comparative Population Genomics of the Borrelia burgdorferi Species Complex Reveals High Degree of Genetic Isolation among Species and Underscores Benefits and Constraints to Studying Intra-Specific Epidemiological Processes

    Science.gov (United States)

    Jacquot, Maude; Gonnet, Mathieu; Ferquel, Elisabeth; Abrial, David; Claude, Alexandre; Gasqui, Patrick; Choumet, Valérie; Charras-Garrido, Myriam; Garnier, Martine; Faure, Benjamin; Sertour, Natacha; Dorr, Nelly; De Goër, Jocelyn; Vourc'h, Gwenaël; Bailly, Xavier

    2014-01-01

    Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France), a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a ∼50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s.s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used to formulate

  10. Multiple gene genealogies and phenotypic data reveal cryptic species of the Botryosphaeriaceae: a case study on the Neofusicoccum parvum/N. ribis complex.

    Science.gov (United States)

    Pavlic, Draginja; Slippers, Bernard; Coutinho, Teresa A; Wingfield, Michael J

    2009-05-01

    Neofusicoccum parvum and N. ribis (Botryosphaeriaceae, Ascomycetes) are closely related, plant pathogenic fungi with a world-wide distribution on a wide range of woody hosts. Species boundaries in the N. parvum/N. ribis complex have eluded definition, despite the application of various tools for characterisation. In this study, we test the hypothesis that only one species exists amongst isolates from the N. parvum/N. ribis complex, identified from Syzygiumcordatum trees across their native distribution in South Africa. Genealogical concordance phylogenetic species recognition (GCPSR) was applied based on concordance of genealogies obtained from DNA sequence data for five nuclear loci. These data showed that the single species hypothesis must be rejected. Rather, all analyses support the existence of three previously unrecognised, cryptic species within the N. parvum/N.ribis complex from S. cordatum, in addition to N. parvum and N. ribis. The three lineages reflecting these cryptic taxa are sympatric across their geographical range, indicating barriers to gene flow other than geographic isolation. Phenotypic characters failed to detect all the species uncovered by the GCPSR. Sequence data of the Internal Transcribed Spacer (ITS) of the ribosomal DNA locus, which is thought to be useful for barcoding in fungi, did not distinguish all the species with confidence. RNA polymerase II subunit (RPB2) was the most informative to distinguish all the species a posteriori to the application of GCPSR. The results reflect the critical importance of using multiple gene genealogies and adequate sampling to identify cryptic species and to characterise the true diversity within the Botryosphaeriaceae.

  11. CRISPR/Cas9 and active genetics-based trans-species replacement of the endogenousDrosophila kni-L2 CRM reveals unexpected complexity.

    Science.gov (United States)

    Xu, Xiang-Ru Shannon; Gantz, Valentino Matteo; Siomava, Natalia; Bier, Ethan

    2017-12-23

    The knirps ( kni ) locus encodes transcription factors required for induction of the L2 wing vein in Drosophila . Here, we employ diverse CRISPR/Cas9 genome editing tools to generate a series of targeted lesions within the endogenous cis-regulatory module (CRM) required for kni expression in the L2 vein primordium. Phenotypic analysis of these ' in locus ' mutations based on both expression of Kni protein and adult wing phenotypes, reveals novel unexpected features of L2-CRM function including evidence for a chromosome pairing-dependent process that promotes transcription. We also demonstrate that self-propagating active genetic elements (CopyCat elements) can efficiently delete and replace the L2-CRM with orthologous sequences from other divergent fly species. Wing vein phenotypes resulting from these trans-species enhancer replacements parallel features of the respective donor fly species. This highly sensitive phenotypic readout of enhancer function in a native genomic context reveals novel features of CRM function undetected by traditional reporter gene analysis. © 2017, Xu et al.

  12. Out of Asia: Biogeography of fungal populations reveals Asian origin of diversification of the Laccaria amethystina complex, and two new species of violet Laccaria.

    Science.gov (United States)

    Vincenot, Lucie; Popa, Flavius; Laso, Francisco; Donges, Kathrin; Rexer, Karl-Heinz; Kost, Gerhard; Yang, Zhu L; Nara, Kazuhide; Selosse, Marc-André

    2017-11-01

    Purple Laccaria are ectomycorrhizal basidiomycetes associated with temperate forests all over the Northern Hemisphere in at least two taxa: Laccaria amethysteo-occidentalis in North America, and L. amethystina complex in Eurasia, as shown by Vincenot et al. (2012). Here, we combine a further study of the genetic structure of L. amethystina populations from Europe to southwestern China and Japan, using neutral Single Sequence Repeat (SSR; microsatellite) markers; and a systematic description of two novel Asian species, namely Laccaria moshuijun and Laccaria japonica, based on ecological, morphological, and molecular criteria (rDNA sequences). Population genetics provides evidence of the ancient isolation of three regional groups, with strong signal for speciation, and suggests a centre of origin of modern populations closest to present-day Chinese populations. Phylogenetic analyses confirm speciation at the molecular level, reflected in morphological features: L. moshuijun samples (from Yunnan, China) display strongly variable cheilocystidia, while L. japonica samples (from Japan) present distinctive globose to subglobose spores and clavate cheilocystidia. This study of a species complex primarily described with an extremely wide ecological and geographical range sheds new light on the biodiversity and biogeography of ectomycorrhizal fungi. Copyright © 2017 British Mycological Society. All rights reserved.

  13. Phylogenetic analysis of two single-copy nuclear genes revealed origin and complex relationships of polyploid species of Hordeum in Triticeae (Poaceae).

    Science.gov (United States)

    Hu, Qianni; Sun, Genlou

    2017-06-01

    Two single-copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and thioredoxin-like gene (HTL), were used to explore the phylogeny and origin of polyploid species in Hordeum. Our results were partly in accord with previous studies, but disclosed additional complexity. Both RPB2 and HTL trees confirmed the presence of Xa genome in H. capense and H. secalinum, and that H. depressum originated from H. californicum together with other American diploids, either H. intercedens or H. pusillum. American diploids solely contributed to the origin of H. depressum. The Asian diploids, either H. bogdanii or H. brevisubulatum, contributed to the formation of American polyploids except H. depressum. RPB2 and HTL sequences showed that H. roshevitzii did not contribute to the origin of American tetraploids. Our data showed a close relationship between the hexaploids H. procerum and H. parodii and the tetraploids H. brachyantherum, H. fuegianum, H. guatemalense, H. jubatum, and H. tetraploidum. The involvement of the diploid H. pusillum and the tetraploid H. jubatum in the formation of H. arizonicum was also indicated in the HTL phylogeny. Our results suggested a possible gene introgression of W- and P-genome species into the tetraploid H. jubatum and the hexaploid H. procerum.

  14. The Colletotrichum gloeosporioides species complex.

    Science.gov (United States)

    Weir, B S; Johnston, P R; Damm, U

    2012-09-15

    The limit of the Colletotrichum gloeosporioides species complex is defined genetically, based on a strongly supported clade within the Colletotrichum ITS gene tree. All taxa accepted within this clade are morphologically more or less typical of the broadly defined C. gloeosporioides, as it has been applied in the literature for the past 50 years. We accept 22 species plus one subspecies within the C. gloeosporioides complex. These include C. asianum, C. cordylinicola, C. fructicola, C. gloeosporioides, C. horii, C. kahawae subsp. kahawae, C. musae, C. nupharicola, C. psidii, C. siamense, C. theobromicola, C. tropicale, and C. xanthorrhoeae, along with the taxa described here as new, C. aenigma, C. aeschynomenes, C. alatae, C. alienum, C. aotearoa, C. clidemiae, C. kahawae subsp. ciggaro, C. salsolae, and C. ti, plus the nom. nov. C. queenslandicum (for C. gloeosporioides var. minus). All of the taxa are defined genetically on the basis of multi-gene phylogenies. Brief morphological descriptions are provided for species where no modern description is available. Many of the species are unable to be reliably distinguished using ITS, the official barcoding gene for fungi. Particularly problematic are a set of species genetically close to C. musae and another set of species genetically close to C. kahawae, referred to here as the Musae clade and the Kahawae clade, respectively. Each clade contains several species that are phylogenetically well supported in multi-gene analyses, but within the clades branch lengths are short because of the small number of phylogenetically informative characters, and in a few cases individual gene trees are incongruent. Some single genes or combinations of genes, such as glyceraldehyde-3-phosphate dehydrogenase and glutamine synthetase, can be used to reliably distinguish most taxa and will need to be developed as secondary barcodes for species level identification, which is important because many of these fungi are of biosecurity

  15. Uncovering the diversity in the Amazophrynella minuta complex: integrative taxonomy reveals a new species of Amazophrynella (Anura, Bufonidae) from southern Peru

    Science.gov (United States)

    Rojas, Rommel R.; Chaparro, Juan C.; Carvalho, Vinícius Tadeu De; Ávila, Robson W.; Farias, Izeni Pires; Hrbek, Tomas; Gordo, Marcelo

    2016-01-01

    Abstract A new species of the genus Amazophrynella (Anura, Bufonidae) is described from the departments of Madre de Dios, Cusco and Junin in Peru. An integrative taxonomy approach is used. A morphological diagnosis, morphometrics comparisons, description of the advertisement call, and the phylogenetic relationships of the new species are provided. Amazophrynella javierbustamantei sp. n. differs from other species of Amazophrynella by: intermediate body-size (snout-vent length 14.9 mm in males, n = 26 and 19.6 mm in females, n = 20), tuberculate skin texture of body, greatest hand length of the Amazophrynella spp. (3.6 mm in males, n = 26 and 4.6 mm in females, n = 20), venter coloration yellowish, tiny rounded black points covering the venter, and thirteen molecular autapomorphies in the 16S RNA gene. Its distribution varies from 215 to 708 m a.s.l. This discovery highlights the importance of the remnant forest in preserving the biodiversity in Peru, and increase in seven the species formally described in the genus Amazophrynella. PMID:27047239

  16. Complexities of bloom dynamics in the toxic dinoflagellate Alexandrium fundyense revealed through DNA measurements by imaging flow cytometry coupled with species-specific rRNA probes

    Science.gov (United States)

    Brosnahan, Michael L.; Farzan, Shahla; Keafer, Bruce A.; Sosik, Heidi M.; Olson, Robert J.; Anderson, Donald M.

    2014-05-01

    Measurements of the DNA content of different protist populations can shed light on a variety of processes, including cell division, sex, prey ingestion, and parasite invasion. Here, we modified an Imaging FlowCytobot (IFCB), a custom-built flow cytometer that records images of microplankton, to measure the DNA content of large dinoflagellates and other high-DNA content species. The IFCB was also configured to measure fluorescence from Cy3-labeled rRNA probes, aiding the identification of Alexandrium fundyense (syn. A. tamarense Group I), a photosynthetic dinoflagellate that causes paralytic shellfish poisoning (PSP). The modified IFCB was used to analyze samples from the development, peak and termination phases of an inshore A. fundyense bloom (Salt Pond, Eastham, MA, USA), and from a rare A. fundyense ‘red tide’ that occurred in the western Gulf of Maine, offshore of Portsmouth, NH (USA). Diploid or G2 phase (‘2C’) A. fundyense cells were frequently enriched at the near-surface, suggesting an important role for aggregation at the air-sea interface during sexual events. Also, our analysis showed that large proportions of A. fundyense cells in both the Salt Pond and red tide blooms were planozygotes during bloom decline, highlighting the importance of sexual fusion to bloom termination. At Salt Pond, bloom decline also coincided with a dramatic rise in infections by the parasite genus Amoebophrya. The samples that were most heavily infected contained many large cells with higher DNA-associated fluorescence than 2C vegetative cells, but these cells' nuclei were also frequently consumed by Amoebophrya trophonts. Neither large cell size nor increased DNA-associated fluorescence could be replicated by infecting an A. fundyense culture of vegetative cells. Therefore, we attribute these characteristics of the large Salt Pond cells to planozygote maturation rather than Amoebophrya infection, though an interaction between infection and planozygote maturation may

  17. The Candida Pathogenic Species Complex

    Science.gov (United States)

    Turner, Siobhán A.; Butler, Geraldine

    2014-01-01

    Candida species are the most common causes of fungal infection. Approximately 90% of infections are caused by five species: Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei. Three (C. albicans, C. tropicalis, and C. parapsilosis) belong to the CTG clade, in which the CTG codon is translated as serine and not leucine. C. albicans remains the most commonly isolated but is decreasing relative to the other species. The increasing incidence of C. glabrata is related to its reduced susceptibility to azole drugs. Genome analysis suggests that virulence in the CTG clade is associated with expansion of gene families, particularly of cell wall genes. Similar independent processes took place in the C. glabrata species group. Gene loss and expansion in an ancestor of C. glabrata may have resulted in preadaptations that enabled pathogenicity. PMID:25183855

  18. Novel multilocus sequence typing scheme reveals high genetic diversity of human pathogenic members of the Fusarium incarnatum-F. equiseti and F. chlamydosporum species complexes within the United States

    NARCIS (Netherlands)

    O'Donnell, K.; Sutton, D.A.; Rinaldi, M.G.; Gueidan, C.; Crous, P.W.; Geiser, D.M.

    2009-01-01

    Species limits within the clinically important Fusarium incarnatum-F. equiseti and F. chlamydosporum species complexes (FIESC and FCSC, respectively) were investigated using multilocus DNA sequence data. Maximum-parsimony and maximum-likelihood analyses of aligned DNA sequences from four loci

  19. The Drosophila bipectinata species complex: phylogenetic ...

    Indian Academy of Sciences (India)

    PARUL BANERJEE

    c Indian Academy of Sciences. RESEARCH ARTICLE. The Drosophila bipectinata species complex: phylogenetic relationship among different members based on chromosomal variations. PARUL BANERJEE and BASHISTH N. SINGH. ∗. Genetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi ...

  20. Species recognition and cryptic species in the Tuber indicum complex.

    Directory of Open Access Journals (Sweden)

    Juan Chen

    Full Text Available Morphological delimitation of Asian black truffles, including Tuber himalayense, T. indicum, T. sinense, T. pseudohimalayense, T. formosanum and T. pseudoexcavatum, has remained problematic and even phylogenetic analyses have been controversial. In this study, we combined five years of field investigation in China with morphological study and DNA sequences analyses (ITS, LSU and β-tubulin of 131 Tuber specimens to show that T. pseudohimalayense and T. pseudoexcavatum are the same species. T. formosanum is a separate species based on its host plants and geographic distribution, combined with minor morphological difference from T. indicum. T. sinense should be treated as a synonym of T. indicum. Our results demonstrate that the present T. indicum, a single described morphological species, should include at least two separate phylogenetic species. These findings are of high importance for truffle taxonomy and reveal and preserve the richness of truffle diversity.

  1. Sequencing the Black Aspergilli species complex

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Salamov, Asaf; Zhou, Kemin; Otillar, Robert; Baker, Scott; Grigoriev, Igor

    2011-03-11

    The ~15 members of the Aspergillus section Nigri species complex (the "Black Aspergilli") are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as food processing and spoilage agents and agricultural toxigens. Despite their utility and ubiquity, the morphological and metabolic distinctiveness of the complex's members, and thus their taxonomy, is poorly defined. We are using short read pyrosequencing technology (Roche/454 and Illumina/Solexa) to rapidly scale up genomic and transcriptomic analysis of this species complex. To date we predict 11197 genes in Aspergillus niger, 11624 genes in A. carbonarius, and 10845 genes in A. aculeatus. A. aculeatus is our most recent genome, and was assembled primarily from 454-sequenced reads and annotated with the aid of >2 million 454 ESTs and >300 million Solexa ESTs. To most effectively deploy these very large numbers of ESTs we developed 2 novel methods for clustering the ESTs into assemblies. We have also developed a pipeline to propose orthologies and paralogies among genes in the species complex. In the near future we will apply these methods to additional species of Black Aspergilli that are currently in our sequencing pipeline.

  2. The Drosophila bipectinata species complex: phylogenetic ...

    Indian Academy of Sciences (India)

    Navya

    Acad. Sci India 82, 99-115. Tomimura Y., Matsuda, M. and Tobari, Y. N. 2005 Chromosomal phylogeny and geographical divergence in the Drosophila bipectinata complex. Genome 48, 487–502. White M. J. D. 1958 Restriction and recombination in grasshopper populations and species. Cold Spr. Harb. Symp. Quant. Biol.

  3. The Drosophila bipectinata species complex: phylogenetic ...

    Indian Academy of Sciences (India)

    [Banerjee P. and Singh B. N. 2017 The Drosophila bipectinata species complex: phylogenetic relationship among different members based on chromosomal variations. J. Genet. 96, 97–107]. Introduction ..... loops touch the chromocenter and in our microphotograph. (depicting both the arms) too, the involvement of chromo-.

  4. New species of Moenkhausia Eigenmann, 1903 (Characiformes: Characidae with comments on the Moenkhausia oligolepis species complex

    Directory of Open Access Journals (Sweden)

    Ricardo C. Benine

    Full Text Available A new species of Moenkhausia is described from tributaries of the rio Paraguay, Brazil. The new species is diagnosed from congeners by characters related to body coloration, the number of lateral line scales, the degree of poring of the lateral line, and number of scales rows above and below the lateral line. Molecular analyses using partial sequences of the mitochondrial gene Cytochrome Oxidase I from specimens of the new species and specimens belonging to morphologically similar species demonstrated that the new species is easily differentiated by their high genetic distance and by their position in the phylogenetic hypothesis obtained through the Maximum Parsimony methodology. The analyses of three samples of M. oligolepis also revealed that they have high genetic distances and belong to different monophyletic groups suggesting that this species corresponds to a species complex rather than a single species.

  5. Cryptic Sebastes norvegicus species in Greenland waters revealed by microsatellites

    DEFF Research Database (Denmark)

    Saha, Atal; Hauser, Lorenz; Hedeholm, Rasmus

    2017-01-01

    Identification of cryptic species can have profound implications in fishery management, conservation and biodiversity contexts. In the North Atlantic, the genus Sebastes is currently represented by four species, although additional cryptic species have been assumed. The connectivity of the gene......-pools within the genus in Greenland waters, in particular, remains largely unexplored. Using a panel of 13 microsatellite markers for 720 fish, we explored the species complex of Sebastes norvegicus in Greenland waters. Genetic analyses provided evidence for three cryptic species in samples that were...... morphologically identified as S. norvegicus. They were termed S. norvegicus-A, S. norvegicus-B, and S. norvegicusgiants. A few phenotypic features exist to identify adult S. norvegicus giants, but no characteristics have been identified for the two other cryptic species. The proposed cryptic species should...

  6. Lactobacillus species: taxonomic complexity and controversial susceptibilities.

    Science.gov (United States)

    Goldstein, Ellie J C; Tyrrell, Kerin L; Citron, Diane M

    2015-05-15

    The genus Lactobacillus is a taxonomically complex and is composed of over 170 species that cannot be easily differentiated phenotypically and often require molecular identification. Although they are part of the normal human gastrointestinal and vaginal flora, they can also be occasional human pathogens. They are extensively used in a variety of commercial products including probiotics. Their antimicrobial susceptibilities are poorly defined in part because of their taxonomic complexity and are compounded by the different methods recommended by Clinical Laboratory Standards Institute and International Dairy Foundation. Their use as probiotics for prevention of Clostridium difficile infection is prevalent among consumers worldwide but raises the question of will the use of any concurrent antibiotic effect their ability to survive. Lactobacillus species are generally acid resistant and are able to survive ingestion. They are generally resistant to metronidazole, aminoglycosides and ciprofloxacin with L. acidophilus being susceptible to penicillin and vancomycin, whereas L. rhamnosus and L. casei are resistant to metronidazole and vancomycin. © The Author 2015. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  7. Evolutionary relationships within the Phytophthora cactorum species complex in Europe.

    Science.gov (United States)

    Pánek, Matěj; Fér, Tomáš; Mráček, Jaroslav; Tomšovský, Michal

    2016-01-01

    The Phytophthora cactorum species complex in Europe is composed of P. cactorum, Phytophthora hedraiandra, and a hybrid species Phytophthora × serendipita. Evolutionary analyses using the amplified fragment length polymorphism (AFLP) method were carried out on 133 isolates from 19 countries. The AFLP data were complemented by sequence analysis of three genes (ITS region of ribosomal RNA gene, phenolic acid decarboxylase - Pheca I, and Cytochrome oxidase - Cox I), morphometric analysis and cardinal temperature data. The high proportion of clonal genotypes, low gene flow among groups, which was defined by the structure analysis, and low Nei's gene diversity confirms the homothallic life cycle of the groups. On the other hand, the ITS, Cox I and Pheca I sequence data support occasional hybridization between species. The structure K = 5 grouping revealed two groups of hybrid origin (C2 and F). While the C2 group resembles P. × serendipita, the F group includes Finnish isolates characterized by high oogonial abortion rates and slow growth. The morphological characters routinely used in identification of Phytophthora species are not useful for delimitation of species from the P. cactorum complex. Therefore, we discuss the status of P. hedraiandra as a separate species. The epitypification of P. cactorum is proposed. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  8. Molecular differentiation of sibling species in the Galactomyces geotrichum complex.

    Science.gov (United States)

    Naumova, E S; Smith MTh; Boekhout, T; de Hoog, G S; Naumov, G I

    2001-12-01

    PCR-analysis, multilocus enzyme electrophoresis and molecular karyotyping were used to characterize 52 strains belonging to the genus Galactomyces. The resultant data revealed that a PCR method employing the universal primer N21 and microsatellite primer (CAC)5 is appropriate for the distinction of four Ga. geotrichum sibling species, Ga. citri-aurantii and Ga. reessii. Better separation was achieved with the UP primer N21; each species displayed a specific pattern with very low intraspecific variation. We propose to use the primer N21 for the differentiation of the six taxa composing the genus Galactomyces. Multilocus enzyme electrophoresis revealed genetic homogeneity of each sibling species within the Ga. geotrichum complex. On the other hand, the four sibling species, having from 41 to 59% of nDNA homology and similar phenotypic characteristics, are clearly distinguished based on their electrophoretic profiles using two enzymes: mannose-6-phosphate isomerase (MPI) and phosphoglucomutase (PGM). Despite the same number of chromosomal bands, different karyotype patterns were found in Ga. geotrichum sensu stricto and its two sibling species A and B. Within each sibling species, chromosome length polymorphism was observed, in particular for small bands, allowing discrimination to the strain level.

  9. Cryptic species in the Terfezia boudieri complex.

    Science.gov (United States)

    Ferdman, Yael; Sitrit, Yaron; Li, Yong-Fang; Roth-Bejerano, Nurit; Kagan-Zur, Varda

    2009-05-01

    Phylogenetic analyses have corroborated the discovery of three internal transcribed spacer (ITS) Types in Terfezia boudieri isolates in the course of earlier studies and have emphasized the divergence of Type 2 from Types 1 and 3. The application of molecular and physiological tools described below, revealed the existence of cryptic species within T. boudieri. The markers used include sequences taken from the 5' end of the ribosomal large subunit gene, a chitin synthase partial sequence, beta-tubulin partial sequence and amplified fragment length polymorphism (AFLP)-based markers. Following initial sequencing of a single PCR amplified sample for each Type, mass analysis of specimens relied on RFLP differences between the Types. Over 100 fruit bodies, 30 or more specimens for each ITS Type, were tested with each of the markers. The markers analysis divided the isolates into three groups, each correlated to a specific ITS Type. Two of the physiological traits examined: mycelial proliferation and mycorrhiza formation, consistently showed responses paralleling the ITS Types; the data presented suggest that T. boudieri is comprised of three cryptic species.

  10. Delimiting Species Boundaries within a Paraphyletic Species Complex: Insights from Morphological, Genetic, and Molecular Data on Paramecium sonneborni (Paramecium aurelia species complex, Ciliophora, Protozoa).

    Science.gov (United States)

    Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Sawka, Natalia

    2015-09-01

    The demarcation of boundaries between protist species is often problematic because of the absence of a uniform species definition, the abundance of cryptic diversity, and the occurrence of convergent morphology. The ciliates belonging to the Paramecium aurelia complex, consisting of 15 species, are a good model for such systematic and evolutionary studies. One member of the complex is P. sonneborni, previously known only from one stand in Texas (USA), but recently found in two new sampling sites in Cyprus (creeks running to Salt Lake and Oroklini Lake near Larnaca). The studied Paramecium sonneborni strains (from the USA and Cyprus) reveal low viability in the F1 and F2 generations of interstrain hybrids and may be an example of ongoing allopatric speciation. Despite its molecular distinctiveness, we postulate that P. sonneborni should remain in the P. aurelia complex, making it a paraphyletic taxon. Morphological studies have revealed that some features of the nuclear apparatus of P. sonneborni correspond to the P. aurelia spp. complex, while others are similar to P. jenningsi and P. schewiakoffi. The observed discordance indicates rapid splitting of the P. aurelia-P. jenningsi-P. schewiakoffi group, in which genetic, morphological, and molecular boundaries between species are not congruent. Copyright © 2015 Elsevier GmbH. All rights reserved.

  11. Morphological evolution and genetic differentiation in Daphnia species complexes

    NARCIS (Netherlands)

    Gießer, S.; Mader, E.; Schwenk, K.

    1999-01-01

    Despite many ecological and evolutionary studies, the history of several species complexes within the freshwater crustacean genus Daphnia (Branchiopoda, Anomopoda) is poorly understood. In particular, the Daphnia longispina group, comprising several large-lake species, is characterized by pronounced

  12. Elucidating the Ramularia eucalypti species complex

    NARCIS (Netherlands)

    Videira, S.I.R.; Groenewald, J.Z.; Kolecka, A.; Haren, van L.; Boekhout, T.; Crous, P.W.

    2015-01-01

    The genus Ramularia includes numerous phytopathogenic species, several of which are economically important. Ramularia eucalypti is currently the only species of this genus known to infect Eucalyptus by causing severe leaf-spotting symptoms on this host. However, several isolates identified as R.

  13. Phylogeny and taxonomy of species in the Grosmannia serpens complex.

    Science.gov (United States)

    Duong, Tuan A; de Beer, Z Wilhelm; Wingfield, Brenda D; Wingfield, Michael J

    2012-01-01

    Grosmannia serpens was first described from pine in Italy in 1936 and it has been recorded subsequently from many countries in both the northern and southern hemispheres. The fungus is vectored primarily by root-infesting bark beetles and has been reported to contribute to pine-root diseases in Italy and South Africa. The objective of this study was to consider the identity of a global collection of isolates not previously available and using DNA sequence-based comparisons not previously applied to most of these isolates. Phylogenetic analyses of the ITS2-LSU, actin, beta-tubulin, calmodulin and translation elongation factor-1 alpha sequences revealed that these morphologically similar isolates represent a complex of five cryptic species. Grosmannia serpens sensu stricto thus is redefined and comprises only isolates from Italy including the ex-type isolate. The ex-type isolate of Verticicladiella alacris was shown to be distinct from G. serpens, and a new holomorphic species, G. alacris, is described. The teleomorph state of G. alacris was obtained through mating studies in the laboratory, confirming that this species is heterothallic. Most of the available isolates, including those from South Africa, USA, France, Portugal and some from Spain, represent G. alacris. The remaining three taxa, known only in their anamorph states, are described as the new species Leptographium gibbsii for isolates from the UK, L. yamaokae for isolates from Japan and L. castellanum for isolates from Spain and the Dominican Republic.

  14. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.

    Directory of Open Access Journals (Sweden)

    Karin Voordeckers

    2015-11-01

    Full Text Available Tolerance to high levels of ethanol is an ecologically and industrially relevant phenotype of microbes, but the molecular mechanisms underlying this complex trait remain largely unknown. Here, we use long-term experimental evolution of isogenic yeast populations of different initial ploidy to study adaptation to increasing levels of ethanol. Whole-genome sequencing of more than 30 evolved populations and over 100 adapted clones isolated throughout this two-year evolution experiment revealed how a complex interplay of de novo single nucleotide mutations, copy number variation, ploidy changes, mutator phenotypes, and clonal interference led to a significant increase in ethanol tolerance. Although the specific mutations differ between different evolved lineages, application of a novel computational pipeline, PheNetic, revealed that many mutations target functional modules involved in stress response, cell cycle regulation, DNA repair and respiration. Measuring the fitness effects of selected mutations introduced in non-evolved ethanol-sensitive cells revealed several adaptive mutations that had previously not been implicated in ethanol tolerance, including mutations in PRT1, VPS70 and MEX67. Interestingly, variation in VPS70 was recently identified as a QTL for ethanol tolerance in an industrial bio-ethanol strain. Taken together, our results show how, in contrast to adaptation to some other stresses, adaptation to a continuous complex and severe stress involves interplay of different evolutionary mechanisms. In addition, our study reveals functional modules involved in ethanol resistance and identifies several mutations that could help to improve the ethanol tolerance of industrial yeasts.

  15. Phylogeny of Fomitopsis pinicola: A species complex

    Science.gov (United States)

    John Haight; Gary A. Laursen; Jessie A. Glaeser; D. Lee. Taylor

    2016-01-01

    Fungal species with a broad distribution may exhibit considerable genetic variation over their geographic ranges. Variation may develop among populations based on geographic isolation, lack of migration, and genetic drift, though this genetic variation may not always be evident when examining phenotypic characters. Fomitopsis pinicola is an...

  16. New species in the New World Natada complex (Lepidoptera: Limacodidae

    Directory of Open Access Journals (Sweden)

    Jorge F Corrales

    2000-06-01

    Full Text Available The following new species in the New World Natada complex are described: Natada minuscula, Natada cecilia, Natada lalogamezi, Natada kokii, Natada monteverdensis, Narosopsis iangauldi, and Euprosterna wemilleri. Natada minuscula is the smallest known species in the complex. Of the new species, only Natada kokii, Natada cecilia and Narosopsis iangauldi are known to occur outside of Costa Rica. Previously the New World Natada complex had 43 species in the neotropics. It is anticipated that the proportion of new species in the complex will exceed other major lineages of Limacodidae found in Costa Rica.Se describe las siguientes especies nuevas del complejo Natada del Nuevo Mundo: Natada minuscula, Natada cecilia, Natada lalogamezi, Natada kokii, Natada monteverdensis, Narosopsis iangauldi, and Euprosterna wemilleri. Natada minuscula es la especie más pequeña del complejo.

  17. Disentangling diatom species complexes: does morphometry suffice?

    Directory of Open Access Journals (Sweden)

    Saúl Blanco

    2017-12-01

    Full Text Available Accurate taxonomic resolution in light microscopy analyses of microalgae is essential to achieve high quality, comparable results in both floristic analyses and biomonitoring studies. A number of closely related diatom taxa have been detected to date co-occurring within benthic diatom assemblages, sharing many morphological, morphometrical and ecological characteristics. In this contribution, we analysed the hypothesis that, where a large sample size (number of individuals is available, common morphometrical parameters (valve length, width and stria density are sufficient to achieve a correct identification to the species level. We focused on some common diatom taxa belonging to the genus Gomphonema. More than 400 valves and frustules were photographed in valve view and measured using Fiji software. Several statistical tools (mixture and discriminant analysis, k-means clustering, classification trees, etc. were explored to test whether mere morphometry, independently of other valve features, leads to correct identifications, when compared to identifications made by experts. In view of the results obtained, morphometry-based determination in diatom taxonomy is discouraged.

  18. The complex hybrid origins of the root knot nematodes revealed through comparative genomics

    Directory of Open Access Journals (Sweden)

    David H. Lunt

    2014-05-01

    Full Text Available Root knot nematodes (RKN can infect most of the world’s agricultural crop species and are among the most important of all plant pathogens. As yet however we have little understanding of their origins or the genomic basis of their extreme polyphagy. The most damaging pathogens reproduce by obligatory mitotic parthenogenesis and it has been suggested that these species originated from interspecific hybridizations between unknown parental taxa. We have sequenced the genome of the diploid meiotic parthenogen Meloidogyne floridensis, and use a comparative genomic approach to test the hypothesis that this species was involved in the hybrid origin of the tropical mitotic parthenogen Meloidogyne incognita. Phylogenomic analysis of gene families from M. floridensis, M. incognita and an outgroup species Meloidogyne hapla was carried out to trace the evolutionary history of these species’ genomes, and we demonstrate that M. floridensis was one of the parental species in the hybrid origins of M. incognita. Analysis of the M. floridensis genome itself revealed many gene loci present in divergent copies, as they are in M. incognita, indicating that it too had a hybrid origin. The triploid M. incognita is shown to be a complex double-hybrid between M. floridensis and a third, unidentified, parent. The agriculturally important RKN have very complex origins involving the mixing of several parental genomes by hybridization and their extreme polyphagy and success in agricultural environments may be related to this hybridization, producing transgressive variation on which natural selection can act. It is now clear that studying RKN variation via individual marker loci may fail due to the species’ convoluted origins, and multi-species population genomics is essential to understand the hybrid diversity and adaptive variation of this important species complex. This comparative genomic analysis provides a compelling example of the importance and complexity of

  19. Comparative genomics reveals evidence of marine adaptation in Salinispora species

    Directory of Open Access Journals (Sweden)

    Penn Kevin

    2012-03-01

    Full Text Available Abstract Background Actinobacteria represent a consistent component of most marine bacterial communities yet little is known about the mechanisms by which these Gram-positive bacteria adapt to life in the marine environment. Here we employed a phylogenomic approach to identify marine adaptation genes in marine Actinobacteria. The focus was on the obligate marine actinomycete genus Salinispora and the identification of marine adaptation genes that have been acquired from other marine bacteria. Results Functional annotation, comparative genomics, and evidence of a shared evolutionary history with bacteria from hyperosmotic environments were used to identify a pool of more than 50 marine adaptation genes. An Actinobacterial species tree was used to infer the likelihood of gene gain or loss in accounting for the distribution of each gene. Acquired marine adaptation genes were associated with electron transport, sodium and ABC transporters, and channels and pores. In addition, the loss of a mechanosensitive channel gene appears to have played a major role in the inability of Salinispora strains to grow following transfer to low osmotic strength media. Conclusions The marine Actinobacteria for which genome sequences are available are broadly distributed throughout the Actinobacterial phylogenetic tree and closely related to non-marine forms suggesting they have been independently introduced relatively recently into the marine environment. It appears that the acquisition of transporters in Salinispora spp. represents a major marine adaptation while gene loss is proposed to play a role in the inability of this genus to survive outside of the marine environment. This study reveals fundamental differences between marine adaptations in Gram-positive and Gram-negative bacteria and no common genetic basis for marine adaptation among the Actinobacteria analyzed.

  20. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

    Science.gov (United States)

    Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

    2015-01-01

    Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional) states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported) face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people) cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits) of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

  1. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

    Directory of Open Access Journals (Sweden)

    Aamena Alshamsi

    Full Text Available Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

  2. Intestinal transcriptome analysis revealed differential salinity adaptation between two tilapiine species.

    Science.gov (United States)

    Ronkin, Dana; Seroussi, Eyal; Nitzan, Tali; Doron-Faigenboim, Adi; Cnaani, Avner

    2015-03-01

    Tilapias are a group of freshwater species, which vary in their ability to adapt to high salinity water. Osmotic regulation in fish is conducted mainly in the gills, kidney, and gastrointestinal tract (GIT). The mechanisms involved in ion and water transport through the GIT is not well-characterized, with only a few described complexes. Comparing the transcriptome of the anterior and posterior intestinal sections of a freshwater and saltwater adapted fish by deep-sequencing, we examined the salinity adaptation of two tilapia species: the high salinity-tolerant Oreochromis mossambicus (Mozambique tilapia), and the less salinity-tolerant Oreochromis niloticus (Nile tilapia). This comparative analysis revealed high similarity in gene expression response to salinity change between species in the posterior intestine and large differences in the anterior intestine. Furthermore, in the anterior intestine 68 genes were saltwater up-regulated in one species and down-regulated in the other species (47 genes up-regulated in O. niloticus and down-regulated in O. mossambicus, with 21 genes showing the reverse pattern). Gene ontology (GO) analysis showed a high proportion of transporter and ion channel function among these genes. The results of this study point to a group of genes that differed in their salinity-dependent regulation pattern in the anterior intestine as potentially having a role in the differential salinity tolerance of these two closely related species. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Molecular evidence for convergent evolution and allopolyploid speciation within the Physcomitrium-Physcomitrella species complex.

    Science.gov (United States)

    Beike, Anna K; von Stackelberg, Mark; Schallenberg-Rüdinger, Mareike; Hanke, Sebastian T; Follo, Marie; Quandt, Dietmar; McDaniel, Stuart F; Reski, Ralf; Tan, Benito C; Rensing, Stefan A

    2014-07-11

    The moss Physcomitrella patens (Hedw.) Bruch & Schimp. is an important experimental model system for evolutionary-developmental studies. In order to shed light on the evolutionary history of Physcomitrella and related species within the Funariaceae, we analyzed the natural genetic diversity of the Physcomitrium-Physcomitrella species complex. Molecular analysis of the nuclear single copy gene BRK1 reveals that three Physcomitrium species feature larger genome sizes than Physcomitrella patens and encode two expressed BRK1 homeologs (polyploidization-derived paralogs), indicating that they may be allopolyploid hybrids. Phylogenetic analyses of BRK1 as well as microsatellite simple sequence repeat (SSR) data confirm a polyphyletic origin for three Physcomitrella lineages. Differences in the conservation of mitochondrial editing sites further support hybridization and cryptic speciation within the Physcomitrium-Physcomitrella species complex. We propose a revised classification of the previously described four subspecies of Physcomitrella patens into three distinct species, namely Physcomitrella patens, Physcomitrella readeri and Physcomitrella magdalenae. We argue that secondary reduction of sporophyte complexity in these species is due to the establishment of an ecological niche, namely spores resting in mud and possible spore dispersal by migratory birds. Besides the Physcomitrium-Physcomitrella species complex, the Funariaceae are host to their type species, Funaria hygrometrica, featuring a sporophyte morphology which is more complex. Their considerable developmental variation among closely related lineages and remarkable trait evolution render the Funariaceae an interesting group for evolutionary and genetic research.

  4. Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea

    Directory of Open Access Journals (Sweden)

    Logue Kyle

    2013-02-01

    Full Text Available Abstract Background Members of the Anopheles punctulatus group (AP group are the primary vectors of human malaria in Papua New Guinea. The AP group includes 13 sibling species, most of them morphologically indistinguishable. Understanding why only certain species are able to transmit malaria requires a better comprehension of their evolutionary history. In particular, understanding relationships and divergence times among Anopheles species may enable assessing how malaria-related traits (e.g. blood feeding behaviours, vector competence have evolved. Methods DNA sequences of 14 mitochondrial (mt genomes from five AP sibling species and two species of the Anopheles dirus complex of Southeast Asia were sequenced. DNA sequences from all concatenated protein coding genes (10,770 bp were then analysed using a Bayesian approach to reconstruct phylogenetic relationships and date the divergence of the AP sibling species. Results Phylogenetic reconstruction using the concatenated DNA sequence of all mitochondrial protein coding genes indicates that the ancestors of the AP group arrived in Papua New Guinea 25 to 54 million years ago and rapidly diverged to form the current sibling species. Conclusion Through evaluation of newly described mt genome sequences, this study has revealed a divergence among members of the AP group in Papua New Guinea that would significantly predate the arrival of humans in this region, 50 thousand years ago. The divergence observed among the mtDNA sequences studied here may have resulted from reproductive isolation during historical changes in sea-level through glacial minima and maxima. This leads to a hypothesis that the AP sibling species have evolved independently for potentially thousands of generations. This suggests that the evolution of many phenotypes, such as insecticide resistance will arise independently in each of the AP sibling species studied here.

  5. Epiverta Dieke (Coleoptera: Coccinellidae: Epilachnini): A Complex of Species, Not a Monotypic Genus.

    Science.gov (United States)

    Tomaszewska, Wioletta; Huo, Lizhi; Szawaryn, Karol; Wang, Xingmin

    2017-01-01

    Rich sampling and modern research techniques, including SEM, revealed that rarely collected epilachnine species Epiverta chelonia is a complex of four closely related species: E. chelonia (Mader, 1933), E. albopilosa, E. angusta, and E. supinata spp. nov. All Epiverta species are described and illustrated, a key to the species and a distribution map are provided. Lectotype of Solanophila cheloniaMader, 1933 is designated and its type locality delimited to Yunnan Province, Deqin County (China). © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

  6. The Drosophila ananassae species complex: Evolutionary relationships among different members

    Directory of Open Access Journals (Sweden)

    Singh B.N.

    2013-01-01

    Full Text Available Information about genetic structure and historical demography of natural populations is central to understanding how natural selection changes genomes. Drosophila ananassae is a widespread species occurring in geographically isolated or partially isolated populations and provides a unique opportunity to investigate population structure and molecular variation. D. ananassae and its closely related species serve as a widely used model in population and evolutionary genetics. The ananassae subgroup belongs to the melanogaster species group. This subgroup contains 22 described species distributed mainly throughout Southeast Asia, with some species expanding into northeastern Australia, South Pacific and Indian subcontinent and Africa. Within the ananassae subgroup, three species complexes-ananassae, bipectinata and ercepeae have been recognized based on male genital morphology. D. ananassae and its relatives have many advantages as a model of genetic differentiation and speciation. In this review, distribution, phylogenies, hybridization, sexual isolation among D. ananassae complex have been discussed. The complex of several cryptic island species provides a useful model for evolutionary studies dealing with the mechanisms of speciation.

  7. Seed sexing revealed female bias in two Rumex species

    Directory of Open Access Journals (Sweden)

    Dagmara Kwolek

    2011-07-01

    Full Text Available Sex-ratio bias in seeds of dioecious Rumex species with sex chromosomes is an interesting and still unsettled issue. To resolve gender among seeds of R. acetosa and R. thyrsiflorus (two species with an XX/XY1Y2 sex chromosome system, this work applied a PCR-based method involving DNA markers located on Y chromosomes. Both species showed female-biased primary sex ratios, with female bias greater in R. acetosa than in R. thyrsiflorus. The observed predominance of female seeds is consistent with the view that the female biased sex ratios in Rumex are conditioned not only postzygotically but also prezygotically.

  8. Geometric Mechanics Reveals Optimal Complex Terrestrial Undulation Patterns

    Science.gov (United States)

    Gong, Chaohui; Astley, Henry; Schiebel, Perrin; Dai, Jin; Travers, Matthew; Goldman, Daniel; Choset, Howie; CMU Team; GT Team

    Geometric mechanics offers useful tools for intuitively analyzing biological and robotic locomotion. However, utility of these tools were previously restricted to systems that have only two internal degrees of freedom and in uniform media. We show kinematics of complex locomotors that make intermittent contacts with substrates can be approximated as a linear combination of two shape bases, and can be represented using two variables. Therefore, the tools of geometric mechanics can be used to analyze motions of locomotors with many degrees of freedom. To demonstrate the proposed technique, we present studies on two different types of snake gaits which utilize combinations of waves in the horizontal and vertical planes: sidewinding (in the sidewinder rattlesnake C. cerastes) and lateral undulation (in the desert specialist snake C. occipitalis). C. cerastes moves by generating posteriorly traveling body waves in the horizontal and vertical directions, with a relative phase offset equal to +/-π/2 while C. occipitalismaintains a π/2 offset of a frequency doubled vertical wave. Geometric analysis reveals these coordination patterns enable optimal movement in the two different styles of undulatory terrestrial locomotion. More broadly, these examples demonstrate the utility of geometric mechanics in analyzing realistic biological and robotic locomotion.

  9. Oogenesis in the Bemisia tabaci MEAM1 species complex.

    Science.gov (United States)

    Guo, Jian-Yang; Wan, Fang-Hao; Ye, Gong-Yin

    2016-04-01

    The whitefly Bemisia tabaci MEAM1 species complex has invaded several parts of the world in the past 30 years and replaced native whitefly populations in the invaded regions, including certain areas of China. One of the possible reasons for the invasion is that MEAM1 whiteflies are more fecund than native species. However, the factors that affect the reproduction of the B. tabaci cryptic species are not clearly known. The regulation of oogenesis is thought to be one of the essential processes for egg formation and ovary development and could affect its population dynamics. In this study, the ovariole structure and oogenesis of the MEAM1 species complex was examined using light and transmission electron microscopy. Telotrophic ovarioles were observed in the MEAM1 species complex. Each ovariole had two well defined regions: the tropharium and the vitellarium. The tropharium always had more than ten trophocytes. The development of a single oocyte in the vitellarium has four phases: oocyte formation, previtellogenesis, vitellogenesis and choriogenesis. Two arrested oocytes, follicular cells and uncompleted oocytes were separated from the tropharium by microtubule and microfilaments. Early previtellogenesis oocytes absorbed nutrients and endosymbiont bacteria through a nutritive cord. However, the vitellogenesis of oocytes transmitted Vg through both the nutritive cord and the space between follicular cells. Each mature oocyte with deposited yolk proteins had only one bacteriocyte and was surrounded by a single layer of follicular cells. The oogenesis in the B. tabaci MEAM1 species complex concluded with the differentiation of oocytes, the transport of yolk and endosymbionts as well as the development and maturation of oocytes. This result provides important information that further defines the regulation of oogenesis in the B. tabaci complex. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Intersubject information mapping: revealing canonical representations of complex natural stimuli

    Directory of Open Access Journals (Sweden)

    Nikolaus Kriegeskorte

    2015-03-01

    Full Text Available Real-world time-continuous stimuli such as video promise greater naturalism for studies of brain function. However, modeling the stimulus variation is challenging and introduces a bias in favor of particular descriptive dimensions. Alternatively, we can look for brain regions whose signal is correlated between subjects, essentially using one subject to model another. Intersubject correlation mapping (ICM allows us to find brain regions driven in a canonical manner across subjects by a complex natural stimulus. However, it requires a direct voxel-to-voxel match between the spatiotemporal activity patterns and is thus only sensitive to common activations sufficiently extended to match up in Talairach space (or in an alternative, e.g. cortical-surface-based, common brain space. Here we introduce the more general approach of intersubject information mapping (IIM. For each brain region, IIM determines how much information is shared between the subjects' local spatiotemporal activity patterns. We estimate the intersubject mutual information using canonical correlation analysis applied to voxels within a spherical searchlight centered on each voxel in turn. The intersubject information estimate is invariant to linear transforms including spatial rearrangement of the voxels within the searchlight. This invariance to local encoding will be crucial in exploring fine-grained brain representations, which cannot be matched up in a common space and, more fundamentally, might be unique to each individual – like fingerprints. IIM yields a continuous brain map, which reflects intersubject information in fine-grained patterns. Performed on data from functional magnetic resonance imaging (fMRI of subjects viewing the same television show, IIM and ICM both highlighted sensory representations, including primary visual and auditory cortices. However, IIM revealed additional regions in higher association cortices, namely temporal pole and orbitofrontal cortex. These

  11. Species Richness and Diversity Reveal that Human-Modified ...

    African Journals Online (AJOL)

    Spider abundance differed significantly between habitat types and was influenced by the sampling methods used. Family diversity and richness showed no significant differences across the sites. The spider species consisted of primarily three functional groups: ground wanderers, web builders and plant wanderers, and ...

  12. Fish introductions reveal the temperature dependence of species interactions.

    Science.gov (United States)

    Hein, Catherine L; Öhlund, Gunnar; Englund, Göran

    2014-01-22

    A major area of current research is to understand how climate change will impact species interactions and ultimately biodiversity. A variety of environmental conditions are rapidly changing owing to climate warming, and these conditions often affect both the strength and outcome of species interactions. We used fish distributions and replicated fish introductions to investigate environmental conditions influencing the coexistence of two fishes in Swedish lakes: brown trout (Salmo trutta) and pike (Esox lucius). A logistic regression model of brown trout and pike coexistence showed that these species coexist in large lakes (more than 4.5 km(2)), but not in small, warm lakes (annual air temperature more than 0.9-1.5°C). We then explored how climate change will alter coexistence by substituting climate scenarios for 2091-2100 into our model. The model predicts that brown trout will be extirpated from approximately half of the lakes where they presently coexist with pike and from nearly all 9100 lakes where pike are predicted to invade. Context dependency was critical for understanding pike-brown trout interactions, and, given the widespread occurrence of context-dependent species interactions, this aspect will probably be critical for accurately predicting climate impacts on biodiversity.

  13. Integrative modelling reveals mechanisms linking productivity and plant species richness

    NARCIS (Netherlands)

    Grace, James B.; Anderson, T. Michael; Seabloom, Eric W.; Borer, Elizabeth T.; Adler, Peter B.; Harpole, W. Stanley; Hautier, Yann; Hillebrand, Helmut; Lind, Eric M.; Pärtel, Meelis; Bakker, Jonathan D.; Buckley, Yvonne M.; Crawley, Michael J.; Damschen, Ellen I.; Davies, Kendi F.; Fay, Philip A.; Firn, Jennifer; Gruner, Daniel S.; Hector, Andy; Knops, Johannes M. H.; MacDougall, Andrew S.; Melbourne, Brett A.; Morgan, John W.; Orrock, John L.; Prober, Suzanne M.; Smith, Melinda D.

    2016-01-01

    How ecosystem productivity and species richness are interrelated is one of the most debated subjects in the history of ecology. Decades of intensive study have yet to discern the actual mechanisms behind observed global patterns. Here, by integrating the predictions from multiple theories into a

  14. The Drosophila bipectinata species complex: degree of sterility and ...

    Indian Academy of Sciences (India)

    Genetica 140, 75–81. Banerjee P. and Singh B. N. 2015 Interspecific hybridization does not affect the level of fluctuating asymmetry (FA) in the. Drosophila bipectinata species complex. Genetica 143, 459–471. Barbash B. A., Awadalla P. and Parone A. M. 2004 Functional divergence caused by ancient positive selection of ...

  15. Species Diversity and Bird Feed in Residential Complex

    Science.gov (United States)

    Hadinoto; Suhesti, Eni

    2017-12-01

    Bird is one component of the ecosystem which has an important role in supporting the occurrence of an organism's life cycle. Therefore, the presence of birds in an area is important, because it can affect the existence and distribution of plant species. The purpose of this study is to calculate the diversity of bird species and identify the source of bird feed in the compound. This study was conducted by field surveys in the residential complex. In addition to the birds as a research object vegetation as habitat / foraging birds were also observed. Data were analyzed by using the bird diversity index, richenes index, bundance index, dominance analysis, analysis of bird distribution and analysis of the level of meeting types, while vegetation will be analyzed based on the type and part of what is eaten by birds. In Pandau Jaya housing complex, found as many as 12 species of birds which consists of seven families. Bird species often present is Cucak Kutilang (Pycnonotus aurigaster) of 20 individuals, Bondol Peking (Lonchura punctulata) 14 individuals and Perkutut Jawa (Geopelia striata) 10 individuals. Bird species diversity (H ‘) in Pandau Jaya housing complex is still relatively moderate with a value of 2.27, while the Evenness Index (E) of 0.91 and Richenes Index (R) of 2.45. Types of vegetation as a food source, among others: mango, guava, cherry, jackfruit, ketapang, coconut, areca, palm, banana, papaya, flowers and grasses.

  16. Pheromones of three ambrosia beetles in the Euwallacea fornicatus species complex: ratios and preferences

    Directory of Open Access Journals (Sweden)

    Miriam F. Cooperband

    2017-10-01

    Full Text Available Three cryptic species in the Euwallacea fornicatus species complex were reared in laboratory colonies and investigated for the presence of pheromones. Collections of volatiles from combinations of diet, fungus, beetles, and galleries from polyphagous shot hole borer (Euwallacea sp. #1 revealed the presence of 2-heneicosanone and 2-tricosanone only in the presence of beetles, regardless of sex. Subsequent examination of volatiles from the other two species, tea shot hole borer (Euwallacea sp. #2 and Kuroshio shot hole borer (Euwallacea sp. #5, revealed these two ketones were present in all three species but in different ratios. In dual choice olfactometer behavioral bioassays, mature mated females were strongly attracted to a synthetic binary blend of ketones matching their own natural ratios. However, females in each species were repelled by ketone blends in ratios corresponding to the other two species. Males of each species responded similarly to females when presented with ratios matching their own or the other two species. The presence of these compounds in the three beetle species, in ratios unique to each species, and their strong species-specific attraction and repellency, suggests they are pheromones. The ecological function of these pheromones is discussed. In addition to the pheromones, the previously known attractant (1S,4R-p-menth-2-en-1-ol (also known as quercivorol was discovered in the presence of the fungal symbionts, but not in association with the beetles. Quercivorol was tested in a dual-choice olfactometer and was strongly attractive to all three species. This evidence suggests quercivorol functions as a kairomone for members of the E. fornicatus species complex, likely produced by the symbiotic fungi.

  17. Defining species boundaries in the Merodon avidus complex (Diptera, Syrphidae using integrative taxonomy, with the description of a new species

    Directory of Open Access Journals (Sweden)

    Jelena Ačanski

    2016-10-01

    Full Text Available Several recent studies have detected and described complexes of cryptic and sibling species in the genus Merodon (Diptera, Syrphidae. One representative of these complexes is the Merodon avidus complex that contains four sibling species, which have proven difficult to distinguish using traditional morphological characters. In the present study, we use two geometric morphometric approaches, as well as molecular characters of the 5’-end of the mtDNA COI gene, to delimit sibling taxa. Analyses based on these data were used to strengthen species boundaries within the complex, and to validate the status of a previously-recognized cryptic taxon from Lesvos Island (Greece, here described as Merodon megavidus Vujić & Radenković sp. nov. Geometric morphometric results of both wing and surstylus shape confirm the present classification for three sibling species-M. avidus (Rossi, 1790, M. moenium Wiedemann in Meigen, 1822 and M. ibericus Vujić, 2015-and, importantly, clearly discriminate the newly-described taxon Merodon megavidus sp. nov. In addition to our geometric morphometric results, supporting characters were obtained from molecular analyses of mtDNA COI sequences, which clearly differentiated M. megavidus sp. nov. from the other members of the M. avidus complex. Molecular analyses revealed that the earliest divergence of M. ibericus occurred around 800 ky BP, while the most recent separation happened between M. avidus and M. moenium around 87 ky BP.

  18. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

    Science.gov (United States)

    Dasmahapatra, Kanchon K; Walters, James R.; Briscoe, Adriana D.; Davey, John W.; Whibley, Annabel; Nadeau, Nicola J.; Zimin, Aleksey V.; Hughes, Daniel S. T.; Ferguson, Laura C.; Martin, Simon H.; Salazar, Camilo; Lewis, James J.; Adler, Sebastian; Ahn, Seung-Joon; Baker, Dean A.; Baxter, Simon W.; Chamberlain, Nicola L.; Chauhan, Ritika; Counterman, Brian A.; Dalmay, Tamas; Gilbert, Lawrence E.; Gordon, Karl; Heckel, David G.; Hines, Heather M.; Hoff, Katharina J.; Holland, Peter W.H.; Jacquin-Joly, Emmanuelle; Jiggins, Francis M.; Jones, Robert T.; Kapan, Durrell D.; Kersey, Paul; Lamas, Gerardo; Lawson, Daniel; Mapleson, Daniel; Maroja, Luana S.; Martin, Arnaud; Moxon, Simon; Palmer, William J.; Papa, Riccardo; Papanicolaou, Alexie; Pauchet, Yannick; Ray, David A.; Rosser, Neil; Salzberg, Steven L.; Supple, Megan A.; Surridge, Alison; Tenger-Trolander, Ayse; Vogel, Heiko; Wilkinson, Paul A.; Wilson, Derek; Yorke, James A.; Yuan, Furong; Balmuth, Alexi L.; Eland, Cathlene; Gharbi, Karim; Thomson, Marian; Gibbs, Richard A.; Han, Yi; Jayaseelan, Joy C.; Kovar, Christie; Mathew, Tittu; Muzny, Donna M.; Ongeri, Fiona; Pu, Ling-Ling; Qu, Jiaxin; Thornton, Rebecca L.; Worley, Kim C.; Wu, Yuan-Qing; Linares, Mauricio; Blaxter, Mark L.; Constant, Richard H. ffrench; Joron, Mathieu; Kronforst, Marcus R.; Mullen, Sean P.; Reed, Robert D.; Scherer, Steven E.; Richards, Stephen; Mallet, James; McMillan, W. Owen; Jiggins, Chris D.

    2012-01-01

    The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation. PMID:22722851

  19. Remember redcedar! An overlooked species reveals its potential

    Science.gov (United States)

    Joan O' Callaghan; Leslie Brodie; Constance Harrington; Peter Gould; Warren Devine

    2012-01-01

    People have long valued mature western redcedar for its strong, lightweight wood that is rot-resistant.The species has cultural importance for Northwest tribes who use the tree’s bark and roots as well as the wood. Redcedar is very shade-tolerant and is often found in the understory and midstory of Pacific Northwest forests. It is also very adaptable and can grow on a...

  20. Genetic relationships among Orobanche species as revealed by RAPD analysis.

    Science.gov (United States)

    Román, B; Alfaro, C; Torres, A M; Moreno, M T; Satovic, Z; Pujadas, A; Rubiales, D

    2003-05-01

    RAPD markers were used to study variation among 20 taxa in the genus OROBANCHE: O. alba, O. amethystea, O. arenaria, O. ballotae, O. cernua, O. clausonis, O. cumana, O. crenata, O. densiflora, O. foetida, O. foetida var. broteri, O. gracilis, O. haenseleri, O. hederae, O. latisquama, O. mutelii, O. nana, O. ramosa, O. rapum-genistae and O. santolinae. A total of 202 amplification products generated with five arbitrary RAPD primers was obtained and species-specific markers were identified. The estimated Jaccard's differences between the species varied between 0 and 0.864. The pattern of interspecific variation obtained is in general agreement with previous taxonomic studies based on morphology, and the partition into two different sections (Trionychon and Orobanche) is generally clear. However, the position in the dendrogram of O. clausonis did not fit this classification since it clustered with members of section TRIONYCHON: Within this section, O. arenaria was relatively isolated from the other members of the section: O. mutelii, O. nana and O. ramosa. Within section Orobanche, all O. ramosa populations showed a similar amplification pattern, whereas differences among O. crenata populations growing on different hosts were found. Orobanche foetida and O. densiflora clustered together, supporting the morphological and cytological similarities and the host preferences of these species.

  1. Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors.

    Directory of Open Access Journals (Sweden)

    Scott B Vafai

    Full Text Available Deficiency of mitochondrial complex I is encountered in both rare and common diseases, but we have limited therapeutic options to treat this lesion to the oxidative phosphorylation system (OXPHOS. Idebenone and menadione are redox-active molecules capable of rescuing OXPHOS activity by engaging complex I-independent pathways of entry, often referred to as "complex I bypass." In the present study, we created a cellular model of complex I deficiency by using CRISPR genome editing to knock out Ndufa9 in mouse myoblasts, and utilized this cell line to develop a high-throughput screening platform for novel complex I bypass factors. We screened a library of ~40,000 natural product extracts and performed bioassay-guided fractionation on a subset of the top scoring hits. We isolated four plant-derived 1,4-naphthoquinone complex I bypass factors with structural similarity to menadione: chimaphilin and 3-chloro-chimaphilin from Chimaphila umbellata and dehydro-α-lapachone and dehydroiso-α-lapachone from Stereospermum euphoroides. We also tested a small number of structurally related naphthoquinones from commercial sources and identified two additional compounds with complex I bypass activity: 2-methoxy-1,4-naphthoquinone and 2-methoxy-3-methyl-1,4,-naphthoquinone. The six novel complex I bypass factors reported here expand this class of molecules and will be useful as tool compounds for investigating complex I disease biology.

  2. Chromosomal evidence for a putative cryptic species in the Gymnotus carapo species-complex (Gymnotiformes, Gymnotidae

    Directory of Open Access Journals (Sweden)

    De Souza Augusto CP

    2008-11-01

    Full Text Available Abstract Background In this study we examined the karyotypes of morphologically indistinguishable populations of the electric knifefish Gymnotus carapo sensu stricto from the Eastern Amazon of Brazil. These were identified unambiguously on the basis of external morphology, meristics, and pigmentation. Results Specimens from one of five localities exhibited a karyotype previously not documented for Gymnotus species in the Amazon basin: 2n = 40 (34M/SM+6ST/A. Samples from the other four localities exhibited a different karyotype: 2n = 42 (30M/SM+12ST/A, which we had previously described. Specimens from all five localities presented constitutive heterochromatin in the centromeric region of almost all chromosomes, including in the distal and interstitial regions. Staining with 4'6-Diamidino-2-phenylindole revealed C-positive banding. In both karyotypes the Nucleolar Organizer Region (NOR was located on the short arm of pair 20, and Chromomycin A3 stained the NORs. Fluorescent in situ hybridization with telomeric probes showed an Interstitial Telomeric Sequence (ITS in the proximal short arm of a metacentric pair in the 2n = 40 karyotype. Conclusion The difference between the two karyotypes on the diploid number and chromosome morphology can be explained by rearrangements of the fusion-fission type and also by pericentric inversions. The presence of ITS in a metacentric pair of the 2n = 40 karyotype suggests that the difference in the diploid number of the karyotypes results from a fusion. The consistent 2n = 42 karyotype at four localities suggests an interbreeding population. However, because fusion-fission and pericentric inversions of this nature typically result in reproductive isolation, we speculate that the form with the 2n = 40 karyotype is a different species to that of the 2n = 42 form. Nonetheless, we did not observe evident differences in external morphology, meristics and pigmentation between the two forms, which suggest that they

  3. Alkylation sensitivity screens reveal a conserved cross-species functionome

    Science.gov (United States)

    Svilar, David; Dyavaiah, Madhu; Brown, Ashley R.; Tang, Jiang-bo; Li, Jianfeng; McDonald, Peter R.; Shun, Tong Ying; Braganza, Andrea; Wang, Xiao-hong; Maniar, Salony; St Croix, Claudette M.; Lazo, John S.; Pollack, Ian F.; Begley, Thomas J.; Sobol, Robert W.

    2013-01-01

    To identify genes that contribute to chemotherapy resistance in glioblastoma, we conducted a synthetic lethal screen in a chemotherapy-resistant glioblastoma derived cell line with the clinical alkylator temozolomide (TMZ) and an siRNA library tailored towards “druggable” targets. Select DNA repair genes in the screen were validated independently, confirming the DNA glycosylases UNG and MYH as well as MPG to be involved in the response to high dose TMZ. The involvement of UNG and MYH is likely the result of a TMZ-induced burst of reactive oxygen species. We then compared the human TMZ sensitizing genes identified in our screen with those previously identified from alkylator screens conducted in E. coli and S. cerevisiae. The conserved biological processes across all three species composes an Alkylation Functionome that includes many novel proteins not previously thought to impact alkylator resistance. This high-throughput screen, validation and cross-species analysis was then followed by a mechanistic analysis of two essential nodes: base excision repair (BER) DNA glycosylases (UNG, human and mag1, S. cerevisiae) and protein modification systems, including UBE3B and ICMT in human cells or pby1, lip22, stp22 and aim22 in S. cerevisiae. The conserved processes of BER and protein modification were dual targeted and yielded additive sensitization to alkylators in S. cerevisiae. In contrast, dual targeting of BER and protein modification genes in human cells did not increase sensitivity, suggesting an epistatic relationship. Importantly, these studies provide potential new targets to overcome alkylating agent resistance. PMID:23038810

  4. A theoretical lens for revealing the complexity of chronic care

    NARCIS (Netherlands)

    Borgermans, L.; de Maeseneer, J.; Wollersheim, H.; Vrijhoef, H.J.M.; Devroey, D.

    2013-01-01

    The increasing prevalence of co-occurring multiple chronic conditions in an aging population has influenced the debate on complexity in chronic care and nowadays provides an impetus to the reform of numerous health systems. This article presents a theoretical lens for understanding the complexity of

  5. Principles of assembly reveal a periodic table of protein complexes.

    Science.gov (United States)

    Ahnert, Sebastian E; Marsh, Joseph A; Hernández, Helena; Robinson, Carol V; Teichmann, Sarah A

    2015-12-11

    Structural insights into protein complexes have had a broad impact on our understanding of biological function and evolution. In this work, we sought a comprehensive understanding of the general principles underlying quaternary structure organization in protein complexes. We first examined the fundamental steps by which protein complexes can assemble, using experimental and structure-based characterization of assembly pathways. Most assembly transitions can be classified into three basic types, which can then be used to exhaustively enumerate a large set of possible quaternary structure topologies. These topologies, which include the vast majority of observed protein complex structures, enable a natural organization of protein complexes into a periodic table. On the basis of this table, we can accurately predict the expected frequencies of quaternary structure topologies, including those not yet observed. These results have important implications for quaternary structure prediction, modeling, and engineering. Copyright © 2015, American Association for the Advancement of Science.

  6. Further insight into reproductive incompatibility between putative cryptic species of the Bemisia tabaci whitefly complex.

    Science.gov (United States)

    Qin, Li; Pan, Li-Long; Liu, Shu-Sheng

    2016-04-01

    The whitefly Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae), with its global distribution and extensive genetic diversity, is now known to be a complex of over 35 cryptic species. However, a satisfactory resolution of the systematics of this species complex is yet to be achieved. Here, we designed experiments to examine reproductive compatibility among species with different levels of mitochondrial cytochrome oxidase I (mtCOI) divergence. The data show that putative species with mtCOI divergence of >8% between them consistently exhibited complete reproductive isolation. However, two of the putative species, Asia II 9 and Asia II 3, with mtCOI divergence of 4.47% between them, exhibited near complete reproductive compatibility in one direction of their cross, and partial reproductive compatibility in the other direction. Together with some recent reports on this topic from the literature, our data indicates that, while divergence in the mtCOI sequences provides a valid molecular marker for species delimitation in most clades, more genetic markers and more sophisticated molecular phylogeny will be required to achieve adequate delimitation of all species in this whitefly complex. While many attempts have been made to examine the reproductive compatibility among genetic groups of the B. tabaci complex, our study represents the first effort to conduct crossing experiments with putative species that were chosen with considerations of their genetic divergence. In light of the new data, we discuss the best strategy and protocols to conduct further molecular phylogenetic analysis and crossing trials, in order to reveal the overall pattern of reproductive incompatibility among species of this whitefly complex. © 2015 Institute of Zoology, Chinese Academy of Sciences.

  7. Differential metabolism of Mycoplasma species as revealed by their genomes

    Directory of Open Access Journals (Sweden)

    Fabricio B.M. Arraes

    2007-01-01

    Full Text Available The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall, has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS. Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms.

  8. Comparative Genome Analysis of Lolium-Festuca Complex Species

    DEFF Research Database (Denmark)

    Czaban, Adrian; Byrne, Stephen; Sharma, Sapna

    2015-01-01

    The Lolium-Festuca complex incorporates species from the Lolium genera and the broad leaf Fescues. Plants belonging to this complex exhibit significant phenotypic plasticity for agriculturally important traits, such as annuality/perenniality, establishment potential, growth speed, nutritional value......, winter hardiness, drought tolerance and resistance to grazing. In this study we have sequenced and assembled the low copy fraction of the genomes of Lolium westerwoldicum, Lolium multiflorum, Festuca pratensis and Lolium temulentum. We have also generated de-novo transcriptome assemblies for each species....... Our dataset enabled us to perform comparative gene family analysis for CBF (C-Repeat Binding Factor) proteins, which are key regulators of cold acclimation and freezing tolerance in plants....

  9. 454 sequencing reveals extreme complexity of the class II Major Histocompatibility Complex in the collared flycatcher

    Directory of Open Access Journals (Sweden)

    Gustafsson Lars

    2010-12-01

    Full Text Available Abstract Background Because of their functional significance, the Major Histocompatibility Complex (MHC class I and II genes have been the subject of continuous interest in the fields of ecology, evolution and conservation. In some vertebrate groups MHC consists of multiple loci with similar alleles; therefore, the multiple loci must be genotyped simultaneously. In such complex systems, understanding of the evolutionary patterns and their causes has been limited due to challenges posed by genotyping. Results Here we used 454 amplicon sequencing to characterize MHC class IIB exon 2 variation in the collared flycatcher, an important organism in evolutionary and immuno-ecological studies. On the basis of over 152,000 sequencing reads we identified 194 putative alleles in 237 individuals. We found an extreme complexity of the MHC class IIB in the collared flycatchers, with our estimates pointing to the presence of at least nine expressed loci and a large, though difficult to estimate precisely, number of pseudogene loci. Many similar alleles occurred in the pseudogenes indicating either a series of recent duplications or extensive concerted evolution. The expressed alleles showed unambiguous signals of historical selection and the occurrence of apparent interlocus exchange of alleles. Placing the collared flycatcher's MHC sequences in the context of passerine diversity revealed transspecific MHC class II evolution within the Muscicapidae family. Conclusions 454 amplicon sequencing is an effective tool for advancing our understanding of the MHC class II structure and evolutionary patterns in Passeriformes. We found a highly dynamic pattern of evolution of MHC class IIB genes with strong signals of selection and pronounced sequence divergence in expressed genes, in contrast to the apparent sequence homogenization in pseudogenes. We show that next generation sequencing offers a universal, affordable method for the characterization and, in perspective

  10. A taxonomic revision of the Wallemia sebi species complex

    DEFF Research Database (Denmark)

    Jančič, Sašo; Nguyen, Hai D. T.; Frisvad, Jens Christian

    2015-01-01

    Wallemia sebi is a xerophilic food- and air-borne fungus. The name has been used for strains that prevail in cold, temperate and tropical climates. In this study, multi-locus phylogenetic analyses, using the internal transcribed spacer (ITS) regions, DNA replication licensing factor (MCM7), pre......-rRNA processing protein (TSR1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2) and a new marker 3´-phosphoadenosine-5´-phosphatase (HAL2), confirmed the previous hypothesis that W. sebi presents a complex of at least four species. Here, we confirm and apply...... the phylogenetic analyses based species hypotheses from a companion study to guide phenotypic assessment of W. sebi like strains from a wide range of substrates, climates and continents allowed the recognition of W. sebi sensu stricto and three new species described as W. mellicola, W. Canadensis, and W...

  11. Allopatric Speciation within a Cryptic Species Complex of Australasian Octopuses

    Science.gov (United States)

    Amor, Michael D.; Norman, Mark D.; Cameron, Hayley E.; Strugnell, Jan M.

    2014-01-01

    Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the ‘tetricus complex’. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide. PMID:24964133

  12. A Taxonomic Revision of the Wallemia sebi Species Complex.

    Directory of Open Access Journals (Sweden)

    Sašo Jančič

    Full Text Available Wallemia sebi is a xerophilic food- and air-borne fungus. The name has been used for strains that prevail in cold, temperate and tropical climates. In this study, multi-locus phylogenetic analyses, using the internal transcribed spacer (ITS regions, DNA replication licensing factor (MCM7, pre-rRNA processing protein (TSR1, RNA polymerase II largest subunit (RPB1, RNA polymerase II second largest subunit (RPB2 and a new marker 3´-phosphoadenosine-5´-phosphatase (HAL2, confirmed the previous hypothesis that W. sebi presents a complex of at least four species. Here, we confirm and apply the phylogenetic analyses based species hypotheses from a companion study to guide phenotypic assessment of W. sebi like strains from a wide range of substrates, climates and continents allowed the recognition of W. sebi sensu stricto and three new species described as W. mellicola, W. Canadensis, and W. tropicalis. The species differ in their conidial size, xerotolerance, halotolerance, chaotolerance, growth temperature regimes, extracellular enzyme activity profiles, and secondary metabolite patterns. A key to all currently accepted Wallemia species is provided that allow their identification on the basis of physiological, micromorphological and culture characters.

  13. A Taxonomic Revision of the Wallemia sebi Species Complex.

    Science.gov (United States)

    Jančič, Sašo; Nguyen, Hai D T; Frisvad, Jens C; Zalar, Polona; Schroers, Hans-Josef; Seifert, Keith A; Gunde-Cimerman, Nina

    2015-01-01

    Wallemia sebi is a xerophilic food- and air-borne fungus. The name has been used for strains that prevail in cold, temperate and tropical climates. In this study, multi-locus phylogenetic analyses, using the internal transcribed spacer (ITS) regions, DNA replication licensing factor (MCM7), pre-rRNA processing protein (TSR1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2) and a new marker 3´-phosphoadenosine-5´-phosphatase (HAL2), confirmed the previous hypothesis that W. sebi presents a complex of at least four species. Here, we confirm and apply the phylogenetic analyses based species hypotheses from a companion study to guide phenotypic assessment of W. sebi like strains from a wide range of substrates, climates and continents allowed the recognition of W. sebi sensu stricto and three new species described as W. mellicola, W. Canadensis, and W. tropicalis. The species differ in their conidial size, xerotolerance, halotolerance, chaotolerance, growth temperature regimes, extracellular enzyme activity profiles, and secondary metabolite patterns. A key to all currently accepted Wallemia species is provided that allow their identification on the basis of physiological, micromorphological and culture characters.

  14. Two new Geosmithia species in G. pallida species complex from bark beetles in eastern USA.

    Science.gov (United States)

    Huang, Y-T; Kolařík, M; Kasson, M T; Hulcr, J

    2017-01-01

    Species of Geosmithia are cosmopolitan but understudied fungi, and most are associated with phloem-feeding bark beetles on various woody hosts. We surveyed 207 bark and ambrosia beetles from 37 species in the eastern USA for associated fungi. The community is dominated by species in the G. pallida species complex (GPSC) and included several Geosmithia isolates that appear to be new to science. The new Geosmithia isolates exhibited the characteristic brownish-colored colonies typical for the G. pallida species complex and were phylogenetically resolved as two genealogically exclusive lineages based on a concatenated multilocus data set based on the internal transcribed spacers (ITS) of the nuc rDNA (ITS1-5.8S-ITS2 = ITS), and the translation elongation factor 1-α (TEF1-α), β-tubulin (TUB2), and RNA polymerase II second largest subunit (RPB2) genes. Two new Geosmithia species, G. brunnea and G. proliferans, are proposed, and their morphological traits and phylogenetic placements are presented.

  15. Social complexity parallels vocal complexity: a comparison of three non-human primate species.

    Science.gov (United States)

    Bouchet, Hélène; Blois-Heulin, Catherine; Lemasson, Alban

    2013-01-01

    Social factors play a key role in the structuring of vocal repertoires at the individual level, notably in non-human primates. Some authors suggested that, at the species level too, social life may have driven the evolution of communicative complexity, but this has rarely been empirically tested. Here, we use a comparative approach to address this issue. We investigated vocal variability, at both the call type and the repertoire levels, in three forest-dwelling species of Cercopithecinae presenting striking differences in their social systems, in terms of social organization as well as social structure. We collected female call recordings from twelve De Brazza's monkeys (Cercopithecus neglectus), six Campbell's monkeys (Cercopithecus campbelli) and seven red-capped mangabeys (Cercocebus torquatus) housed in similar conditions. First, we noted that the level of acoustic variability and individual distinctiveness found in several call types was related to their importance in social functioning. Contact calls, essential to intra-group cohesion, were the most individually distinctive regardless of the species, while threat calls were more structurally variable in mangabeys, the most "despotic" of our three species. Second, we found a parallel between the degree of complexity of the species' social structure and the size, diversity, and usage of its vocal repertoire. Mangabeys (most complex social structure) called twice as often as guenons and displayed the largest and most complex repertoire. De Brazza's monkeys (simplest social structure) displayed the smallest and simplest repertoire. Campbell's monkeys displayed an intermediate pattern. Providing evidence of higher levels of vocal variability in species presenting a more complex social system, our results are in line with the theory of a social-vocal coevolution of communicative abilities, opening new perspectives for comparative research on the evolution of communication systems in different animal taxa.

  16. Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.

    Directory of Open Access Journals (Sweden)

    Pierre Lefeuvre

    Full Text Available Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.

  17. Systematics of the Platyrrhinus helleri species complex (Chiroptera: Phyllostomidae), with descriptions of two new species

    Science.gov (United States)

    Velazco, Paúl M.; Gardner, Alfred L.; Patterson, Bruce D.

    2010-01-01

    Platyrrhinus is a diverse genus of small to large phyllostomid bats characterized by a comparatively narrow uropatagium thickly fringed with hair, a white dorsal stripe, comparatively large inner upper incisors that are convergent at the tips, and three upper and three lower molars. Eighteen species are currently recognized, the majority occurring in the Andes. Molecular, morphological, and morphometric analyses of specimens formerly identified as Platyrrhinus helleri support recognition of Platyrrhinus incarum as a separate species and reveal the presence of two species from western and northern South America that we describe herein as new (Platyrrhinus angustirostris sp. nov. from eastern Colombia and Ecuador, north-eastern Peru, and Venezuela and Platyrrhinus fusciventris sp. nov. from Guyana, Suriname, French Guiana, Trinidad and Tobago, northern Brazil, eastern Ecuador, and southern Venezuela). These two new species are sister taxa and, in turn, sister to Platyrrhinus incarum.

  18. Exotic plant species around Jeongeup Research Complex and RFT industrial complex

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jin Kyu; Cha, Min Kyoung; Ryu, Tae Ho; Lee, Yun Jong; Kim, Jin Hong [Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup(Korea, Republic of)

    2015-08-15

    In Shinjeong-dong of Jeongeup, there are three government-supported research institutes and an RFT industrial complex which is currently being established. Increased human activities can affect flora and fauna as a man-made pressure onto the region. As a baseline study, status of exotic plants was investigated prior to a full operation of the RFT industrial complex. A total of 54 species and 1 variety of naturalized or introduced plants were found in the study area. Among them, three species (Ambrosia artemisifolia var. elatior, Rumex acetocella and Aster pilosus) belong to 'nuisance species', and four species (Phytolacca americana, Iopomoea hederacea, Ereechtites hieracifolia and Rudbeckia laciniata) to ‘monitor species’ designated by the ministry of Environment. Some of naturalized trees and plants were intentionally introduced in this area, while others naturally immigrated. Physalis angulata seems to immigrate in the study area in the form of mixture with animal feeds as its distribution coincided with the transportation route of the animal feeds. Liquidambar styraciflua is amenable to the ecological investigation on the possible expansion of the species to the nearby Naejang National Park as its leave shape and autumn color are very similar to those of maple trees. The number of naturalized plants around the RFT industrial complex will increase with an increase in floating population, in human activities in association with constructions of factories and operations of the complex. The result of this study provides baseline data for assessing the ecological change of the region according to the operation of the RFT industrial complex.

  19. Exotic plant species around Jeongeup Research Complex and RFT industrial complex

    International Nuclear Information System (INIS)

    Kim, Jin Kyu; Cha, Min Kyoung; Ryu, Tae Ho; Lee, Yun Jong; Kim, Jin Hong

    2015-01-01

    In Shinjeong-dong of Jeongeup, there are three government-supported research institutes and an RFT industrial complex which is currently being established. Increased human activities can affect flora and fauna as a man-made pressure onto the region. As a baseline study, status of exotic plants was investigated prior to a full operation of the RFT industrial complex. A total of 54 species and 1 variety of naturalized or introduced plants were found in the study area. Among them, three species (Ambrosia artemisifolia var. elatior, Rumex acetocella and Aster pilosus) belong to 'nuisance species', and four species (Phytolacca americana, Iopomoea hederacea, Ereechtites hieracifolia and Rudbeckia laciniata) to ‘monitor species’ designated by the ministry of Environment. Some of naturalized trees and plants were intentionally introduced in this area, while others naturally immigrated. Physalis angulata seems to immigrate in the study area in the form of mixture with animal feeds as its distribution coincided with the transportation route of the animal feeds. Liquidambar styraciflua is amenable to the ecological investigation on the possible expansion of the species to the nearby Naejang National Park as its leave shape and autumn color are very similar to those of maple trees. The number of naturalized plants around the RFT industrial complex will increase with an increase in floating population, in human activities in association with constructions of factories and operations of the complex. The result of this study provides baseline data for assessing the ecological change of the region according to the operation of the RFT industrial complex

  20. Social complexity parallels vocal complexity: a comparison of three nonhuman primate species

    Directory of Open Access Journals (Sweden)

    Hélène eBOUCHET

    2013-07-01

    Full Text Available Social factors play a key role in the structuring of vocal repertoires at the individual level, notably in nonhuman primates. Some authors suggested that, at the species level too, social life may have driven the evolution of communicative complexity, but this has rarely been empirically tested. Here, we use a comparative approach to address this issue. We investigated vocal variability, at both the call type and the repertoire levels, in three forest-dwelling species of Cercopithecinae presenting striking differences in their social systems, in terms of social organization as well as social structure. We collected female call recordings from twelve De Brazza’s monkeys (Cercopithecus neglectus, six Campbell’s monkeys (Cercopithecus campbelli and seven red-capped mangabeys (Cercocebus torquatus housed in similar conditions. First, we noted that the level of acoustic variability and individual distinctiveness found in several call types was related to their importance in social functioning. Contact calls, essential to intra-group cohesion, were the most individually distinctive regardless of the species, while threat calls were more structurally variable in mangabeys, the most ‘despotic’ of our three species. Second, we found a parallel between the degree of complexity of the species’ social structure and the size, diversity, and usage of its vocal repertoire. Mangabeys (most complex social structure called twice as often as guenons and displayed the largest and most complex repertoire. De Brazza’s monkeys (simplest social structure displayed the smallest and simplest repertoire. Campbell’s monkeys displayed an intermediate pattern. Providing evidence of higher levels of vocal variability in species presenting a more complex social system, our results are in line with the theory of a social-vocal coevolution of communicative abilities, opening new perspectives for comparative research on the evolution of communication systems in

  1. Hierarchicality of trade flow networks reveals complexity of products.

    Directory of Open Access Journals (Sweden)

    Peiteng Shi

    Full Text Available With globalization, countries are more connected than before by trading flows, which amounts to at least 36 trillion dollars today. Interestingly, around 30-60 percents of exports consist of intermediate products in global. Therefore, the trade flow network of particular product with high added values can be regarded as value chains. The problem is weather we can discriminate between these products from their unique flow network structure? This paper applies the flow analysis method developed in ecology to 638 trading flow networks of different products. We claim that the allometric scaling exponent η can be used to characterize the degree of hierarchicality of a flow network, i.e., whether the trading products flow on long hierarchical chains. Then, it is pointed out that the flow networks of products with higher added values and complexity like machinary, transport equipment etc. have larger exponents, meaning that their trade flow networks are more hierarchical. As a result, without the extra data like global input-output table, we can identify the product categories with higher complexity, and the relative importance of a country in the global value chain by the trading network solely.

  2. Hierarchicality of trade flow networks reveals complexity of products.

    Science.gov (United States)

    Shi, Peiteng; Zhang, Jiang; Yang, Bo; Luo, Jingfei

    2014-01-01

    With globalization, countries are more connected than before by trading flows, which amounts to at least 36 trillion dollars today. Interestingly, around 30-60 percents of exports consist of intermediate products in global. Therefore, the trade flow network of particular product with high added values can be regarded as value chains. The problem is weather we can discriminate between these products from their unique flow network structure? This paper applies the flow analysis method developed in ecology to 638 trading flow networks of different products. We claim that the allometric scaling exponent η can be used to characterize the degree of hierarchicality of a flow network, i.e., whether the trading products flow on long hierarchical chains. Then, it is pointed out that the flow networks of products with higher added values and complexity like machinary, transport equipment etc. have larger exponents, meaning that their trade flow networks are more hierarchical. As a result, without the extra data like global input-output table, we can identify the product categories with higher complexity, and the relative importance of a country in the global value chain by the trading network solely.

  3. Hierarchicality of Trade Flow Networks Reveals Complexity of Products

    Science.gov (United States)

    Shi, Peiteng; Zhang, Jiang; Yang, Bo; Luo, Jingfei

    2014-01-01

    With globalization, countries are more connected than before by trading flows, which amounts to at least trillion dollars today. Interestingly, around percents of exports consist of intermediate products in global. Therefore, the trade flow network of particular product with high added values can be regarded as value chains. The problem is weather we can discriminate between these products from their unique flow network structure? This paper applies the flow analysis method developed in ecology to 638 trading flow networks of different products. We claim that the allometric scaling exponent can be used to characterize the degree of hierarchicality of a flow network, i.e., whether the trading products flow on long hierarchical chains. Then, it is pointed out that the flow networks of products with higher added values and complexity like machinary, transport equipment etc. have larger exponents, meaning that their trade flow networks are more hierarchical. As a result, without the extra data like global input-output table, we can identify the product categories with higher complexity, and the relative importance of a country in the global value chain by the trading network solely. PMID:24905753

  4. Mosaic genome architecture of the Anopheles gambiae species complex.

    Directory of Open Access Journals (Sweden)

    Rui Wang-Sattler

    2007-11-01

    Full Text Available Attempts over the last three decades to reconstruct the phylogenetic history of the Anopheles gambiae species complex have been important for developing better strategies to control malaria transmission.We used fingerprint genotyping data from 414 field-collected female mosquitoes at 42 microsatellite loci to infer the evolutionary relationships of four species in the A. gambiae complex, the two major malaria vectors A. gambiae sensu stricto (A. gambiae s.s. and A. arabiensis, as well as two minor vectors, A. merus and A. melas.We identify six taxonomic units, including a clear separation of West and East Africa A. gambiae s.s. S molecular forms. We show that the phylogenetic relationships vary widely between different genomic regions, thus demonstrating the mosaic nature of the genome of these species. The two major malaria vectors are closely related and closer to A. merus than to A. melas at the genome-wide level, which is also true if only autosomes are considered. However, within the Xag inversion region of the X chromosome, the M and two S molecular forms are most similar to A. merus. Near the X centromere, outside the Xag region, the two S forms are highly dissimilar to the other taxa. Furthermore, our data suggest that the centromeric region of chromosome 3 is a strong discriminator between the major and minor malaria vectors.Although further studies are needed to elucidate the basis of the phylogenetic variation among the different regions of the genome, the preponderance of sympatric admixtures among taxa strongly favor introgression of different genomic regions between species, rather than lineage sorting of ancestral polymorphism, as a possible mechanism.

  5. The Capsaspora genome reveals a complex unicellular prehistory of animals.

    Science.gov (United States)

    Suga, Hiroshi; Chen, Zehua; de Mendoza, Alex; Sebé-Pedrós, Arnau; Brown, Matthew W; Kramer, Eric; Carr, Martin; Kerner, Pierre; Vervoort, Michel; Sánchez-Pons, Núria; Torruella, Guifré; Derelle, Romain; Manning, Gerard; Lang, B Franz; Russ, Carsten; Haas, Brian J; Roger, Andrew J; Nusbaum, Chad; Ruiz-Trillo, Iñaki

    2013-01-01

    To reconstruct the evolutionary origin of multicellular animals from their unicellular ancestors, the genome sequences of diverse unicellular relatives are essential. However, only the genome of the choanoflagellate Monosiga brevicollis has been reported to date. Here we completely sequence the genome of the filasterean Capsaspora owczarzaki, the closest known unicellular relative of metazoans besides choanoflagellates. Analyses of this genome alter our understanding of the molecular complexity of metazoans' unicellular ancestors showing that they had a richer repertoire of proteins involved in cell adhesion and transcriptional regulation than previously inferred only with the choanoflagellate genome. Some of these proteins were secondarily lost in choanoflagellates. In contrast, most intercellular signalling systems controlling development evolved later concomitant with the emergence of the first metazoans. We propose that the acquisition of these metazoan-specific developmental systems and the co-option of pre-existing genes drove the evolutionary transition from unicellular protists to metazoans.

  6. Gastrin release: Antrum microdialysis reveals a complex neural control

    DEFF Research Database (Denmark)

    Ericsson, P; Håkanson, R; Rehfeld, Jens F.

    2010-01-01

    We used microdialysis to monitor local gastrin release in response to food, acid blockade and acute vagal excitation. For the first time, gastrin release has been monitored continuously in intact conscious rats in a physiologically relevant experimental setting in a fashion that minimizes...... the gastrin concentration in blood as well as microdialysate. The high gastrin concentration following omeprazole treatment was not affected by vagotomy. Vagal excitation stimulated the G cells: electrical vagal stimulation and pylorus ligation (fasted rats) raised the gastrin concentration transiently...... that the vagus has not only a prompt stimulatory but also a slow inhibitory effect on gastrin release. 2) Although vagal denervation did not affect the gastrin response to anacidity, the TTX experiments revealed that both food-evoked and anacidity-evoked gastrin release depends on neural input....

  7. Gastrin release: Antrum microdialysis reveals a complex neural control

    DEFF Research Database (Denmark)

    Ericsson, P; Håkanson, R; Rehfeld, Jens F.

    2010-01-01

    that the vagus has not only a prompt stimulatory but also a slow inhibitory effect on gastrin release. 2) Although vagal denervation did not affect the gastrin response to anacidity, the TTX experiments revealed that both food-evoked and anacidity-evoked gastrin release depends on neural input.......We used microdialysis to monitor local gastrin release in response to food, acid blockade and acute vagal excitation. For the first time, gastrin release has been monitored continuously in intact conscious rats in a physiologically relevant experimental setting in a fashion that minimizes...... in both serum and microdialysate. Food intake induced a 2- to 3-fold increase in serum gastrin, while gastrin in antral microdialysate increased 10- to 15-fold. In unilaterally vagotomized rats (fasted, 3 days post-op.), food evoked a prompt peak gastrin release followed by a gradual decline on the intact...

  8. Ancestral polymorphism at the major histocompatibility complex (MHCIIß in the Nesospiza bunting species complex and its sister species (Rowettia goughensis

    Directory of Open Access Journals (Sweden)

    van Rensburg Alexandra

    2012-08-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to other avian taxa. The Nesospiza bunting species complex (two species on Nightingale Island; one species with three sub-species on Inaccessible Island represents a rapid adaptive radiation at a small, isolated archipelago, and is thus an excellent model for the study of adaptation and speciation. In this first study of MHC in Nesospiza buntings, we aim to characterize MHCIIß variation, determine the strength of selection acting at this gene region and assess the level of shared polymorphism between the Nesospiza species complex and its putative sister taxon, Rowettia goughensis, from Gough Island. Results In total, 23 unique alleles were found in 14 Nesospiza and 2 R. goughensis individuals encoding at least four presumably functional loci and two pseudogenes. There was no evidence of ongoing selection on the peptide binding region (PBR. Of the 23 alleles, 15 were found on both the islands inhabited by Nesospiza species, and seven in both Nesospiza and Rowettia; indications of shared, ancestral polymorphism. A gene tree of Nesospiza MHCIIß alleles with several other passerine birds shows three highly supported Nesospiza-specific groups. All R. goughensis alleles were shared with Nesospiza, and these alleles were found in all three Nesospiza sequence groups in the gene tree, suggesting that most of the observed variation predates their phylogenetic split. Conclusions Lack of evidence of selection on the PBR, together with shared polymorphism across the gene tree, suggests that population variation of MHCIIß among Nesospiza and Rowettia is due to ancestral polymorphism rather than local selective

  9. Molecular approaches identify known species, reveal cryptic species and verify host specificity of Chinese Philotrypesis (Hymenoptera: Pteromalidae).

    Science.gov (United States)

    Zhou, Mei-Jiao; Xiao, Jin-Hua; Bian, Sheng-Nan; Li, Yan-Wei; Niu, Li-Ming; Hu, Hao-Yuan; Wu, Wen-Shan; Murphy, Robert W; Huang, Da-Wei

    2012-07-01

    Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a model taxon for studying male fighting and mating behaviour. Its extreme sexual dimorphism and male polymorphism render species identification uncertain and in-depth research on its ecology, behaviour and other evolutionary topics challenging. The fig wasps' enclosed habitat within the syconia makes their mating behaviour inaccessible, to the extent of matching conspecific females and males. In this study, we combine morphological and molecular analyses to identify species of Philotrypesis sampled from south China and to associate their extraordinarily dimorphic genders and labile male morphologies. Morphological evaluations of females identify 22 species and 28 male morphs. The mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 2 data detect 21 species using females, and 15 species among the males. Most of the males match the species as delimited by females. Both markers reveal cryptic species in P. quadrisetosa on Ficus vasculosa. Most species of wasps live on one species of fig but three species co-occur in two hosts (F. microcarpa and F. benjamina), which indicates host switching. © 2012 Blackwell Publishing Ltd.

  10. Tephritid Integrative Taxonomy: Where We Are Now, with a Focus on the Resolution of Three Tropical Fruit Fly Species Complexes.

    Science.gov (United States)

    Schutze, Mark K; Virgilio, Massimiliano; Norrbom, Allen; Clarke, Anthony R

    2017-01-31

    Accurate species delimitation underpins good taxonomy. Formalization of integrative taxonomy in the past decade has provided a framework for using multidisciplinary data to make species delimitation hypotheses more rigorous. We address the current state of integrative taxonomy by using as a case study an international project targeted at resolving three important tephritid species complexes: Bactrocera dorsalis complex, Anastrepha fraterculus complex, and Ceratitis FAR (C. fasciventris, C. anonae, C. rosa) complex. The integrative taxonomic approach has helped deliver significant advances in resolving these complexes: It has been used to identify some taxa as belonging to the same biological species as well as to confirm hidden cryptic diversity under a single taxonomic name. Nevertheless, the general application of integrative taxonomy has not been without issue, revealing challenges that must be considered when undertaking an integrative taxonomy project. Scrutiny of this international case study provides a unique opportunity to document lessons learned for the benefit of not only tephritid taxonomists, but also the wider taxonomic community.

  11. Transcriptomic analyses reveal the adaptive features and biological differences of guts from two invasive whitefly species.

    Science.gov (United States)

    Ye, Xiao-Dong; Su, Yun-Lin; Zhao, Qiong-Yi; Xia, Wen-Qiang; Liu, Shu-Sheng; Wang, Xiao-Wei

    2014-05-15

    The gut of phloem feeding insects is critical for nutrition uptake and xenobiotics degradation. However, partly due to its tiny size, genomic information for the gut of phloem feeding insects is limited. In this study, the gut transcriptomes of two species of invasive whiteflies in the Bemisia tabaci complex, Middle East Asia Minor 1 (MEAM1) and Mediterranean (MED), were analyzed using the Illumina sequencing. A total of 12,879 MEAM1 transcripts and 11,246 MED transcripts were annotated with a significant Blastx hit. In addition, 7,000 and 5,771 gut specific genes were respectively identified for MEAM1 and MED. Functional analyses on these gut specific genes demonstrated the important roles of gut in metabolism of insecticides and secondary plant chemicals. To reveal the molecular difference between guts of MEAM1 and MED, a comparison between gut transcriptomes of the two species was conducted and 3,910 pairs of orthologous genes were identified. Based on the ratio of nonsynonymous and synonymous substitutions, 15 genes were found evolving under positive selection. Many of those genes are predicted to be involved in metabolism and insecticide resistance. Furthermore, many genes related to detoxification were expressed at an elevated level in the gut of MED compared to MEAM1, which might be responsible for the MED's higher resistance to insecticides and environmental stresses. The sequencing of MED and MEAM1 gut transcriptomes and extensive comparisons of MEAM1 and MED gut transcripts provide substantial sequence information for revealing the role of gut in whiteflies.

  12. 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.

  13. In vitro photodynamic inactivation of Sporothrix schenckii complex species.

    Science.gov (United States)

    Nunes Mario, Débora Alves; Denardi, Laura Bedin; Brayer Pereira, Daniela Isabel; Santurio, Janio Morais; Alves, Sydney Hartz

    2014-10-01

    Photodynamic therapy has been applied successfully against cutaneous and subcutaneous mycoses. We applied methylene blue as a photosensitizing agent and light emitting diode (InGaAlP) against Sporothrix schenckii complex species in an in vitro assay. The viability of the conidia was determined by counting colony-forming units. Methylene blue in conjunction with laser irradiation was able to inhibit the growth of all tested samples. The in vitro inhibition of Sporothrix spp. isolates by laser light deserves in vivo experimental and clinical studies since it may be a promising treatment for cutaneous and subcutaneous sporotrichosis. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. The Ophiostoma clavatum species complex: a newly defined group in the Ophiostomatales including three novel taxa.

    Science.gov (United States)

    Linnakoski, Riikka; Jankowiak, Robert; Villari, Caterina; Kirisits, Thomas; Solheim, Halvor; de Beer, Z Wilhelm; Wingfield, Michael J

    2016-07-01

    Two species of blue-stain fungi with similar morphologies, Ophiostoma brunneo-ciliatum and Ophiostoma clavatum, are associates of bark beetles infesting Pinus spp. in Europe. This has raised questions whether they represent distinct taxa. Absence of herbarium specimens and contaminated or mistakenly identified cultures of O. brunneo-ciliatum and O. clavatum have accentuated the uncertainty regarding their correct identification. The aim of this study was to reconsider the identity of European isolates reported as O. brunneo-ciliatum and O. clavatum by applying DNA-based identification methods, and to provide appropriate type specimens for them. Phylogenetic analyses of the ITS, βT, TEF-1α and CAL gene sequences revealed that the investigated isolates represent a complex of seven cryptic species. The study confirmed that ITS data is insufficient to delineate species in some Ophiostoma species clusters. Lectotypes and epitypes were designated for O. clavatum and O. brunneo-ciliatum, and three new species, Ophiostoma brunneolum, Ophiostoma macroclavatum and Ophiostoma pseudocatenulatum, are described in the newly defined O. clavatum-complex. The other two species included in the complex are Ophiostoma ainoae and Ophiostoma tapionis. The results suggest co-evolution of these fungi in association with specific bark beetles. The results also confirm the identity of the fungus associated with the pine bark beetle Ips acuminatus as O. clavatum, while O. brunneo-ciliatum appears to be mainly associated with another pine bark beetle, Ips sexdentatus.

  15. Evidence of constrained phenotypic evolution in a cryptic species complex of agamid lizards.

    Science.gov (United States)

    Smith, Katie L; Harmon, Luke J; Shoo, Luke P; Melville, Jane

    2011-04-01

    Lineages that exhibit little morphological change over time provide a unique opportunity to explore whether nonadaptive or adaptive processes explain the conservation of morphology over evolutionary time scales. We provide the most comprehensive evaluation to date of the evolutionary processes leading to morphological similarity among species in a cryptic species complex, incorporating two agamid lizard species (Diporiphora magna and D. bilineata). Phylogenetic analysis of mitochondrial (ND2) and nuclear (RAG-1) gene regions revealed the existence of eight deeply divergent clades. Analysis of morphological data confirmed the presence of cryptic species among these clades. Alternative evolutionary hypotheses for the morphological similarity of species were tested using a combination of phylogenetic, morphological, and ecological data. Likelihood model testing of morphological data suggested a history of constrained phenotypic evolution where lineages have a tendency to return to their medial state, whereas ecological data showed support for both Brownian motion and constrained evolution. Thus, there was an overriding signature of constrained evolution influencing morphological divergence between clades. Our study illustrates the utility of using a combination of phylogenetic, morphological, and ecological data to investigate evolutionary mechanisms maintaining cryptic species. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  16. Multifaceted roles of metabolic enzymes of the Paracoccidioides species complex

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    Caroline Maria Marcos

    2014-12-01

    Full Text Available Paracoccidioides species are dimorphic fungi, and are the etiologic agents of paracoccidioidomycosis (PCM, a serious disease of multiple organs. The large number of tissues colonized by this fungus suggests the presence of a variety of surface molecules involved in adhesion. A surprising finding is that the majority of enzymes in the glycolytic pathway, tricarboxylic acid (TCA cycle and glyoxylate cycle in Paracoccidioides spp. has adhesive properties that aid in the interaction with the host extracellular matrix, and so act as ‘moonlighting’ proteins. Moonlighting proteins have multiple functions and add another dimension to cellular complexity, while benefiting cells in several ways. This phenomenon occurs in both eukaryotes and prokaryotes. For example, moonlighting proteins from the glycolytic pathway or TCA cycle can play roles in bacterial pathogens, either by acting as proteins secreted in a conventional pathway or not and/or as cell surface component that facilitate adhesion or adherence . This review outlines the multifuncionality exposed by a variety of Paracoccidioides spp. enzymes including aconitase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, isocitrate lyase, malate synthase, triose phosphate isomerase, fumarase and enolase. The roles that moonlighting activities play in the virulence characteristics of this fungus and several other human pathogens during their interactions with the host are discussed.

  17. Origin of Boundary Populations in Medaka (Oryzias latipes Species Complex).

    Science.gov (United States)

    Takehana, Yusuke; Sakai, Masato; Narita, Takanori; Sato, Tadashi; Naruse, Kiyoshi; Sakaizumi, Mitsuru

    2016-04-01

    The Japanese wild population of the medaka fish (Oryzias latipes species complex) comprises two genetically distinct groups, the Northern and the Southern Populations, with boundary populations having a unique genotype. It is thought that the boundary populations have been formed through introgressive hybridization between the two groups, because they are fixed with the Northern alleles at two allozymic loci, with the Southern alleles at two other loci, and have a unique allele at one locus. In this study, we examined the genetic population structure of the boundary populations using genome-wide single nucleotide polymorphism (SNP) data. Most SNPs of the Toyooka population, a typical boundary population, were shared with the Northern Population, some were shared with the Southern Population, and the remaining SNPs were unique to this population, suggesting that the boundary populations originated and diverged from the Northern Population. Further analyses of different populations using SNPs at eight genomic loci indicated that the boundary populations at different locations share similar genomic constitutions, and can be genetically distinguished from typical Northern Populations by unique SNPs. In addition, the boundary populations in the Maruyama River Basin had Northern mitochondrial DNA (mtDNA), while others, from the Fukuda and Kishida River Basins and from the Kumihama Bay area, had Southern mtDNA. These findings suggested that the boundary populations originated from the Northern Population, and then their genomes diverged as a result of geographical isolation, followed by mtDNA introgression from the Southern Population that occurred independently in some populations.

  18. Cross-mating experiments detect reproductive compatibility between Triatoma sherlocki and other members of the Triatoma brasiliensis species complex.

    Science.gov (United States)

    Correia, Nathália; Almeida, Carlos E; Lima-Neiva, Vanessa; Gumiel, Márcia; Dornak, L Lynnette; Lima, Marli M; Medeiros, Lívia M O; Mendonça, Vagner J; da Rosa, João A; Costa, Jane

    2013-10-01

    Phylogenetic approaches based on mitochondrial DNA variation (fragments of Cyt B and 16S ribosomal RNA) have revealed Triatoma sherlocki as the most recent species addition to the Triatoma brasiliensis species complex; a monophyletic group which includes T. brasiliensis, Triatoma melanica, and Triatoma juazeirensis. T. sherlocki is the most differentiated among all species of this complex: it is unable to fly, possesses longer legs than the other members, and has reddish tonality in some parts of its exochorion. We question whether these species are reproductively compatible because of this pronounced morphological differentiation, and therefore, we present a series of cross breeding experiments that test compatibility between T. sherlocki and other members of the T. brasiliensis complex. We extended our analyses to include crosses between T. sherlocki and Triatoma lenti, because the latter has been suggested as a possible member of this complex. T. sherlocki male×T. lenti female pairs failed to produce hybrids. All other crosses of T. sherlocki and members of T. brasiliensis species complex, as well as backcrosses, produced viable offspring through the third generation. This study stresses the importance of searching for the features that may isolate members of the T. brasiliensis species complex. Copyright © 2013 Elsevier B.V. All rights reserved.

  19. The Tetramorium tortuosum species group (Hymenoptera, Formicidae, Myrmicinae revisited - taxonomic revision of the Afrotropical T. capillosum species complex

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    Francisco Hita Garcia

    2013-05-01

    Full Text Available In this study we revise the taxonomy of the Tetramorium tortuosum species group members encountered in the Afrotropical region, which we have placed in its own subgroup: the T. capillosum species complex. We re-describe the two previously known species T. capillosum Bolton and T. tabarum Bolton, and describe the new species T. hecate sp. n. The geographic distribution of the three species appears to be restricted to the equatorial rainforests of Central Africa. We provide a diagnosis of the T. capillosum species complex, an illustrated identification key to species level, and worker-based species descriptions, which include diagnoses, discussions, high-quality montage images, and distribution maps. Furthermore, we discuss biogeography and composition of the globally distributed T. tortuosum group.

  20. Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species.

    Science.gov (United States)

    Oono, Ryoko; Lutzoni, François; Arnold, A Elizabeth; Kaye, Laurel; U'Ren, Jana M; May, Georgiana; Carbone, Ignazio

    2014-08-01

    • Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.• We take a multilocus approach to examine genetic variation within and among populations of Lophodermium australe, an endophytic fungus commonly associated with healthy foliage of pines in the southeastern United States. Sampling focused on two pine species ranging from montane to coastal regions of North Carolina and Virginia.• Our sampling revealed two genetically distinct groups within Lophodermium australe. Our analysis detected less than one migrant per generation between them, indicating that they are distinct species. The species comprising the majority of isolates (major species) demonstrated a panmictic structure, whereas the species comprising the minority of isolates (cryptic species) demonstrated isolation by distance. Distantly related pine species hosted the same Lophodermium species, and host species did not influence genetic structure.• We present the first evidence for isolation by distance in a foliar fungal endophyte that is horizontally transmitted. Cryptic species may be common among microbial symbionts and are important to delimit when exploring their genetic structure and microevolutionary processes. The hyperdiversity of endophytic fungi may be explained in part by cryptic species without apparent ecological and morphological differences as well as genetic diversification within rare fungal species across large spatial scales. © 2014 Botanical Society of America, Inc.

  1. MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species.

    Science.gov (United States)

    Cicconardi, Francesco; Borges, Paulo A V; Strasberg, Dominique; Oromí, Pedro; López, Heriberto; Pérez-Delgado, Antonio J; Casquet, Juliane; Caujapé-Castells, Juli; Fernández-Palacios, José María; Thébaud, Christophe; Emerson, Brent C

    2017-06-01

    Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil-dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human-mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions. © 2017 John Wiley & Sons Ltd.

  2. Four new species of Pyropia (Bangiales, Rhodophyta from the west coast of North America: the Pyropia lanceolata species complex updated

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    Sandra C. Lindstrom

    2015-06-01

    Full Text Available Recent molecular studies indicate that the Pyropia lanceolata species complex on the west coast of North America is more speciose than previously thought. Based on extensive rbcL gene sequencing of representative specimens we recognize seven species in the complex, three of which are newly described: Py. montereyensis sp. nov., Py. columbiensis sp. nov., and Py. protolanceolata sp. nov. The new species are all lanceolate, at least when young, and occur in the upper mid to high intertidal zone primarily in winter and early spring. Pyropia montereyensis and Py. columbiensis are sister taxa that are distributed south and north of Cape Mendocino, respectively, and both occur slightly lower on the shore than Py. lanceolata or Py. pseudolanceolata. Pyropia protolanceolata is known thus far only from Morro Rock and the Monterey Peninsula, California; it occurs basally to the other species in the complex in the molecular phylogeny. A fourth newly described species, Pyropia bajacaliforniensis sp. nov., is more closely related to Py. nereocystis than to species in this complex proper. It is a thin species with undulate margins known only from Moss Landing, Monterey Bay, California, and northern Baja California; it also occurs in the high intertidal in spring. Porphyra mumfordii, a high intertidal winter species that has frequently been confused with species in the Py. lanceolata complex, has now been confirmed to occur from Calvert Island, British Columbia, to Pescadero State Park, California.

  3. Four new species of Pyropia (Bangiales, Rhodophyta) from the west coast of North America: the Pyropialanceolata species complex updated.

    Science.gov (United States)

    Lindstrom, Sandra C; Hughey, Jeffery R; Rosas, Luis E Aguilar

    2015-01-01

    Recent molecular studies indicate that the Pyropialanceolata species complex on the west coast of North America is more speciose than previously thought. Based on extensive rbcL gene sequencing of representative specimens we recognize seven species in the complex, three of which are newly described: Pyropiamontereyensis sp. nov., Pyropiacolumbiensis sp. nov., and Pyropiaprotolanceolata sp. nov. The new species are all lanceolate, at least when young, and occur in the upper mid to high intertidal zone primarily in winter and early spring. Pyropiamontereyensis and Pyropiacolumbiensis are sister taxa that are distributed south and north of Cape Mendocino, respectively, and both occur slightly lower on the shore than Pyropialanceolata or Pyropiapseudolanceolata. Pyropiaprotolanceolata is known thus far only from Morro Rock and the Monterey Peninsula, California; it occurs basally to the other species in the complex in the molecular phylogeny. A fourth newly described species, Pyropiabajacaliforniensis sp. nov., is more closely related to Pyropianereocystis than to species in this complex proper. It is a thin species with undulate margins known only from Moss Landing, Monterey Bay, California, and northern Baja California; it also occurs in the high intertidal in spring. Porphyramumfordii, a high intertidal winter species that has frequently been confused with species in the Pyropialanceolata complex, has now been confirmed to occur from Calvert Island, British Columbia, to Pescadero State Park, California.

  4. Spatial genetics of wild tomato species reveals roles of the Andean geography on demographic history.

    Science.gov (United States)

    Nakazato, Takuya; Housworth, Elizabeth A

    2011-01-01

    Understanding the demographic history of natural populations in relation to the geographic features in their habitats is an important step toward deciphering the mechanisms of evolutionary processes in nature. This study investigates how the complex geographic and ecological features of the Andes play a role in demographic history, species divergence, dispersal patterns, and hybridization in wild tomato species. We investigated spatial genetics of two closely related wild tomato species, Solanum lycopersicum and S. pimpinellifolium, by integrating amplified fragment length polymorphism (AFLP) marker data and geographic information system (GIS)-derived geographic and climatic data. The two species represent genetically distinct lineages largely separated by the Andes, but hybridize extensively in central to northern Ecuador, likely mediated by the transitional climatic conditions between those of the two species. Solanum lycospericum has likely experienced a severe population bottleneck during the colonization of the eastern Andes followed by a rapid population expansion. The study demonstrates that the evolutionary patterns of the two wild tomatoes, including demographic history, dispersal patterns, interspecific divergence, and hybridization, are intimately related to the complex geographic and ecological features of the Andes. Integrating genetic data across the genome and GIS-derived environmental data can provide insights into the patterns of complex evolutionary processes in nature.

  5. Mitochondrial sequence data expose the putative cosmopolitan polychaete Scoloplos armiger (Annelida, Orbiniidae as a species complex

    Directory of Open Access Journals (Sweden)

    Albrecht Sylvia

    2006-06-01

    Full Text Available Abstract Background Polychaetes assigned as Scoloplos armiger (Orbiniidae show a cosmopolitan distribution and have been encountered in all zoogeographic regions. Sibling S. armiger-like species have been revealed by recent studies using RAPDs and AFLP genetic data. We sequenced a ~12 kb fragment of the Scoloplos cf. armiger mitochondrial genome and developed primers for variable regions including the 3' end of the cox3 gene, trnQ, and most of nad6. A phylogenetic analysis of this 528-nucleotide fragment was carried out for S. armiger-like individuals from the Eastern North Atlantic as well as Pacific regions. The aim of this study is to test the cosmopolitan status, as well as to clarify the systematics of this species complex in the Eastern North Atlantic, while using a few specimens from the Pacific Ocean for comparision. Results Phylogenetic analysis of the cox3-trnQ-nad6 data set recovered five different clades of Scoloplos cf. armiger. The fragment of the mitochondrial genome of Scoloplos cf. armiger is 12,042 bp long and contains 13 protein coding genes, 15 of the 22 expected tRNAs, and the large ribosomal subunit (rrnl. Conclusion The sequenced cox3-trnQ-nad6 fragment proved to be very useful in phylogenetic analyses of Scoloplos cf. armiger. Due to its larger sampling scale this study goes beyond previous analyses which used RAPD and AFLP markers. The results of this study clearly supports that Scoloplos armiger represents a species complex and not a cosmopolitan species. We find at least two S. armiger-like species within the Pacific region and three different S. armiger-like species in the North Atlantic. Implications for the taxonomy and the impact on ecological studies are discussed.

  6. Existence of species complex largely reduced barcoding success for invasive species of Tephritidae: a case study in Bactrocera spp.

    Science.gov (United States)

    Jiang, F; Jin, Q; Liang, L; Zhang, A B; Li, Z H

    2014-11-01

    Fruit flies in the family Tephritidae are the economically important pests that have many species complexes. DNA barcoding has gradually been verified as an effective tool for identifying species in a wide range of taxonomic groups, and there are several publications on rapid and accurate identification of fruit flies based on this technique; however, comprehensive analyses of large and new taxa for the effectiveness of DNA barcoding for fruit flies identification have been rare. In this study, we evaluated the COI barcode sequences for the diagnosis of fruit flies using 1426 sequences for 73 species of Bactrocera distributed worldwide. Tree-based [neighbour-joining (NJ)]; distance-based, such as Best Match (BM), Best Close Match (BCM) and Minimum Distance (MD); and character-based methods were used to evaluate the barcoding success rates obtained with maintaining the species complex in the data set, treating a species complex as a single taxon unit, and removing the species complex. Our results indicate that the average divergence between species was 14.04% (0.00-25.16%), whereas within a species this was 0.81% (0.00-9.71%); the existence of species complexes largely reduced the barcoding success for Tephritidae, for example relatively low success rates (74.4% based on BM and BCM and 84.8% based on MD) were obtained when the sequences from species complexes were included in the analysis, whereas significantly higher success rates were achieved if the species complexes were treated as a single taxon or removed from the data set - BM (98.9%), BCM (98.5%) and MD (97.5%), or BM (98.1%), BCM (97.4%) and MD (98.2%). © 2014 John Wiley & Sons Ltd.

  7. 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.

  8. How complex is the Bufo bufo species group?

    NARCIS (Netherlands)

    Arntzen, J.W.; Recuero, E.; Canestrelli, D.; Martínez-Solano, I.

    2013-01-01

    Species delineation remains one of the most challenging tasks in the study of biodiversity, mostly owing to the application of different species concepts, which results in contrasting taxonomic arrangements. This has important practical consequences, since species are basic units in fields like

  9. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea.

    Science.gov (United States)

    Lee, On On; Wang, Yong; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

    2011-04-01

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored.

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

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    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.

  11. Enhanced reactive oxygen species through direct copper sulfide nanoparticle-doxorubicin complexation

    Science.gov (United States)

    Li, Yajuan; Cupo, Michela; Guo, Liangran; Scott, Julie; Chen, Yi-Tzai; Yan, Bingfang; Lu, Wei

    2017-12-01

    CuS-based nanostructures loading the chemotherapeutic agent doxorubicin (DOX) exerted excellent cancer photothermal chemotherapy under multi-external stimuli. The DOX loading was generally designed through electrostatic interaction or chemical linkers. However, the interaction between DOX molecules and CuS nanoparticles has not been investigated. In this work, we use PEGylated hollow copper sulfide nanoparticles (HCuSNPs) to directly load DOX through the DOX/Cu2+ chelation process. Distinctively, the synthesized PEG–HCuSNPs–DOX release the DOX/Cu2+ complexes into surrounding environment, which generate significant reactive oxygen species (ROS) in a controlled manner by near-infrared laser. The CuS nanoparticle-mediated photothermal ablation facilitates the ROS-induced cancer cell killing effect. Our current work reveals a DOX/Cu2+-mediated ROS-enhanced cell-killing effect in addition to conventional photothermal chemotherapy through the direct CuS nanoparticle-DOX complexation.

  12. Functional redundancy patterns reveal non-random assembly rules in a species-rich marine assemblage.

    Directory of Open Access Journals (Sweden)

    Nicolas Guillemot

    Full Text Available The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species.

  13. 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.

  14. DNA barcoding reveal patterns of species diversity among northwestern Pacific molluscs

    Science.gov (United States)

    Sun, Shao’e; Li, Qi; Kong, Lingfeng; Yu, Hong; Zheng, Xiaodong; Yu, Ruihai; Dai, Lina; Sun, Yan; Chen, Jun; Liu, Jun; Ni, Lehai; Feng, Yanwei; Yu, Zhenzhen; Zou, Shanmei; Lin, Jiping

    2016-01-01

    This study represents the first comprehensive molecular assessment of northwestern Pacific molluscs. In total, 2801 DNA barcodes belonging to 569 species from China, Japan and Korea were analyzed. An overlap between intra- and interspecific genetic distances was present in 71 species. We tested the efficacy of this library by simulating a sequence-based specimen identification scenario using Best Match (BM), Best Close Match (BCM) and All Species Barcode (ASB) criteria with three threshold values. BM approach returned 89.15% true identifications (95.27% when excluding singletons). The highest success rate of congruent identifications was obtained with BCM at 0.053 threshold. The analysis of our barcode library together with public data resulted in 582 Barcode Index Numbers (BINs), 72.2% of which was found to be concordantly with morphology-based identifications. The discrepancies were divided in two groups: sequences from different species clustered in a single BIN and conspecific sequences divided in one more BINs. In Neighbour-Joining phenogram, 2,320 (83.0%) queries fromed 355 (62.4%) species-specific barcode clusters allowing their successful identification. 33 species showed paraphyletic and haplotype sharing. 62 cases are represented by deeply diverged lineages. This study suggest an increased species diversity in this region, highlighting taxonomic revision and conservation strategy for the cryptic complexes. PMID:27640675

  15. Double keystone bird in a keystone species complex.

    OpenAIRE

    Daily, G C; Ehrlich, P R; Haddad, N M

    1993-01-01

    Species in a Colorado subalpine ecosystem show subtle interdependences. Red-naped sapsuckers play two distinct keystone roles. They excavate nest cavities in fungus-infected aspens that are required as nest sites by two species of swallows, and they drill sap wells into willows that provide abundant nourishment for themselves, hummingbirds, orange-crowned warblers, chipmunks, and an array of other sap robbers. The swallows thus depend on, and the sap robbers benefit from, a keystone species c...

  16. Higher order structures of Adalimumab, Infliximab and their complexes with TNFα revealed by electron microscopy.

    Science.gov (United States)

    Tran, Bich Ngoc; Chan, Siew Leong; Ng, Chloe; Shi, Jian; Correia, Ivan; Radziejewski, Czeslaw; Matsudaira, Paul

    2017-12-01

    Adalimumab and Infliximab are recombinant IgG1 monoclonal antibodies (mAbs) that bind and neutralize human tumor necrosis factor alpha (TNFα). TNFα forms a stable homotrimer with unique surface-exposed sites for Adalimumab, Infliximab, and TNF receptor binding. Here, we report the structures of Adalimumab-TNFα and Infliximab-TNFα complexes modeled from negative stain EM and cryo-EM images. EM images reveal complex structures consisting of 1:1, 1:2, 2:2, and 3:2 complexes of Adalimumab-TNFα and Infliximab-TNFα. The 2:2 complex structures of Adalimumab-TNFα and Infliximab-TNFα show diamond-shaped profiles and the 2D class averages reveal distinct orientations of the Fab domains, indicating different binding modes by Adalimumab and Infliximab to TNFα. After separation by size exclusion chromatography and analysis by negative stain EM, the 3:2 complexes of Adalimumab-TNFα or Infliximab-TNFα complexes are more complicated but retain features recognized in the 2:2 complexes. Preliminary cryo-EM analysis of 3:2 Adalimumab-TNFα complex generated a low-resolution density consistent with a TNFα trimer bound with three Fab domains from three individual antibody molecules, while each antibody molecule binds to two molecules of TNFα trimer. The Fc domains are not visible in the reconstruction. These results show the two mAbs form structurally distinct complexes with TNFα. © 2017 The Protein Society.

  17. Combination antimicrobial susceptibility testing of Burkholderia cepacia complex: significance of species.

    Science.gov (United States)

    Abbott, Felicity K; Milne, Kathleen E N; Stead, David A; Gould, Ian M

    2016-11-01

    The Burkholderia cepacia complex (Bcc) is notorious for the life-threatening pulmonary infections it causes in patients with cystic fibrosis. The multidrug-resistant nature of Bcc and differing infective Bcc species make the design of appropriate treatment regimens challenging. Previous synergy studies have failed to take account of the species of Bcc isolates. Etest methodology was used to facilitate minimum inhibitory concentration (MIC) and antimicrobial combination testing on 258 isolates of Bcc, identified to species level by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). The most active antimicrobials were trimethoprim/sulphamethoxazole, doxycycline and minocycline (52.5%, 46.4% and 45.9% of isolates susceptible, respectively). Synergy was observed in 9.2% of the 1799 combinations tested; the most common synergistic combinations were tobramycin + ceftazidime, meropenem + tobramycin and levofloxacin + piperacillin/tazobactam (35.4%, 32.3% and 22.2% synergy, respectively). Antimicrobial susceptibility analysis revealed differences between Burkholderia cenocepacia and Burkholderia multivorans. Disparity in clinical outcome during infection with these two micro-organisms necessitates further investigation into the clinical outcomes of treatment regimens in light of species identification and in vitro antimicrobial susceptibility studies. Copyright © 2016 Elsevier B.V. and International Society of Chemotherapy. All rights reserved.

  18. The bladed Bangiales (Rhodophyta) of the South Eastern Pacific: Molecular species delimitation reveals extensive diversity.

    Science.gov (United States)

    Guillemin, Marie-Laure; Contreras-Porcia, Loretto; Ramírez, María Eliana; Macaya, Erasmo C; Contador, Cristian Bulboa; Woods, Helen; Wyatt, Christopher; Brodie, Juliet

    2016-01-01

    A molecular taxonomic study of the bladed Bangiales of the South Eastern Pacific (coast of Chile) was undertaken based on sequence data of the mitochondrial COI and chloroplast rbcL for 193 specimens collected from Arica (18°S) in the north to South Patagonia (53°S) in the south. The results revealed for the first time that four genera, Porphyra, Pyropia, Fuscifolium and Wildemania were present in the region. Species delimitation was determined based on a combination of a General Mixed Yule Coalescence model (GMYC) and Automatic Barcode Gap Discovery (ABGD) coupled with detection of monophyly in tree reconstruction. The overall incongruence between the species delimitation methods within each gene was 29%. The GMYC method led to over-splitting groups, whereas the ABGD method had a tendency to lump groups. Taking a conservative approach to the number of putative species, at least 18 were recognized and, with the exception of the recently described Pyropia orbicularis, all were new to the Chilean flora. Porphyra and Pyropia were the most diverse genera with eight 'species' each, whereas only a 'single' species each was found for Fuscifolium and Wildemania. There was also evidence of recently diverging groups: Wildemania sp. was distinct but very closely related to W. amplissima from the Northern Hemisphere and raises questions in relation to such disjunct distributions. Pyropia orbicularis was very closely related to two other species, making species delimitation very difficult but provides evidence of an incipient speciation. The difference between the 'species' discovered and those previously reported for the region is discussed in relation to the difficulty of distinguishing species based on morphological identification. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Review of the Trifolium amabile Complex in Peru, with the Description of a New Species.

    Science.gov (United States)

    Molinari-Novoa, Eduardo Antonio

    2016-01-01

    Here, we describe Trifolium absconditum sp. nov., a new species of the T. amabile complex from South America. It differs from other Peruvian Trifolia of the complex by having smaller stipules, leaves, inflorescences, and floral pieces. A key for Peruvian species of the complex is presented, and typifications for them are made when necessary and material is available in Peruvian herbaria. Thus, the number of Peruvian species in the complex is elevated to three: T. amabile, T. absconditum, and a resurrected T. peruvianum. Finally, it is suggested that Chile must be excluded from the distribution of this complex.

  20. Review of the Trifolium amabile Complex in Peru, with the Description of a New Species

    Directory of Open Access Journals (Sweden)

    Eduardo Antonio Molinari-Novoa

    2016-01-01

    Full Text Available Here, we describe Trifolium absconditum sp. nov., a new species of the T. amabile complex from South America. It differs from other Peruvian Trifolia of the complex by having smaller stipules, leaves, inflorescences, and floral pieces. A key for Peruvian species of the complex is presented, and typifications for them are made when necessary and material is available in Peruvian herbaria. Thus, the number of Peruvian species in the complex is elevated to three: T. amabile, T. absconditum, and a resurrected T. peruvianum. Finally, it is suggested that Chile must be excluded from the distribution of this complex.

  1. The geography of demography: long-term demographic studies and species distribution models reveal a species border limited by adaptation.

    Science.gov (United States)

    Eckhart, V M; Geber, M A; Morris, W F; Fabio, E S; Tiffin, P; Moeller, D A

    2011-10-01

    Potential causes of species' geographic distribution limits fall into two broad classes: (1) limited adaptation across spatially variable environments and (2) limited opportunities to colonize unoccupied areas. Combining demographic studies, analyses of demographic responses to environmental variation, and species distribution models, we investigated the causes of range limits in a model system, the eastern border of the California annual plant Clarkia xantiana ssp. xantiana. Vital rates of 20 populations varied with growing season temperature and precipitation: fruit number and overwinter survival of 1-year-old seeds declined steeply, while current-year seed germination increased modestly along west-to-east gradients in decreasing temperature, decreasing mean precipitation, and increasing variation in precipitation. Long-term stochastic finite rate of increase, λ(s), exhibited a fourfold range and varied among geologic surface materials as well as with temperature and precipitation. Growth rate declined significantly toward the eastern border, falling below 1 in three of the five easternmost populations. Distribution models employing demographically important environmental variables predicted low habitat favorability beyond the eastern border. Models that filtered or weighted population presences by λ(s) predicted steeper eastward declines in favorability and assigned greater roles in setting the distribution to among-year variation in precipitation and to geologic surface material. These analyses reveal a species border likely set by limited adaptation to declining environmental quality.

  2. Conjunctival lymphangioma in a 4-year-old girl revealed tuberous sclerosis complex

    Directory of Open Access Journals (Sweden)

    Freiberg, Florentina Joyce

    2016-09-01

    Full Text Available Background: To present a case of conjunctival lymphangioma in a girl with tuberous sclerosis complex.Methods/results: A 4-year-old girl presented with a relapsing cystic lesion of the bulbar conjunctiva in the right eye with string-of-pearl-like dilation of lymphatic vessels and right-sided facial swelling with mild pain. Best-corrected vision was not impaired. Examination of the skin revealed three hypomelanotic macules and a lumbal Shagreen patch. Magnetic resonance imaging (MRI findings displayed minimal enhancement of buccal fat on the right side. Cranial and orbital MRI showed signal enhancement in the right cortical and subcortical areas. Genetic analysis revealed a heterozygous deletion encompassing exon 1 and 2 of the gene (tuberous sclerosis complex 1 gene, confirming the diagnosis of tuberous sclerosis complex.Conclusion: In conjunctival lymphangioma, tuberous sclerosis complex should be considered as the primary disease.

  3. Evidence of tree species' range shifts in a complex landscape.

    Directory of Open Access Journals (Sweden)

    Vicente J Monleon

    Full Text Available Climate change is expected to change the distribution of species. For long-lived, sessile species such as trees, tracking the warming climate depends on seedling colonization of newly favorable areas. We compare the distribution of seedlings and mature trees for all but the rarest tree species in California, Oregon and Washington, United States of America, a large, environmentally diverse region. Across 46 species, the mean annual temperature of the range of seedlings was 0.120°C colder than that of the range of trees (95% confidence interval from 0.096 to 0.144°C. The extremes of the seedling distributions also shifted towards colder temperature than those of mature trees, but the change was less pronounced. Although the mean elevation and mean latitude of the range of seedlings was higher than and north of those of the range of mature trees, elevational and latitudinal shifts run in opposite directions for the majority of the species, reflecting the lack of a direct biological relationship between species' distributions and those variables. The broad scale, environmental diversity and variety of disturbance regimes and land uses of the study area, the large number and exhaustive sampling of tree species, and the direct causal relationship between the temperature response and a warming climate, provide strong evidence to attribute the observed shifts to climate change.

  4. Ichthyobodo necator (Kinetoplastida)--a complex of sibling species.

    Science.gov (United States)

    Todal, Jan Arvid; Karlsbakk, Egil; Isaksen, Trond E; Plarre, Heidrun; Urawa, Shigehiko; Mouton, Anna; Hoel, Erik; Koren, Christian W R; Nylund, Are

    2004-01-28

    Ichthyobodo necator is a parasitic flagellate that attacks fishes, causing disease problems in freshwater worldwide. Findings of similar flagellates in strictly marine fishes have indicated that ichthyobodiosis may be caused by more than 1 flagellate species. We obtained partial small subunit rDNA (ssu rDNA) sequences of 14 Ichthyobodo isolates originating from fishes in Norway, Japan, Singapore, South Africa and Brazil, and identified 8 strains or species, including 2 species infecting cultured salmon in Norway. An Ichthyobodo species isolated from the skin of Atlantic salmon parr in freshwater is suggested to represent L. necator sensu stricto, while another species, showing particular affinity for the gills, infects salmon in both fresh- and seawater. Atlantic cod is infected with a marine Ichthyobodo species unrelated to those infecting salmonids; 2 cyprinids originating from different parts of the world had related Ichthyobodo strains/species, and 2 isolates from unrelated North and South American fishes were also closely related. The phylogenetic relationships of the Ichthyobodo isolates is described, and the implications of the molecular findings on past and future morphological studies of Ichthyobodo spp. are discussed.

  5. Substrate recognition by complement convertases revealed in the C5-cobra venom factor complex

    DEFF Research Database (Denmark)

    Laursen, Nick Stub; Andersen, Kasper Røjkjær; Braren, Ingke

    2011-01-01

    with a protease subunit (Bb or C2a). We determined the crystal structures of the C3b homologue cobra venom factor (CVF) in complex with C5, and in complex with C5 and the inhibitor SSL7 at 4.3 Å resolution. The structures reveal a parallel two-point attachment between C5 and CVF, where the presence of SSL7 only...

  6. Chromosomal structures and repetitive sequences divergence in Cucumis species revealed by comparative cytogenetic mapping.

    Science.gov (United States)

    Zhang, Yunxia; Cheng, Chunyan; Li, Ji; Yang, Shuqiong; Wang, Yunzhu; Li, Ziang; Chen, Jinfeng; Lou, Qunfeng

    2015-09-25

    Differentiation and copy number of repetitive sequences affect directly chromosome structure which contributes to reproductive isolation and speciation. Comparative cytogenetic mapping has been verified an efficient tool to elucidate the differentiation and distribution of repetitive sequences in genome. In present study, the distinct chromosomal structures of five Cucumis species were revealed through genomic in situ hybridization (GISH) technique and comparative cytogenetic mapping of major satellite repeats. Chromosome structures of five Cucumis species were investigated using GISH and comparative mapping of specific satellites. Southern hybridization was employed to study the proliferation of satellites, whose structural characteristics were helpful for analyzing chromosome evolution. Preferential distribution of repetitive DNAs at the subtelomeric regions was found in C. sativus, C hystrix and C. metuliferus, while majority was positioned at the pericentromeric heterochromatin regions in C. melo and C. anguria. Further, comparative GISH (cGISH) through using genomic DNA of other species as probes revealed high homology of repeats between C. sativus and C. hystrix. Specific satellites including 45S rDNA, Type I/II, Type III, Type IV, CentM and telomeric repeat were then comparatively mapped in these species. Type I/II and Type IV produced bright signals at the subtelomeric regions of C. sativus and C. hystrix simultaneously, which might explain the significance of their amplification in the divergence of Cucumis subgenus from the ancient ancestor. Unique positioning of Type III and CentM only at the centromeric domains of C. sativus and C. melo, respectively, combining with unique southern bands, revealed rapid evolutionary patterns of centromeric DNA in Cucumis. Obvious interstitial telomeric repeats were observed in chromosomes 1 and 2 of C. sativus, which might provide evidence of the fusion hypothesis of chromosome evolution from x = 12 to x = 7 in

  7. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    OpenAIRE

    Lee, On On; Wang, Yong; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

    2010-01-01

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla w...

  8. Genetic Diversity of Selected Mangifera Species Revealed by Inter Simple Sequence Repeats Markers

    OpenAIRE

    Ariffin, Zulhairil; Md Sah, Muhammad Shafie; Idris, Salma; Hashim, Nuradni

    2015-01-01

    ISSR markers were employed to reveal genetic diversity and genetic relatedness among 28 Mangifera accessions collected from Yan (Kedah), Bukit Gantang (Perak), Sibuti (Sarawak), and Papar (Sabah). A total of 198 markers were generated using nine anchored primers and one nonanchored primer. Genetic variation among the 28 accessions of Mangifera species including wild relatives, landraces, and clonal varieties is high, with an average degree of polymorphism of 98% and mean Shannon index, H0=7.5...

  9. How complex is the Bufo bufo species group?

    Science.gov (United States)

    Arntzen, Jan W; Recuero, Ernesto; Canestrelli, Daniele; Martínez-Solano, Iñigo

    2013-12-01

    Species delineation remains one of the most challenging tasks in the study of biodiversity, mostly owing to the application of different species concepts, which results in contrasting taxonomic arrangements. This has important practical consequences, since species are basic units in fields like ecology and conservation biology. We here review molecular genetic evidence relevant to the systematics of toads in the Bufo bufo species group (Anura, Bufonidae). Two studies recently published in this journal (Recuero et al., MPE 62: 71-86 and García-Porta et al., MPE 63: 113-130) addressed this issue but reached opposing conclusions on the taxonomy of the group (four versus two species). In particular, allozyme data in the latter paper were interpreted as evidence for hybridization across species (between B. bufo-B. spinosus and B. bufo-B. verrucosissimus). We tested claims for hybridization through re-analysis of allozyme data for individuals instead of populations, to be able to distinguish between sympatry with and without admixture, and found no evidence of hybridization across taxa. We propose alternative explanations for the observed patterns that García-Porta et al. (2012) failed to consider. In the absence of unequivocal evidence for hybridization and introgression, we reject the proposal to downgrade Bufo spinosus and Bufo verrucosissimus to the subspecies level. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  10. Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities.

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    Suleyman Yildirim

    Full Text Available BACKGROUND: Host-associated microbes comprise an integral part of animal digestive systems and these interactions have a long evolutionary history. It has been hypothesized that the gastrointestinal microbiome of humans and other non-human primates may have played significant roles in host evolution by facilitating a range of dietary adaptations. We have undertaken a comparative sequencing survey of the gastrointestinal microbiomes of several non-human primate species, with the goal of better understanding how these microbiomes relate to the evolution of non-human primate diversity. Here we present a comparative analysis of gastrointestinal microbial communities from three different species of Old World wild monkeys. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed fecal samples from three different wild non-human primate species (black-and-white colobus [Colubus guereza], red colobus [Piliocolobus tephrosceles], and red-tailed guenon [Cercopithecus ascanius]. Three samples from each species were subjected to small subunit rRNA tag pyrosequencing. Firmicutes comprised the vast majority of the phyla in each sample. Other phyla represented were Bacterioidetes, Proteobacteria, Spirochaetes, Actinobacteria, Verrucomicrobia, Lentisphaerae, Tenericutes, Planctomycetes, Fibrobacateres, and TM7. Bray-Curtis similarity analysis of these microbiomes indicated that microbial community composition within the same primate species are more similar to each other than to those of different primate species. Comparison of fecal microbiota from non-human primates with microbiota of human stool samples obtained in previous studies revealed that the gut microbiota of these primates are distinct and reflect host phylogeny. CONCLUSION/SIGNIFICANCE: Our analysis provides evidence that the fecal microbiomes of wild primates co-vary with their hosts, and that this is manifested in higher intraspecies similarity among wild primate species, perhaps reflecting species

  11. Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

    KAUST Repository

    Lee, Onon

    2010-11-18

    Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

  12. Genetic modifier screens reveal new components that interact with the Drosophila dystroglycan-dystrophin complex.

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    Mariya M Kucherenko

    Full Text Available The Dystroglycan-Dystrophin (Dg-Dys complex has a capacity to transmit information from the extracellular matrix to the cytoskeleton inside the cell. It is proposed that this interaction is under tight regulation; however the signaling/regulatory components of Dg-Dys complex remain elusive. Understanding the regulation of the complex is critical since defects in this complex cause muscular dystrophy in humans. To reveal new regulators of the Dg-Dys complex, we used a model organism Drosophila melanogaster and performed genetic interaction screens to identify modifiers of Dg and Dys mutants in Drosophila wing veins. These mutant screens revealed that the Dg-Dys complex interacts with genes involved in muscle function and components of Notch, TGF-beta and EGFR signaling pathways. In addition, components of pathways that are required for cellular and/or axonal migration through cytoskeletal regulation, such as Semaphorin-Plexin, Frazzled-Netrin and Slit-Robo pathways show interactions with Dys and/or Dg. These data suggest that the Dg-Dys complex and the other pathways regulating extracellular information transfer to the cytoskeletal dynamics are more intercalated than previously thought.

  13. 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

  14. Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea.

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    Kirill Borziak

    Full Text Available Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs, is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA, which in archaea is typically encoded by two genes (LplA-N and LplA-C, or by a lipoyl(octanoyl transferase (LipB or LipM plus a lipoic acid synthetase (LipA. Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across

  15. Scorpions from Mexico: From Species Diversity to Venom Complexity

    Science.gov (United States)

    Santibáñez-López, Carlos E.; Francke, Oscar F.; Ureta, Carolina; Possani, Lourival D.

    2015-01-01

    Scorpions are among the oldest terrestrial arthropods, which are distributed worldwide, except for Antarctica and some Pacific islands. Scorpion envenomation represents a public health problem in several parts of the world. Mexico harbors the highest diversity of scorpions in the world, including some of the world’s medically important scorpion species. The systematics and diversity of Mexican scorpion fauna has not been revised in the past decade; and due to recent and exhaustive collection efforts as part of different ongoing major revisionary systematic projects, our understanding of this diversity has changed compared with previous assessments. Given the presence of several medically important scorpion species, the study of their venom in the country is also important. In the present contribution, the diversity of scorpion species in Mexico is revised and updated based on several new systematic contributions; 281 different species are recorded. Commentaries on recent venomic, ecological and behavioral studies of Mexican scorpions are also provided. A list containing the most important peptides identified from 16 different species is included. A graphical representation of the different types of components found in these venoms is also revised. A map with hotspots showing the current knowledge on scorpion distribution and areas explored in Mexico is also provided. PMID:26712787

  16. On the dangers of model complexity without ecological justification in species distribution modeling

    Science.gov (United States)

    David M. Bell; Daniel R. Schlaepfer

    2016-01-01

    Although biogeographic patterns are the product of complex ecological processes, the increasing com-plexity of correlative species distribution models (SDMs) is not always motivated by ecological theory,but by model fit. The validity of model projections, such as shifts in a species’ climatic niche, becomesquestionable particularly during extrapolations, such as for...

  17. Distribution of Burkholderia cepacia complex species among isolates recovered from persons with or without cystic fibrosis.

    Science.gov (United States)

    Reik, Rebecca; Spilker, Theodore; Lipuma, John J

    2005-06-01

    We analyzed Burkholderia cepacia complex isolates recovered from 1,218 cystic fibrosis (CF) patients and 90 patients without CF. Although all B. cepacia complex species were found, some were rarely identified. The distribution of species differed between the CF and non-CF populations and appears to be changing over time among CF patients.

  18. Metabolomics Analysis Reveals Specific Novel Tetrapeptide and Potential Anti-Inflammatory Metabolites in Pathogenic Aspergillus species

    Directory of Open Access Journals (Sweden)

    Kim-Chung Lee

    2015-06-01

    Full Text Available Infections related to Aspergillus species have emerged to become an important focus in infectious diseases, as a result of the increasing use of immunosuppressive agents and high fatality associated with invasive aspergillosis. However, laboratory diagnosis of Aspergillus infections remains difficult. In this study, by comparing the metabolomic profiles of the culture supernatants of 30 strains of six pathogenic Aspergillus species (A. fumigatus, A. flavus, A. niger, A. terreus, A. nomius and A. tamarii and 31 strains of 10 non-Aspergillus fungi, eight compounds present in all strains of the six Aspergillus species but not in any strain of the non-Aspergillus fungi were observed. One of the eight compounds, Leu–Glu–Leu–Glu, is a novel tetrapeptide and represents the first linear tetrapeptide observed in Aspergillus species, which we propose to be named aspergitide. Two other closely related Aspergillus-specific compounds, hydroxy-(sulfooxybenzoic acid and (sulfooxybenzoic acid, may possess anti-inflammatory properties, as 2-(sulfooxybenzoic acid possesses a structure similar to those of aspirin [2-(acetoxybenzoic acid] and salicylic acid (2-hydroxybenzoic acid. Further studies to examine the potentials of these Aspergillus-specific compounds for laboratory diagnosis of aspergillosis are warranted and further experiments will reveal whether Leu–Glu–Leu–Glu, hydroxy-(sulfooxybenzoic acid and (sulfooxybenzoic acid are virulent factors of the pathogenic Aspergillus species.

  19. Revealing historic invasion patterns and potential invasion sites for two non-native plant species.

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    Jacob N Barney

    Full Text Available The historical spatio-temporal distribution of invasive species is rarely documented, hampering efforts to understand invasion dynamics, especially at regional scales. Reconstructing historical invasions through use of herbarium records combined with spatial trend analysis and modeling can elucidate spreading patterns and identify susceptible habitats before invasion occurs. Two perennial species were chosen to contrast historic and potential phytogeographies: Japanese knotweed (Polygonum cuspidatum, introduced intentionally across the US; and mugwort (Artemisia vulgaris, introduced largely accidentally to coastal areas. Spatial analysis revealed that early in the invasion, both species have a stochastic distribution across the contiguous US, but east of the 90(th meridian, which approximates the Mississippi River, quickly spread to adjacent counties in subsequent decades. In contrast, in locations west of the 90(th meridian, many populations never spread outside the founding county, probably a result of encountering unfavorable environmental conditions. Regression analysis using variables categorized as environmental or anthropogenic accounted for 24% (Japanese knotweed and 30% (mugwort of the variation in the current distribution of each species. Results show very few counties with high habitat suitability (>/=80% remain un-invaded (5 for Japanese knotweed and 6 for mugwort, suggesting these perennials are reaching the limits of large-scale expansion. Despite differences in initial introduction loci and pathways, Japanese knotweed and mugwort demonstrate similar historic patterns of spread and show declining rates of regional expansion. Invasion mitigation efforts should be concentrated on areas identified as highly susceptible that border invaded regions, as both species demonstrate secondary expansion from introduction loci.

  20. Experiments Are Revealing a Foundation Species: A Case Study of Eastern Hemlock (Tsuga canadensis

    Directory of Open Access Journals (Sweden)

    Aaron M. Ellison

    2014-01-01

    Full Text Available Foundation species are species that create and define particular ecosystems; control in large measure the distribution and abundance of associated flora and fauna; and modulate core ecosystem processes, such as energy flux and biogeochemical cycles. However, whether a particular species plays a foundational role in a system is not simply asserted. Rather, it is a hypothesis to be tested, and such tests are best done with large-scale, long-term manipulative experiments. The utility of such experiments is illustrated through a review of the Harvard Forest Hemlock Removal Experiment (HF-HeRE, a multidecadal, multihectare experiment designed to test the foundational role of eastern hemlock, Tsuga canadensis, in eastern North American forests. Experimental removal of T. canadensis has revealed that after 10 years, this species has pronounced, long-term effects on associated flora and fauna, but shorter-term effects on energy flux and nutrient cycles. We hypothesize that on century-long scales, slower changes in soil microbial associates will further alter ecosystem processes in T. canadensis stands. HF-HeRE may indeed continue for >100 years, but at such time scales, episodic disturbances and changes in regional climate and land cover can be expected to interact in novel ways with these forests and their foundation species.

  1. Identification and Characterization of Two Novel RNA Viruses from Anopheles gambiae Species Complex Mosquitoes.

    Science.gov (United States)

    Carissimo, Guillaume; Eiglmeier, Karin; Reveillaud, Julie; Holm, Inge; Diallo, Mawlouth; Diallo, Diawo; Vantaux, Amélie; Kim, Saorin; Ménard, Didier; Siv, Sovannaroth; Belda, Eugeni; Bischoff, Emmanuel; Antoniewski, Christophe; Vernick, Kenneth D

    2016-01-01

    Mosquitoes of the Anopheles gambiae complex display strong preference for human bloodmeals and are major malaria vectors in Africa. However, their interaction with viruses or role in arbovirus transmission during epidemics has been little examined, with the exception of O'nyong-nyong virus, closely related to Chikungunya virus. Deep-sequencing has revealed different RNA viruses in natural insect viromes, but none have been previously described in the Anopheles gambiae species complex. Here, we describe two novel insect RNA viruses, a Dicistrovirus and a Cypovirus, found in laboratory colonies of An. gambiae taxa using small-RNA deep sequencing. Sequence analysis was done with Metavisitor, an open-source bioinformatic pipeline for virus discovery and de novo genome assembly. Wild-collected Anopheles from Senegal and Cambodia were positive for the Dicistrovirus and Cypovirus, displaying high sequence identity to the laboratory-derived virus. Thus, the Dicistrovirus (Anopheles C virus, AnCV) and Cypovirus (Anopheles Cypovirus, AnCPV) are components of the natural virome of at least some anopheline species. Their possible influence on mosquito immunity or transmission of other pathogens is unknown. These natural viruses could be developed as models for the study of Anopheles-RNA virus interactions in low security laboratory settings, in an analogous manner to the use of rodent malaria parasites for studies of mosquito anti-parasite immunity.

  2. A newly recognized species in the Anopheles (Nyssorhynchus) albitarsis complex (Diptera: Culicidae) from Puerto Carreno, Colombia.

    Science.gov (United States)

    Brochero, Helena H L; Li, Cong; Wilkerson, Richard C

    2007-06-01

    We report a previously unrecognized mosquito species from eastern Colombia belonging to the Anopheles (Nyssorhynchus) albitarsis complex. We provisionally name this taxon An. albitarsis species "F." Until now, the only members of the Albitarsis Complex recorded from north of the Amazon River have been An. marajoara and a putative phylogenetic species, An. albitarsis "E." As with the other largely monomorphic species in the complex, we were able to detect its presence using ribosomal DNA internal transcribed spacer 2 (rDNA ITS2) and partial white gene sequences. Unlike An. marajoara, but in common with other species in the complex, An. albitarsis F lacks the white gene fourth intron. This species is sympatric with An. marajoara in a malaria-endemic area in Puerto Carreño, Vichada Department, Colombia. It could be an important current and/or historical vector of human malaria parasites at this locality and, depending on its actual distribution, elsewhere in Colombia and Venezuela.

  3. Diversification in species complexes: tests of species origin and delimitation in the Bursera simaruba clade of tropical trees (Burseraceae).

    Science.gov (United States)

    Rosell, Julieta A; Olson, Mark E; Weeks, Andrea; De-Nova, J Arturo; Lemos, Rosalinda Medina; Camacho, Jacqueline Pérez; Feria, Teresa P; Gómez-Bermejo, Roberto; Montero, Juan C; Eguiarte, Luis E

    2010-11-01

    Molecular phylogenies are invaluable for testing morphology-based species delimitation in species complexes, as well as for examining hypotheses regarding the origination of species in these groups. Using five nucleotide markers, we reconstructed the phylogeny of the Bursera simaruba species complex of neotropical trees to test the notion that four "satellite" species originated from populations of the most widely distributed member of the genus, B. simaruba, which the satellites strongly resemble. In addition to molecular phylogenetic reconstruction, we tested species delimitation of B. simaruba and the satellites using multivariate analyses of morphological and ecological characters. The analyses evaluated the taxonomic value of these traditional characters and pinpointed those in need of further study, such as the expression of pubescence. Phylogenetic data rejected the origin of three satellite species from their purported ancestor, B. simaruba, and we ascribe their morphological similarity to convergence or parallelism. The fourth satellite species likely represents one end of a spectrum of inflorescence length variation within B. simaruba and is conspecific. Despite its marked morphological variability, we recovered B. simaruba as a single valid species, which implies that it maintains genetic cohesion among distant populations throughout its vast range. Copyright © 2010 Elsevier Inc. All rights reserved.

  4. The Drosophila bipectinata species complex: degree of sterility and ...

    Indian Academy of Sciences (India)

    Haldane (1922) said that, in general, when one sex of hybrids between species is sterile or inviable, it is more frequently the heterogametic one. As suggested by numerous workers, the reason behind this phenomenon is attributed to the X chromosome, which occurs in hemizygous condition in the heterogametic sex.

  5. Comparative "Omics" of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

    NARCIS (Netherlands)

    Niehaus, E.-M.; Münsterkötter, M.; Proctor, R.H.; Brown, D.W.; Sharon, A.; Idan, Y.; Oren-Young, L.; Sieber, C.M.; Novák, O.; Pěnčík, A.; Tarkowská, D.; Hromadová, K.; Freeman, S.; Maymon, M.; Elazar, M.; Youssef, S.A.; El-Shabrawy, E.S.M.; Shalaby, A.B.A.; Houterman, P.; Brock, N.L.; Burkhardt, I.; Tsavkelova, E.A.; Dickschat, J.S.; Galuszka, P.; Güldener, U.; Tudzynski, B.

    2016-01-01

    Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share

  6. Identification of Genes under Positive Selection Reveals Differences in Evolutionary Adaptation between Brown-Algal Species

    Directory of Open Access Journals (Sweden)

    Linhong Teng

    2017-08-01

    Full Text Available Brown algae are an important taxonomic group in coastal ecosystems. The model brown algal species Ectocarpus siliculosus and Saccharina japonica are closely related lineages. Despite their close phylogenetic relationship, they vary greatly in morphology and physiology. To obtain further insights into the evolutionary forces driving divergence in brown algae, we analyzed 3,909 orthologs from both species to identify Genes Under Positive Selection (GUPS. About 12% of the orthologs in each species were considered to be under positive selection. Many GUPS are involved in membrane transport, regulation of homeostasis, and sexual reproduction in the small sporophyte of E. siliculosus, which is known to have a complex life cycle and to occupy a wide range of habitats. Genes involved in photosynthesis and cell division dominated the group of GUPS in the large kelp of S. japonica, which might explain why this alga has evolved the ability to grow very rapidly and to form some of the largest sporophytes. A significant number of molecular chaperones (e.g., heat-shock proteins involved in stress responses were identified to be under positive selection in both species, potentially indicating their important roles for macroalgae to cope with the relatively variable environment of coastal ecosystems. Moreover, analysis of previously published microarray data of E. siliculosus showed that many GUPS in E. siliculosus were responsive to stress conditions, such as oxidative and hyposaline stress, whereas our RNA-seq data of S. japonica showed that GUPS in this species were most highly expressed in large sporophytes, which supports the suggestion that selection largely acts on different sets of genes in both marcoalgal species, potentially reflecting their adaptation to different ecological niches.

  7. Molecular approaches to identify cryptic species and polymorphic species within a complex community of fig wasps.

    Directory of Open Access Journals (Sweden)

    Jin-Hua Xiao

    2010-11-01

    Full Text Available Cryptic and polymorphic species can complicate traditional taxonomic research and both of these concerns are common in fig wasp communities. Species identification is very difficult, despite great effort and the ecological importance of fig wasps. Herein, we try to identify all chalcidoid wasp species hosted by one species of fig, using both morphological and molecular methods. We compare the efficiency of four different DNA regions and find that ITS2 is highly effective for species identification, while mitochondrial COI and Cytb regions appear less reliable, possibly due to the interference signals from either nuclear copies of mtDNA, i.e. NUMTs, or the effects of Wolbachia infections. The analyses suggest that combining multiple markers is the best choice for inferring species identifications as any one marker may be unsuitable in a given case.

  8. Predicting invasive species impacts: a community module functional response approach reveals context dependencies.

    Science.gov (United States)

    Paterson, Rachel A; Dick, Jaimie T A; Pritchard, Daniel W; Ennis, Marilyn; Hatcher, Melanie J; Dunn, Alison M

    2015-03-01

    Predatory functional responses play integral roles in predator-prey dynamics, and their assessment promises greater understanding and prediction of the predatory impacts of invasive species. Other interspecific interactions, however, such as parasitism and higher-order predation, have the potential to modify predator-prey interactions and thus the predictive capability of the comparative functional response approach. We used a four-species community module (higher-order predator; focal native or invasive predators; parasites of focal predators; native prey) to compare the predatory functional responses of native Gammarus duebeni celticus and invasive Gammarus pulex amphipods towards three invertebrate prey species (Asellus aquaticus, Simulium spp., Baetis rhodani), thus, quantifying the context dependencies of parasitism and a higher-order fish predator on these functional responses. Our functional response experiments demonstrated that the invasive amphipod had a higher predatory impact (lower handling time) on two of three prey species, which reflects patterns of impact observed in the field. The community module also revealed that parasitism had context-dependent influences, for one prey species, with the potential to further reduce the predatory impact of the invasive amphipod or increase the predatory impact of the native amphipod in the presence of a higher-order fish predator. Partial consumption of prey was similar for both predators and occurred increasingly in the order A. aquaticus, Simulium spp. and B. rhodani. This was associated with increasing prey densities, but showed no context dependencies with parasitism or higher-order fish predator. This study supports the applicability of comparative functional responses as a tool to predict and assess invasive species impacts incorporating multiple context dependencies. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

  9. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.

    Science.gov (United States)

    Montefusco, David J; Chen, Lujia; Matmati, Nabil; Lu, Songjian; Newcomb, Benjamin; Cooper, Gregory F; Hannun, Yusuf A; Lu, Xinghua

    2013-10-29

    Ceramide, the central molecule of sphingolipid metabolism, is an important bioactive molecule that participates in various cellular regulatory events and that has been implicated in disease. Deciphering ceramide signaling is challenging because multiple ceramide species exist, and many of them may have distinct functions. We applied systems biology and molecular approaches to perturb ceramide metabolism in the yeast Saccharomyces cerevisiae and inferred causal relationships between ceramide species and their potential targets by combining lipidomic, genomic, and transcriptomic analyses. We found that during heat stress, distinct metabolic mechanisms controlled the abundance of different groups of ceramide species and provided experimental support for the importance of the dihydroceramidase Ydc1 in mediating the decrease in dihydroceramides during heat stress. Additionally, distinct groups of ceramide species, with different N-acyl chains and hydroxylations, regulated different sets of functionally related genes, indicating that the structural complexity of these lipids produces functional diversity. The transcriptional modules that we identified provide a resource to begin to dissect the specific functions of ceramides.

  10. COI and ITS2 sequences delimit species, reveal cryptic taxa and host specificity of fig-associated Sycophila (Hymenoptera, Eurytomidae).

    Science.gov (United States)

    Li, Yanwei; Zhou, Xin; Feng, Gui; Hu, Haoyuan; Niu, Liming; Hebert, Paul D N; Huang, Dawei

    2010-01-01

    Although the genus Sycophila has broad host preferences, some species are specifically associated with figs as nonpollinator wasps. Because of their sexual dimorphism, morphological plasticity, cryptic mating behaviour and poorly known biology, species identifications are often uncertain. It is particularly difficult to match conspecific females and males. In this study, we employed two molecular markers, mitochondrial COI and nuclear ITS2, to identify Sycophila from six Chinese fig species. Morphological studies revealed 25 female and male morphs, while sequence results for both genes were consistent in supporting the presence of 15 species, of which 13 were host specialists and two used dual hosts. A single species of Sycophila was respectively found on four fig species, but six species were isolated from Ficus benjamina and a same number was reared from Ficus microcarpa. Sequence results revealed three male morphs in one species and detected two species that were overlooked by morphological analysis. © 2009 Blackwell Publishing Ltd.

  11. Karyotype relationships among selected deer species and cattle revealed by bovine FISH probes.

    Directory of Open Access Journals (Sweden)

    Jan Frohlich

    Full Text Available The Cervidae family comprises more than fifty species divided into three subfamilies: Capreolinae, Cervinae and Hydropotinae. A characteristic attribute for the species included in this family is the great karyotype diversity, with the chromosomal numbers ranging from 2n = 6 observed in female Muntiacus muntjak vaginalis to 2n = 70 found in Mazama gouazoubira as a result of numerous Robertsonian and tandem fusions. This work reports chromosomal homologies between cattle (Bos taurus, 2n = 60 and nine cervid species using a combination of whole chromosome and region-specific paints and BAC clones derived from cattle. We show that despite the great diversity of karyotypes in the studied species, the number of conserved chromosomal segments detected by 29 cattle whole chromosome painting probes was 35 for all Cervidae samples. The detailed analysis of the X chromosomes revealed two different morphological types within Cervidae. The first one, present in the Capreolinae is a sub/metacentric X with the structure more similar to the bovine X. The second type found in Cervini and Muntiacini is an acrocentric X which shows rearrangements in the proximal part that have not yet been identified within Ruminantia. Moreover, we characterised four repetitive sequences organized in heterochromatic blocks on sex chromosomes of the reindeer (Rangifer tarandus. We show that these repeats gave no hybridization signals to the chromosomes of the closely related moose (Alces alces and are therefore specific to the reindeer.

  12. Karyotype relationships among selected deer species and cattle revealed by bovine FISH probes.

    Science.gov (United States)

    Frohlich, Jan; Kubickova, Svatava; Musilova, Petra; Cernohorska, Halina; Muskova, Helena; Vodicka, Roman; Rubes, Jiri

    2017-01-01

    The Cervidae family comprises more than fifty species divided into three subfamilies: Capreolinae, Cervinae and Hydropotinae. A characteristic attribute for the species included in this family is the great karyotype diversity, with the chromosomal numbers ranging from 2n = 6 observed in female Muntiacus muntjak vaginalis to 2n = 70 found in Mazama gouazoubira as a result of numerous Robertsonian and tandem fusions. This work reports chromosomal homologies between cattle (Bos taurus, 2n = 60) and nine cervid species using a combination of whole chromosome and region-specific paints and BAC clones derived from cattle. We show that despite the great diversity of karyotypes in the studied species, the number of conserved chromosomal segments detected by 29 cattle whole chromosome painting probes was 35 for all Cervidae samples. The detailed analysis of the X chromosomes revealed two different morphological types within Cervidae. The first one, present in the Capreolinae is a sub/metacentric X with the structure more similar to the bovine X. The second type found in Cervini and Muntiacini is an acrocentric X which shows rearrangements in the proximal part that have not yet been identified within Ruminantia. Moreover, we characterised four repetitive sequences organized in heterochromatic blocks on sex chromosomes of the reindeer (Rangifer tarandus). We show that these repeats gave no hybridization signals to the chromosomes of the closely related moose (Alces alces) and are therefore specific to the reindeer.

  13. Environmental Screening for the Scedosporium apiospermum Species Complex in Public Parks in Bangkok, Thailand.

    Directory of Open Access Journals (Sweden)

    Natthanej Luplertlop

    Full Text Available The Scedosporium apiospermum species complex, comprising filamentous fungal species S. apiospermum sensu stricto, S. boydii, S. aurantiacum, S. dehoogii and S. minutispora, are important pathogens that cause a wide variety of infections. Although some species (S. boydii and S. apiospermum have been isolated from patients in Thailand, no environmental surveys of these fungi have been performed in Thailand or surrounding countries. In this study, we isolated and identified species of these fungi from 68 soil and 16 water samples randomly collected from 10 parks in Bangkok. After filtration and subsequent inoculation of samples on Scedo-Select III medium, colony morphological examinations and microscopic observations were performed. Scedosporium species were isolated from soil in 8 of the 10 parks, but were only detected in one water sample. Colony morphologies of isolates from 41 of 68 soil samples (60.29% and 1 of 15 water samples (6.67% were consistent with that of the S. apiospermum species complex. Each morphological type was selected for species identification based on DNA sequencing and phylogenetic analysis of the β-tubulin gene. Three species of the S. apiospermum species complex were identified: S. apiospermum (71 isolates, S. aurantiacum (6 isolates and S. dehoogii (5 isolates. In addition, 16 sequences could not be assigned to an exact Scedosporium species. According to our environmental survey, the S. apiospermum species complex is widespread in soil in Bangkok, Thailand.

  14. Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species

    Science.gov (United States)

    Claußen, Maike; Lingner, Thomas; Pommerenke, Claudia; Opitz, Lennart; Salinas, Gabriela; Pieler, Tomas

    2015-01-01

    RNAs that localize to the vegetal cortex during Xenopus laevis oogenesis have been reported to function in germ layer patterning, axis determination, and development of the primordial germ cells. Here we report on the genome-wide, comparative analysis of differentially localizing RNAs in Xenopus laevis and Xenopus tropicalis oocytes, revealing a surprisingly weak degree of conservation in respect to the identity of animally as well as vegetally enriched transcripts in these closely related species. Heterologous RNA injections and protein binding studies indicate that the different RNA localization patterns in these two species are due to gain/loss of cis-acting localization signals rather than to differences in the RNA-localizing machinery. PMID:26337391

  15. Morphology informed by phylogeny reveals unexpected patterns of species differentiation in the aquatic moss Rhynchostegium riparioides s.l.

    Science.gov (United States)

    Hutsemékers, Virginie; Vieira, Cristiana C; Ros, Rosa María; Huttunen, Sanna; Vanderpoorten, Alain

    2012-02-01

    Bryophyte floras typically exhibit extremely low levels of endemism. The interpretation, that this might reflect taxonomic shortcomings, is tested here for the Macaronesian flora, using the moss species complex of Rhynchostegium riparioides as a model. The deep polyphyly of R. riparioides across its distribution range reveals active differentiation that better corresponds to geographic than morphological differences. Morphometric analyses are, in fact, blurred by a size gradient that accounts for 80% of the variation observed among gametophytic traits. The lack of endemic diversification observed in R. riparioides in Macaronesia weakens the idea that the low rates of endemism observed in the Macaronesian bryophyte flora might solely be explained by taxonomic shortcomings. To the reverse, the striking polyphyly of North American and European lineages of R. riparioides suggests that the similarity between the floras of these continents has been over-emphasized. Discriminant analyses point to the existence of morphological discontinuities among the lineages resolved by the molecular phylogeny. The global rate of error associated to species identification based on morphology (0.23) indicates, however, that intergradation of shape and size characters among species in the group challenges their identification. Copyright © 2011 Elsevier Inc. All rights reserved.

  16. Long-term changes in abundances of Sonoran Desert lizards reveal complex responses to climatic variation.

    Science.gov (United States)

    Flesch, Aaron D; Rosen, Philip C; Holm, Peter

    2017-12-01

    Understanding how climatic variation affects animal populations and communities is essential for addressing threats posed by climate change, especially in systems where impacts are projected to be high. We evaluated abundance dynamics of five common species of diurnal lizards over 25 years in a Sonoran Desert transition zone where precipitation decreased and temperature increased across time, and assessed hypotheses for the influence of climatic flux on spatiotemporal variation in abundances. We repeatedly surveyed lizards in spring and summer of each year at up to 32 sites, and used hierarchical mixture models to estimate detection probabilities, abundances, and population growth rates. Among terrestrial species, abundances of a short-lived, winter-spring breeder increased markedly by an estimated 237%-285% across time, while two larger spring-summer breeders with higher thermal preferences declined by up to 64%. Abundances of two arboreal species that occupy shaded and thus sheltered microhabitats fluctuated but did not decline systematically. Abundances of all species increased with precipitation at short lag times (1-1.5 years) likely due to enhanced food availability, but often declined after periods of high precipitation at longer lag times (2-4 years) likely due to predation and other biotic pressures. Although rising maximum daily temperatures (T max ) are expected to drive global declines of lizards, associations with T max were variable and weak for most species. Instead, abundances of all species declined with rising daily minimum temperatures, suggesting degradation of cool refugia imposed widespread metabolic or other costs. Our results suggest climate warming and drying are having major impacts on lizard communities by driving declines in species with traits that augment exposure to abiotic extremes and by modifying species interactions. The complexity of patterns we report indicates that evaluating and responding to the influence of climate change

  17. Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates.

    Directory of Open Access Journals (Sweden)

    Bo Yuan

    2015-12-01

    Full Text Available Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100 is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases-about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual's susceptibility to acquiring disease-associated alleles.

  18. The complex biogeographic history of a widespread tropical tree species.

    Science.gov (United States)

    Dick, Christopher W; Heuertz, Myriam

    2008-11-01

    Many tropical forest tree species have broad geographic ranges, and fossil records indicate that population disjunctions in some species were established millions of years ago. Here we relate biogeographic history to patterns of population differentiation, mutational and demographic processes in the widespread rainforest tree Symphonia globulifera using ribosomal (ITS) and chloroplast DNA sequences and nuclear microsatellite (nSSR) loci. Fossil records document sweepstakes dispersal origins of Neotropical S. globulifera populations from Africa during the Miocene. Despite historical long-distance gene flow, nSSR differentiation across 13 populations from Costa Rica, Panama, Ecuador (east and west of Andes) and French Guiana was pronounced (F(ST)= 0.14, R(ST)= 0.39, P F(ST)) to the divergences between cis- and trans-Andean populations. Both DNA sequence and nSSR data reflect contrasting demographic histories in lower Mesoamerica and Amazonia. Amazon populations show weak phylogeographic structure and deviation from drift-mutation equilibrium indicating recent population expansion. In Mesoamerica, genetic drift was strong and contributed to marked differentiation among populations. The genetic structure of S. globulifera contains fingerprints of drift-dispersal processes and phylogeographic footprints of geological uplifts and sweepstakes dispersal.

  19. Delimitating cryptic species in the Gracilaria domingensis complex (Gracilariaceae, Rhodophyta) using molecular and morphological data.

    Science.gov (United States)

    Lyra, Goia de M; Gurgel, C Frederico D; Costa, Emmanuelle da S; de Jesus, Priscila B; Oliveira, Mariana C; Oliveira, Eurico C; Davis, Charles C; Nunes, José Marcos de Castro

    2016-12-01

    Species in the genus Gracilaria that display conspicuously flattened vegetative morphologies are a taxonomically challenging group of marine benthic red algae. This is a result of their species richness, morphological similarity, and broad phenotypic plasticity. Within this group, the Gracilaria domingensis complex is one of the most common, conspicuous, and morphologically variable species along the tropical western Atlantic Ocean. Previous research has identified that members of this complex belong to two distantly related clades. However, despite this increased phylogentic resolution, species delimitations within each of these clades remain unclear. Our study assessed the species diversity within this difficult complex using morphological and molecular data from three genetic markers (cox1, UPA, and rbcL). We additionally applied six single-marker species delimitation methods (SDM: ABGD, GMYCs, GMYCm, SPN, bPTP, and PTP) to rbcL, which were largely in agreement regarding species delimitation. These results, combined with our analysis of morphology, indicate that the G. domingensis complex includes seven distinct species, each of which are not all most closely related: G. cervicornis; a ressurected G. ferox; G. apiculata subsp. apiculata; a new species, Gracilaria baiana sp. nov.; G. intermedia subsp. intermedia; G. venezuelensis; and G. domingensis sensu stricto, which includes the later heterotypic synonym, G. yoneshigueana. Our study demonstrates the value of multipronged strategies, including the use of both molecular and morphological approaches, to decipher cryptic species of red algae. © 2016 Phycological Society of America.

  20. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    Directory of Open Access Journals (Sweden)

    Borja Milá

    Full Text Available The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%, yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%, with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In

  1. Molecular systematics reveals increased diversity within the South African Laurencia complex (Rhodomelaceae, Rhodophyta).

    Science.gov (United States)

    Francis, Caitlynne; Bolton, John J; Mattio, Lydiane; Mandiwana-Neudani, Tshifhiwa G; Anderson, Robert J

    2017-08-01

    Previous publications list ten species in the Laurencia complex from South Africa with all ascribed to the genus Laurencia sensu stricto. However, the diversity of the complex in South Africa has not yet been re-assessed following the numerous recent taxonomic changes. This study investigated the phylogenetic relationships and taxonomy of this group in South Africa using recent collections. Methods included molecular phylogenetic analyses of plastid rbcL gene sequences (a total of 146; including eleven outgroup taxa) using Maximum Likelihood and Bayesian Inference, and the examination of morphological and anatomical characters, including the number of corps en cerise when present. The seven genera of the Laurencia complex formed monophyletic clades with high posterior probabilities. Seventeen morphotypes were identified: 14 in the genus Laurencia sensu stricto, among which eight corresponded to Laurencia species currently recognized from South Africa and one each to species of Palisada, Chondrophycus, and Laurenciella. The six remaining morphotypes in Laurencia sensu stricto did not match any descriptions and are described here as five new species: Laurencia alfredensis sp. nov., Laurencia dichotoma sp. nov., Laurencia digitata sp. nov., Laurencia multiclavata sp. nov. and Laurencia sodwaniensis sp. nov. and a new variety: Laurencia pumila var. dehoopiensis var. nov. Laurencia stegengae nom. nov. is established to replace Laurencia peninsularis Stegenga, Bolton and Anderson nom. illeg. The diversity is likely greater, with six additional unidentified specimens found in this molecular investigation. These findings place South Africa alongside Australia in having one of the most diverse floras of this group in the world. © 2017 Phycological Society of America.

  2. Population Genomics Reveals Speciation and Introgression between Brown Norway Rats and Their Sibling Species.

    Science.gov (United States)

    Teng, Huajing; Zhang, Yaohua; Shi, Chengmin; Mao, Fengbiao; Cai, Wanshi; Lu, Liang; Zhao, Fangqing; Sun, Zhongsheng; Zhang, Jianxu

    2017-09-01

    Murine rodents are excellent models for study of adaptive radiations and speciation. Brown Norway rats (Rattus norvegicus) are successful global colonizers and the contributions of their domesticated laboratory strains to biomedical research are well established. To identify nucleotide-based speciation timing of the rat and genomic information contributing to its colonization capabilities, we analyzed 51 whole-genome sequences of wild-derived Brown Norway rats and their sibling species, R. nitidus, and identified over 20 million genetic variants in the wild Brown Norway rats that were absent in the laboratory strains, which substantially expand the reservoir of rat genetic diversity. We showed that divergence of the rat and its siblings coincided with drastic climatic changes that occurred during the Middle Pleistocene. Further, we revealed that there was a geographically widespread influx of genes between Brown Norway rats and the sibling species following the divergence, resulting in numerous introgressed regions in the genomes of admixed Brown Norway rats. Intriguing, genes related to chemical communications among these introgressed regions appeared to contribute to the population-specific adaptations of the admixed Brown Norway rats. Our data reveals evolutionary history of the Brown Norway rat, and offers new insights into the role of climatic changes in speciation of animals and the effect of interspecies introgression on animal adaptation. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  3. Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins.

    Science.gov (United States)

    Grosser, Stefanie; Rawlence, Nicolas J; Anderson, Christian N K; Smith, Ian W G; Scofield, R Paul; Waters, Jonathan M

    2016-02-10

    The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional 'cryptic' invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts. © 2016 The Author(s).

  4. Comprehensive genetic analysis of OEIS complex reveals no evidence for a recurrent microdeletion or duplication.

    Science.gov (United States)

    Vlangos, Christopher N; Siuniak, Amanda; Ackley, Todd; van Bokhoven, Hans; Veltman, Joris; Iyer, Ram; Park, John M; Keppler-Noreuil, Kim; Keegan, Catherine E

    2011-01-01

    Omphalocele-exstrophy of the bladder-imperforate anus-spinal defects (OEIS) complex, or cloacal exstrophy (EC), is a rare constellation of malformations in humans involving the urogenital, gastrointestinal, and skeletal systems, and less commonly the central nervous system. Although OEIS complex is well-recognized in the clinical setting, there remains a significant lack of understanding of this condition at both the developmental and the genetic level. While most cases are sporadic, familial cases have been reported, suggesting that one or more specific genes may play a significant role in this condition. Several developmental mechanisms have been proposed to explain the etiology of OEIS complex, and it is generally considered to be a defect early in caudal mesoderm development and ventral body wall closure. The goal of this study was to identify genetic aberrations in 13 patients with OEIS/EC using a combination of candidate gene analysis and microarray studies. Analysis of 14 candidate genes in combination with either high resolution SNP or oligonucleotide microarray did not reveal any disease-causing mutations, although novel variants were identified in five patients. To our knowledge, this is the most comprehensive genetic analysis of patients with OEIS complex to date. We conclude that OEIS is a complex disorder from an etiological perspective, likely involving a combination of genetic and environmental predispositions. Based on our data, OEIS complex is unlikely to be caused by a recurrent chromosomal aberration. Copyright © 2010 Wiley-Liss, Inc.

  5. Adding complexity to the complex: new insights into the phylogeny, diversification and origin of parthenogenesis in the Aporrectodea caliginosa species complex (Oligochaeta, Lumbricidae).

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    Fernández, Rosa; Almodóvar, Ana; Novo, Marta; Simancas, Bárbara; Díaz Cosín, Darío J

    2012-08-01

    The importance of the Aporrectodea caliginosa species complex lies in the great abundance and wide distribution of the species which exist within it. For more than a century, chaos has surrounded this complex; morphological criteria has failed to solve the taxonomic status of these species. This present body of work aims to study the phylogeny of this complex by increasing the number of samples used in previous molecular works and by including morphologically-similar species that were never studied using molecular tools (A. giardi, Nicodrilus monticola, N. carochensis and N. tetramammalis). Two basal clades were obtained: one formed by A. caliginosa and A. tuberculata and the other by the rest of the species. This second clade was divided into two more: one with Eurosiberian and another with Mediterranean forms. A. caliginosa and A. longa were divided into two paraphyletic groups. Both A. giardi and A. nocturna showed characteristics consistent with monophyletic groups. Each of the two recovered lineages of A. trapezoides were phylogenetically related to different sexual species. While lineage I of A. trapezoides was monophyletic, lineage II resulted to be paraphyletic, as well as the three Nicodrilus 'species'. The diversification of the complex occurred during the Late Miocene-Early Pliocene (6.92-11.09 Mya). The parthenogenetic forms within the Mediterranean clade would have diversified before the ones in the Eurosiberian clade (3.13-4.64 Mya and 1.05-3.48 Mya, respectively), thus implying the existence not only of at least two different moments in which parthenogenesis arose within this complex of species, but also of two different and independent evolutionary lines. Neither the 4× rule nor the GMYC method for species delimitation were successful for distinguishing taxonomically-distinct species. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Delineation of a new species of the Borrelia burgdorferi Sensu Lato Complex, Borrelia americana sp. nov.

    Science.gov (United States)

    Rudenko, Nataliia; Golovchenko, Maryna; Lin, Tao; Gao, Lihui; Grubhoffer, Libor; Oliver, James H

    2009-12-01

    Analysis of borrelia isolates collected from ticks, birds, and rodents from the southeastern United States revealed the presence of well-established populations of Borrelia burgdorferi sensu stricto, Borrelia bissettii, Borrelia carolinensis, and Borrelia sp. nov. Multilocus sequence analysis of five genomic loci from seven samples representing Borrelia sp. nov. isolated from nymphal Ixodes minor collected in South Carolina showed their close relatedness to California strains known as genomospecies 1 and separation from any other known species of the B. burgdorferi sensu lato complex. One nucleotide difference in the size of the 5S-23S intergenic spacer region, one substitution in 16S rRNA gene signature nucleotides, and silent nucleotide substitutions in sequences of the gene encoding flagellin and the gene p66 clearly separate Borrelia sp. nov. isolates from South Carolina into two subgroups. The sequences of isolates of each subgroup share the same restriction fragment length polymorphism patterns of the 5S-23S intergenic spacer region and contain unique signature nucleotides in the 16S rRNA gene. We propose that seven Borrelia sp. nov. isolates from South Carolina and two California isolates designated as genomospecies 1 comprise a single species, which we name Borrelia americana sp. nov. The currently recognized geographic distribution of B. americana is South Carolina and California. All strains are associated with Ixodes pacificus or Ixodes minor and their rodent and bird hosts.

  7. Evidence of diversity and recombination in Arsenophonus symbionts of the Bemisia tabaci species complex

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    Mouton Laurence

    2012-01-01

    Full Text Available Abstract Background Maternally inherited bacterial symbionts infecting arthropods have major implications on host ecology and evolution. Among them, the genus Arsenophonus is particularly characterized by a large host spectrum and a wide range of symbiotic relationships (from mutualism to parasitism, making it a good model to study the evolution of host-symbiont associations. However, few data are available on the diversity and distribution of Arsenophonus within host lineages. Here, we propose a survey on Arsenophonus diversity in whitefly species (Hemiptera, in particular the Bemisia tabaci species complex. This polyphagous insect pest is composed of genetic groups that differ in many ecological aspects. They harbor specific bacterial communities, among them several lineages of Arsenophonus, enabling a study of the evolutionary history of these bacteria at a fine host taxonomic level, in association to host geographical range and ecology. Results Among 152 individuals, our analysis identified 19 allelic profiles and 6 phylogenetic groups, demonstrating this bacterium's high diversity. These groups, based on Arsenophonus phylogeny, correlated with B. tabaci genetic groups with two exceptions reflecting horizontal transfers. None of three genes analyzed provided evidence of intragenic recombination, but intergenic recombination events were detected. A mutation inducing a STOP codon on one gene in a strain infecting one B. tabaci genetic group was also found. Phylogenetic analyses of the three concatenated loci revealed the existence of two clades of Arsenophonus. One, composed of strains found in other Hemiptera, could be the ancestral clade in whiteflies. The other, which regroups strains found in Hymenoptera and Diptera, may have been acquired more recently by whiteflies through lateral transfers. Conclusions This analysis of the genus Arsenophonus revealed a diversity within the B. tabaci species complex which resembles that reported on the

  8. Comparative “Omics” of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

    Science.gov (United States)

    Niehaus, Eva-Maria; Münsterkötter, Martin; Proctor, Robert H.; Brown, Daren W.; Sharon, Amir; Idan, Yifat; Oren-Young, Liat; Sieber, Christian M.; Novák, Ondřej; Pěnčík, Aleš; Tarkowská, Danuše; Hromadová, Kristýna; Freeman, Stanley; Maymon, Marcel; Elazar, Meirav; Youssef, Sahar A.; El-Shabrawy, El Said M.; Shalaby, Abdel Baset A.; Houterman, Petra; Brock, Nelson L.; Burkhardt, Immo; Tsavkelova, Elena A.; Dickschat, Jeroen S.; Galuszka, Petr; Güldener, Ulrich; Tudzynski, Bettina

    2016-01-01

    Species of the Fusarium fujikuroi species complex (FFC) cause a wide spectrum of often devastating diseases on diverse agricultural crops, including coffee, fig, mango, maize, rice, and sugarcane. Although species within the FFC are difficult to distinguish by morphology, and their genes often share 90% sequence similarity, they can differ in host plant specificity and life style. FFC species can also produce structurally diverse secondary metabolites (SMs), including the mycotoxins fumonisins, fusarins, fusaric acid, and beauvericin, and the phytohormones gibberellins, auxins, and cytokinins. The spectrum of SMs produced can differ among closely related species, suggesting that SMs might be determinants of host specificity. To date, genomes of only a limited number of FFC species have been sequenced. Here, we provide draft genome sequences of three more members of the FFC: a single isolate of F. mangiferae, the cause of mango malformation, and two isolates of F. proliferatum, one a pathogen of maize and the other an orchid endophyte. We compared these genomes to publicly available genome sequences of three other FFC species. The comparisons revealed species-specific and isolate-specific differences in the composition and expression (in vitro and in planta) of genes involved in SM production including those for phytohormome biosynthesis. Such differences have the potential to impact host specificity and, as in the case of F. proliferatum, the pathogenic versus endophytic life style. PMID:28040774

  9. Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development.

    Science.gov (United States)

    Wang, Yong-Qiang; Yang, Yong; Fei, Zhangjun; Yuan, Hui; Fish, Tara; Thannhauser, Theodore W; Mazourek, Michael; Kochian, Leon V; Wang, Xiaowu; Li, Li

    2013-02-01

    Chromoplasts are unique plastids that accumulate massive amounts of carotenoids. To gain a general and comparative characterization of chromoplast proteins, this study performed proteomic analysis of chromoplasts from six carotenoid-rich crops: watermelon, tomato, carrot, orange cauliflower, red papaya, and red bell pepper. Stromal and membrane proteins of chromoplasts were separated by 1D gel electrophoresis and analysed using nLC-MS/MS. A total of 953-2262 proteins from chromoplasts of different crop species were identified. Approximately 60% of the identified proteins were predicted to be plastid localized. Functional classification using MapMan bins revealed large numbers of proteins involved in protein metabolism, transport, amino acid metabolism, lipid metabolism, and redox in chromoplasts from all six species. Seventeen core carotenoid metabolic enzymes were identified. Phytoene synthase, phytoene desaturase, ζ-carotene desaturase, 9-cis-epoxycarotenoid dioxygenase, and carotenoid cleavage dioxygenase 1 were found in almost all crops, suggesting relative abundance of them among the carotenoid pathway enzymes. Chromoplasts from different crops contained abundant amounts of ATP synthase and adenine nucleotide translocator, which indicates an important role of ATP production and transport in chromoplast development. Distinctive abundant proteins were observed in chromoplast from different crops, including capsanthin/capsorubin synthase and fibrillins in pepper, superoxide dismutase in watermelon, carrot, and cauliflower, and glutathione-S-transferease in papaya. The comparative analysis of chromoplast proteins among six crop species offers new insights into the general metabolism and function of chromoplasts as well as the uniqueness of chromoplasts in specific crop species. This work provides reference datasets for future experimental study of chromoplast biogenesis, development, and regulation in plants.

  10. Comprehensive species set revealing the phylogeny and biogeography of Feliformia (Mammalia, Carnivora based on mitochondrial DNA.

    Directory of Open Access Journals (Sweden)

    Yu Zhou

    Full Text Available Extant Feliformia species are one of the most diverse radiations of Carnivora (~123 species. Despite substantial recent interest in their conservation, diversification, and systematic study, no previous phylogeny contains a comprehensive species set, and no biogeography of this group is available. Here, we present a phylogenetic estimate for Feliformia with a comprehensive species set and establish a historical biogeography based on mitochondrial DNA. Both the Bayesian and maximum likelihood phylogeny for Feliformia are elucidated in our analyses and are strongly consistent with many groups recognized in previous studies. The mitochondrial phylogenetic relationships of Felidae were for the first time successfully reconstructed in our analyses with strong supported. When divergence times and dispersal/vicariance histories were compared with historical sea level changes, four dispersal and six vicariance events were identified. These vicariance events were closely related with global sea level changes. The transgression of sea into the lowland plains between Eurasia and Africa may have caused the vicariance in these regions. A fall in the sea level during late Miocene to Pliocene produced the Bering strait land bridge, which assisted the migration of American Feliformia ancestors from Asia to North America. In contrast with the 'sweepstakes hypothesis', our results suggest that the climate cooling during 30-27 Ma assisted Feliformia migration from the African mainland to Madagascar by creating a short-lived ice bridge across the Mozambique Channel. Lineages-through-time plots revealed a large increase in lineages since the Mid-Miocene. During the Mid-Miocene Climatic Optimum, the ecosystems and population of Feliformia rapidly expanded. Subsequent climate cooling catalyzed immigration, speciation, and the extinction of Feliformia.

  11. The occurrence of Toxocara species in naturally infected broiler chickens revealed by molecular approaches.

    Science.gov (United States)

    Zibaei, M; Sadjjadi, S M; Maraghi, S

    2017-09-01

    Consuming raw and undercooked meat is known to enhance the risk of human toxocariasis because Toxocara species have a wide range of paratenic hosts, including chickens. The aim of this study was to identify species of Toxocara in naturally infected broiler chickens using molecular approaches. A polymerase chain reaction (PCR) method was used for the differentiation of Toxocara canis and Toxocara cati larvae recovered from tissues and organs, and identified by microscopic observations. Thirty-three 35- to 47-day-old broiler chickens were used for examination of Toxocara larvae. The duodenum, liver, lungs, heart, kidneys, skeletal muscles and brain of each chicken were examined using the pepsin method, and DNA from each tissue was extracted as the template for PCR assay. The findings revealed that 5 of 33 (15.2%) broiler chickens were infected with Toxocara larvae. Larvae were recovered from the liver (n = 19), duodenum (n = 8), skeletal muscles (n = 8) and brain (n = 2) of broiler chickens naturally infected with Toxocara spp. The results showed that the frequencies of the species in the chickens were T. canis larvae (n = 5, 83.3%) and T. cati larvae (n = 1, 16.7%). Our data from the present study demonstrated the importance of broiler chickens as a paratenic host for the parasite's life cycle in the environment. The implementation of DNA amplification as a routine diagnostic technique is a specific and alternative method for identification of Toxocara larvae, and allowed the observation of specific species under field conditions within the locations where broiler chickens are typically raised and exposed to Toxocara spp. eggs or larvae.

  12. Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control.

    Science.gov (United States)

    Krug, Patrick J; Vendetti, Jann E; Rodriguez, Albert K; Retana, Jennifer N; Hirano, Yayoi M; Trowbridge, Cynthia D

    2013-12-01

    DNA barcoding can highlight taxa in which conventional taxonomy underestimates species richness, identifying mitochondrial lineages that may correspond to unrecognized species. However, key assumptions of barcoding remain untested for many groups of soft-bodied marine invertebrates with poorly resolved taxonomy. Here, we applied an integrative approach for species delimitation to herbivorous sea slugs in clade Sacoglossa, in which unrecognized diversity may complicate studies of drug discovery, plastid endosymbiosis, and biological control. Using the mitochondrial barcoding COI gene and the nuclear histone 3 gene, we tested the hypothesis that three widely distributed "species" each comprised a complex of independently evolving lineages. Morphological and reproductive characters were then used to evaluate whether each lineage was distinguishable as a candidate species. The "circumtropical" Elysia ornata comprised a Caribbean species and four Indo-Pacific candidate species that are potential sources of kahalalides, anti-cancer compounds. The "monotypic" and highly photosynthetic Plakobranchus ocellatus, used for over 60 years to study chloroplast symbiosis, comprised 10 candidate species. Finally, six candidate species were distinguished in the Elysia tomentosa complex, including potential biological control agents for invasive green algae (Caulerpa spp.). We show that a candidate species approach developed for vertebrates effectively categorizes cryptic diversity in marine invertebrates, and that integrating threshold COI distances with non-molecular character data can delimit species even when common assumptions of DNA barcoding are violated. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Comparative proteomics of tuber induction, development and maturation reveal the complexity of tuberization process in potato (Solanum tuberosum L.).

    Science.gov (United States)

    Agrawal, Lalit; Chakraborty, Subhra; Jaiswal, Dinesh Kumar; Gupta, Sonika; Datta, Asis; Chakraborty, Niranjan

    2008-09-01

    Tuberization in potato ( Solanum tuberosum L.) is a developmental process that serves a double function, as a storage organ and as a vegetative propagation system. It is a multistep, complex process and the underlying mechanisms governing these overlapping steps are not fully understood. To understand the molecular basis of tuberization in potato, a comparative proteomic approach has been applied to monitor differentially expressed proteins at different development stages using two-dimensional gel electrophoresis (2-DE). The differentially displayed proteomes revealed 219 protein spots that change their intensities more than 2.5-fold. The LC-ES-MS/MS analyses led to the identification of 97 differentially regulated proteins that include predicted and novel tuber-specific proteins. Nonhierarchical clustering revealed coexpression patterns of functionally similar proteins. The expression of reactive oxygen species catabolizing enzymes, viz., superoxide dismutase, ascorbate peroxidase and catalase, were induced by more than 2-fold indicating their possible role during the developmental transition from stolons into tubers. We demonstrate that nearly 100 proteins, some presumably associated with tuber cell differentiation, regulate diverse functions like protein biogenesis and storage, bioenergy and metabolism, and cell defense and rescue impinge on the complexity of tuber development in potato.

  14. Evidence for the robustness of protein complexes to inter-species hybridization.

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    Jean-Baptiste Leducq

    Full Text Available Despite the tremendous efforts devoted to the identification of genetic incompatibilities underlying hybrid sterility and inviability, little is known about the effect of inter-species hybridization at the protein interactome level. Here, we develop a screening platform for the comparison of protein-protein interactions (PPIs among closely related species and their hybrids. We examine in vivo the architecture of protein complexes in two yeast species (Saccharomyces cerevisiae and Saccharomyces kudriavzevii that diverged 5-20 million years ago and in their F1 hybrids. We focus on 24 proteins of two large complexes: the RNA polymerase II and the nuclear pore complex (NPC, which show contrasting patterns of molecular evolution. We found that, with the exception of one PPI in the NPC sub-complex, PPIs were highly conserved between species, regardless of protein divergence. Unexpectedly, we found that the architecture of the complexes in F1 hybrids could not be distinguished from that of the parental species. Our results suggest that the conservation of PPIs in hybrids likely results from the slow evolution taking place on the very few protein residues involved in the interaction or that protein complexes are inherently robust and may accommodate protein divergence up to the level that is observed among closely related species.

  15. Good species behaving badly: Non-monophyly of black fly sibling species in the Simulium arcticum complex (Diptera: Simuliidae).

    Science.gov (United States)

    Conflitti, Ida M; Kratochvil, Michael J; Spironello, Michael; Shields, Gerald F; Currie, Douglas C

    2010-10-01

    Mitochondrial based phylogenetic reconstructions often show deviations from species-level monophyly. We used the Simulium arcticum species complex (Diptera: Simuliidae) as a model system for interpreting non-monophyly in light of chromosomal data supporting species status of siblings. For cytogenetic identification of morphologically indistinguishable black fly sibling species, larvae must be preserved in Carnoy's solution, a fixative known to degrade DNA. Consequently, we reconstructed phylogenetic relationships based on 12S, COII, cyt b, and ITS-1 gene sequences obtained from larvae sampled from presumed taxon-pure localities. As species composition at 'taxon-pure' sites may have changed at the time of sampling, we performed a second study that aimed to: (1) assess phylogenetic relationships among cytologically verified members of the S. arcticum species complex using COI and COII gene sequences; (2) determine whether useable genetic information could be gleaned from Carnoy's fixed specimens; and (3) determine the extent to which Carnoy's fixative degrades DNA over time. We consistently obtained genetic data from material stored in Carnoy's solution for two to three months. Genetic analysis of samples fixed in Carnoy's solution for up to six years indicates that larvae preserved for a maximum of five years can provide useable information for molecular analysis. Our preliminary and cytologically confirmed phylogenetic analyses demonstrate that mitochondrial DNA fails to resolve species-level monophyly of chromosomally distinct S. arcticum taxa. As results of analyses based on cytologically verified larvae mirror those of our preliminary study, we rule out imperfect taxonomy as the reason for species-level non-monophyly. Although we cannot confidently reject either inadequate phylogenetic information or incomplete lineage sorting as the cause of non-monophyly, the sharing of alleles between sympatric siblings suggests introgressive hybridization between taxa. We

  16. Taxonomy and phylogeny of Pluteus glaucotinctus sensu lato (Agaricales, Basidiomycota), a multicontinental species complex

    Science.gov (United States)

    Nelson Menolli; Alfredo Justo; Pedro Arrillaga; C.K. Pradeep; Andrew M. Minnis; Marina. Capelari

    2014-01-01

    In order to better understand species delimitation in the Pluteus glaucotinctus species complex, we present a detailed study based on morphological and DNA sequence (nrITS + tef1) data. Pluteus glaucotinctus sensu stricto is known only from the type collection (Democratic Republic of the Congo), which is re-...

  17. Species of the Colletotrichum acutatum complex associated with anthracnose diseases of fruit in Brazil

    NARCIS (Netherlands)

    Bragança, Carlos A.D.; Damm, Ulrike; Baroncelli, Riccardo; Massola Júnior, Nelson S.; Crous, Pedro W.

    Abstract Although Colletotrichum acutatum was recently investigated and shown to be a species complex comprising about 30 species, the name is still used in its broad sense for anthracnose pathogens of fruits in Brazil. In this study, a multilocus molecular analysis was carried out based on a

  18. Genetic population structure of Fusarium graminearum species complex in Korean cereals

    Science.gov (United States)

    Small grain cereals are frequently contaminated with toxigenic Fusarium species. Members of the Fusarium graminearum species complex (FGSC) are known as a head blight pathogens and mycotoxin producers. In order to characterize the FGSC populations associated with cereals in Korea, barley, corn, maiz...

  19. Crystal structure of TAZ-TEAD complex reveals a distinct interaction mode from that of YAP-TEAD complex.

    Science.gov (United States)

    Kaan, Hung Yi Kristal; Chan, Siew Wee; Tan, Siew Kim Joyce; Guo, Fusheng; Lim, Chun Jye; Hong, Wanjin; Song, Haiwei

    2017-05-17

    The Hippo pathway is a tumor suppressor pathway that is implicated in the regulation of organ size. The pathway has three components: the upstream regulatory factors, the kinase core, and the downstream transcriptional machinery, which consists of YAP, TAZ (transcription co-activators) and TEAD (transcription factor). Formation of YAP/TAZ-TEAD complexes leads to the transcription of growth-promoting genes. Herein, we report the crystal structure of TAZ-TEAD4 complex, which reveals two binding modes. The first is similar to the published YAP-TEAD structure. The second is a unique binding mode, whereby two molecules of TAZ bind to and bridge two molecules of TEAD4. We validated the latter using cross-linking and multi-angle light scattering. Using siRNA, we showed that TAZ knockdown leads to a decrease in TEAD4 dimerization. Lastly, results from luciferase assays, using YAP/TAZ transfected or knockdown cells, give support to the non-redundancy of YAP/TAZ co-activators in regulating gene expression in the Hippo pathway.

  20. Lutzomyia umbratilis, the main vector of Leishmania guyanensis, represents a novel species complex?

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    Vera Margarete Scarpassa

    Full Text Available BACKGROUND: Lutzomyia umbratilis is an important Leishmania guyanensis vector in South America. Previous studies have suggested differences in the vector competence between L. umbratilis populations situated on opposite banks of the Amazonas and Negro Rivers in the central Amazonian Brazil region, likely indicating a species complex. However, few studies have been performed on these populations and the taxonomic status of L. umbratilis remains unclear. METHODOLOGY/PRINCIPAL FINDINGS: Phylogeographic structure was estimated for six L. umbratilis samples from the central Amazonian region in Brazil by analyzing mtDNA using 1181 bp of the COI gene to assess whether the populations on opposite banks of these rivers consist of incipient or distinct species. The genetic diversity was fairly high and the results revealed two distinct clades ( = lineages with 1% sequence divergence. Clade I consisted of four samples from the left bank of the Amazonas and Negro Rivers, whereas clade II comprised two samples from the right bank of Negro River. No haplotypes were shared between samples of two clades. Samples within clades exhibited low to moderate genetic differentiation (F(ST = -0.0390-0.1841, whereas samples between clades exhibited very high differentiation (F(ST = 0.7100-0.8497 and fixed differences. These lineages have diverged approximately 0.22 Mya in the middle Pleistocene. Demographic expansion was detected for the lineages I and II approximately 30,448 and 15,859 years ago, respectively, in the late Pleistocene. CONCLUSIONS/SIGNIFICANCE: The two genetic lineages may represent an advanced speciation stage suggestive of incipient or distinct species within L. umbratilis. These findings suggest that the Amazonas and Negro Rivers may be acting as effective barriers, thus preventing gene flow between populations on opposite sides. Such findings have important implications for epidemiological studies, especially those related to vector

  1. Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulex species complex

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    Cristescu Melania E

    2011-07-01

    Full Text Available Abstract Background Evidence for historical, demographic and selective factors affecting enzyme evolution can be obtained by examining nucleotide sequence variation in candidate genes such as Lactate dehydrogenase (Ldh. Two closely related Daphnia species can be distinguished by their electrophoretic Ldh genotype and habitat. Daphnia pulex populations are fixed for the S allele and inhabit temporary ponds, while D. pulicaria populations are fixed for the F allele and inhabit large stratified lakes. One locus is detected in most allozyme surveys, but genome sequencing has revealed two genes, LdhA and LdhB. Results We sequenced both Ldh genes from 70 isolates of these two species from North America to determine if the association between Ldh genotype and habitat shows evidence for selection, and to elucidate the evolutionary history of the two genes. We found that alleles in the pond-dwelling D. pulex and in the lake-dwelling D. pulicaria form distinct groups at both loci, and the substitution of Glutamine (S for Glutamic acid (F at amino acid 229 likely causes the electrophoretic mobility shift in the LDHA protein. Nucleotide diversity in both Ldh genes is much lower in D. pulicaria than in D. pulex. Moreover, the lack of spatial structuring of the variation in both genes over a wide geographic area is consistent with a recent demographic expansion of lake populations. Neutrality tests indicate that both genes are under purifying selection, but the intensity is much stronger on LdhA. Conclusions Although lake-dwelling D. pulicaria hybridizes with the other lineages in the pulex species complex, it remains distinct ecologically and genetically. This ecological divergence, coupled with the intensity of purifying selection on LdhA and the strong association between its genotype and habitat, suggests that experimental studies would be useful to determine if variation in molecular function provides evidence that LDHA variants are adaptive.

  2. Lutzomyia umbratilis, the main vector of Leishmania guyanensis, represents a novel species complex?

    Science.gov (United States)

    Scarpassa, Vera Margarete; Alencar, Ronildo Baiatone

    2012-01-01

    Lutzomyia umbratilis is an important Leishmania guyanensis vector in South America. Previous studies have suggested differences in the vector competence between L. umbratilis populations situated on opposite banks of the Amazonas and Negro Rivers in the central Amazonian Brazil region, likely indicating a species complex. However, few studies have been performed on these populations and the taxonomic status of L. umbratilis remains unclear. Phylogeographic structure was estimated for six L. umbratilis samples from the central Amazonian region in Brazil by analyzing mtDNA using 1181 bp of the COI gene to assess whether the populations on opposite banks of these rivers consist of incipient or distinct species. The genetic diversity was fairly high and the results revealed two distinct clades ( = lineages) with 1% sequence divergence. Clade I consisted of four samples from the left bank of the Amazonas and Negro Rivers, whereas clade II comprised two samples from the right bank of Negro River. No haplotypes were shared between samples of two clades. Samples within clades exhibited low to moderate genetic differentiation (F(ST) = -0.0390-0.1841), whereas samples between clades exhibited very high differentiation (F(ST) = 0.7100-0.8497) and fixed differences. These lineages have diverged approximately 0.22 Mya in the middle Pleistocene. Demographic expansion was detected for the lineages I and II approximately 30,448 and 15,859 years ago, respectively, in the late Pleistocene. The two genetic lineages may represent an advanced speciation stage suggestive of incipient or distinct species within L. umbratilis. These findings suggest that the Amazonas and Negro Rivers may be acting as effective barriers, thus preventing gene flow between populations on opposite sides. Such findings have important implications for epidemiological studies, especially those related to vector competence and anthropophily, and for vector control strategies. In addition, L

  3. Comparative Analysis of Four Calypogeia Species Revealed Unexpected Change in Evolutionarily-Stable Liverwort Mitogenomes

    Directory of Open Access Journals (Sweden)

    Monika Ślipiko

    2017-12-01

    Full Text Available Liverwort mitogenomes are considered to be evolutionarily stable. A comparative analysis of four Calypogeia species revealed differences compared to previously sequenced liverwort mitogenomes. Such differences involve unexpected structural changes in the two genes, cox1 and atp1, which have lost three and two introns, respectively. The group I introns in the cox1 gene are proposed to have been lost by two-step localized retroprocessing, whereas one-step retroprocessing could be responsible for the disappearance of the group II introns in the atp1 gene. These cases represent the first identified losses of introns in mitogenomes of leafy liverworts (Jungermanniopsida contrasting the stability of mitochondrial gene order with certain changes in the gene content and intron set in liverworts.

  4. Multi-locus Analyses Reveal Four Giraffe Species Instead of One.

    Science.gov (United States)

    Fennessy, Julian; Bidon, Tobias; Reuss, Friederike; Kumar, Vikas; Elkan, Paul; Nilsson, Maria A; Vamberger, Melita; Fritz, Uwe; Janke, Axel

    2016-09-26

    Traditionally, one giraffe species and up to eleven subspecies have been recognized [1]; however, nine subspecies are commonly accepted [2]. Even after a century of research, the distinctness of each giraffe subspecies remains unclear, and the genetic variation across their distribution range has been incompletely explored. Recent genetic studies on mtDNA have shown reciprocal monophyly of the matrilines among seven of the nine assumed subspecies [3, 4]. Moreover, until now, genetic analyses have not been applied to biparentally inherited sequence data and did not include data from all nine giraffe subspecies. We sampled natural giraffe populations from across their range in Africa, and for the first time individuals from the nominate subspecies, the Nubian giraffe, Giraffa camelopardalis camelopardalis Linnaeus 1758 [5], were included in a genetic analysis. Coalescence-based multi-locus and population genetic analyses identify at least four separate and monophyletic clades, which should be recognized as four distinct giraffe species under the genetic isolation criterion. Analyses of 190 individuals from maternal and biparental markers support these findings and further suggest subsuming Rothschild's giraffe into the Nubian giraffe, as well as Thornicroft's giraffe into the Masai giraffe [6]. A giraffe survey genome produced valuable data from microsatellites, mobile genetic elements, and accurate divergence time estimates. Our findings provide the most inclusive analysis of giraffe relationships to date and show that their genetic complexity has been underestimated, highlighting the need for greater conservation efforts for the world's tallest mammal. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

    Science.gov (United States)

    Tian, Xinpeng; Zhang, Zhewen; Yang, Tingting; Chen, Meili; Li, Jie; Chen, Fei; Yang, Jin; Li, Wenjie; Zhang, Bing; Zhang, Zhang; Wu, Jiayan; Zhang, Changsheng; Long, Lijuan; Xiao, Jingfa

    2016-01-01

    Over 200 genomes of streptomycete strains that were isolated from various environments are available from the NCBI. However, little is known about the characteristics that are linked to marine adaptation in marine-derived streptomycetes. The particularity and complexity of the marine environment suggest that marine streptomycetes are genetically diverse. Here, we sequenced nine strains from the Streptomyces genus that were isolated from different longitudes, latitudes, and depths of the South China Sea. Then we compared these strains to 22 NCBI downloaded streptomycete strains. Thirty-one streptomycete strains are clearly grouped into a marine-derived subgroup and multiple source subgroup-based phylogenetic tree. The phylogenetic analyses have revealed the dynamic process underlying streptomycete genome evolution, and lateral gene transfer is an important driving force during the process. Pan-genomics analyses have revealed that streptomycetes have an open pan-genome, which reflects the diversity of these streptomycetes and guarantees the species a quick and economical response to diverse environments. Functional and comparative genomics analyses indicate that the marine-derived streptomycetes subgroup possesses some common characteristics of marine adaptation. Our findings have expanded our knowledge of how ocean isolates of streptomycete strains adapt to marine environments. The availability of streptomycete genomes from the South China Sea will be beneficial for further analysis on marine streptomycetes and will enrich the South China Sea’s genetic data sources. PMID:27446038

  6. Metabolite analysis of Mycobacterium species under aerobic and hypoxic conditions reveals common metabolic traits.

    Science.gov (United States)

    Drapal, Margit; Wheeler, Paul R; Fraser, Paul D

    2016-08-01

    A metabolite profiling approach has been implemented to elucidate metabolic adaptation at set culture conditions in five Mycobacterium species (two fast- and three slow-growing) with the potential to act as model organisms for Mycobacterium tuberculosis (Mtb). Analysis has been performed over designated growth phases and under representative environments (nutrient and oxygen depletion) experienced by Mtb during infection. The procedure was useful in determining a range of metabolites (60-120 compounds) covering nucleotides, amino acids, organic acids, saccharides, fatty acids, glycerols, -esters, -phosphates and isoprenoids. Among these classes of compounds, key biomarker metabolites, which can act as indicators of pathway/process activity, were identified. In numerous cases, common metabolite traits were observed for all five species across the experimental conditions (e.g. uracil indicating DNA repair). Amino acid content, especially glutamic acid, highlighted the different properties between the fast- and slow-growing mycobacteria studied (e.g. nitrogen assimilation). The greatest similarities in metabolite composition between fast- and slow-growing mycobacteria were apparent under hypoxic conditions. A comparison to previously reported transcriptomic data revealed a strong correlation between changes in transcription and metabolite content. Collectively, these data validate the changes in the transcription at the metabolite level, suggesting transcription exists as one of the predominant modes of cellular regulation in Mycobacterium. Sectors with restricted correlation between metabolites and transcription (e.g. hypoxic cultivation) warrant further study to elucidate and exploit post-transcriptional modes of regulation. The strong correlation between the laboratory conditions used and data derived from in vivo conditions, indicate that the approach applied is a valuable addition to our understanding of cell regulation in these Mycobacterium species.

  7. Quantification of ploidy in proteobacteria revealed the existence of monoploid, (mero-oligoploid and polyploid species.

    Directory of Open Access Journals (Sweden)

    Vito Pecoraro

    Full Text Available Bacteria are generally assumed to be monoploid (haploid. This assumption is mainly based on generalization of the results obtained with the most intensely studied model bacterium, Escherichia coli (a gamma-proteobacterium, which is monoploid during very slow growth. However, several species of proteobacteria are oligo- or polyploid, respectively. To get a better overview of the distribution of ploidy levels, genome copy numbers were quantified in four species of three different groups of proteobacteria. A recently developed Real Time PCR approach, which had been used to determine the ploidy levels of halophilic archaea, was optimized for the quantification of genome copy numbers of bacteria. Slow-growing (doubling time 103 minutes and fast-growing (doubling time 25 minutes E. coli cultures were used as a positive control. The copy numbers of the origin and terminus region of the chromosome were determined and the results were in excellent agreement with published data. The approach was also used to determine the ploidy levels of Caulobacter crescentus (an alpha-proteobacterium and Wolinella succinogenes (an epsilon-proteobacterium, both of which are monoploid. In contrast, Pseudomonas putida (a gamma-proteobacterium contains 20 genome copies and is thus polyploid. A survey of the proteobacteria with experimentally-determined genome copy numbers revealed that only three to four of 11 species are monoploid and thus monoploidy is not typical for proteobacteria. The ploidy level is not conserved within the groups of proteobacteria, and there are no obvious correlations between the ploidy levels with other parameters like genome size, optimal growth temperature or mode of life.

  8. Echinostoma 'revolutum' (Digenea: Echinostomatidae) species complex revisited: species delimitation based on novel molecular and morphological data gathered in Europe.

    Science.gov (United States)

    Georgieva, Simona; Faltýnková, Anna; Brown, Rebecca; Blasco-Costa, Isabel; Soldánová, Miroslava; Sitko, Jiljí; Scholz, Tomáš; Kostadinova, Aneta

    2014-11-27

    The systematics of echinostomes within the so-called 'revolutum' group of the genus Echinostoma, which encompasses the type-species E. revolutum and a number of morphologically similar species, has long been controversial. Recent molecular studies indicate the existence of more species than previously considered valid, thus stressing the need for wider taxon sampling from natural host populations. This is especially true for Europe where morphological evidence indicates higher species diversity than previously thought, but where molecular data are virtually lacking. This gap in our knowledge was addressed in the present study through an integration of morphological and molecular approaches in the investigation of a dataset with larger taxonomic and geographical coverage. More than 20,000 freshwater snails belonging to 16 species were collected during 1998-2012 from various localities in eight countries in Europe. Snail screening provided representative larval isolates for five species of the 'revolutum' group, identified by their morphology. Adult isolates for four species recovered from natural and experimental infections were also identified. Partial fragments of the mitochondrial nad1 and 28S rRNA genes were amplified for 74 and 16 isolates, respectively; these were analysed together with the sequences of Echinostoma spp. available on GenBank. Delineation of the European Echinostoma spp. was carried out based on molecular, morphological and ecological data. The large-scale screening revealed infections with five Echinostoma spp., including one new species: E. revolutum (sensu stricto), E. miyagawai, E. paraulum, E. bolschewense and Echinostoma n. sp. The newly-generated nad1 sequences from Europe fall into six distinct, well-supported, reciprocally monophyletic lineages corresponding to the species identifications based on morphology; this was corroborated by the 28S rDNA sequences. The analyses of the total nad1 dataset provided evidence for 12 monophyletic

  9. DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

    Science.gov (United States)

    Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

    2015-10-01

    The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (pentropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies.

    Directory of Open Access Journals (Sweden)

    Masakazu Kohda

    2016-01-01

    Full Text Available Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4 as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3 and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21 as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder.

  11. Predictive ethoinformatics reveals the complex migratory behaviour of a pelagic seabird, the Manx Shearwater

    Science.gov (United States)

    Freeman, Robin; Dean, Ben; Kirk, Holly; Leonard, Kerry; Phillips, Richard A.; Perrins, Chris M.; Guilford, Tim

    2013-01-01

    Understanding the behaviour of animals in the wild is fundamental to conservation efforts. Advances in bio-logging technologies have offered insights into the behaviour of animals during foraging, migration and social interaction. However, broader application of these systems has been limited by device mass, cost and longevity. Here, we use information from multiple logger types to predict individual behaviour in a highly pelagic, migratory seabird, the Manx Shearwater (Puffinus puffinus). Using behavioural states resolved from GPS tracking of foraging during the breeding season, we demonstrate that individual behaviours can be accurately predicted during multi-year migrations from low cost, lightweight, salt-water immersion devices. This reveals a complex pattern of migratory stopovers: some involving high proportions of foraging, and others of rest behaviour. We use this technique to examine three consecutive years of global migrations, revealing the prominence of foraging behaviour during migration and the importance of highly productive waters during migratory stopover. PMID:23635496

  12. Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis

    Directory of Open Access Journals (Sweden)

    Takahiro Tsujikawa

    2017-04-01

    Full Text Available Here, we describe a multiplexed immunohistochemical platform with computational image processing workflows, including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination and revealed that response to therapy correlated with degree of mono-myelocytic cell density and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification and provide digital image processing pipelines to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to improve biomarker discovery and assessment.

  13. Hydra meiosis reveals unexpected conservation of structural synaptonemal complex proteins across metazoans

    Science.gov (United States)

    Fraune, Johanna; Alsheimer, Manfred; Volff, Jean-Nicolas; Busch, Karoline; Fraune, Sebastian; Bosch, Thomas C. G.; Benavente, Ricardo

    2012-01-01

    The synaptonemal complex (SC) is a key structure of meiosis, mediating the stable pairing (synapsis) of homologous chromosomes during prophase I. Its remarkable tripartite structure is evolutionarily well conserved and can be found in almost all sexually reproducing organisms. However, comparison of the different SC protein components in the common meiosis model organisms Saccharomyces cerevisiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus revealed no sequence homology. This discrepancy challenged the hypothesis that the SC arose only once in evolution. To pursue this matter we focused on the evolution of SYCP1 and SYCP3, the two major structural SC proteins of mammals. Remarkably, our comparative bioinformatic and expression studies revealed that SYCP1 and SYCP3 are also components of the SC in the basal metazoan Hydra. In contrast to previous assumptions, we therefore conclude that SYCP1 and SYCP3 form monophyletic groups of orthologous proteins across metazoans. PMID:23012415

  14. Green and brown bridges between weeds and crops reveal novel Diaporthe species in Australia

    NARCIS (Netherlands)

    Thompson, S.M.; Tan, Y.P.; Shivas, R.G.; Neate, S.M.; Morin, L.; Bissett, A.; Aitken, E.A.B.

    2015-01-01

    Diaporthe (syn. Phomopsis) species are well-known saprobes, endophytes or pathogens on a range of plants. Several species have wide host ranges and multiple species may sometimes colonise the same host species. This study describes eight novel Diaporthe species isolated from live and/or dead tissue

  15. Morphology and DNA barcoding reveal a new species of Eudicella from East Africa (Coleoptera: Scarabaeidae: Cetoniinae).

    Science.gov (United States)

    Seidel, Matthias

    2016-07-13

    A new species of Eudicella White, 1839 (Coleoptera: Scarabaeidae: Cetoniinae), is described from Uganda and Kenya: E. nana new species. Morphological and genetic analyses of the new taxon and phenotypically allied species are given. Eudicella nana is compared with its hypothesized sister species, E. darwiniana Kraatz, 1880, and diagnostic characters that distinguish it from other species occurring in the same region are provided.

  16. Continental Drift and Speciation of the Cryptococcus neoformans and Cryptococcus gattii Species Complexes.

    Science.gov (United States)

    Casadevall, Arturo; Freij, Joudeh B; Hann-Soden, Christopher; Taylor, John

    2017-01-01

    Genomic analysis has placed the origins of two human-pathogenic fungi, the Cryptococcus gattii species complex and the Cryptococcus neoformans species complex, in South America and Africa, respectively. Molecular clock calculations suggest that the two species separated ~80 to 100 million years ago. This time closely approximates the breakup of the supercontinent Pangea, which gave rise to South America and Africa. On the basis of the geographic distribution of these two species complexes and the coincidence of the evolutionary divergence and Pangea breakup times, we propose that a spatial separation caused by continental drift resulted in the emergence of the C. gattii and C. neoformans species complexes from a Pangean ancestor. We note that, despite the spatial and temporal separation that occurred approximately 100 million years ago, these two species complexes are morphologically similar, share virulence factors, and cause very similar diseases. Continuation of these phenotypic characteristics despite ancient separation suggests the maintenance of similar selection pressures throughout geologic ages.

  17. Continental Drift and Speciation of the Cryptococcus neoformans and Cryptococcus gattii Species Complexes

    Directory of Open Access Journals (Sweden)

    Arturo Casadevall

    2017-04-01

    Full Text Available Genomic analysis has placed the origins of two human-pathogenic fungi, the Cryptococcus gattii species complex and the Cryptococcus neoformans species complex, in South America and Africa, respectively. Molecular clock calculations suggest that the two species separated ~80 to 100 million years ago. This time closely approximates the breakup of the supercontinent Pangea, which gave rise to South America and Africa. On the basis of the geographic distribution of these two species complexes and the coincidence of the evolutionary divergence and Pangea breakup times, we propose that a spatial separation caused by continental drift resulted in the emergence of the C. gattii and C. neoformans species complexes from a Pangean ancestor. We note that, despite the spatial and temporal separation that occurred approximately 100 million years ago, these two species complexes are morphologically similar, share virulence factors, and cause very similar diseases. Continuation of these phenotypic characteristics despite ancient separation suggests the maintenance of similar selection pressures throughout geologic ages.

  18. 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 ...

  19. Simulation ofDeepwater Horizonoil plume reveals substrate specialization within a complex community of hydrocarbon degraders.

    Science.gov (United States)

    Hu, Ping; Dubinsky, Eric A; Probst, Alexander J; Wang, Jian; Sieber, Christian M K; Tom, Lauren M; Gardinali, Piero R; Banfield, Jillian F; Atlas, Ronald M; Andersen, Gary L

    2017-07-11

    The Deepwater Horizon (DWH) accident released an estimated 4.1 million barrels of oil and 10 10 mol of natural gas into the Gulf of Mexico, forming deep-sea plumes of dispersed oil droplets and dissolved gases that were largely degraded by bacteria. During the course of this 3-mo disaster a series of different bacterial taxa were enriched in succession within deep plumes, but the metabolic capabilities of the different populations that controlled degradation rates of crude oil components are poorly understood. We experimentally reproduced dispersed plumes of fine oil droplets in Gulf of Mexico seawater and successfully replicated the enrichment and succession of the principal oil-degrading bacteria observed during the DWH event. We recovered near-complete genomes, whose phylogeny matched those of the principal biodegrading taxa observed in the field, including the DWH Oceanospirillales (now identified as a Bermanella species), multiple species of Colwellia , Cycloclasticus , and other members of Gammaproteobacteria, Flavobacteria, and Rhodobacteria. Metabolic pathway analysis, combined with hydrocarbon compositional analysis and species abundance data, revealed substrate specialization that explained the successional pattern of oil-degrading bacteria. The fastest-growing bacteria used short-chain alkanes. The analyses also uncovered potential cooperative and competitive relationships, even among close relatives. We conclude that patterns of microbial succession following deep ocean hydrocarbon blowouts are predictable and primarily driven by the availability of liquid petroleum hydrocarbons rather than natural gases.

  20. Molecular systematics of new world gopher, bull, and pinesnakes (Pituophis: Colubridae), a transcontinental species complex.

    Science.gov (United States)

    Rodríguez-Robles, J A; De Jesús-Escobar, J M

    2000-01-01

    Pituophis melanoleucus (gopher, bull, and pinesnakes) is among the most widely distributed polytypic species complexes in North America, with most authors recognizing from a single transcontinental species (the melanoleucus complex, composed of 15 subspecies) to four (monotypic and polytypic) species. We used mitochondrial gene sequences from the two middle American species, P. deppei and P. lineaticollis, and from 13 subspecies from most of the range of the melanoleucus complex to test various phylogenetic hypotheses for Pituophis. Maximum parsimony and maximum likelihood methods identified the same major clades within Pituophis and indicated that two segments of the melanoleucus complex, the lodingi-melanoleucus-mugitus eastern pinesnake clade and the affinis-annectens-bimaris-catenifer-deserticola- sayi-ruthveni-vertebr alis clade from central and western United States and northern Mexico, represent divergent, allopatric lineages with no known intergradation zone. We recognize each of these two groupings as a different species. Our data also indicate that some ruthveni are more closely related to sayi than to other ruthveni. Nonetheless, ruthveni is an allopatric taxon diagnosable from its closest relatives by a combination of morphometric characters, and because it is likely that at least some of these traits are independent and genetically inherited, we interpret this as evidence that ruthveni has attained the status of independent evolutionary lineage, despite the fact that it retains strong genetic affinities with sayi. The endemic Baja Californian gopher snakes (bimaris and vertebralis) are considered by some taxonomists as a different species, P. vertebralis, but we discovered that these serpents belong to two different clades and hence we do not agree with the recognition of P. vertebralis as presently defined. In summary, we believe that three distinct species are included in the melanoleucus complex, Pituophis melanoleucus (sensu stricto), P. catenifer

  1. Historical perspective on the synonymization of the four major pest species belonging to the Bactrocera dorsalis species complex (Diptera, Tephritidae).

    Science.gov (United States)

    Hee, Alvin K W; Wee, Suk-Ling; Nishida, Ritsuo; Ono, Hajime; Hendrichs, Jorge; Haymer, David S; Tan, Keng-Hong

    2015-01-01

    An FAO/IAEA-sponsored coordinated research project on integrative taxonomy, involving close to 50 researchers from at least 20 countries, culminated in a significant breakthrough in the recognition that four major pest species, Bactrocera dorsalis, Bactrocera philippinensis, Bactrocera papayae and Bactrocera invadens, belong to the same biological species, Bactrocera dorsalis. The successful conclusion of this initiative is expected to significantly facilitate global agricultural trade, primarily through the lifting of quarantine restrictions that have long affected many countries, especially those in regions such as Asia and Africa that have large potential for fresh fruit and vegetable commodity exports. This work stems from two taxonomic studies: a revision in 1994 that significantly increased the number of described species in the Bactrocera dorsalis species complex; and the description in 2005 of Bactrocera invadens, then newly incursive in Africa. While taxonomically valid species, many biologists considered that these were different names for one biological species. Many disagreements confounded attempts to develop a solution for resolving this taxonomic issue, before the FAO/IAEA project commenced. Crucial to understanding the success of that initiative is an accounting of the historical events and perspectives leading up to the international, multidisciplinary collaborative efforts that successfully achieved the final synonymization. This review highlights the 21 year journey taken to achieve this outcome.

  2. Cryptic Species Identification and Composition of Bemisia tabaci (Hemiptera: Aleyrodidae) Complex in Henan Province, China.

    Science.gov (United States)

    Jiu, Min; Hu, Jian; Wang, Lun-Ji; Dong, Jun-Feng; Song, Yue-Qin; Sun, Hui-Zhong

    2017-05-01

    Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex, causing significant crop losses in China during the last decade. Although knowledge of cryptic species composition and dynamics within B. tabaci complex is critical for developing sustainable pest management strategies, limited information is available on this pest in the Henan province of China. A systematic survey of the cryptic species composition and distribution of B. tabaci complex in different locations of Henan province was conducted in 2012. The results of RAPD-PCR and the gene for the mitochondrial cytochrome oxidase subunit-1 (mtCOI) based phylogenetic relationships established using Bayesian method indicated there were four known cryptic species MEAM1, MED, Asia II 3, Asia II 9 and a new cryptic species named China 6 in Henan province. In the survey, the invasive cryptic species MED and MEAM1 were found to be predominant with wide spread distribution across the surveyed regions. On the contrary, the indigenous B. tabaci cryptic species including Asia II 3, Asia II 9 and China 6 remained with low prevalence in some surveyed regions. Cryptic species MEAM1 and MED have not completely displaced the native B. tabaci in Henan province. This current study for the first time unifies our knowledge of the diversity and distribution of B. tabaci across Henan province of China. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America.

  3. Echinostoma 'revolutum' (Digenea: Echinostomatidae) species complex revisited: species delimitation based on novel molecular and morphological data gathered in Europe

    Czech Academy of Sciences Publication Activity Database

    Georgieva, Simona; Faltýnková, Anna; Brown, Rebecca; Blasco-Costa, Maria Isabel; Soldánová, Miroslava; Sitko, J.; Scholz, Tomáš; Kostadinova, Aneta

    2014-01-01

    Roč. 7, NOV 27 2014 (2014), s. 520 ISSN 1756-3305 R&D Projects: GA ČR GAP505/10/1562; GA ČR GBP505/12/G112 Institutional support: RVO:60077344 Keywords : Echinostoma 'revolutum' species complex * Molecular and morphological data * nad1 * 28S rDNA * Europe Subject RIV: EH - Ecology, Behaviour Impact factor: 3.430, year: 2014

  4. Transmitter receptors reveal segregation of the arcopallium/amygdala complex in pigeons (Columba livia).

    Science.gov (United States)

    Herold, Christina; Paulitschek, Christina; Palomero-Gallagher, Nicola; Güntürkün, Onur; Zilles, Karl

    2018-02-15

    At the beginning of the 20th century it was suggested that a complex group of nuclei in the avian posterior ventral telencephalon is comparable to the mammalian amygdala. Subsequent findings, however, revealed that most of these structures share premotor characteristics, while some indeed constitute the avian amygdala. These developments resulted in 2004 in a change of nomenclature of these nuclei, which from then on were named arcopallial or amygdala nuclei and referred to as the arcopallium/amygdala complex. The structural basis for the similarities between avian and mammalian arcopallial and amygdala subregions is poorly understood. Therefore, we analyzed binding site densities for glutamatergic AMPA, NMDA and kainate, GABAergic GABA A , muscarinic M 1 , M 2 and nicotinic acetylcholine (nACh; α 4 β 2 subtype), noradrenergic α 1 and α 2 , serotonergic 5-HT 1A and dopaminergic D 1/5 receptors using quantitative in vitro receptor autoradiography combined with a detailed analysis of the cyto- and myelo-architecture. Our approach supports a segregation of the pigeon's arcopallium/amygdala complex into the following subregions: the arcopallium anterius (AA), the arcopallium ventrale (AV), the arcopallium dorsale (AD), the arcopallium intermedium (AI), the arcopallium mediale (AM), the arcopallium posterius (AP), the nucleus posterioris amygdalopallii pars basalis (PoAb) and pars compacta (PoAc), the nucleus taeniae amgygdalae (TnA) and the area subpallialis amygdalae (SpA). Some of these subregions showed further subnuclei and each region of the arcopallium/amygdala complex are characterized by a distinct multi-receptor density expression. Here we provide a new detailed map of the pigeon's arcopallium/amygdala complex and compare the receptor architecture of the subregions to their possible mammalian counterparts. © 2017 Wiley Periodicals, Inc.

  5. Protein-carbohydrate complex reveals circulating metastatic cells in a microfluidic assay

    KAUST Repository

    Simone, Giuseppina

    2013-02-11

    Advances in carbohydrate sequencing technologies reveal the tremendous complexity of the glycome and the role that glycomics might have to bring insight into the biological functions. Carbohydrate-protein interactions, in particular, are known to be crucial to most mammalian physiological processes as mediators of cell adhesion and metastasis, signal transducers, and organizers of protein interactions. An assay is developed here to mimic the multivalency of biological complexes that selectively and sensitively detect carbohydrate-protein interactions. The binding of β-galactosides and galectin-3 - a protein that is correlated to the progress of tumor and metastasis - is examined. The efficiency of the assay is related to the expression of the receptor while anchoring to the interaction\\'s strength. Comparative binding experiments reveal molecular binding preferences. This study establishes that the assay is robust to isolate metastatic cells from colon affected patients and paves the way to personalized medicine. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae.

    Directory of Open Access Journals (Sweden)

    Yongmin Li

    Full Text Available Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%. The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045-0.245 Ma from multiple refugia prior to the Last Glacial Maximum (LGM. Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.

  7. Vicariance and Its Impact on the Molecular Ecology of a Chinese Ranid Frog Species-Complex (Odorrana schmackeri, Ranidae).

    Science.gov (United States)

    Li, Yongmin; Wu, Xiaoyou; Zhang, Huabin; Yan, Peng; Xue, Hui; Wu, Xiaobing

    2015-01-01

    Paleogeological events and Pleistocene climatic fluctuations have had profound influences on the genetic patterns and phylogeographic structure of species in southern China. In this study, we investigated the population genetic structure and Phylogeography of the Odorrana schmackeri species complex, mountain stream-dwelling odorous frogs, endemic to southern China. We obtained mitochondrial sequences (1,151bp) of the complete ND2 gene and two flanking tRNAs of 511 individuals from 25 sites for phylogeographic analyses. Phylogenetic reconstruction revealed seven divergent evolutionary lineages, with mean pairwise (K2P) sequence distances from 7.8% to 21.1%, except for a closer ND2 distance (3.4%). The complex geological history of southern China drove matrilineal divergence in the O. schmackeri species complex into highly structured geographical units. The first divergence between lineage A+B and other lineages (C-G) had likely been influenced by the uplift of coastal mountains of Southeast China during the Mio-Pliocene period. The subsequent divergences between the lineages C-G may have followed the formation of the Three Gorges and the intensification of the East Asian summer monsoon during the late Pliocene and early Pleistocene. Demographic analyses indicated that major lineages A and C have been experienced recent population expansion (c. 0.045-0.245 Ma) from multiple refugia prior to the Last Glacial Maximum (LGM). Molecular analysis suggest that these seven lineages may represent seven different species, three described species and four cryptic species and should at least be separated into seven management units corresponding to these seven geographic lineages for conservation.

  8. Systematics of the Osteocephalus buckleyi species complex (Anura, Hylidae) from Ecuador and Peru

    Science.gov (United States)

    Ron, Santiago R.; Venegas, Pablo J.; Toral, Eduardo; Morley Read; Diego A. Ortiz; Manzano, Andrea L.

    2012-01-01

    Abstract We present a new phylogeny, based on DNA sequences of mitochondrial and nuclear genes, for frogs of the genus Osteocephalus with emphasis in the Osteocephalus buckleyi species complex. Genetic, morphologic, and advertisement call data are combined to define species boundaries and describe new species. The phylogeny shows strong support for: (1) a basal position of Osteocephalus taurinus + Osteocephalus oophagus, (2) a clade containing phytotelmata breeding species, and (3) a clade that corresponds to the Osteocephalus buckleyi species complex. Our results document a large proportion of hidden diversity within a set of populations that were previously treated as a single, widely distributed species, Osteocephalus buckleyi. Individuals assignable to Osteocephalus buckleyi formed a paraphyletic group relative to Osteocephalus verruciger and Osteocephalus cabrerai and contained four species, one of which is Osteocephalus buckleyi sensu stricto and three are new. Two of the new species are shared between Ecuador and Peru (Osteocephalus vilmae sp. n. and Osteocephalus cannatellai sp. n.) and one is distributed in the Amazon region of southern Peru (Osteocephalus germani sp. n.) We discuss the difficulties of using morphological characters to define species boundaries and propose a hypothesis to explain them. PMID:23166473

  9. Systematics of the Osteocephalus buckleyi species complex (Anura, Hylidae from Ecuador and Peru

    Directory of Open Access Journals (Sweden)

    Santiago Ron

    2012-10-01

    Full Text Available We present a new phylogeny, based on DNA sequences of mitochondrial and nuclear genes, for frogs of the genus Osteocephalus with emphasis in the Osteocephalus buckleyi species complex. Genetic, morphologic, and advertisement call data are combined to define species boundaries and describe new species. The phylogeny shows strong support for: (1 a basal position of O. taurinus + O. oophagus, (2 a clade containing phytotelmata breeding species, and (3 a clade that corresponds to the O. buckleyi species complex. Our results document a large proportion of hidden diversity within a set of populations that were previously treated as a single, widely distributed species, O. buckleyi. Individuals assignable to O. buckleyi formed a paraphyletic group relative to O. verruciger and O. cabrerai and contained four species, one of which is O. buckleyi sensu stricto and three are new. Two of the new species are shared between Ecuador and Peru (O. vilmae sp. n. and O. cannatellai sp. n. and one is distributed in the Amazon region of southern Peru (O. germani sp. n.. We discuss the difficulties of using morphological characters to define species boundaries and propose a hypothesis to explain them.

  10. Heterogeneity of large macromolecular complexes revealed by 3-D cryo-EM variance analysis

    Science.gov (United States)

    Zhang, Wei; Kimmel, Marek; Spahn, Christian M.T.; Penczek, Pawel A.

    2008-01-01

    Macromolecular structure determination by cryo-electron microscopy (EM) and single particle analysis are based on the assumption that imaged molecules have identical structure. With the increased size of processed datasets it becomes apparent that many complexes coexist in a mixture of conformational states or contain flexible regions. As the cryo-EM data is collected in form of projections of imaged molecules, the information about variability of reconstructed density maps is not directly available. To address this problem, we describe a new implementation of the bootstrap resampling technique that yields estimates of voxel-by-voxel variance of a structure reconstructed from the set of its projections. We introduced a novel highly efficient reconstruction algorithm that is based on direct Fourier inversion and which incorporates correction for the transfer function of the microscope, thus extending the resolution limits of variance estimation. We also describe a validation method to determine the number of resampled volumes required to achieve stable estimate of the variance. The proposed bootstrap method was applied to a dataset of 70S ribosome complexed with tRNA and the elongation factor G. The variance map revealed regions of high variability: the L1 protein, the EF-G and the 30S head and the ratchet-like subunit rearrangement. The proposed method of variance estimation opens new possibilities for single particle analysis, by extending applicability of the technique to heterogeneous datasets of macromolecules, and to complexes with significant conformational variability. PMID:19081053

  11. Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex.

    Science.gov (United States)

    Jeong, Hanbin; Park, Jumi; Lee, Changwook

    2016-12-01

    The endoplasmic reticulum-mitochondria encounter structure (ERMES) is a protein complex that plays a tethering role in physically connecting ER and mitochondria membranes. The ERMES complex is composed of Mdm12, Mmm1, and Mdm34, which have a SMP domain in common, and Mdm10. Here, we report the crystal structure of S. cerevisiae Mdm12. The Mdm12 forms a dimeric SMP structure through domain swapping of the β1-strand comprising residues 1-7. Biochemical experiments reveal a phospholipid-binding site located along a hydrophobic channel of the Mdm12 structure and that Mdm12 might have a binding preference for glycerophospholipids harboring a positively charged head group. Strikingly, both full-length Mdm12 and Mdm12 truncated to exclude the disordered region (residues 74-114) display the same organization in the asymmetric unit, although they crystallize as a tetramer and hexamer, respectively. Taken together, these studies provide a novel understanding of the overall organization of SMP domains in the ERMES complex, indicating that Mdm12 interacts with Mdm34 through head-to-head contact, and with Mmm1 through tail-to-tail contact of SMP domains. © 2016 The Authors.

  12. Functional diversity measures revealed impacts of non-native species and habitat degradation on species-poor freshwater fish assemblages.

    Science.gov (United States)

    Colin, Nicole; Villéger, Sébastien; Wilkes, Martin; de Sostoa, Adolfo; Maceda-Veiga, Alberto

    2018-06-01

    Trait-based ecology has been developed for decades to infer ecosystem responses to stressors based on the functional structure of communities, yet its value in species-poor systems is largely unknown. Here, we used an extensive dataset in a Spanish region highly prone to non-native fish invasions (15 catchments, N=389 sites) to assess for the first time how species-poor communities respond to large-scale environmental gradients using a taxonomic and functional trait-based approach in riverine fish. We examined total species richness and three functional trait-based indices available when many sites have ≤3 species (specialization, FSpe; originality, FOri and entropy, FEnt). We assessed the responses of these taxonomic and functional indices along gradients of altitude, water pollution, physical habitat degradation and non-native fish biomass. Whilst species richness was relatively sensitive to spatial effects, functional diversity indices were responsive across natural and anthropogenic gradients. All four diversity measures declined with altitude but this decline was modulated by physical habitat degradation (richness, FSpe and FEnt) and the non-native:total fish biomass ratio (FSpe and FOri) in ways that varied between indices. Furthermore, FSpe and FOri were significantly correlated with Total Nitrogen. Non-native fish were a major component of the taxonomic and functional structure of fish communities, raising concerns about potential misdiagnosis between invaded and environmentally-degraded river reaches. Such misdiagnosis was evident in a regional fish index widely used in official monitoring programs. We recommend the application of FSpe and FOri to extensive datasets from monitoring programs in order to generate valuable cross-system information about the impacts of non-native species and habitat degradation, even in species-poor systems. Scoring non-native species apart from habitat degradation in the indices used to determine ecosystem health is

  13. Phylogenetic relationships among members of the Fusarium solani species complex in human infections and the descriptions of F. keratoplasticum sp. nov. and F. petroliphilum stat. nov

    DEFF Research Database (Denmark)

    Short, Dylan P.G.; O’Donnell, Kerry; Thrane, Ulf

    2013-01-01

    Fusarium species are frequently associated with mycotic keratitis and, to a lesser extent, cases of localized and disseminated infections. The Fusarium solani species complex (FSSC) is the most common group of fusaria associated with human infectious diseases. Several studies to date have revealed...... dozens of strongly supported phylogenetic species within this important evolutionary clade, though little work has been done to improve the taxonomy and understanding of the reproductive mode and phenotypes of the predominant clinically relevant species. Here we described Fusarium keratoplasticum sp. nov...

  14. Antifungal susceptibilities of Candida glabrata species complex, Candida krusei, Candida parapsilosis species complex and Candida tropicalis causing invasive candidiasis in China: 3 year national surveillance.

    Science.gov (United States)

    Xiao, Meng; Fan, Xin; Chen, Sharon C-A; Wang, He; Sun, Zi-Yong; Liao, Kang; Chen, Shu-Lan; Yan, Yan; Kang, Mei; Hu, Zhi-Dong; Chu, Yun-Zhuo; Hu, Tie-Shi; Ni, Yu-Xing; Zou, Gui-Ling; Kong, Fanrong; Xu, Ying-Chun

    2015-03-01

    To define the antifungal susceptibility patterns of the most common non-albicans Candida spp. in China. We evaluated the susceptibilities to nine antifungal drugs of Candida parapsilosis species complex, Candida tropicalis, Candida glabrata species complex and Candida krusei isolates from patients with invasive candidiasis at 11 hospitals over 3 years. Isolates were identified by MALDI-TOF MS supplemented by DNA sequencing. MICs were determined by Sensititre YeastOne(TM) using current clinical breakpoints/epidemiological cut-off values to assign susceptibility (or WT), and by CLSI M44-A2 disc diffusion for fluconazole and voriconazole. Of 1072 isolates, 392 (36.6%) were C. parapsilosis species complex. C. tropicalis, C. glabrata species complex and C. krusei comprised 35.4%, 24.3% and 3.7% of the isolates, respectively. Over 99.3% of the isolates were of WT phenotype to amphotericin B and 5-flucytosine. Susceptibility/WT rates to azoles among C. parapsilosis species complex were ≥97.5%. However, 11.6% and 9.5% of C. tropicalis isolates were non-susceptible to fluconazole and voriconazole, respectively (7.1% were resistant to both). Approximately 14.3% of C. glabrata sensu stricto isolates (n = 258) were fluconazole resistant, and 11.6% of C. glabrata sensu stricto isolates were cross-resistant to fluconazole and voriconazole. All C. krusei isolates were susceptible/WT to voriconazole, posaconazole and itraconazole. Overall, 97.7%-100% of isolates were susceptible to caspofungin, micafungin and anidulafungin, but 2.3% of C. glabrata were non-susceptible to anidulafungin. There was no azole/echinocandin co-resistance. Disc diffusion and Sensititre YeastOne(TM) methods showed >95% categorical agreement for fluconazole and voriconazole. In summary, reduced azole susceptibility was seen among C. tropicalis. Resistance to echinocandins was uncommon. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial

  15. Review of the Ambrysus stali La Rivers species complex (Heteroptera: Nepomorpha: Naucoridae) with the description of a new species from Mesoamerica.

    Science.gov (United States)

    Sites, Robert W; Reynoso-Velasco, Daniel

    2015-09-15

    The Neotropical Ambrysus stali La Rivers species complex is reviewed and includes A. bifidus La Rivers & Nieser, A. scolius La Rivers, A. stali La Rivers, and A. tricuspis La Rivers. Ambrysus oblongulus Montandon is removed as a member of this complex. Features uniting these species are related to male genitalia and associated structures. Ambrysus maya n. sp. is the fifth species in the complex and is described from Belize, Guatemala, and Mexico based on specimens from recent collecting and museum collections.

  16. Functional gene polymorphism to reveal species history: the case of the CRTISO gene in cultivated carrots.

    Directory of Open Access Journals (Sweden)

    Vanessa Soufflet-Freslon

    Full Text Available Carrot is a vegetable cultivated worldwide for the consumption of its root. Historical data indicate that root colour has been differentially selected over time and according to geographical areas. Root pigmentation depends on the relative proportion of different carotenoids for the white, yellow, orange and red types but only internally for the purple one. The genetic control for root carotenoid content might be partially associated with carotenoid biosynthetic genes. Carotenoid isomerase (CRTISO has emerged as a regulatory step in the carotenoid biosynthesis pathway and could be a good candidate to show how a metabolic pathway gene reflects a species genetic history.In this study, the nucleotide polymorphism and the linkage disequilibrium among the complete CRTISO sequence, and the deviation from neutral expectation were analysed by considering population subdivision revealed with 17 microsatellite markers. A sample of 39 accessions, which represented different geographical origins and root colours, was used. Cultivated carrot was divided into two genetic groups: one from Middle East and Asia (Eastern group, and another one mainly from Europe (Western group. The Western and Eastern genetic groups were suggested to be differentially affected by selection: a signature of balancing selection was detected within the first group whereas the second one showed no selection. A focus on orange-rooted carrots revealed that cultivars cultivated in Asia were mainly assigned to the Western group but showed CRTISO haplotypes common to Eastern carrots.The carotenoid pathway CRTISO gene data proved to be complementary to neutral markers in order to bring critical insight in the cultivated carrot history. We confirmed the occurrence of two migration events since domestication. Our results showed a European background in material from Japan and Central Asia. While confirming the introduction of European carrots in Japanese resources, the history of Central Asia

  17. What do we gain from simplicity versus complexity in species distribution models?

    Science.gov (United States)

    Merow, Cory; Smith, Matthew J.; Edwards, Thomas C.; Guisan, Antoine; McMahon, Sean M.; Normand, Signe; Thuiller, Wilfried; Wuest, Rafael O.; Zimmermann, Niklaus E.; Elith, Jane

    2014-01-01

    Species distribution models (SDMs) are widely used to explain and predict species ranges and environmental niches. They are most commonly constructed by inferring species' occurrence–environment relationships using statistical and machine-learning methods. The variety of methods that can be used to construct SDMs (e.g. generalized linear/additive models, tree-based models, maximum entropy, etc.), and the variety of ways that such models can be implemented, permits substantial flexibility in SDM complexity. Building models with an appropriate amount of complexity for the study objectives is critical for robust inference. We characterize complexity as the shape of the inferred occurrence–environment relationships and the number of parameters used to describe them, and search for insights into whether additional complexity is informative or superfluous. By building ‘under fit’ models, having insufficient flexibility to describe observed occurrence–environment relationships, we risk misunderstanding the factors shaping species distributions. By building ‘over fit’ models, with excessive flexibility, we risk inadvertently ascribing pattern to noise or building opaque models. However, model selection can be challenging, especially when comparing models constructed under different modeling approaches. Here we argue for a more pragmatic approach: researchers should constrain the complexity of their models based on study objective, attributes of the data, and an understanding of how these interact with the underlying biological processes. We discuss guidelines for balancing under fitting with over fitting and consequently how complexity affects decisions made during model building. Although some generalities are possible, our discussion reflects differences in opinions that favor simpler versus more complex models. We conclude that combining insights from both simple and complex SDM building approaches best advances our knowledge of current and future species

  18. The locus coeruleus complex of the bottlenose dolphin (Tursiops truncatus) as revealed by tyrosine hydroxylase immunohistochemistry.

    Science.gov (United States)

    Manger, Paul R; Ridgway, Sam H; Siegel, Jerome M

    2003-06-01

    Using tyrosine hydroxylase immunohistochemistry we examined the structure of the pontine, or rostral rhombencephalic, catecholaminergic cells groups, which may be collectively termed the locus coeruleus complex (LC), in the bottlenose dolphin. The present study is the first to describe the LC in a cetacean species and, at 1.3 kg, represents the largest non-human brain to date in which the LC has been investigated. We identified four catecholaminergic cell groups in the dorsal pontine tegementum and peri-aqueductal gray matter: A6 dorsal (locus coeruleus), A6 ventral (locus coeruleus alpha), A7 (subcoeruleus), and A5 (fifth arcuate nucleus). No patterns of cellular distribution, nuclear subdivision, or cellular morphology indicate specialization of the LC, which might have been anticipated because of the large absolute brain size and unihemispheric sleep phenomenology of cetaceans.

  19. Botrytis californica, a new cryptic species in the B. cinerea species complex causing gray mold in blueberries and table grapes.

    Science.gov (United States)

    Saito, S; Margosan, D; Michailides, T J; Xiao, C L

    2016-01-01

    The Botrytis cinerea species complex comprises two cryptic species, originally referred to Group I and Group II based on Bc-hch gene RFLP haplotyping. Group I was described as a new cryptic species B. pseudocinerea During a survey of Botrytis spp. causing gray mold in blueberries and table grapes in the Central Valley of California, six isolates, three from blueberries and three from table grapes, were placed in Group I but had a distinct morphological character with conidiophores significantly longer than those of B. cinerea and B. pseudocinerea We compared these with B. cinerea and B. pseudocinerea by examining morphological and physiological characters, sensitivity to fenhexamid and phylogenetic analysis inferred from sequences of three nuclear genes. Phylogenetic analysis with the three partial gene sequences encoding glyceraldehyde-3-phosate dehydrogenase (G3PDH), heat-shock protein 60 (HSP60) and DNA-dependent RNA polymerase subunit II (RPB2) supported the proposal of a new Botrytis species, B. californica, which is closely related genetically to B. cinerea, B. pseudocinerea and B. sinoviticola, all known as causal agents of gray mold of grapes. Botrytis californica caused decay on blueberry and table grape fruit inoculated with the fungus. This study suggests that B. californica is a cryptic species sympatric with B. cinerea on blueberries and table grapes in California. © 2016 by The Mycological Society of America.

  20. Multilocus Analysis of Divergence and Introgression in Sympatric and Allopatric Sibling Species of the Lutzomyia longipalpis Complex in Brazil

    Science.gov (United States)

    Mazzoni, Camila J.; Souza, Nataly A.; Machado, Ricardo C.; Bruno, Rafaela V.

    2013-01-01

    Background Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Latin America, is a complex of sibling species. In Brazil, a number of very closely related sibling species have been revealed by the analyses of copulation songs, sex pheromones and molecular markers. However, the level of divergence and gene flow between the sibling species remains unclear. Brazilian populations of this vector can be divided in two main groups: one producing Burst-type songs and the Cembrene-1 pheromone and a second more diverse group producing various Pulse song subtypes and different pheromones. Methodology/Principal Findings We analyzed 21 nuclear loci in two pairs of Brazilian populations: two sympatric populations from the Sobral locality (1S and 2S) in northeastern Brazil and two allopatric populations from the Lapinha and Pancas localities in southeastern Brazil. Pancas and Sobral 2S are populations of the Burst/Cembrene-1 species while Lapinha and Sobral 1S are two putative incipient species producing the same pheromone and similar Pulse song subtypes. The multilocus analysis strongly suggests the occurrence of gene flow during the divergence between the sibling species, with different levels of introgression between loci. Moreover, this differential introgression is asymmetrical, with estimated gene flow being higher in the direction of the Burst/Cembrene-1 species. Conclusions/Significance The results indicate that introgressive hybridization has been a crucial phenomenon in shaping the genome of the L. longipalpis complex. This has possible epidemiological implications and is particularly interesting considering the potential for increased introgression caused by man-made environmental changes and the current trend of leishmaniasis urbanization in Brazil. PMID:24147172

  1. Competitive PCR reveals the complexity of postcopulatory sexual selection in Teleogryllus commodus.

    Science.gov (United States)

    Hall, Matthew D; Bussière, Luc F; Demont, Marco; Ward, Paul I; Brooks, Robert C

    2010-02-01

    The outcome of mate choice depends on complex interactions between males and females both before and after copulation. Although the competition between males for access to mates and premating choice by females are relatively well understood, the nature of interactions between cryptic female choice and male sperm competition within the female reproductive tract is less clear. Understanding the complexity of postcopulatory sexual selection requires an understanding of how anatomy, physiology and behaviour mediate sperm transfer and storage within multiply mated females. Here we use a newly developed molecular technique to directly quantify mixed sperm stores in multiple mating females of the black field cricket, Teleogryllus commodus. In this species, female postcopulatory choice is easily observed and manipulated as females delay the removal of the spermatophore in favour of preferred males. Using twice-mated females, we find that the proportion of sperm in the spermatheca attributed to the second male to mate with a female (S2) increases linearly with the time of spermatophore attachment. Moreover, we show that the insemination success of a male increases with its attractiveness and decreases with the size of the female. The effect of male attractiveness in this context suggests a previously unknown episode of mate choice in this species that reinforces the sexual selection imposed by premating choice and conflicts with the outcome of postmating male harassment. Our results provide some of the clearest evidence yet for how sperm transfer and displacement in multiply mated females can lead directly to cryptic female choice, and that three distinct periods of sexual selection operate in black field crickets.

  2. Sequence exploration reveals information bias among molecular markers used in phylogenetic reconstruction for Colletotrichum species.

    Science.gov (United States)

    Rampersad, Sephra N; Hosein, Fazeeda N; Carrington, Christine Vf

    2014-01-01

    The Colletotrichum gloeosporioides species complex is among the most destructive fungal plant pathogens in the world, however, identification of isolates of quarantine importance to the intra-specific level is confounded by a number of factors that affect phylogenetic reconstruction. Information bias and quality parameters were investigated to determine whether nucleotide sequence alignments and phylogenetic trees accurately reflect the genetic diversity and phylogenetic relatedness of individuals. Sequence exploration of GAPDH, ACT, TUB2 and ITS markers indicated that the query sequences had different patterns of nucleotide substitution but were without evidence of base substitution saturation. Regions of high entropy were much more dispersed in the ACT and GAPDH marker alignments than for the ITS and TUB2 markers. A discernible bimodal gap in the genetic distance frequency histograms was produced for the ACT and GAPDH markers which indicated successful separation of intra- and inter-specific sequences in the data set. Overall, analyses indicated clear differences in the ability of these markers to phylogenetically separate individuals to the intra-specific level which coincided with information bias.

  3. RNA profiles of porcine embryos during genome activation reveal complex metabolic switch sensitive to in vitro conditions.

    Directory of Open Access Journals (Sweden)

    Olga Østrup

    Full Text Available Fertilization is followed by complex changes in cytoplasmic composition and extensive chromatin reprogramming which results in the abundant activation of totipotent embryonic genome at embryonic genome activation (EGA. While chromatin reprogramming has been widely studied in several species, only a handful of reports characterize changing transcriptome profiles and resulting metabolic changes in cleavage stage embryos. The aims of the current study were to investigate RNA profiles of in vivo developed (ivv and in vitro produced (ivt porcine embryos before (2-cell stage and after (late 4-cell stage EGA and determine major metabolic changes that regulate totipotency. The period before EGA was dominated by transcripts responsible for cell cycle regulation, mitosis, RNA translation and processing (including ribosomal machinery, protein catabolism, and chromatin remodelling. Following EGA an increase in the abundance of transcripts involved in transcription, translation, DNA metabolism, histone and chromatin modification, as well as protein catabolism was detected. The further analysis of members of overlapping GO terms revealed that despite that comparable cellular processes are taking place before and after EGA (RNA splicing, protein catabolism, different metabolic pathways are involved. This strongly suggests that a complex metabolic switch accompanies EGA. In vitro conditions significantly altered RNA profiles before EGA, and the character of these changes indicates that they originate from oocyte and are imposed either before oocyte aspiration or during in vitro maturation. IVT embryos have altered content of apoptotic factors, cell cycle regulation factors and spindle components, and transcription factors, which all may contribute to reduced developmental competence of embryos produced in vitro. Overall, our data are in good accordance with previously published, genome-wide profiling data in other species. Moreover, comparison with mouse and

  4. A two-locus DNA sequence database for typing plant and human pathogens within the Fusarium oxysporum species complex

    DEFF Research Database (Denmark)

    O'Donnell, Kerry; Gueidan, C; Sink, S

    2009-01-01

    We constructed a two-locus database, comprising partial translation elongation factor (EF-1alpha) gene sequences and nearly full-length sequences of the nuclear ribosomal intergenic spacer region (IGS rDNA) for 850 isolates spanning the phylogenetic breadth of the Fusarium oxysporum species complex...... (FOSC). Of the 850 isolates typed, 101 EF-1alpha, 203 IGS rDNA, and 256 two-locus sequence types (STs) were differentiated. Analysis of the combined dataset suggests that two-thirds of the STs might be associated with a single host plant. This analysis also revealed that the 26 STs associated with human...

  5. The current status of the Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) species complex.

    Science.gov (United States)

    Souza, Nataly A; Brazil, Reginaldo P; Araki, Alejandra S

    2017-03-01

    Lutzomyia longipalpis s.l. is a complex of sibling species and is the principal vector of American visceral leishmaniasis. The present review summarises the diversity of efforts that have been undertaken to elucidate the number of unnamed species in this species complex and the phylogenetic relationships among them. A wide variety of evidence, including chemical, behavioral and molecular traits, suggests very recent speciation events and complex population structure in this group. Although significant advances have been achieved to date, differential vector capacity and the correlation between structure of parasite and vector populations have yet to be elucidated. Furthermore, increased knowledge about recent epidemiological changes, such as urbanisation, is essential for pursuing effective strategies for sandfly control in the New World.

  6. Colour patterns do not diagnose species: quantitative evaluation of a DNA barcoded cryptic bumblebee complex.

    Directory of Open Access Journals (Sweden)

    James C Carolan

    Full Text Available Cryptic diversity within bumblebees (Bombus has the potential to undermine crucial conservation efforts designed to reverse the observed decline in many bumblebee species worldwide. Central to such efforts is the ability to correctly recognise and diagnose species. The B. lucorum complex (Bombus lucorum, B. cryptarum and B. magnus comprises one of the most abundant and important group of wild plant and crop pollinators in northern Europe. Although the workers of these species are notoriously difficult to diagnose morphologically, it has been claimed that queens are readily diagnosable from morphological characters. Here we assess the value of colour-pattern characters in species identification of DNA-barcoded queens from the B. lucorum complex. Three distinct molecular operational taxonomic units were identified each representing one species. However, no uniquely diagnostic colour-pattern character state was found for any of these three molecular units and most colour-pattern characters showed continuous variation among the units. All characters previously deemed to be unique and diagnostic for one species were displayed by specimens molecularly identified as a different species. These results presented here raise questions on the reliability of species determinations in previous studies and highlights the benefits of implementing DNA barcoding prior to ecological, taxonomic and conservation studies of these important key pollinators.

  7. First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns.

    Science.gov (United States)

    Knapp, Michael; Rohland, Nadin; Weinstock, Jacobo; Baryshnikov, Gennady; Sher, Andrei; Nagel, Doris; Rabeder, Gernot; Pinhasi, Ron; Schmidt, Heiko A; Hofreiter, Michael

    2009-03-01

    Until recently, cave bears were believed to have only inhabited Europe. However, recent morphological evidence suggests that cave bears' geographic range extended as far east as Transbaikalia, Eastern Siberia. These Asian cave bears were morphologically distinct from European cave bears. However, how they related to European lineages remains unclear, stressing the need to assess the phylogenetic and phylogeographic relationship between Asian cave bears and their European relatives. In this work, we address this issue using a 227 base-pair fragment of the mitochondrial control region obtained from nine fossil bone samples from eight sites from the Urals, Caucasus, Altai Mountains, Ukraine and Yana River region in Eastern Siberia. Results of the phylogenetic analyses indicate that (i) the cave bear from the Yana River is most closely related to cave bears from the Caucasus region; (ii) the Caucasus/Yana group of bears is genetically very distinct from both European cave bears and brown bears, suggesting that these bears could represent an independent species; and (iii) the Western European cave bear lineage reached at least temporarily to the Altai Mountains, 7000 km east of their known centre of distribution. These results suggest that the diversity of cave bears was greater than previously believed, and that they could survive in a much wider range of ecological conditions than previously assumed. They also agree with recent studies on other extinct and extant species, such as wolves, hyenas and steppe bison, which have also revealed higher genetic and ecological diversity in Pleistocene populations than previously known.

  8. A New Species of the Fejervarya limnocharis Complex from Japan (Anura, Dicroglossidae)

    OpenAIRE

    Djong, Hon Tjong; Matsui, Masafumi; Kuramoto, Mitsuru; Nishioka, Midori; Sumida, Masayuki

    2011-01-01

    We describe a new species of dicroglossid frog of the Fejervarya limnocharis complex from western Honshu, Japan Mainland. The new species, Fejervarya kawamurai, is genetically closer to F. sakishimensis than to F. limnocharis. It differs from F. sakishimensis by smaller tympanum, head, forelimb, hindlimb, foot, and tibia lengths, all relative to snout-vent length, and from F. multistriata by relatively shorter forelimb, hindlimb, foot, and tibia. From F. limnocharis and F. iskandari, it is di...

  9. Evolutionary scenarios associated with the Pteronotus parnellii cryptic species-complex (Chiroptera: Mormoopidae).

    OpenAIRE

    López-Wilchis, Ricardo; Flores-Romero, Mayela; Guevara-Chumacero, Luis M.; Serrato-Díaz, Alejandra; Díaz-Larrea, Jhoana; Salgado-Mejía, Fernando; Ibáñez, Carlos; Salles, Leandro O.; Juste, Javier

    2016-01-01

    One of the major challenges to understanding the evolution of Neotropical bats concerns our capacity to successfully scrutinize phylogenetic patterns associated with cases of cryptic species complexes. In this study Pteronotus parnellii is examined as a selected example of a known lineage of mormoopid bat that potentially contains several cryptic species. A samples of 452 individuals from 83 different localities, essentially covering its entire mainland distribution, was evaluated using two g...

  10. Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

    Energy Technology Data Exchange (ETDEWEB)

    Resch, M.

    2014-09-08

    Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution imaging techniques. Also, translating findings between model substrates to intact biomass is critical for evaluating enzyme performance. Here we employ a fungal free enzyme cocktail, a complexed cellulosomal system, and a combination of the two to investigate saccharification mechanisms on cellulose I, II and III along with corn stover from Clean Fractionation (CF), which is an Organosolv pretreatment. The insoluble Cellulose Enriched Fraction (CEF) from CF contains mainly cellulose with minor amounts of residual hemicellulose and lignin, the amount of which depends on the CF pretreatment severity. Enzymatic digestions at both low and high-solids loadings demonstrate that CF reduces the amount of enzyme required to depolymerize polysaccharides relative to deacetylated, dilute acid pretreated corn stover. Transmission and scanning electron microscopy of the biomass provides evidence for the different mechanisms of enzymatic deconstruction between free and complexed enzyme systems, and reveals the basis for the synergistic relationship between the two enzyme paradigms on a process-relevant substrate for the first time. These results also demonstrate that the presence of lignin, rather than cellulose morphology, is more detrimental to cellulosome action than to free cellulases. As enzyme costs are a major economic driver for biorefineries, this study provides key inputs for the evaluation of CF as a pretreatment method for biomass conversion.

  11. Discrimination of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species by Fourier transform infrared spectroscopy.

    Science.gov (United States)

    Sousa, C; Silva, L; Grosso, F; Nemec, A; Lopes, J; Peixe, L

    2014-08-01

    The main goal of this work was to assess the ability of Fourier transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR) to discriminate between the species of the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex, i.e. A. baumannii, A. nosocomialis, A. pittii, A. calcoaceticus, genomic species "Between 1 and 3" and genomic species "Close to 13TU". A total of 122 clinical isolates of the Acb complex previously identified by rpoB sequencing were studied. FTIR-ATR spectra was analysed by partial least squares discriminant analysis (PLSDA) and the model scores were presented in a dendrogram form. This spectroscopic technique proved to be effective in the discrimination of the Acb complex species, with sensitivities from 90 to 100%. Moreover, a flowchart aiming to help with species identification was developed and tested with 100% correct predictions for A. baumannii, A. nosocomialis and A. pittii test isolates. This rapid, low cost and environmentally friendly technique proved to be a reliable alternative for the identification of these closely related Acinetobacter species that share many clinical and epidemiological characteristics and are often difficult to distinguish. Its validation towards application on a routine basis could revolutionise high-throughput bacterial identification.

  12. Epidemiological survey in single-species flocks from Poland reveals expanded genetic and antigenic diversity of small ruminant lentiviruses

    Science.gov (United States)

    Valas, Stephen; Kuźmak, Jacek

    2018-01-01

    Small ruminant lentivirus (SRLV) infections are widespread in Poland and circulation of subtypes A1, A12, A13, B1 and B2 was detected. The present work aimed at extending previous study based on the analysis of a larger number of animals from single-species flocks. Animals were selected for genetic analysis based on serological reactivity towards a range of recombinant antigens derived from Gag and Env viral proteins. Phylogenetic analysis revealed the existence of subtypes B2 and A12 in both goats and sheep and subtypes A1 and B1 in goats only. In addition, two novel subtypes, A16 and A17, were found in goats. Co-infections with strains belonging to different subtypes within A and B groups were detected in 1 sheep and 4 goats originating from four flocks. Although the reactivity of serum samples towards the recombinant antigens confirmed immunological relatedness between Gag epitopes of different subtypes and the cross-reactive nature of Gag antibodies, eleven serum samples failed to react with antigens representing all subtypes detected up-to-date in Poland, highlighting the limitations of the serological diagnosis. These data showed the complex nature of SRLV subtypes circulating in sheep and goats in Poland and the need for improving SRLV-related diagnostic capacity. PMID:29505612

  13. Systematics and biogeography of the Automolus infuscatus complex (Aves; Furnariidae): Cryptic diversity reveals western Amazonia as the origin of a transcontinental radiation.

    Science.gov (United States)

    Schultz, Eduardo D; Burney, Curtis W; Brumfield, Robb T; Polo, Erico M; Cracraft, Joel; Ribas, Camila C

    2017-02-01

    A revision of the avian Neotropical genus Automolus and the Furnariidae family points to the paraphyly of A. infuscatus and reveals a species complex comprising A. infuscatus, A. ochrolaemus, A. paraensis, A. leucophthalmus, A. lammi and A. subulatus, the latter historically classified in the genus Hyloctistes. Detailed knowledge of the taxonomy, geographic distribution, phylogenetic relationship and divergence times of a taxon allows exploration of its evolutionary history and the testing of different scenarios of diversification. In this context, we studied the A. infuscatus complex using molecular data in order to unveil its cryptic diversity and reveal its evolutionary history. For that we sequenced two mitochondrial (ND2 and cytb) and three nuclear markers (G3PDH, ACO, Fib7) for 302 individuals belonging to all species in the complex and most described subspecies. Our analysis supports the paraphyly of A. infuscatus, indicating the existence of at least two distinct clades not closely related. The remaining species were all recovered as monophyletic. Notwithstanding, a well-structured intraspecific diversity was found with 19 lineages suggesting substantial cryptic diversity within the described species. A. subulatus was recovered within the complex, corroborating its position inside the genus. In spite of the high congruence between distributions of different lineages, with several sister lineages currently separated by the same barriers, the temporal incongruence between divergences over the same barriers reveals a complex evolutionary history. While older events might be related to the emergence of barriers such as the Andes and major Amazonian rivers, younger events suggest dispersal after the consolidation of those barriers. Our analysis suggests that the complex had its origin around 6million years (Ma) and inhabited Western Amazonia in Late Miocene-Early Pliocene. Considering the riparian habit of species in its sister clade, the rise and early

  14. Novel taxa in the Fusarium fujikuroi species complex from Pinus spp.

    Science.gov (United States)

    Herron, D.A.; Wingfield, M.J.; Wingfield, B.D.; Rodas, C.A.; Marincowitz, S.; Steenkamp, E.T.

    2015-01-01

    The pitch canker pathogen Fusarium circinatum has caused devastation to Pinus spp. in natural forests and non-natives in commercially managed plantations. This has drawn attention to the potential importance of Fusarium species as pathogens of forest trees. In this study, we explored the diversity of Fusarium species associated with diseased Pinus patula, P. tecunumanii, P. kesiya and P. maximinoi in Colombian plantations and nurseries. Plants displaying symptoms associated with a F. circinatum-like infection (i.e., stem cankers and branch die-back on trees in plantations and root or collar rot of seedlings) were sampled. A total of 57 isolates were collected and characterised based on DNA sequence data for the translation elongation factor 1-α and β-tubulin gene regions. Phylogenetic analyses of these data allowed for the identification of more than 10 Fusarium species. These included F. circinatum, F. oxysporum, species within the Fusarium solani species complex and seven novel species in the Fusarium fujikuroi species complex (formerly the Gibberella fujikuroi species complex), five of which are described here as new. Selected isolates of the new species were tested for their pathogenicity on Pinus patula and compared with that of F. circinatum. Of these, F. marasasianum, F. parvisorum and F. sororula displayed levels of pathogenicity to P. patula that were comparable with that of F. circinatum. These apparently emerging pathogens thus pose a significant risk to forestry in Colombia and other parts of the world. PMID:26955193

  15. Seeing the forest and the trees: multilevel models reveal both species and community patterns

    Science.gov (United States)

    Michelle M. Jackson; Monica G. Turner; Scott M. Pearson; Anthony R. Ives

    2012-01-01

    Studies designed to understand species distributions and community assemblages typically use separate analytical approaches (e.g., logistic regression and ordination) to model the distribution of individual species and to relate community composition to environmental variation. Multilevel models (MLMs) offer a promising strategy for integrating species and community-...

  16. Burning reveals cryptic diversity and promotes coexistence of native species in a restored California prairie

    Science.gov (United States)

    Grassland and prairie restoration projects in California often result in long-term establishment of only a few native plant species, even when they begin with a diverse palette of species. A likely explanation for the disappearance of certain native species over time is that they are outcompeted by ...

  17. Species-specific detection and identification of fusarium species complex, the causal agent of sugarcane pokkah boeng in China.

    Directory of Open Access Journals (Sweden)

    Zhenyue Lin

    Full Text Available BACKGROUND: Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. METHODS: A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. RESULT: Two Fusarium species (F. verticillioides and F. proliferatum that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. CONCLUSIONS/SIGNIFICANCE: This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng.

  18. Proteomic amino-termini profiling reveals targeting information for protein import into complex plastids.

    Directory of Open Access Journals (Sweden)

    Pitter F Huesgen

    Full Text Available In organisms with complex plastids acquired by secondary endosymbiosis from a photosynthetic eukaryote, the majority of plastid proteins are nuclear-encoded, translated on cytoplasmic ribosomes, and guided across four membranes by a bipartite targeting sequence. In-depth understanding of this vital import process has been impeded by a lack of information about the transit peptide part of this sequence, which mediates transport across the inner three membranes. We determined the mature N-termini of hundreds of proteins from the model diatom Thalassiosira pseudonana, revealing extensive N-terminal modification by acetylation and proteolytic processing in both cytosol and plastid. We identified 63 mature N-termini of nucleus-encoded plastid proteins, deduced their complete transit peptide sequences, determined a consensus motif for their cleavage by the stromal processing peptidase, and found evidence for subsequent processing by a plastid methionine aminopeptidase. The cleavage motif differs from that of higher plants, but is shared with other eukaryotes with complex plastids.

  19. Revealing complete complex KIR haplotypes phased by long-read sequencing technology.

    Science.gov (United States)

    Roe, D; Vierra-Green, C; Pyo, C-W; Eng, K; Hall, R; Kuang, R; Spellman, S; Ranade, S; Geraghty, D E; Maiers, M

    2017-09-01

    The killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to 16 genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins fulfill functional roles in infections, pregnancy, autoimmune diseases and transplantation. However, their characterization remains a constant challenge. Not only are the genes highly homologous due to their recent evolution by tandem duplications, but the region is structurally dynamic due to frequent transposon-mediated recombination. A sequencing approach that precisely captures the complexity of KIR haplotypes for functional annotation is desirable. We present a unique approach to haplotype the KIR loci using single-molecule, real-time (SMRT) sequencing. Using this method, we have-for the first time-comprehensively sequenced and phased sixteen KIR haplotypes from eight individuals without imputation. The information revealed four novel haplotype structures, a novel gene-fusion allele, novel and confirmed insertion/deletion events, a homozygous individual, and overall diversity for the structural haplotypes and their alleles. These KIR haplotypes augment our existing knowledge by providing high-quality references, evolutionary informers, and source material for imputation. The haplotype sequences and gene annotations provide alternative loci for the KIR region in the human genome reference GrCh38.p8.

  20. The laminA/NF-Y protein complex reveals an unknown transcriptional mechanism on cell proliferation.

    Science.gov (United States)

    Cicchillitti, Lucia; Manni, Isabella; Mancone, Carmine; Regazzo, Giulia; Spagnuolo, Manuela; Alonzi, Tonino; Carlomosti, Fabrizio; Dell'Anna, Maria Lucia; Dell'Omo, Giulia; Picardo, Mauro; Ciana, Paolo; Capogrossi, Maurizio C; Tripodi, Marco; Magenta, Alessandra; Rizzo, Maria Giulia; Gurtner, Aymone; Piaggio, Giulia

    2017-01-10

    Lamin A is a component of the nuclear matrix that also controls proliferation by largely unknown mechanisms. NF-Y is a ubiquitous protein involved in cell proliferation composed of three subunits (-YA -YB -YC) all required for the DNA binding and transactivation activity. To get clues on new NF-Y partner(s) we performed a mass spectrometry screening of proteins that co-precipitate with the regulatory subunit of the complex, NF-YA. By this screening we identified lamin A as a novel putative NF-Y interactor. Co-immunoprecipitation experiments and confocal analysis confirmed the interaction between the two endogenous proteins. Interestingly, this association occurs on euchromatin regions, too. ChIP experiments demonstrate lamin A enrichment in several promoter regions of cell cycle related genes in a NF-Y dependent manner. Gain and loss of function experiments reveal that lamin A counteracts NF-Y transcriptional activity. Taking advantage of a recently generated transgenic reporter mouse, called MITO-Luc, in which an NF-Y-dependent promoter controls luciferase expression, we demonstrate that lamin A counteracts NF-Y transcriptional activity not only in culture cells but also in living animals. Altogether, our data demonstrate the occurrence of lamin A/NF-Y interaction and suggest a possible role of this protein complex in regulation of NF-Y function in cell proliferation.

  1. Revealing the Structural Complexity of Component Interactions of Topic-Specific PCK when Planning to Teach

    Science.gov (United States)

    Mavhunga, Elizabeth

    2018-04-01

    Teaching pedagogical content knowledge (PCK) at a topic-specific level requires clarity on the content-specific nature of the components employed, as well as the specific features that bring about the desirable depth in teacher explanations. Such understanding is often hazy; yet, it influences the nature of teacher tasks and learning opportunities afforded to pre-service teachers in a teaching program. The purpose of this study was twofold: firstly, to illuminate the emerging complexity when content-specific components of PCK interact when planning to teach a chemistry topic; and secondly, to identify the kinds of teacher tasks that promote the emergence of such complexity. Data collected were content representations (CoRes) in chemical equilibrium accompanied by expanded lesson outlines from 15 pre-service teachers in their final year of study towards a first degree in teaching (B Ed). The analysis involved extraction of episodes that exhibited component interaction by using a qualitative in-depth analysis method. The results revealed the structure in which the components of PCK in a topic interact among each other to be linear, interwoven, or a combination of the two. The interwoven interactions contained multiple components that connected explanations on different aspects of a concept, all working in a complementary manner. The most sophisticated component interactions emerged from teacher tasks on descriptions of a lesson sequence and a summary of a lesson. Recommendations in this study highlight core practices for making pedagogical transformation of topic content knowledge more accessible.

  2. Structure of the Leanyer orthobunyavirus nucleoprotein-RNA complex reveals unique architecture for RNA encapsidation.

    Science.gov (United States)

    Niu, Fengfeng; Shaw, Neil; Wang, Yao E; Jiao, Lianying; Ding, Wei; Li, Xiaomin; Zhu, Ping; Upur, Halmurat; Ouyang, Songying; Cheng, Genhong; Liu, Zhi-Jie

    2013-05-28

    Negative-stranded RNA viruses cover their genome with nucleoprotein (N) to protect it from the human innate immune system. Abrogation of the function of N offers a unique opportunity to combat the spread of the viruses. Here, we describe a unique fold of N from Leanyer virus (LEAV, Orthobunyavirus genus, Bunyaviridae family) in complex with single-stranded RNA refined to 2.78 Å resolution as well as a 2.68 Å resolution structure of LEAV N-ssDNA complex. LEAV N is made up of an N- and a C-terminal lobe, with the RNA binding site located at the junction of these lobes. The LEAV N tetramer binds a 44-nucleotide-long single-stranded RNA chain. Hence, oligomerization of N is essential for encapsidation of the entire genome and is accomplished by using extensions at the N and C terminus. Molecular details of the oligomerization of N are illustrated in the structure where a circular ring-like tertiary assembly of a tetramer of LEAV N is observed tethering the RNA in a positively charged cavity running along the inner edge. Hydrogen bonds between N and the C2 hydroxyl group of ribose sugar explain the specificity of LEAV N for RNA over DNA. In addition, base-specific hydrogen bonds suggest that some regions of RNA bind N more tightly than others. Hinge movements around F20 and V125 assist in the reversal of capsidation during transcription and replication of the virus. Electron microscopic images of the ribonucleoprotein complexes of LEAV N reveal a filamentous assembly similar to those found in phleboviruses.

  3. A Systemic Analysis of Transcriptomic and Epigenomic Data To Reveal Regulation Patterns for Complex Disease.

    Science.gov (United States)

    Xu, Chao; Zhang, Ji-Gang; Lin, Dongdong; Zhang, Lan; Shen, Hui; Deng, Hong-Wen

    2017-07-05

    Integrating diverse genomics data can provide a global view of the complex biological processes related to the human complex diseases. Although substantial efforts have been made to integrate different omics data, there are at least three challenges for multi-omics integration methods: (i) How to simultaneously consider the effects of various genomic factors, since these factors jointly influence the phenotypes; (ii) How to effectively incorporate the information from publicly accessible databases and omics datasets to fully capture the interactions among (epi)genomic factors from diverse omics data; and (iii) Until present, the combination of more than two omics datasets has been poorly explored. Current integration approaches are not sufficient to address all of these challenges together. We proposed a novel integrative analysis framework by incorporating sparse model, multivariate analysis, Gaussian graphical model, and network analysis to address these three challenges simultaneously. Based on this strategy, we performed a systemic analysis for glioblastoma multiforme (GBM) integrating genome-wide gene expression, DNA methylation, and miRNA expression data. We identified three regulatory modules of genomic factors associated with GBM survival time and revealed a global regulatory pattern for GBM by combining the three modules, with respect to the common regulatory factors. Our method can not only identify disease-associated dysregulated genomic factors from different omics, but more importantly, it can incorporate the information from publicly accessible databases and omics datasets to infer a comprehensive interaction map of all these dysregulated genomic factors. Our work represents an innovative approach to enhance our understanding of molecular genomic mechanisms underlying human complex diseases. Copyright © 2017 Xu et al.

  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. Molecular Phylogeny and Zoogeography of the Capoeta damascina Species Complex (Pisces: Teleostei: Cyprinidae.

    Directory of Open Access Journals (Sweden)

    Nisreen Alwan

    Full Text Available Capoeta damascina was earlier considered by many authors as one of the most common freshwater fish species found throughout the Levant, Mesopotamia, Turkey, and Iran. However, owing to a high variation in morphological characters among and within its various populations, 17 nominal species were described, several of which were regarded as valid by subsequent revising authors. Capoeta damascina proved to be a complex of closely related species, which had been poorly studied. The current study aims at defining C. damascina and the C. damascina species complex. It investigates phylogenetic relationships among the various members of the C. damascina complex, based on mitochondrial and nuclear DNA sequences. Phylogenetic relationships were projected against paleogeographical events to interpret the geographic distribution of the taxa under consideration in relation to the area's geological history. Samples were obtained from throughout the geographic range and were subjected to genetic analyses, using two molecular markers targeting the mitochondrial cytochrome oxidase I (n = 103 and the two adjacent divergence regions (D1-D2 of the nuclear 28S rRNA genes (n = 65. Six closely related species were recognized within the C. damascina complex, constituting two main lineages: A western lineage represented by C. caelestis, C. damascina, and C. umbla and an eastern lineage represented by C. buhsei, C. coadi, and C. saadii. The results indicate that speciation of these taxa is rather a recent event. Dispersal occurred during the Pleistocene, resulting in present-day distribution patterns. A coherent picture of the phylogenetic relationships and evolutionary history of the C. damascina species complex is drawn, explaining the current patterns of distribution as a result of paleogeographic events and ecological adaptations.

  6. The Syllis gracilis species complex: A molecular approach to a difficult taxonomic problem (Annelida, Syllidae).

    Science.gov (United States)

    Álvarez-Campos, Patricia; Giribet, Gonzalo; Riesgo, Ana

    2017-04-01

    Syllis gracilis is an emblematic member of the subfamily Syllinae (Syllidae, Annelida), which inhabits shallow, temperate coastal waters and can be found on algae, coral rubble, and sponges. Their distinctive ypsiloid chaetae, usually found in specimens from populations all around the world, led to the consideration of the species as cosmopolitan, even though four other species have similar chaetae: Syllis magellanica, S. picta, S. mayeri and S. ypsiloides. The discovery of deeply divergent lineages in the Mediterranean Sea, that were morphologically similar, questioned the cosmopolitanism of S. gracilis and suggested the possibility of it being a species complex. In order to assess the speciation patterns within the putative S. gracilis complex, we undertook species delimitation and phylogenetic analyses on 61 specimens morphologically ascribed to Syllis gracilis and closely related species using a multilocus molecular dataset (two mitochondrial and two nuclear markers). Our results suggest high levels of genetic differentiation between the S. gracilis populations analyzed, some of which have morphologically distinctive features. Five to eight distinct lineages (depending on the analysis) were identified, all with geographically restricted distributions. Although the presence of ypsiloid chaetae has been traditionally considered the main character to identify S. gracilis, we conclude that this feature is homoplastic. Instead, we propose that characters such as the degree of fusion of blades and shafts in chaetae, the morphology of the posterior chaetae or the animal color pattern should be considered to differentiate lineages within the S. gracilis species complex. Our study does not support the cosmopolitanism of S. gracilis, and instead provides morphological and molecular evidence of the existence of a complex of pseudo-cryptic species. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Different localization patterns of anthocyanin species in the pericarp of black rice revealed by imaging mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Yukihiro Yoshimura

    Full Text Available Black rice (Oryza sativa L. Japonica contains high levels of anthocyanins in the pericarp and is considered an effective health-promoting food. Several studies have identified the molecular species of anthocyanins in black rice, but information about the localization of each anthocyanin species is limited because methodologies for investigating the localization such as determining specific antibodies to anthocyanin, have not yet been developed Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS is a suitable tool for investigating the localization of metabolites. In this study, we identified 7 species of anthocyanin monoglycosides and 2 species of anthocyanin diglycosides in crude extracts from black rice by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS analysis. We also analyzed black rice sections by MALDI-IMS and found 2 additional species of anthocyanin pentosides and revealed different localization patterns of anthocyanin species composed of different sugar moieties. Anthocyanin species composed of a pentose moiety (cyanidin-3-O-pentoside and petunidin-3-O-pentoside were localized in the entire pericarp, whereas anthocyanin species composed of a hexose moiety (cyanidin-3-O-hexoside and peonidin-3-O-hexoside were focally localized in the dorsal pericarp. These results indicate that anthocyanin species composed of different sugar moieties exhibit different localization patterns in the pericarp of black rice. This is the first detailed investigation into the localization of molecular species of anthocyanins by MALDI-IMS.

  8. Nitrogen complex species and its chemical nature in TiO2 for visible-light sensitized photocatalysis

    International Nuclear Information System (INIS)

    Asahi, Ryoji; Morikawa, Takeshi

    2007-01-01

    A photocatalyst with high reactivity under visible-light has been desired to utilize solar irradiation or interior lighting efficiently. Nitrogen-doped TiO 2 revealed significant improvement in optical absorption and photocatalytic activity over TiO 2 under visible light. We have performed the first-principles calculations to study the detailed N complex species introduced in TiO 2 . The results include stable geometries, densities of states, formation energies, and core levels. The present systematic studies account for the long-term controversial issue on N-doped TiO 2 , in particular, regarding the detailed assignment of N 1s binding energies observed in the XPS measurement. The detailed analyses of the formation energies show that introducing the N species more in a controlled way via process conditions is crucial to achieve the optimized photocatalytic performance

  9. Quantum mechanical calculation of aqueuous uranium complexes: carbonate, phosphate, organic and biomolecular species

    Directory of Open Access Journals (Sweden)

    Jha Prashant

    2009-08-01

    Full Text Available Abstract Background Quantum mechanical calculations were performed on a variety of uranium species representing U(VI, U(V, U(IV, U-carbonates, U-phosphates, U-oxalates, U-catecholates, U-phosphodiesters, U-phosphorylated N-acetyl-glucosamine (NAG, and U-2-Keto-3-doxyoctanoate (KDO with explicit solvation by H2O molecules. These models represent major U species in natural waters and complexes on bacterial surfaces. The model results are compared to observed EXAFS, IR, Raman and NMR spectra. Results Agreement between experiment and theory is acceptable in most cases, and the reasons for discrepancies are discussed. Calculated Gibbs free energies are used to constrain which configurations are most likely to be stable under circumneutral pH conditions. Reduction of U(VI to U(IV is examined for the U-carbonate and U-catechol complexes. Conclusion Results on the potential energy differences between U(V- and U(IV-carbonate complexes suggest that the cause of slower disproportionation in this system is electrostatic repulsion between UO2 [CO3]35- ions that must approach one another to form U(VI and U(IV rather than a change in thermodynamic stability. Calculations on U-catechol species are consistent with the observation that UO22+ can oxidize catechol and form quinone-like species. In addition, outer-sphere complexation is predicted to be the most stable for U-catechol interactions based on calculated energies and comparison to 13C NMR spectra. Outer-sphere complexes (i.e., ion pairs bridged by water molecules are predicted to be comparable in Gibbs free energy to inner-sphere complexes for a model carboxylic acid. Complexation of uranyl to phosphorus-containing groups in extracellular polymeric substances is predicted to favor phosphonate groups, such as that found in phosphorylated NAG, rather than phosphodiesters, such as those in nucleic acids.

  10. Mistletoe lectin I in complex with galactose and lactose reveals distinct sugar-binding properties

    Energy Technology Data Exchange (ETDEWEB)

    Mikeska, Ruth [Institute of Biochemistry and Food Chemistry, University of Hamburg, c/o DESY, Notkestrasse 85, Building 22a, 22603 Hamburg (Germany); Wacker, Roland [Institute of Physiological Chemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen (Germany); Arni, Raghuvir [Department of Physics, IBILCE/UNESP, São Jose do Rio Preto, São Paul (Brazil); Singh, Tej P. [Department of Biophysics, All India Institute of Medical Sciences, New Delhi (India); Mikhailov, Albert; Gabdoulkhakov, Azat [Institute of Crystallography of Russian Academy of Sciences, Leninsky Prospect 59, 117333 Moscow (Russian Federation); Voelter, Wolfgang [Institute of Physiological Chemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen (Germany); Betzel, Christian, E-mail: betzel@unisgi1.desy.de [Institute of Biochemistry and Food Chemistry, University of Hamburg, c/o DESY, Notkestrasse 85, Building 22a, 22603 Hamburg (Germany)

    2005-01-01

    The structures of mistletoe lectin I in complex with lactose and galactose reveal differences in binding by the two known sites in subdomains α1 and γ2 and suggest the presence of a third low-affinity site in subdomain β1. The structures of mistletoe lectin I (ML-I) from Viscum album complexed with lactose and galactose have been determined at 2.3 Å resolution and refined to R factors of 20.9% (R{sub free} = 23.6%) and 20.9 (R{sub free} = 24.6%), respectively. ML-I is a heterodimer and belongs to the class of ribosome-inactivating proteins of type II, which consist of two chains. The A-chain has rRNA N-glycosidase activity and irreversibly inhibits eukaryotic ribosomes. The B-chain is a lectin and preferentially binds to galactose-terminated glycolipids and glycoproteins on cell membranes. Saccharide binding is performed by two binding sites in subdomains α1 and γ2 of the ML-I B-chain separated by ∼62 Å from each other. The favoured binding of galactose in subdomain α1 is achieved via hydrogen bonds connecting the 4-hydroxyl and 3-hydroxyl groups of the sugar moiety with the side chains of Asp23B, Gln36B and Lys41B and the main chain of 26B. The aromatic ring of Trp38B on top of the preferred binding pocket supports van der Waals packing of the apolar face of galactose and stabilizes the sugar–lectin complex. In the galactose-binding site II of subdomain γ2, Tyr249B provides the hydrophobic stacking and the side chains of Asp235B, Gln238B and Asn256B are hydrogen-bonding partners for galactose. In the case of the galactose-binding site I, the 2-hydroxyl group also stabilizes the sugar–protein complex, an interaction thus far rarely detected in galactose-specific lectins. Finally, a potential third low-affinity galactose-binding site in subunit β1 was identified in the present ML-I structures, in which a glycerol molecule from the cryoprotectant buffer has bound, mimicking the sugar compound.

  11. Global analysis of threat status reveals higher extinction risk in tropical than in temperate bird sister species

    Directory of Open Access Journals (Sweden)

    Reif Jiří

    2016-06-01

    Full Text Available Given increasing pressures upon biodiversity, identification of species’ traits related to elevated extinction risk is useful for more efficient allocation of limited resources for nature conservation. Despite its need, such a global analysis was lacking in the case of birds. Therefore, we performed this exercise for avian sister species using information about their global extinction risk from IUCN Red List. We focused on 113 pairs of sister species, each containing a threatened and an unthreatened species to factor out the effects of common evolutionary history on the revealed relationship. We collected data on five traits with expected relationships to species’ extinction risk based on previous studies performed at regional or national levels: breeding habitat (recognizing forest, grassland, wetland and oceanic species, latitudinal range position (temperate and tropics species, migration strategy (migratory and resident species, diet (carnivorous, insectivorous, herbivorous and omnivorous species and body mass. We related the extinction risk using IUCN threat level categories to species’ traits using generalised linear mixed effects models expecting lower risk for forest, temperate, omnivorous and smaller-bodied species. Our expectation was confirmed only in the case of latitudinal range position, as we revealed higher threat level for tropical than for temperate species. This relationship was robust to different methods of threat level expression and cannot be explained by a simple association of high bird species richness with the tropical zone. Instead, it seems that tropical species are more threatened because of their intrinsic characteristics such as slow life histories, adaptations to stable environments and small geographic ranges. These characteristics are obviously disadvantageous in conditions of current human-induced environmental perturbations. Moreover, given the absence of habitat effects, our study indicates that such

  12. Geographically predominant genotypes of Aspergillus terreus species complex in Austria: s microsatellite typing study

    NARCIS (Netherlands)

    Lackner, M.; Coassin, S.; Haun, M.; Binder, U.; Kronenberg, F.; Haas, H. de; Jank, M.; Maurer, E.; Meis, J.F.; Hagen, F.; Lass-Florl, C.

    2016-01-01

    Aspergillus terreus species complex is recognized as a frequent agent of invasive aspergillosis in Tyrol. The reason for this specific epidemiological situation is unclear. Aspergillus terreus strains isolated from environmental and clinical sources were genotyped using a novel panel of short tandem

  13. Comparison of the cattle leukocyte receptor complex with related livestock species

    Science.gov (United States)

    The natural killer (NK) cell receptor gene complexes are highly variable between species, and their repetitive nature makes genomic assembly and characterization problematic. As a result, most reference genome assemblies are heavily fragmented and/or misassembled over these regions. However, new lon...

  14. Proposals for treating four species complexes in Ficus subgenus Urostigma section Americanae (Moraceae)

    NARCIS (Netherlands)

    Berg, C.C.

    2007-01-01

    Four species complexes of Ficus subg. Urostigma sect. Americanae (Moraceae) are discussed. Four new combinations are made in Ficus americana Aubl.: subsp. andicola (Standl.) C.C. Berg, subsp. greiffiana (Dugand) C.C. Berg, subsp. guianensis (Desv.) C.C. Berg, and subsp. subapiculata (Miq.) C.C.

  15. An unrecognized species of the Culicoides obsoletus complex feeding on livestock in the Netherlands

    NARCIS (Netherlands)

    Meiswinkel, R.; Bree, de F.M.; Vries, de Ruth; Elbers, A.R.W.

    2015-01-01

    In studies on Culicoides attacking livestock in the Netherlands, we chanced upon a species of the Obsoletus complex that we do not recognize, but whose dark wing pattern is distinctive. Nine cytochrome c oxidase (CO1) sequences of our so-called ‘dark obsoletus’ support its status as a separate

  16. Delineation of a New Species of the Borrelia burgdorferi Sensu Lato Complex, Borrelia americana sp. nov

    Czech Academy of Sciences Publication Activity Database

    Rudenko, Natalia; Golovchenko, Maryna; Lin, T.; Gao, L.; Grubhoffer, Libor; Oliver, J. H., Jr.

    2009-01-01

    Roč. 47, č. 12 (2009), s. 3875-3880 ISSN 0095-1137 R&D Projects: GA MŠk(CZ) LC06009 Institutional research plan: CEZ:AV0Z60220518 Keywords : multilocus sequence analysis * B. burgdorferi sl complex * new borrelia species * Borrelia americana Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 4.162, year: 2009

  17. Method of analysis of polymerizable monomeric species in a complex mixture

    Science.gov (United States)

    Hermes, Robert E

    2014-03-18

    Method of selective quantitation of a polymerizable monomeric species in a well spacer fluid, said method comprising the steps of adding at least one solvent having a refractive index of less than about 1.33 to a sample of the complex mixture to produce a solvent phase, and measuring the refractive index of the solvent phase.

  18. Differential triazole sensitivity among members of the Fusarium graminearum species complex infecting barley grains in Brazil

    Science.gov (United States)

    Fusarium head blight (FHB) is an important disease of small grains and is caused mainly by members of the Fusarium graminearum species complex (FGSC). Barley growers in Brazil rely on fungicides, especially triazoles, to suppress the disease and limit mycotoxin contamination of grain. Information on...

  19. A Polychaete's powerful punch: venom gland transcriptomics of Glycera reveals a complex cocktail of toxin homologs.

    Science.gov (United States)

    von Reumont, Björn M; Campbell, Lahcen I; Richter, Sandy; Hering, Lars; Sykes, Dan; Hetmank, Jörg; Jenner, Ronald A; Bleidorn, Christoph

    2014-09-05

    Glycerids are marine annelids commonly known as bloodworms. Bloodworms have an eversible proboscis adorned with jaws connected to venom glands. Bloodworms prey on invertebrates, and it is known that the venom glands produce compounds that can induce toxic effects in animals. Yet, none of these putative toxins has been characterized on a molecular basis. Here we present the transcriptomic profiles of the venom glands of three species of bloodworm, Glycera dibranchiata, Glycera fallax and Glycera tridactyla, as well as the body tissue of G. tridactyla. The venom glands express a complex mixture of transcripts coding for putative toxin precursors. These transcripts represent 20 known toxin classes that have been convergently recruited into animal venoms, as well as transcripts potentially coding for Glycera-specific toxins. The toxins represent five functional categories: Pore-forming and membrane-disrupting toxins, neurotoxins, protease inhibitors, other enzymes, and CAP domain toxins. Many of the transcripts coding for putative Glycera toxins belong to classes that have been widely recruited into venoms, but some are homologs of toxins previously only known from the venoms of scorpaeniform fish and monotremes (stonustoxin-like toxin), turrid gastropods (turripeptide-like peptides), and sea anemones (gigantoxin I-like neurotoxin). This complex mixture of toxin homologs suggests that bloodworms employ venom while predating on macroscopic prey, casting doubt on the previously widespread opinion that G. dibranchiata is a detritivore. Our results further show that researchers should be aware that different assembly methods, as well as different methods of homology prediction, can influence the transcriptomic profiling of venom glands. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. Comprehensive analysis of RNA-seq data reveals the complexity of the transcriptome in Brassica rapa.

    Science.gov (United States)

    Tong, Chaobo; Wang, Xiaowu; Yu, Jingyin; Wu, Jian; Li, Wanshun; Huang, Junyan; Dong, Caihua; Hua, Wei; Liu, Shengyi

    2013-10-07

    sequence, which will advance our understanding of the dynamics and complexity of the B. rapa transcriptome. The atlas of gene expression in different tissues will be useful for accelerating research on functional genomics and genome evolution in Brassica species.

  1. Integrative taxonomy reveals a new species of Callisto ( Lepidoptera , Gracillariidae ) in the Alps

    OpenAIRE

    Kirichenko, Natalia; Huemer, Peter; Deutsch, Helmut; Triberti, Paolo; Rougerie, Rodolphe; Lopez-Vaamonde, Carlos

    2015-01-01

    Abstract Europe has one of the best-known Lepidopteran faunas in the world, yet many species are still being discovered, especially in groups of small moths. Here we describe a new gracillariid species from the south-eastern Alps, Callisto basistrigella Huemer, Deutsch & Triberti, sp. n. It shows differences from its sister species Callisto coffeella in morphology, the barcode region of the cytochrome c oxidase I gene and the nuclear gene histone H3. Both Callisto basistrigella and Callisto c...

  2. Ultrastructural characteristics of nurse cell-larva complex of four species of Trichinella in several hosts

    Directory of Open Access Journals (Sweden)

    Sacchi L.

    2001-06-01

    Full Text Available The nurse cell-larva complex of nematodes of the genus Trichinella plays an Important role in the survival of the larva in decaying muscles, frequently favouring the transmission of the parasite in extreme environmental conditions. The ultrastructure of the nurse cell-larva complex in muscles from different hosts infected with T. nativa (a walrus and a polar bear, T. spiralis (horses and humans, T. pseudospiralis (a laboratory mouse and T. papuae (a laboratory mouse were examined. Analysis with transmission electron microscope showed that the typical nurse cell structure was present in all examined samples, irrespective of the species of larva, of the presence of a collagen capsule, of the age of infection and of the host species, suggesting that there exists a molecular mechanism that in the first stage of larva invasion is similar for encapsulated and non-encapsulated species.

  3. RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis

    Directory of Open Access Journals (Sweden)

    Garcia Tzintzuni I

    2012-09-01

    Full Text Available Abstract Background The release of oil resulting from the blowout of the Deepwater Horizon (DH drilling platform was one of the largest in history discharging more than 189 million gallons of oil and subject to widespread application of oil dispersants. This event impacted a wide range of ecological habitats with a complex mix of pollutants whose biological impact is still not yet fully understood. To better understand the effects on a vertebrate genome, we studied gene expression in the salt marsh minnow Fundulus grandis, which is local to the northern coast of the Gulf of Mexico and is a sister species of the ecotoxicological model Fundulus heteroclitus. To assess genomic changes, we quantified mRNA expression using high throughput sequencing technologies (RNA-Seq in F. grandis populations in the marshes and estuaries impacted by DH oil release. This application of RNA-Seq to a non-model, wild, and ecologically significant organism is an important evaluation of the technology to quickly assess similar events in the future. Results Our de novo assembly of RNA-Seq data produced a large set of sequences which included many duplicates and fragments. In many cases several of these could be associated with a common reference sequence using blast to query a reference database. This reduced the set of significant genes to 1,070 down-regulated and 1,251 up-regulated genes. These genes indicate a broad and complex genomic response to DH oil exposure including the expected AHR-mediated response and CYP genes. In addition a response to hypoxic conditions and an immune response are also indicated. Several genes in the choriogenin family were down-regulated in the exposed group; a response that is consistent with AH exposure. These analyses are in agreement with oligonucleotide-based microarray analyses, and describe only a subset of significant genes with aberrant regulation in the exposed set. Conclusion RNA-Seq may be successfully applied to feral and

  4. Species identification within Acinetobacter calcoaceticus-baumannii complex using MALDI-TOF MS.

    Science.gov (United States)

    Toh, Benjamin E W; Paterson, David L; Kamolvit, Witchuda; Zowawi, Hosam; Kvaskoff, David; Sidjabat, Hanna; Wailan, Alexander; Peleg, Anton Y; Huber, Charlotte A

    2015-11-01

    Acinetobacter baumannii, one of the more clinically relevant species in the Acinetobacter genus is well known to be multi-drug resistant and associated with bacteremia, urinary tract infection, pneumonia, wound infection and meningitis. However, it cannot be differentiated from closely related species such as Acinetobacter calcoaceticus, Acinetobacter pittii and Acinetobacter nosocomialis by most phenotypic tests and can only be differentiated by specific, time consuming genotypic tests with very limited use in clinical microbiological laboratories. As a result, these species are grouped into the A. calcoaceticus-A. baumannii (Acb) complex. Herein we investigated the mass spectra of 73 Acinetobacter spp., representing ten different species, using an AB SCIEX 5800 MALDI-TOF MS to differentiate members of the Acinetobacter genus, including the species of the Acb complex. RpoB gene sequencing, 16S rRNA sequencing, and gyrB multiplex PCR were also evaluated as orthogonal methods to identify the organisms used in this study. We found that whilst 16S rRNA and rpoB gene sequencing could not differentiate A. pittii or A. calcoaceticus, they can be differentiated using gyrB multiplex PCR and MALDI-TOF MS. All ten Acinetobacter species investigated could be differentiated by their MALDI-TOF mass spectra. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences.

    Science.gov (United States)

    Bunawan, Hamidun; Yen, Choong Chee; Yaakop, Salmah; Noor, Normah Mohd

    2017-01-26

    The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus. Phylogeny reconstruction was carried out using neighbor-joining, maximum parsimony and Bayesian analyses. All the trees revealed two major clusters, a lowland group consisting of N. ampullaria, N. mirabilis, N. gracilis and N. rafflesiana, and another containing both intermediately distributed species (N. albomarginata and N. benstonei) and four highland species (N. sanguinea, N. macfarlanei, N. ramispina and N. alba). The trnL intron and ITS sequences proved to provide phylogenetic informative characters for deriving a phylogeny of Nepenthes species in Peninsular Malaysia. To our knowledge, this is the first molecular phylogenetic study of Nepenthes species occurring along an altitudinal gradient in Peninsular Malaysia.

  6. Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other’s development

    Science.gov (United States)

    Friedl, Martina A.

    2012-01-01

    In this paper, we report on the in situ diversity of the mycotrophic fungus Trichoderma (teleomorph Hypocrea, Ascomycota, Dikarya) revealed by a taxon-specific metagenomic approach. We designed a set of genus-specific internal transcribed spacer (ITS)1 and ITS2 rRNA primers and constructed a clone library containing 411 molecular operational taxonomic units (MOTUs). The overall species composition in the soil of the two distinct ecosystems in the Danube floodplain consisted of 15 known species and two potentially novel taxa. The latter taxa accounted for only 1.5 % of all MOTUs, suggesting that almost no hidden or uncultivable Hypocrea/Trichoderma species are present at least in these temperate forest soils. The species were unevenly distributed in vertical soil profiles although no universal factors controlling the distribution of all of them (chemical soil properties, vegetation type and affinity to rhizosphere) were revealed. In vitro experiments simulating infrageneric interactions between the pairs of species that were detected in the same soil horizon showed a broad spectrum of reactions from very strong competition over neutral coexistence to the pronounced synergism. Our data suggest that only a relatively small portion of Hypocrea/Trichoderma species is adapted to soil as a habitat and that the interaction between these species should be considered in a screening for Hypocrea/Trichoderma as an agent(s) of biological control of pests. PMID:22075025

  7. Taxon-specific metagenomics of Trichoderma reveals a narrow community of opportunistic species that regulate each other's development.

    Science.gov (United States)

    Friedl, Martina A; Druzhinina, Irina S

    2012-01-01

    In this paper, we report on the in situ diversity of the mycotrophic fungus Trichoderma (teleomorph Hypocrea, Ascomycota, Dikarya) revealed by a taxon-specific metagenomic approach. We designed a set of genus-specific internal transcribed spacer (ITS)1 and ITS2 rRNA primers and constructed a clone library containing 411 molecular operational taxonomic units (MOTUs). The overall species composition in the soil of the two distinct ecosystems in the Danube floodplain consisted of 15 known species and two potentially novel taxa. The latter taxa accounted for only 1.5 % of all MOTUs, suggesting that almost no hidden or uncultivable Hypocrea/Trichoderma species are present at least in these temperate forest soils. The species were unevenly distributed in vertical soil profiles although no universal factors controlling the distribution of all of them (chemical soil properties, vegetation type and affinity to rhizosphere) were revealed. In vitro experiments simulating infrageneric interactions between the pairs of species that were detected in the same soil horizon showed a broad spectrum of reactions from very strong competition over neutral coexistence to the pronounced synergism. Our data suggest that only a relatively small portion of Hypocrea/Trichoderma species is adapted to soil as a habitat and that the interaction between these species should be considered in a screening for Hypocrea/Trichoderma as an agent(s) of biological control of pests.

  8. Complex cytogeographical patterns reveal a dynamic tetraploid–octoploid contact zone

    Science.gov (United States)

    Castro, Mariana; Castro, Sílvia; Figueiredo, Albano; Husband, Brian; Loureiro, João

    2018-01-01

    Abstract The distribution of cytotypes in mixed-ploidy species is crucial for evaluating ecological processes involved in the establishment and evolution of polyploid taxa. Here, we use flow cytometry and chromosome counts to explore cytotype diversity and distributions within a tetraploid–octoploid contact zone. We then use niche modelling and ploidy seed screening to assess the roles of niche differentiation among cytotypes and reproductive interactions, respectively, in promoting cytotype coexistence. Two cytotypes, tetraploids and octoploids, were dominant within the contact zone. They were most often distributed parapatrically or allopatrically, resulting in high geographic isolation. Still, 16.7 % of localities comprised two or more cytotypes, including the intermediate hexaploid cytotype. Tetraploids and octoploids had high environmental niche overlap and associated with similar climatic environments, suggesting they have similar ecological requirements. Given the geographical separation and habitat similarity among cytotypes, mixed-ploidy populations may be transitional and subject to the forces of minority cytotype exclusion which lead to pure-ploidy populations. However, seed ploidy analysis suggests that strong reproductive barriers may enforce assortative mating which favours stable cytotype coexistence. High cytogenetic diversity detected in the field suggests that unreduced gamete formation and hybridization events seem frequent in the studied polyploid complex and might be involved with the recurrent polyploid formation, governing, as well, the gene flow between cytogenetic entities. PMID:29593853

  9. Generalized additive models reveal the intrinsic complexity of wood formation dynamics.

    Science.gov (United States)

    Cuny, Henri E; Rathgeber, Cyrille B K; Kiessé, Tristan Senga; Hartmann, Felix P; Barbeito, Ignacio; Fournier, Meriem

    2013-04-01

    The intra-annual dynamics of wood formation, which involves the passage of newly produced cells through three successive differentiation phases (division, enlargement, and wall thickening) to reach the final functional mature state, has traditionally been described in conifers as three delayed bell-shaped curves followed by an S-shaped curve. Here the classical view represented by the 'Gompertz function (GF) approach' was challenged using two novel approaches based on parametric generalized linear models (GLMs) and 'data-driven' generalized additive models (GAMs). These three approaches (GFs, GLMs, and GAMs) were used to describe seasonal changes in cell numbers in each of the xylem differentiation phases and to calculate the timing of cell development in three conifer species [Picea abies (L.), Pinus sylvestris L., and Abies alba Mill.]. GAMs outperformed GFs and GLMs in describing intra-annual wood formation dynamics, showing two left-skewed bell-shaped curves for division and enlargement, and a right-skewed bimodal curve for thickening. Cell residence times progressively decreased through the season for enlargement, whilst increasing late but rapidly for thickening. These patterns match changes in cell anatomical features within a tree ring, which allows the separation of earlywood and latewood into two distinct cell populations. A novel statistical approach is presented which renews our understanding of xylogenesis, a dynamic biological process in which the rate of cell production interplays with cell residence times in each developmental phase to create complex seasonal patterns.

  10. Long-term monitoring reveals an avian species credit in secondary forest patches of Costa Rica

    Directory of Open Access Journals (Sweden)

    Steven C. Latta

    2017-06-01

    Full Text Available Degraded and secondary forests comprise approximately 50% of remaining tropical forest. Bird community characteristics and population trends in secondary forests are infrequently studied, but secondary forest may serve as a “safety net” for tropical biodiversity. Less understood is the occurrence of time-delayed, community-level dynamics such as an extinction debt of specialist species or a species credit resulting from the recolonization of forest patches by extirpated species. We sought to elucidate patterns and magnitudes of temporal change in avian communities in secondary forest patches in Southern Costa Rica biannually over a 10 year period during the late breeding season and mid-winter. We classified birds caught in mist nets or recorded in point counts by residency status, and further grouped them based on preferred habitat, sensitivity to disturbance, conservation priority, foraging guild, and foraging strata. Using hierarchical, mixed-effects models we tested for trends among species that share traits. We found that permanent-resident species increased over time relative to migrants. In both seasons, primary forest species generally increased while species typical of secondary forest, scrub, or edge declined. Species relatively sensitive to habitat disturbance increased significantly over time, whereas birds less sensitive to disturbance decreased. Similarly, generalists with higher habitat breadth scores declined. Because, we found very few changes in vegetation characteristics in secondary forest patches, shifts in the avian community toward primary forest species represent a species credit and are likely related to vegetation changes in the broader landscape. We suggest that natural regeneration and maturation of secondary forests should be recognized as a positive conservation development of potential benefit even to species typical of primary forest.

  11. The first European stand of Paramecium sonneborni (P. aurelia complex), a species known only from North America (Texas, USA).

    Science.gov (United States)

    Przyboś, Ewa; Tarcz, Sebastian; Rautian, Maria; Lebedeva, Natalia

    2014-06-01

    P. aurelia is currently defined as a complex of 15 sibling species including 14 species designated by Sonneborn (1975) and one, P. sonneborni, by Aufderheide et al. (1983). The latter was known from only one stand (Texas, USA). The main reason for the present study was a new stand of Paramecium in Cyprus, with strains recognized as P. sonneborni based on the results of strain crosses, cytological slides, and molecular analyses of three loci (ITS1-5.8S-ITS2-5'LSU rDNA, COI, CytB). The new stand of P. sonneborni in Europe shows that the species, previously considered endemic, may have a wider range. This demonstrates the impact of under-sampling on the knowledge of the biogeography of microbial eukaryotes. Phylogenetic trees based on all the studied fragments revealed that P. sonneborni forms a separate cluster that is closer to P. jenningsi and P. schewiakoffi than to the other members of the P. aurelia complex. Copyright © 2014 Elsevier GmbH. All rights reserved.

  12. Cross-fostering reveals seasonal changes in the relative fitness of two competing species of flycatchers

    NARCIS (Netherlands)

    Qvarnstrom, A; Svedin, N; Wiley, C; Veen, T; Gustafsson, L

    Spatial and temporal heterogeneity in relative fitness of competing species is a key factor affecting the structure of communities. However, it is not intuitive whys species that are ecologically similar should differ in their response to environmental changes. Here we show that two sympatric

  13. Patterns of phenotypic variation reveal substantial differentiation in sexual dimorphism of three Psammodromus (Squamata, Lacertidae) species

    NARCIS (Netherlands)

    San-Jose, L.M.; Gonzalez-Jimena, V.; Fitze, P.S.

    2012-01-01

    The Spanish sand racer (Psammodromus hispanicus) has been recently split into three distinct species: P. hispanicus, P. edwardsianus, and P. occidentalis. Some morphological differences have been reported but there is as yet no description allowing unambiguous identification of the three species.

  14. Comparative Cytogenetics of Hoplerythrinus unitaeniatus (Agassiz, 1829) (Characiformes, Erythrinidae) Species Complex from Different Brazilian Hydrographic Basins.

    Science.gov (United States)

    Martinez, Juliana F; Lui, Roberto L; Traldi, Josiane B; Blanco, Daniel R; Moreira-Filho, Orlando

    2016-01-01

    Chromosomal characteristics of Hoplerythrinus unitaeniatus populations from 5 Brazilian river basins, namely Arinos (Amazonas basin), Araguaia, Paraguai, Alto Paraná, and São Francisco were analyzed by conventional Giemsa staining, C-banding, silver nitrate impregnation, and fluorescence in situ hybridization (FISH) with 18S and 5S rDNA and telomeric sequence (TTAGGG)n probes. The diploid chromosome number was 2n = 48 in representatives of the populations from Paraguai and Alto Paraná River basins and 2n = 52 for those from the Arinos and Araguaia River basins. The São Francisco population had individuals with 2n = 50 and 52 occurring in sympatry. C-banding showed heterochromatic blocks mainly located at interstitial and pericentromeric positions in most of the chromosomes. Silver nitrate impregnation demonstrated simple NORs for representatives from Arinos and Araguaia River populations and multiple NORs for specimens from Paraguai, Alto Paraná, and São Francisco River populations. FISH with 18S and 5S rDNA probes revealed many chromosomes carrying these cistrons, with up to 21 chromosomes bearing 18S rDNA sites (Alto Rio Paraná basin) and up to 12 chromosomes with 5S rDNA sites (Paraguai basin), besides the occurrence of colocalization in all populations. FISH with telomeric sequence (TTAGGG)n detected sites in the terminal portion of the chromosomes in all populations. These data reinforce the idea that H. unitaeniatus is a species complex. Evolutionary and biogeographical aspects of the group in the Neotropical region are discussed. © 2016 S. Karger AG, Basel.

  15. Identification and Genetic Characterization of Ralstonia solanacearum Species Complex Isolates from Cucurbita maxima in China.

    Science.gov (United States)

    She, Xiaoman; Yu, Lin; Lan, Guobing; Tang, Yafei; He, Zifu

    2017-01-01

    Ralstonia solanacearum species complex is a devastating phytopathogen with an unusually wide host range, and new host plants are continuously being discovered. In June 2016, a new bacterial wilt on Cucurbita maxima was observed in Guangdong province, China. Initially, in the adult plant stage, several leaves of each plant withered suddenly and drooped; the plant then wilted completely, and the color of their vasculature changed to dark brown, ultimately causing the entire plant to die. Creamy-whitish bacterial masses were observed to ooze from crosscut stems of these diseased plants. To develop control strategies for C. maxima bacterial wilt, the causative pathogenic isolates were identified and characterized. Twenty-four bacterial isolates were obtained from diseased C. maxima plants, and 16S rRNA gene sequencing and pathogenicity analysis results indicated that the pathogen of C. maxima bacterial wilt was Ralstonia solanacearum . The results from DNA-based analysis, host range determination and bacteriological identification confirmed that the 24 isolates belonged to R. solanacearum phylotype I, race 1, and eight of these isolates belonged to biovar 3, while 16 belonged to biovar 4. Based on the results of partial egl gene sequence analysis, the 24 isolates clustered into three egl- sequence type groups, sequevars 17, 45, and 56. Sequevar 56 is a new sequevar which is described for the first time in this paper. An assessment of the resistance of 21 pumpkin cultivars revealed that C. moschata cv. Xiangyu1 is resistant to strain RS378, C. moschata cv. Xiangmi is moderately resistant to strain RS378, and 19 other pumpkin cultivars, including four C. maxima cultivars and 15 C. moschata cultivars, are susceptible to strain RS378. To the best of our knowledge, this is the first report of C. maxima bacterial wilt caused by R. solanacearum race 1 in the world. Our results provide valuable information for the further development of control strategies for C. maxima wilt

  16. Identification and Genetic Characterization of Ralstonia solanacearum Species Complex Isolates from Cucurbita maxima in China

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    Xiaoman She

    2017-10-01

    Full Text Available Ralstonia solanacearum species complex is a devastating phytopathogen with an unusually wide host range, and new host plants are continuously being discovered. In June 2016, a new bacterial wilt on Cucurbita maxima was observed in Guangdong province, China. Initially, in the adult plant stage, several leaves of each plant withered suddenly and drooped; the plant then wilted completely, and the color of their vasculature changed to dark brown, ultimately causing the entire plant to die. Creamy-whitish bacterial masses were observed to ooze from crosscut stems of these diseased plants. To develop control strategies for C. maxima bacterial wilt, the causative pathogenic isolates were identified and characterized. Twenty-four bacterial isolates were obtained from diseased C. maxima plants, and 16S rRNA gene sequencing and pathogenicity analysis results indicated that the pathogen of C. maxima bacterial wilt was Ralstonia solanacearum. The results from DNA-based analysis, host range determination and bacteriological identification confirmed that the 24 isolates belonged to R. solanacearum phylotype I, race 1, and eight of these isolates belonged to biovar 3, while 16 belonged to biovar 4. Based on the results of partial egl gene sequence analysis, the 24 isolates clustered into three egl- sequence type groups, sequevars 17, 45, and 56. Sequevar 56 is a new sequevar which is described for the first time in this paper. An assessment of the resistance of 21 pumpkin cultivars revealed that C. moschata cv. Xiangyu1 is resistant to strain RS378, C. moschata cv. Xiangmi is moderately resistant to strain RS378, and 19 other pumpkin cultivars, including four C. maxima cultivars and 15 C. moschata cultivars, are susceptible to strain RS378. To the best of our knowledge, this is the first report of C. maxima bacterial wilt caused by R. solanacearum race 1 in the world. Our results provide valuable information for the further development of control strategies

  17. Fractal dimension does not adequately describe the complexity of leaf margin in seedlings of Quercus species

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    Camarero, Jesús Julio

    2002-06-01

    Full Text Available We quantified the complexity of leaf margin in a set of Quercus tree species using fractal dimension estimated by the box-counting method (FDb. Leaves were sampled from seedlings in a set of 15 Quercus species with a wide range of leaf morphology (Q. agrifolia, Q. alba, Q. cerris, Q. chrysolepis, Q. coccifera, Q.faginea, Q. frainetto, Q. ilex subsp. ballota, Q. ilex subsp. ilex, Q. petraea, Q. pyrenaica, Q. robur, Q. rubra, Q. suber, and Q. velutina. To describe leaf-edge roughness, we used simple indices: P/L - the ratio of leaf perimeter (P to maximum leaf length (L along the main nerve; P/A - the ratio of leaf perimeter to leaf-blade area (A and its dimensionless version (P/A0'; and WM/Wm -the ratio of maximum distance from the lobe tip to the main nerve (WM to minimum distance from the lobe incision to the main nerve (Wm. There was a strong positive relationship between FDb and P/A. Clustering analysis revealed the existence of three groups of leaves, namely those with: smooth or spiny margins (e.g., Q. coccifera, Q. velutina, shallow lobes (e.g., Q. petraea, and deep lobes (e.g., Q. pyrenaica. In the studied Quercus species, the ratio WM/Wm is a simple and suitable leaflobation index. It is suggested that the flux rate along the leaf edge is related to the complexity of this boundary.Se ha cuantificado la complejidad del margen de las hojas de varias especies arboreas del genero Quercus utilizando la dimension fractal estimada mediante el modo del recuento de cajas (FDb. Se tomaron hojas procedentes de plantulas pertenecientes a 15 especies de Quercus con un amplio rango de morfologfa foliar (Q. agrifolia, Q. alba, Q. cerris, Q. chrysolepis, Q. coccifera, Q. faginea, Q. frainetto, Q. ilex subsp. ballota, Q. ilex subsp. ilex, Q. petraea, Q. pyrenaica, Q. robur, Q. rubra, Q. suber y Q. velutina. Se usaron varios Indices sencillos para describir la complejidad del borde de la hoja: P/L, la relation entre el perimetro foliar (P y la longitud

  18. Forced-rupture of cell-adhesion complexes reveals abrupt switch between two brittle states

    Science.gov (United States)

    Toan, Ngo Minh; Thirumalai, D.

    2018-03-01

    Cell adhesion complexes (CACs), which are activated by ligand binding, play key roles in many cellular functions ranging from cell cycle regulation to mediation of cell extracellular matrix adhesion. Inspired by single molecule pulling experiments using atomic force spectroscopy on leukocyte function-associated antigen-1 (LFA-1), expressed in T-cells, bound to intercellular adhesion molecules (ICAM), we performed constant loading rate (rf) and constant force (F) simulations using the self-organized polymer model to describe the mechanism of ligand rupture from CACs. The simulations reproduce the major experimental finding on the kinetics of the rupture process, namely, the dependence of the most probable rupture forces (f*s) on ln rf (rf is the loading rate) exhibits two distinct linear regimes. The first, at low rf, has a shallow slope, whereas the slope at high rf is much larger, especially for a LFA-1/ICAM-1 complex with the transition between the two occurring over a narrow rf range. Locations of the two transition states (TSs) extracted from the simulations show an abrupt change from a high value at low rf or constant force, F, to a low value at high rf or F. This unusual behavior in which the CACs switch from one brittle (TS position is a constant over a range of forces) state to another brittle state is not found in forced-rupture in other protein complexes. We explain this novel behavior by constructing the free energy profiles, F(Λ)s, as a function of a collective reaction coordinate (Λ), involving many key charged residues and a critical metal ion (Mg2+). The TS positions in F(Λ), which quantitatively agree with the parameters extracted using the Bell-Evans model, change abruptly at a critical force, demonstrating that it, rather than the molecular extension, is a good reaction coordinate. Our combined analyses using simulations performed in both the pulling modes (constant rf and F) reveal a new mechanism for the two loading regimes observed in the

  19. Identification of the non-pertechnetate species in Hanford waste tanks, Tc(I) carbonyl complexes

    Energy Technology Data Exchange (ETDEWEB)

    Lukens, Wayne W.; Shuh, David K.; Schroeder, Norman C.; Ashley, Kenneth R.

    2003-10-16

    Immobilization of the high-level nuclear waste stored at the Hanford Reservation has been complicated by the presence of soluble, lower-valent technetium species. Previous work by Schroeder and Blanchard has shown that these species cannot be removed by ion-exchange and are difficult to oxidize. The Tc-K edge XANES spectra of the species in Tanks SY-101 and SY-103 were reported by Blanchard, but they could not be assigned to any known technetium complex. We report that the XANES spectra are most likely those of Tc(I) carbonyl species, especially fac-Tc(CO){sub 3}(gluconate){sup 2-}. This is further supported by EXAFS and {sup 99}Tc-NMR studies in nonradioactive simulants of these tank wastes.

  20. Perched Lava Pond Complex on South Rift of Axial Volcano Revealed in AUV Mapping

    Science.gov (United States)

    Paduan, J. B.; Clague, D. A.; Caress, D. W.; Thomas, H. J.

    2013-12-01

    An extraordinary lava pond complex is located on Axial Volcano's distal south rift. It was discovered in EM300 multibeam bathymetry collected in 1998, and explored and sampled with ROVs Tiburon in 2005 and Doc Ricketts in 2013. It was surveyed with the MBARI Mapping AUV D. Allan B. in 2011, in a complicated mission first flying above the levees at constant depth, then skimming ~5 m over the levees at a different constant depth to survey the floors, then twice switching to constant altitude mode to map outside the ponds. The AUV navigation was adjusted using the MB-System tool mbnavadjust so that bathymetric features match in overlapping and crossing swaths. The ~1-m resolution AUV bathymetry reveals extremely rough terrain, where low-resolution EM300 data had averaged acoustic returns and obscured details of walls, floors, a breach and surrounding flows, and gives context to the ROV observations and samples. The 6 x 1.5 km pond complex has 4 large and several smaller drained ponds with rims 67 to 106 m above the floors. The combined volume before draining was 0.56 km3. The ponds overflowed to build lobate-flow levees with elongate pillows draping outer flanks, then drained, leaving lava veneer on vertical inner walls. Levee rim depths vary by only 10 m and are deeper around the southern ponds. Deep collapse-pits in the levees suggest porosity of pond walls. The eastern levee of the northeastern pond breached, draining the interconnected ponds, and fed thick, rapidly-emplaced, sheet-flows along the complex's east side. These flows travelled at least 5.5 km down-rift and have 19-33 m deep drained ponds. They extended up-rift as well, forming a 10 x 2.5 km ponded flow with level 'bathtub rings' as high as 35 m above the floor marking that flow's high-stand. Despite the breach, at least 0.066 km3 of the molten interior of the large ponds also drained back down the eruptive fissures, as the pond floors are deeper than the sill and sea floor outside the complex. Tumulus

  1. Ecological speciation in anemone-associated snapping shrimps (Alpheus armatus species complex).

    Science.gov (United States)

    Hurt, C; Silliman, K; Anker, A; Knowlton, N

    2013-09-01

    Divergent natural selection driven by competition for limited resources can promote speciation, even in the presence of gene flow. Reproductive isolation is more likely to result from divergent selection when the partitioned resource is closely linked to mating. Obligate symbiosis and host fidelity (mating on or near the host) can provide this link, creating ideal conditions for speciation in the absence of physical barriers to dispersal. Symbiotic organisms often experience competition for hosts, and host fidelity ensures that divergent selection for a specific host or host habitat can lead to speciation and strengthen pre-existing reproductive barriers. Here, we present evidence that diversification of a sympatric species complex occurred despite the potential for gene flow and that partitioning of host resources (both by species and by host habitat) has contributed to this diversification. Four species of snapping shrimps (Alpheus armatus, A. immaculatus, A. polystictus and A. roquensis) are distributed mainly sympatrically in the Caribbean, while the fifth species (A. rudolphi) is restricted to Brazil. All five species are obligate commensals of sea anemones with a high degree of fidelity and ecological specificity for host species and habitat. We analysed sequence data from 10 nuclear genes and the mitochondrial COI gene in 11-16 individuals from each of the Caribbean taxa and from the only available specimen of the Brazilian taxon. Phylogenetic analyses support morphology-based species assignments and a well-supported Caribbean clade. The Brazilian A. rudolphi is recovered as an outgroup to the Caribbean taxa. Isolation-migration coalescent analysis provides evidence for historical gene flow among sympatric sister species. Our data suggest that both selection for a novel host and selection for host microhabitat may have promoted diversification of this complex despite gene flow. © 2013 John Wiley & Sons Ltd.

  2. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping

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    Eileen eLuders

    2013-07-01

    Full Text Available Scientific studies addressing anatomical variations in meditators’ brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM. To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls, where meditators have been practicing close to twenty years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentate, entorhinal cortex, subiculum as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri- hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators – perhaps due to an attenuated release of stress hormones and decreased neurotoxicity.

  3. Crystal structure of Clostridium botulinum whole hemagglutinin reveals a huge triskelion-shaped molecular complex.

    Science.gov (United States)

    Amatsu, Sho; Sugawara, Yo; Matsumura, Takuhiro; Kitadokoro, Kengo; Fujinaga, Yukako

    2013-12-06

    Clostridium botulinum HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. At least two properties of HA contribute to these roles: the sugar-binding activity and the barrier-disrupting activity that depends on E-cadherin binding of HA. HA consists of three different proteins, HA1, HA2, and HA3, whose structures have been partially solved and are made up mainly of β-strands. Here, we demonstrate structural and functional reconstitution of whole HA and present the complete structure of HA of serotype B determined by x-ray crystallography at 3.5 Å resolution. This structure reveals whole HA to be a huge triskelion-shaped molecule. Our results suggest that whole HA is functionally and structurally separable into two parts: HA1, involved in recognition of cell-surface carbohydrates, and HA2-HA3, involved in paracellular barrier disruption by E-cadherin binding.

  4. Comparative functional genomic analysis of two Vibrio phages reveals complex metabolic interactions with the host cell

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    Dimitrios Skliros

    2016-11-01

    Full Text Available Sequencing and annotation was performed for two giant double stranded DNA bacteriophages, φGrn1 and φSt2 of the Myoviridae family, considered to be of great interest for phage therapy against Vibrios in aquaculture live feeds. In addition, phage-host metabolic interactions and exploitation was studied by transcript profiling of selected viral and host genes. Comparative genomic analysis with other giant Vibrio phages was also performed to establish the presence and location of homing endonucleases highlighting distinct features for both phages. Phylogenetic analysis revealed that they belong to the schizoT4like clade. Although many reports of newly sequenced viruses have provided a large set of information, basic research related to the shift of the bacterial metabolism during infection remains stagnant. The function of many viral protein products in the process of infection is still unknown. Genome annotation identified the presence of several viral ORFs participating in metabolism, including a Sir2/cobB (sirtuin protein and a number of genes involved in auxiliary NAD+ and nucleotide biosynthesis, necessary for phage DNA replication. Key genes were subsequently selected for detail study of their expression levels during infection. This work suggests a complex metabolic interaction and exploitation of the host metabolic pathways and biochemical processes, including a possible post-translational protein modification, by the virus during infection.

  5. Crystal Structures of Cyclohexanone Monooxygenase Reveal Complex Domain Movements and a Sliding Cofactor

    Energy Technology Data Exchange (ETDEWEB)

    Mirza, I.; Yachnin, B; Wang, S; Grosse, S; Bergeron, H; Imura, A; Iwaki, H; Hasegawa, Y; Lau, P; Berghuis, A

    2009-01-01

    Cyclohexanone monooxygenase (CHMO) is a flavoprotein that carries out the archetypical Baeyer-Villiger oxidation of a variety of cyclic ketones into lactones. Using NADPH and O{sub 2} as cosubstrates, the enzyme inserts one atom of oxygen into the substrate in a complex catalytic mechanism that involves the formation of a flavin-peroxide and Criegee intermediate. We present here the atomic structures of CHMO from an environmental Rhodococcus strain bound with FAD and NADP+ in two distinct states, to resolutions of 2.3 and 2.2 {angstrom}. The two conformations reveal domain shifts around multiple linkers and loop movements, involving conserved arginine 329 and tryptophan 492, which effect a translation of the nicotinamide resulting in a sliding cofactor. Consequently, the cofactor is ideally situated and subsequently repositioned during the catalytic cycle to first reduce the flavin and later stabilize formation of the Criegee intermediate. Concurrent movements of a loop adjacent to the active site demonstrate how this protein can effect large changes in the size and shape of the substrate binding pocket to accommodate a diverse range of substrates. Finally, the previously identified BVMO signature sequence is highlighted for its role in coordinating domain movements. Taken together, these structures provide mechanistic insights into CHMO-catalyzed Baeyer-Villiger oxidation.

  6. An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme.

    Science.gov (United States)

    Esquirol, Lygie; Peat, Thomas S; Wilding, Matthew; Liu, Jian-Wei; French, Nigel G; Hartley, Carol J; Onagi, Hideki; Nebl, Thomas; Easton, Christopher J; Newman, Janet; Scott, Colin

    2018-03-09

    Cyanuric acid is a metabolic intermediate of s-triazines, such as atrazine (a common herbicide) and melamine (used in resins and plastics). Cyanuric acid is mineralized to ammonia and carbon dioxide by the soil bacterium Pseudomonas sp. strain ADP via three hydrolytic enzymes (AtzD, AtzE, and AtzF). Here, we report the purification and biochemical and structural characterization of AtzE. Contrary to previous reports, we found that AtzE is not a biuret amidohydrolase, but instead catalyzes the hydrolytic deamination of 1-carboxybiuret. X-ray crystal structures of apo AtzE and AtzE bound with the suicide inhibitor phenyl phosphorodiamidate revealed that the AtzE enzyme complex consists of two independent molecules in the asymmetric unit. We also show that AtzE forms an α2β2 heterotetramer with a hitherto unidentified 68-amino-acid-long protein (AtzG) encoded in the cyanuric acid mineralization operon from Pseudomonas sp. strain ADP. Moreover, we observed that AtzG is essential for the production of soluble, active AtzE and that this obligate interaction is a vestige of their shared evolutionary origin. We propose that AtzEG was likely recruited into the cyanuric acid-mineralizing pathway from an ancestral glutamine transamidosome that required protein-protein interactions to enforce the exclusion of solvent from the transamidation reaction. Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

  7. Proteomic analysis reveals the diversity and complexity of membrane proteins in chickpea (Cicer arietinum L.

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    Jaiswal Dinesh Kumar

    2012-10-01

    Full Text Available Abstract Background Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. Results To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the identified proteins are putative integral membrane proteins, possessing transmembrane domains. Conclusions The proteomic analysis revealed many resident integral membrane proteins as well as membrane-associated proteins including those not reported earlier. To our knowledge, this is the first report of membrane proteome from aerial tissues of a crop plant. The findings may provide a better understanding of the biochemical machinery of the plant membranes at the molecular level that might help in functional genomics studies of different developmental pathways and stress-responses.

  8. DNA barcoding of twelve shrimp species (Crustacea: Decapoda from Turkish seas reveals cryptic diversity

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    R. BILGIN

    2014-05-01

    Full Text Available DNA barcoding is a useful tool for the identification and potential discovery of new species. In this study, DNA barcoding was employed by sequencing the mitochondrial cytochrome oxidase subunit I gene (COI to characterize the genetic diversity of 12 shrimp species inhabiting Turkish coastal waters and, when possible, to compare with the genetic data available from different parts of the Mediterranean and eastern Atlantic. This study also comprises the first DNA barcoding study performed in the Turkish Seas using COI. A total of 40 shrimp specimens were collected and analyzed from 9 sites. Generally, the barcoding gap criterion was successful at identifying species; hence COI appeared to be a good marker of choice for DNA barcoding in this group. Out of the 12 species investigated, five were barcoded for the first time. In six species two intraspecific clades were retrieved after the analyses. The results suggest the presence of cryptic diversity in a genetically understudied marine area, Turkish coastal waters, and further investigation in these species using population genetics, taxonomic approaches and nuclear markers is likely to result in designation of new species.

  9. Epicuticular chemistry reinforces the new taxonomic classification of the Bactrocera dorsalis species complex (Diptera: Tephritidae, Dacinae.

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    Lucie Vaníčková

    Full Text Available Bactrocera invadens Drew, Tsuruta & White, Bactrocera papayae Drew & Hancock, and Bactrocera philippinensis Drew & Hancock, key pest species within the Bactrocera dorsalis species complex, have been recently synonymized under the name Bactrocera dorsalis (Hendel. The closely related Bactrocera carambolae Drew & Hancock remains as a discrete taxonomic entity. Although the synonymizations have been accepted by most researchers, debate about the species limits remains. Because of the economic importance of this group of taxa, any new information available to support or deny the synonymizations is valuable. We investigated the chemical epicuticle composition of males and females of B. dorsalis, B. invadens, B. papayae, B. philippinensis, and B. carambolae by means of one- and two-dimensional gas chromatography-mass spectrometry, followed by multiple factor analyses and principal component analysis. Clear segregation of complex cuticule profiles of both B. carambolae sexes from B. dorsalis (Hendel was observed. In addition to cuticular hydrocarbons, abundant complex mixtures of sex-specific oxygenated lipids (three fatty acids and 22 fatty acid esters with so far unknown function were identified in epicuticle extracts from females of all species. The data obtained supports both taxonomic synonymization of B. invadens, B. papayae, and B. philippinensis with B. dorsalis, as well as the exclusion of B. carambolae from B. dorsalis.

  10. Epicuticular chemistry reinforces the new taxonomic classification of the Bactrocera dorsalis species complex (Diptera: Tephritidae, Dacinae).

    Science.gov (United States)

    Vaníčková, Lucie; Nagy, Radka; Pompeiano, Antonio; Kalinová, Blanka

    2017-01-01

    Bactrocera invadens Drew, Tsuruta & White, Bactrocera papayae Drew & Hancock, and Bactrocera philippinensis Drew & Hancock, key pest species within the Bactrocera dorsalis species complex, have been recently synonymized under the name Bactrocera dorsalis (Hendel). The closely related Bactrocera carambolae Drew & Hancock remains as a discrete taxonomic entity. Although the synonymizations have been accepted by most researchers, debate about the species limits remains. Because of the economic importance of this group of taxa, any new information available to support or deny the synonymizations is valuable. We investigated the chemical epicuticle composition of males and females of B. dorsalis, B. invadens, B. papayae, B. philippinensis, and B. carambolae by means of one- and two-dimensional gas chromatography-mass spectrometry, followed by multiple factor analyses and principal component analysis. Clear segregation of complex cuticule profiles of both B. carambolae sexes from B. dorsalis (Hendel) was observed. In addition to cuticular hydrocarbons, abundant complex mixtures of sex-specific oxygenated lipids (three fatty acids and 22 fatty acid esters) with so far unknown function were identified in epicuticle extracts from females of all species. The data obtained supports both taxonomic synonymization of B. invadens, B. papayae, and B. philippinensis with B. dorsalis, as well as the exclusion of B. carambolae from B. dorsalis.

  11. Three gene phylogeny of the Thoreales (Rhodophyta) reveals high species diversity.

    Science.gov (United States)

    Johnston, Emily T; Dixon, Kyatt R; West, John A; Buhari, Nurliah; Vis, Morgan L

    2018-04-01

    The freshwater red algal order Thoreales has triphasic life history composed of a diminutive diploid "Chantransia" stage, a distinctive macroscopic gametophyte with multi-axial growth and carposporophytes that develop on the gametophyte thallus. This order is comprised of two genera, Thorea and Nemalionopsis. Thorea has been widely reported with numerous species, whereas Nemalionopsis has been more rarely observed with only a few species described. DNA sequences from three loci (rbcL, cox1, and LSU) were used to examine the phylogenetic affinity of specimens collected from geographically distant locations including North America, South America, Europe, Pacific Islands, Southeast Asia, China, and India. Sixteen species of Thorea and two species of Nemalionopsis were recognized. Morphological observations confirmed the distinctness of the two genera and also provided some characters to distinguish species. However, many of the collections were in "Chantransia" stage rather than gametophyte stage, meaning that key diagnostic morphological characters were unavailable. Three new species are proposed primarily based on the DNA sequence data generated in this study, Thorea kokosinga-pueschelii, T. mauitukitukii, and T. quisqueyana. In addition to these newly described species, one DNA sequence from GenBank was not closely associated with other Thorea clades and may represent further diversity in the genus. Two species in Nemalionopsis are recognized, N. shawii and N. parkeri nom. et stat. nov. Thorea harbors more diversity than had been recognized by morphological data alone. Distribution data indicated that Nemalionopsis is common in the Pacific region, whereas Thorea is more globally distributed. Most species of Thorea have a regional distribution, but Thorea hispida appears to be cosmopolitan. © 2018 Phycological Society of America.

  12. Analysis of patterns of bushmeat consumption reveals extensive exploitation of protected species in eastern Madagascar.

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    Richard K B Jenkins

    Full Text Available Understanding the patterns of wild meat consumption from tropical forests is important for designing approaches to address this major threat to biodiversity and mitigate potential pathways for transmission of emerging diseases. Bushmeat consumption has been particularly poorly studied in Madagascar, one of the world's hottest biodiversity hotspots. Studying bushmeat consumption is challenging as many species are protected and researchers must consider the incentives faced by informants. Using interviews with 1154 households in 12 communes in eastern Madagascar, as well as local monitoring data, we investigated the importance of socio-economic variables, taste preference and traditional taboos on consumption of 50 wild and domestic species. The majority of meals contain no animal protein. However, respondents consume a wide range of wild species and 95% of respondents have eaten at least one protected species (and nearly 45% have eaten more than 10. The rural/urban divide and wealth are important predictors of bushmeat consumption, but the magnitude and direction of the effect varies between species. Bushmeat species are not preferred and are considered inferior to fish and domestic animals. Taboos have provided protection to some species, particularly the Endangered Indri, but we present evidence that this taboo is rapidly eroding. By considering a variety of potential influences on consumption in a single study we have improved understanding of who is eating bushmeat and why. Evidence that bushmeat species are not generally preferred meats suggest that projects which increase the availability of domestic meat and fish may have success at reducing demand. We also suggest that enforcement of existing wildlife and firearm laws should be a priority, particularly in areas undergoing rapid social change. The issue of hunting as an important threat to biodiversity in Madagascar is only now being fully recognised. Urgent action is required to ensure

  13. Of Least Concern? Systematics of a cryptic species complex: Limnonectes kuhlii (Amphibia: Anura: Dicroglossidae).

    Science.gov (United States)

    McLeod, David S

    2010-09-01

    Several recent studies have demonstrated that a tremendous amount of biological diversity can be masked by phenotypic similarity in a cryptic species complex. It has been speculated that the widely distributed and relatively common Southeast Asian frog Limnonectes kuhlii represents a complex of multiple species. The phylogeny within the L. kuhlii Complex is estimated in this study based on approximately 2400bp of mtDNA data (tRNA(Phe), 12S, tRNA(Val), and 16S genes) from 244 individuals representing multiple populations from throughout the known distribution of this anuran. Analyses are conducted using parsimony, maximum likelihood and Bayesian methods. The results suggest that what has been recognized historically as a single species is a complex of more than 22 distinct evolutionary lineages, 16 of which are currently subsumed under the nominal L. kuhlii. Several cases of sympatric lineages were detected, and in all cases co-occurring lineages were not each other's closest relatives. Copyright 2010 Elsevier Inc. All rights reserved.

  14. High Species Richness of Scinax Treefrogs (Hylidae) in a Threatened Amazonian Landscape Revealed by an Integrative Approach

    Science.gov (United States)

    Ferrão, Miquéias; Colatreli, Olavo; de Fraga, Rafael; Kaefer, Igor L.; Moravec, Jiří; Lima, Albertina P.

    2016-01-01

    Rising habitat loss is one of the main drivers of the global amphibian decline. Nevertheless, knowledge of amphibian diversity needed for effective habitat protection is still highly inadequate in remote tropical regions, the greater part of the Amazonia. In this study we integrated molecular, morphological and bioacoustic evidence to evaluate the species richness of the treefrogs genus Scinax over a 1000 km transect across rainforest of the Purus-Madeira interfluve, and along the east bank of the upper Madeira river, Brazilian Amazonia. Analysis revealed that 82% of the regional species richness of Scinax is still undescribed; two nominal species, seven confirmed candidate species, two unconfirmed candidate species, and one deep conspecific lineage were detected in the study area. DNA barcoding based analysis of the 16s rRNA gene indicates possible existence of three discrete species groups within the genus Scinax, in addition to the already-known S. rostratus species Group. Quantifying and characterizing the number of undescribed Scinax taxa on a regional scale, we provide a framework for future taxonomic study in Amazonia. These findings indicate that the level to which Amazonian anura species richness has been underestimated is far greater than expected. Consequently, special attention should be paid both to taxonomic studies and protection of the still-neglected Amazonian Scinax treefrogs. PMID:27806089

  15. Detection of recent hybridization between sympatric Chilean Puya species (Bromeliaceae) using AFLP markers and reconstruction of complex relationships.

    Science.gov (United States)

    Schulte, Katharina; Silvestro, Daniele; Kiehlmann, Elke; Vesely, Sanja; Novoa, Patricio; Zizka, Georg

    2010-12-01

    The Chilean Puya species constitute a monophyletic group, co-occurring in different species combinations within the country and displaying a remarkable morphological variability. Here, we studied the importance of recent hybridization and introgression in the group and reconstructed the complex inter- and intraspecific relationships. Amplified fragment length polymorphism (AFLP) analysis, including 109 accessions of all Chilean Puya species and four putative hybrids, yielded 984 characters. Three main genetic groups were revealed, with the chilensis group (P. chilensis, P. gilmartiniae, P. boliviensis) diverging first, and the alpestris (P. alpestris, P. berteroniana) and coerulea group (P. venusta, P. coerulea) forming sister groups. STRUCTURE analyses confirmed a hybrid origin of morphologically intermediate individuals, and detected several additional hybrids. Hybrids were found between the chilensis and alpestris group, and between the alpestris and coerulea group. Exclusion of hybrids improved phylogenetic reconstructions. The study demonstrates that the detection of hybrids within Bromeliaceae can be difficult based on morphological characters alone and that efficient reproductive barriers may only slowly establish, leading to hybridization between closely related sympatric species. The importance of hybridization for the rapid diversification of Puya is discussed. Copyright © 2010 Elsevier Inc. All rights reserved.

  16. Integrative taxonomy and preliminary assessment of species limits in the Liolaemus walkeri complex (Squamata, Liolaemidae with descriptions of three new species from Peru

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    Cesar Aguilar

    2013-12-01

    Full Text Available Species delimitation studies based on integrative taxonomic approaches have received considerable attention in the last few years, and have provided the strongest hypotheses of species boundaries. We used three lines of evidence (molecular, morphological, and niche envelopes to test for species boundaries in Peruvian populations of the Liolaemus walkeri complex. Our results show that different lines of evidence and analyses are congruent in different combinations, for unambiguous delimitation of three lineages that were “hidden” within known species, and now deserve species status. Our phylogenetic analysis shows that L. walkeri, L. tacnae and the three new species are strongly separated from other species assigned to the alticolor-bibronii group. Few conventional morphological characters distinguish the new species from closely related taxa and this highlights the need to integrate other sources of data to erect strong hypothesis of species limits. A taxonomic key for known Peruvian species of the subgenus Lioalemus is provided.

  17. Root transcript profiling of two Rorippa (brassicaceae) species reveals gene clusters associated with extreme submergence tolerance.

    NARCIS (Netherlands)

    Sasidharan, R.; Mustroph, A.; Boonman, A.; Akman, M.; Ammerlaan, A.M.H.; Breit, T.M.; Schranz, M.E.; Voesenek, L.A.C.J.; Tienderen, van P.H.

    2013-01-01

    Complete submergence represses photosynthesis and aerobic respiration, causing rapid mortality in most terrestrial plants. However, some plants have evolved traits allowing them to survive prolonged flooding, such as species of the genus Rorippa, close relatives of Arabidopsis (Arabidopsis

  18. Integrated Taxonomy Reveals Hidden Diversity in Northern Australian Fishes: A New Species of Seamoth (Genus Pegasus.

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    Deborah Osterhage

    Full Text Available Fishes are one of the most intensively studied marine taxonomic groups yet cryptic species are still being discovered. An integrated taxonomic approach is used herein to delineate and describe a new cryptic seamoth (genus Pegasus from what was previously a wide-ranging species. Preliminary mitochondrial DNA barcoding indicated possible speciation in Pegasus volitans specimens collected in surveys of the Torres Strait and Great Barrier Reef off Queensland in Australia. Morphological and meristic investigations found key differences in a number of characters between P. volitans and the new species, P. tetrabelos. Further mt DNA barcoding of both the COI and the slower mutating 16S genes of additional specimens provided strong support for two separate species. Pegasus tetrabelos and P. volitans are sympatric in northern Australia and were frequently caught together in trawls at the same depths.

  19. Comparative transcriptomic analyses revealed divergences of two agriculturally important aphid species

    OpenAIRE

    Wang, Dahai; Liu, Qi; Jones, Huw D; Bruce, Toby; Xia, Lanqin

    2014-01-01

    Background Grain aphid (Sitobion avenae F) and pea aphid (Acyrthosiphon pisum) are two agriculturally important pest species, which cause significant yield losses to crop plants each year by inflicting damage both through the direct effects of feeding and by vectoring debilitating plant viruses. Although a close phylogenetic relationship between grain aphid and pea aphid was proposed, the biological variations between these two aphid species are obvious. While the host ranges of grain aphid i...

  20. Bioinformatic analysis of the neprilysin (M13 family of peptidases reveals complex evolutionary and functional relationships

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    Pinney John W

    2008-01-01

    Full Text Available Abstract Background The neprilysin (M13 family of endopeptidases are zinc-metalloenzymes, the majority of which are type II integral membrane proteins. The best characterised of this family is neprilysin, which has important roles in inactivating signalling peptides involved in modulating neuronal activity, blood pressure and the immune system. Other family members include the endothelin converting enzymes (ECE-1 and ECE-2, which are responsible for the final step in the synthesis of potent vasoconstrictor endothelins. The ECEs, as well as neprilysin, are considered valuable therapeutic targets for treating cardiovascular disease. Other members of the M13 family have not been functionally characterised, but are also likely to have biological roles regulating peptide signalling. The recent sequencing of animal genomes has greatly increased the number of M13 family members in protein databases, information which can be used to reveal evolutionary relationships and to gain insight into conserved biological roles. Results The phylogenetic analysis successfully resolved vertebrate M13 peptidases into seven classes, one of which appears to be specific to mammals, and insect genes into five functional classes and a series of expansions, which may include inactive peptidases. Nematode genes primarily resolved into groups containing no other taxa, bar the two nematode genes associated with Drosophila DmeNEP1 and DmeNEP4. This analysis reconstructed only one relationship between chordate and invertebrate clusters, that of the ECE sub-group and the DmeNEP3 related genes. Analysis of amino acid utilisation in the active site of M13 peptidases reveals a basis for their biochemical properties. A relatively invariant S1' subsite gives the majority of M13 peptidases their strong preference for hydrophobic residues in P1' position. The greater variation in the S2' subsite may be instrumental in determining the specificity of M13 peptidases for their substrates

  1. A reinvestigation of phylogeny and divergence times of the Ablepharus kitaibelii species complex (Sauria, Scincidae) based on mtDNA and nuDNA genes.

    Science.gov (United States)

    Skourtanioti, Eirini; Kapli, Paschalia; Ilgaz, Çetin; Kumlutaş, Yusuf; Avcı, Aziz; Ahmadzadeh, Faraham; Crnobrnja-Isailović, Jelka; Gherghel, Iulian; Lymberakis, Petros; Poulakakis, Nikos

    2016-10-01

    Morphological and DNA data support that the East Mediterranean snake-eyed skink Ablepharus kitaibelii represents a species complex that includes four species A. kitaibelii, A. budaki, A. chernovi, and A. rueppellii, highlighting the need of its taxonomic reevaluation. Here, we used Bayesian and Maximum Likelihood methods to estimate the phylogenetic relationships of all members of the complex based on two mitochondrial (cyt b, 16S rRNA) and two nuclear markers (MC1R, and NKTR) and using Chalcides, Eumeces, and Eutropis as outgroups. The biogeographic history of the complex was also investigated through the application of several phylogeographic (BEAST) and biogeographic (BBM) analyses. Paleogeographic and paleoclimatic data were used to support the inferred phylogeographic patterns. The A. kitaibelli species complex exhibits high genetic diversity, revealing cases of hidden diversity and cases of non-monophyletic species such as A. kitaibelii and A. budaki. Our results indicate that A. pannonicus branches off first and a group that comprises specimens of A. kitaibelli and A. budaki from Kastelorizo Island group (southeast Greece) and southwest Turkey, respectively is differentiated from the rest A. kitaibelli and A. budaki populations and may represent a new species. The estimated divergence times place the origin of the complex in the Middle Miocene (∼16Mya) and the divergence of most currently recognized species in the Late Miocene. The inferred ancestral distribution suggests that the complex originated in Anatolia, supposing that several vicariance and dispersal events that are related with the formation of the Mid-Aegean Trench, the Anatolian Diagonal and the orogenesis of the mountain chains in southern and eastern Anatolia have led to current distribution pattern of A. kitaibelii species complex in the Balkans and Middle East. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. A new species of Labidocera (Copepoda, Calanoida, Pontellidae) collected from Okinawa, southwestern Japan, with establishment of five Indo-West Pacific species groups in the L.detruncata species complex.

    Science.gov (United States)

    Hirabayashi, Takeshi; Ohtsuka, Susumu

    2014-01-01

    Labidocerachuraumi sp. n. is described from Okinawa, southwestern Japan. The female of the new species differs from other congeners in genital compound somite with right postero-lateral and left antero-lateral processes. The male is distinguished from other congeners by the structure of the fifth leg. This new species is assigned to a newly proposed species group, the Labidoceramadurae species group, within the Labidoceradetruncata species complex. In this species complex five Indo-West Pacific species groups are recognized (cervi, detruncata, gangetica, madurae, and pavo) and defined on the basis of difference in sexual dimorphism.

  3. Nuclear species-diagnostic SNP markers mined from 454 amplicon sequencing reveal admixture genomic structure of modern citrus varieties.

    Directory of Open Access Journals (Sweden)

    Franck Curk

    Full Text Available Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105 were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species

  4. Spatial distribution of cryptic species diversity in european freshwater amphipods (Gammarus fossarum as revealed by pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Anja Marie Westram

    Full Text Available In order to understand and protect ecosystems, local gene pools need to be evaluated with respect to their uniqueness. Cryptic species present a challenge in this context because their presence, if unrecognized, may lead to serious misjudgement of the distribution of evolutionarily distinct genetic entities. In this study, we describe the current geographical distribution of cryptic species of the ecologically important stream amphipod Gammarus fossarum (types A, B and C. We use a novel pyrosequencing assay for molecular species identification and survey 62 populations in Switzerland, plus several populations in Germany and eastern France. In addition, we compile data from previous publications (mainly Germany. A clear transition is observed from type A in the east (Danube and Po drainages to types B and, more rarely, C in the west (Meuse, Rhone, and four smaller French river systems. Within the Rhine drainage, the cryptic species meet in a contact zone which spans the entire G. fossarum distribution range from north to south. This large-scale geographical sorting indicates that types A and B persisted in separate refugia during Pleistocene glaciations. Within the contact zone, the species rarely co-occur at the same site, suggesting that ecological processes may preclude long-term coexistence. The clear phylogeographical signal observed in this study implies that, in many parts of Europe, only one of the cryptic species is present.

  5. Spatial Distribution of Cryptic Species Diversity in European Freshwater Amphipods (Gammarus fossarum) as Revealed by Pyrosequencing

    Science.gov (United States)

    Westram, Anja Marie; Jokela, Jukka; Baumgartner, Caroline; Keller, Irene

    2011-01-01

    In order to understand and protect ecosystems, local gene pools need to be evaluated with respect to their uniqueness. Cryptic species present a challenge in this context because their presence, if unrecognized, may lead to serious misjudgement of the distribution of evolutionarily distinct genetic entities. In this study, we describe the current geographical distribution of cryptic species of the ecologically important stream amphipod Gammarus fossarum (types A, B and C). We use a novel pyrosequencing assay for molecular species identification and survey 62 populations in Switzerland, plus several populations in Germany and eastern France. In addition, we compile data from previous publications (mainly Germany). A clear transition is observed from type A in the east (Danube and Po drainages) to types B and, more rarely, C in the west (Meuse, Rhone, and four smaller French river systems). Within the Rhine drainage, the cryptic species meet in a contact zone which spans the entire G. fossarum distribution range from north to south. This large-scale geographical sorting indicates that types A and B persisted in separate refugia during Pleistocene glaciations. Within the contact zone, the species rarely co-occur at the same site, suggesting that ecological processes may preclude long-term coexistence. The clear phylogeographical signal observed in this study implies that, in many parts of Europe, only one of the cryptic species is present. PMID:21909373

  6. Microsatellite markers for Grosmannia alacris (Ophiostomataceae, Ascomycota) and other species in the G. serpens complex.

    Science.gov (United States)

    Duong, Tuan A; de Beer, Z Wilhelm; Zanzot, James W; Wingfield, Michael J; Wingfield, Brenda D

    2012-05-01

    Polymorphic microsatellite markers were developed for the pine-infecting fungus, Grosmannia alacris. Sixteen microsatellite markers were developed by using inter-simple sequence repeat (ISSR)-PCRs and 454 sequencing methods. Seven of these markers showed polymorphisms for a South African population of G. alacris, and 13 markers showed polymorphism when European isolates were included. Most of the primer pairs also amplified four closely related species: G. serpens, Leptographium gibbsii, L. castellanum, and L. yamaokae. These new markers will be useful for population studies of G. alacris and other species in the G. serpens complex.

  7. A new species of the Fejervarya limnocharis complex from Japan (Anura, Dicroglossidae).

    Science.gov (United States)

    Djong, Hon Tjong; Matsui, Masafumi; Kuramoto, Mitsuru; Nishioka, Midori; Sumida, Masayuki

    2011-12-01

    We describe a new species of dicroglossid frog of the Fejervarya limnocharis complex from western Honshu, Japan Mainland. The new species, Fejervarya kawamurai, is genetically closer to F. sakishimensis than to F. limnocharis. It differs from F. sakishimensis by smaller tympanum, head, forelimb, hindlimb, foot, and tibia lengths, all relative to snout-vent length, and from F. multistriata by relatively shorter forelimb, hindlimb, foot, and tibia. From F. limnocharis and F. iskandari, it is differentiated by relatively smaller forelimb, hindlimb, foot, and tibia lengths. Taxonomic problems of Fejervarya populations occurring in Central Ryukyus, continental China, and Taiwan are discussed.

  8. Evolutionary patterns of two major reproduction candidate genes (Zp2 and Zp3 reveal no contribution to reproductive isolation between bovine species

    Directory of Open Access Journals (Sweden)

    Beja-Pereira Albano

    2011-01-01

    Full Text Available Abstract Background It has been established that mammalian egg zona pellucida (ZP glycoproteins are responsible for species-restricted binding of sperm to unfertilized eggs, inducing the sperm acrosome reaction, and preventing polyspermy. In mammals, ZP apparently represents a barrier to heterospecific fertilization and thus probably contributes to reproductive isolation between species. The evolutionary relationships between some members of the tribe Bovini are complex and highly debatable, particularly, those involving Bos and Bison species for which interspecific hybridization is extensively documented. Because reproductive isolation is known to be a major precursor of species divergence, testing evolutionary patterns of ZP glycoproteins may shed some light into the speciation process of these species. To this end, we have examined intraspecific and interspecific genetic variation of two ZP genes (Zp2 and Zp3 for seven representative species (111 individuals from the Bovini tribe, including five species from Bos and Bison, and two species each from genera Bubalus and Syncerus. Results A pattern of low levels of intraspecific polymorphism and interspecific divergence was detected for the two sequenced fragments each for Zp2 and Zp3. At intraspecific level, none of neutrality tests detected deviations from neutral equilibrium expectations for the two genes. Several haplotypes in both genes were shared by multiple species from Bos and Bison. Conclusions Here we argue that neither ancestral polymorphism nor introgressive hybridization alone can fully account for haplotype sharing among species from Bos and Bison, and that both scenarios have contributed to such a pattern of haplotype sharing observed here. Additionally, codon-based tests revealed strong evidence for purifying selection in the Zp3 coding haplotype sequences and weak evidence for purifying selection in the Zp2 coding haplotype sequences. Contrary to a general genetic pattern that

  9. Lineage diversification and hybridization in the Cayratia japonica-Cayratia tenuifolia species complex.

    Science.gov (United States)

    Ishikawa, Naoko; Ikeda, Hajime; Yi, Ting-shuang; Takabe-Ito, Eriko; Okada, Hiroshi; Tsukaya, Hirokazu

    2014-06-01

    The Cayratia japonica-Cayratia tenuifolia species complex (Vitaceae) is distributed from temperate to tropical East Asia, Southeast Asia, India, and Australia. The spatiotemporal diversification history of this complex was assessed through phylogenetic and biogeographic analyses. Maximum parsimony, neighbor-joining, and maximum likelihood methods were used to analyze sequences of one nuclear (AS1) and two plastid regions (trnL-F and trnC-petN). Bayesian dating analysis was conducted to estimate the divergence times of clades. The likelihood method LAGRANGE was used to infer ancestral areas. The Asian C. japonica and C. tenuifolia should be treated as an unresolved complex, and Australian C. japonica is distinct from the Asian C. japonica-C. tenuifolia species complex and should be treated as separate taxa. The Asian C. japonica-C. tenuifolia species complex was estimated to have diverged from its closest relatives during the Late Eocene (35.1 million years ago [Ma], 95% highest posterior densities [HPD]=23.3-47.3Ma) and most likely first diverged in mid-continental Asia. This complex was first divided into a northern clade and a southern clade during the middle Oligocene (27.3Ma; 95% HPD=17.4-38.1Ma), which is consistent with a large southeastward extrusion of the Indochina region relative to South China along the Red River. Each of the northern and southern clades then further diverged into multiple subclades through a series of dispersal and divergence events following significant geological and climatic changes in East and Southeast Asia during the Miocene. Multiple inter-lineage hybridizations among four lineages were inferred to have occurred following this diversification process, which caused some Asian lineages to be morphologically cryptic. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. EVALUATING THE NOVEL METHODS ON SPECIES DISTRIBUTION MODELING IN COMPLEX FOREST

    Directory of Open Access Journals (Sweden)

    C. H. Tu

    2012-07-01

    Full Text Available The prediction of species distribution has become a focus in ecology. For predicting a result more effectively and accurately, some novel methods have been proposed recently, like support vector machine (SVM and maximum entropy (MAXENT. However, high complexity in the forest, like that in Taiwan, will make the modeling become even harder. In this study, we aim to explore which method is more applicable to species distribution modeling in the complex forest. Castanopsis carlesii (long-leaf chinkapin, LLC, growing widely in Taiwan, was chosen as the target species because its seeds are an important food source for animals. We overlaid the tree samples on the layers of altitude, slope, aspect, terrain position, and vegetation index derived from SOPT-5 images, and developed three models, MAXENT, SVM, and decision tree (DT, to predict the potential habitat of LLCs. We evaluated these models by two sets of independent samples in different site and the effect on the complexity of forest by changing the background sample size (BSZ. In the forest with low complex (small BSZ, the accuracies of SVM (kappa = 0.87 and DT (0.86 models were slightly higher than that of MAXENT (0.84. In the more complex situation (large BSZ, MAXENT kept high kappa value (0.85, whereas SVM (0.61 and DT (0.57 models dropped significantly due to limiting the habitat close to samples. Therefore, MAXENT model was more applicable to predict species’ potential habitat in the complex forest; whereas SVM and DT models would tend to underestimate the potential habitat of LLCs.

  11. Complex patterns of faulting revealed by 3D seismic data at the West Galicia rifted margin

    Science.gov (United States)

    Reston, Timothy; Cresswell, Derren; Sawyer, Dale; Ranero, Cesar; Shillington, Donna; Morgan, Julia; Lymer, Gael

    2015-04-01

    The west Galicia margin is characterised by crust thinning to less than 3 km, well-defined fault blocks, which overlie a bright reflection (the S reflector) generally interpreted as a tectonic Moho. The margin exhibits neither voluminous magmatism nor thick sediment piles to obscure the structures and the amount of extension. As such is represents an ideal location to study the process of continental breakup both through seismic imaging and potentially through drilling. Prestack depth migration of existing 2D profiles has strongly supported the interpretation of the S reflector as both a detachment and as the crust-mantle boundary; wide-angle seismic has also shown that the mantle beneath S is serpentinised. Despite the quality of the existing 2D seismic images, a number of competing models have been advanced to explain the formation of this margin, including sequential faulting, polyphase faulting, multiple detachments and the gravitational collapse of the margin over exhumed mantle. As these models, all developed for the Galicia margin, have been subsequently applied to other margins, distinguishing between them has implications not only for the structure of the Galicia margin but for the process of rifting through to breakup more generally. To address these issues in summer of 2013 we collected a 3D combined seismic reflection and wide-angle dataset over this margin. Here we present some of the results of ongoing processing of the 3D volume, focussing on the internal structure of some of the fault blocks that overlies the S detachment. 2D processing of the data shows a relatively simple series of tilted fault block, bound by west-dipping faults that detach downwards onto the bright S reflector. However, inspection of the 3D volume produced by 3D pre-stack time migration reveals that the fault blocks contain a complex set of sedimentary packages, with strata tilted to the east, west, north and south, each package bound by faults. Furthermore, the top of crustal

  12. Transmission electron microscopy of Tuberculina species (Helicobasidiales) reveals an unique mode of conidiogenesis within Basidiomycota.

    Science.gov (United States)

    Aghayeva, Dilzara N; Lutz, Matthias; Piątek, Marcin

    2016-08-01

    Tuberculina species represent the asexual life stage of the plant-parasitic sexual genus Helicobasidium. Tuberculina species are distributed all over the world, living in antagonistic symbiosis with over 150 rust species from at least 15 genera. Within the Basidiomycota, besides the spermogonia of rust fungi, only Tuberculina species develop distinct fructifications in the haplophase. However, the knowledge of conidiogenesis in Tuberculina is meagre. Therefore, conidial development in Tuberculina maxima, Tuberculina persicina, and Tuberculina sbrozzii was studied using transmission electron microscopy, and compared to each other as well as to spermatia formation in rust fungi. Significant ultrastructural characteristics such as the movement of nuclei in the process of conidium formation, and formation of the initial and late stages of conidiogenesis are documented. The mode of conidiogenesis of Tuberculina species is unique within the Basidiomycota in that (1) it is realized by haploid fructifications, (2) it is holoblastic, without annellidic proliferation, (3) the nucleus of the conidiogenous cell moves towards the forming conidium, divides, and no daughter nucleus remains inside the conidiogenous cell, and (4) the conidiogenous cell retains only cytoplasmic residues after the development of a single conidium, and a successive conidium is not produced. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  13. Mitochondrial genome sequences reveal evolutionary relationships of the Phytophthora 1c clade species.

    Science.gov (United States)

    Lassiter, Erica S; Russ, Carsten; Nusbaum, Chad; Zeng, Qiandong; Saville, Amanda C; Olarte, Rodrigo A; Carbone, Ignazio; Hu, Chia-Hui; Seguin-Orlando, Andaine; Samaniego, Jose A; Thorne, Jeffrey L; Ristaino, Jean B

    2015-11-01

    Phytophthora infestans is one of the most destructive plant pathogens of potato and tomato globally. The pathogen is closely related to four other Phytophthora species in the 1c clade including P. phaseoli, P. ipomoeae, P. mirabilis and P. andina that are important pathogens of other wild and domesticated hosts. P. andina is an interspecific hybrid between P. infestans and an unknown Phytophthora species. We have sequenced mitochondrial genomes of the sister species of P. infestans and examined the evolutionary relationships within the clade. Phylogenetic analysis indicates that the P. phaseoli mitochondrial lineage is basal within the clade. P. mirabilis and P. ipomoeae are sister lineages and share a common ancestor with the Ic mitochondrial lineage of P. andina. These lineages in turn are sister to the P. infestans and P. andina Ia mitochondrial lineages. The P. andina Ic lineage diverged much earlier than the P. andina Ia mitochondrial lineage and P. infestans. The presence of two mitochondrial lineages in P. andina supports the hybrid nature of this species. The ancestral state of the P. andina Ic lineage in the tree and its occurrence only in the Andean regions of Ecuador, Colombia and Peru suggests that the origin of this species hybrid in nature may occur there.

  14. Splice variants of the relaxin and INSL3 receptors reveal unanticipated molecular complexity.

    Science.gov (United States)

    Muda, Marco; He, Chaomei; Martini, Paolo G V; Ferraro, Tania; Layfield, Sharon; Taylor, Deanne; Chevrier, Colette; Schweickhardt, Rene; Kelton, Christie; Ryan, Peter L; Bathgate, Ross A D

    2005-08-01

    LGR7 and LGR8 are G protein-coupled receptors that belong to the leucine-rich repeat-containing G-protein coupled receptor (LGR) family, including the thyroid-stimulating hormone (TSH), LH and FSH receptors. LGR7 and LGR8 stimulate cAMP production upon binding of the cognate ligands, relaxin and insulin-like peptide 3 (INSL3), respectively. We cloned several novel splice variants of both LGR7 and LGR8 and analysed the function of four variants. LGR7.1 is a truncated receptor, including only the N-terminal region of the receptor and two leucine rich repeats. In contrast, LGR7.2, LGR7.10 and LGR 8.1 all contain an intact seven transmembrane domain and most of the extracellular region, lacking only one or two exons in the ectodomain. Our analysis demonstrates that although LGR7.10 and LGR8.1 are expressed at the cell surface, LGR7.2 is predominantly retained within cells and LGR7.1 is partially secreted. mRNA expression analysis revealed that several variants are co-expressed in various tissues. None of these variants were able to stimulate cAMP production following relaxin or INSL3 treatment. Unexpectedly, we did not detect any direct specific relaxin or INSL3 binding on any of the splice variants. The large number of receptor splice variants identified suggests an unforeseen complexity in the physiology of this novel hormone-receptor system.

  15. The Noah's Ark experiment: species dependent biodistributions of cationic 99mTc complexes

    International Nuclear Information System (INIS)

    Deutsch, Edward; Ketring, A.R.; Libson, Karen; Vanderheyden, J.-L.; Hirth, W.W.

    1989-01-01

    The time dependent biodistributions of three related 99m Tc complexes of 1, 2-bis(dimethylphosphino)ethane (DMPE) were evaluated in several animal species including humans: trans-[ 99m Tc v (DMPE) 2 O 2 ] + , trans-[ 99m Tc III (DMPE) 2 Cl 2 ] + and [ 99m Tc I (DMPE) 3 ] + . Imaging studies were performed in 10 animal species to evaluate these complexes as myocardial perfusion imaging agents. Animal models adequately predict the uninteresting behaviour of the Tc(V) cation in humans, predict to only a very limited extent the behaviour of the Tc(III) cation in humans and totally fail to predict the behaviour of the Tc(I) cation in humans. (U.K.)

  16. Identity effects dominate the impacts of multiple species extinctions on the functioning of complex food webs.

    Science.gov (United States)

    Harvey, Eric; Séguin, Annie; Nozais, Christian; Archambault, Philippe; Gravel, Dominique

    2013-01-01

    Understanding the impacts of species extinctions on the functioning of food webs is a challenging task because of the complexity of ecological interactions. We report the impacts of experimental species extinctions on the functioning of two food webs of freshwater and marine systems. We used a linear model to partition the variance among the multiple components of the diversity effect (linear group richness, nonlinear group richness, and identity). The identity of each functional group was the best explaining variable of ecosystem functioning for both systems. We assessed the contribution of each functional group in multifunctional space and found that, although the effect of functional group varied across ecosystem functions, some functional groups shared common effects on functions. This study is the first experimental demonstration that functional identity dominates the effects of extinctions on ecosystem functioning, suggesting that generalizations are possible despite the inherent complexity of interactions.

  17. Comparative transcriptome analysis reveals whole-genome duplications and gene selection patterns in cultivated and wild Chrysanthemum species.

    Science.gov (United States)

    Won, So Youn; Kwon, Soo-Jin; Lee, Tae-Ho; Jung, Jae-A; Kim, Jung Sun; Kang, Sang-Ho; Sohn, Seong-Han

    2017-11-01

    Comparative transcriptome analysis of wild and cultivated chrysanthemums provides valuable genomic resources and helps uncover common and divergent patterns of genome and gene evolution in these species. Plants are unique in that they employ polyploidy (or whole-genome duplication, WGD) as a key process for speciation and evolution. The Chrysanthemum genus is closely associated with hybridization and polyploidization, with Chrysanthemum species exhibiting diverse ploidy levels. The commercially important species, C. morifolium is an allohexaploid plant that is thought to have originated via the hybridization of several Chrysanthemum species, but the genomic and molecular evolutionary mechanisms remain poorly understood. In the present study, we sequenced and compared the transcriptomes of C. morifolium and the wild Korean diploid species, C. boreale. De novo transcriptome assembly revealed 11,318 genes in C. morifolium and 10,961 genes in C. boreale, whose functions were annotated by homology searches. An analysis of synonymous substitution rates (Ks) of paralogous and orthologous genes suggested that the two Chrysanthemum species commonly experienced the Asteraceae paleopolyploidization and recent genome duplication or triplication before the divergence of these species. Intriguingly, C. boreale probably underwent rapid diploidization, with a reduction in chromosome number, whereas C. morifolium maintained the original chromosome number. Analysis of the ratios of non-synonymous to synonymous nucleotide substitutions (Ka/Ks) between orthologous gene pairs indicated that 107 genes experienced positive selection, which may have been crucial for the adaptation, domestication, and speciation of Chrysanthemum.

  18. A new morphologically cryptic species of Phyllomedusa (Anura: Phyllomedusidae) from Amazonian forests of northern Peru revealed by DNA sequences.

    Science.gov (United States)

    Castroviejo-Fisher, Santiago; Köhler, Jörn; Riva, Ignacio DE LA; Padial, José M

    2017-05-22

    We describe and name Phyllomedusa chaparroi sp. nov., a medium-sized species (snout-vent length in adult males 67.9-77.5 mm) of monkey frog from Amazonian rainforests of northern Peru. Although morphologically most similar to P. boliviana and P. camba (indistinguishable from the latter in external qualitative and quantitative traits), phylogenetic analysis of combined mitochondrial and nuclear markers place the new species sister to a clade containing P. neildi, P. tarsius, and P. trinitatis. Phyllomedusa chaparroi can be readily differentiated from these species by having a dark reddish-brown iris with indistinct tiny orange spots versus an orange iris with marked dark reticulation found in P. neildi, P. tarsius, and P. trinitatis. Furthermore, genetic distances for a 532 bp sequence of the 16S gene between the new species and its sister species are 2.8-4.1 %, whereas distances are 4.5-5.5 % to the morphologically cryptic P. camba. We briefly discuss the importance of DNA sequences in revealing morphologically cryptic species and modify the content of the P. tarsius species group based on phylogenetic analyses and observations on iris coloration.

  19. Origin and Dispersal History of Two Colonial Ascidian Clades in the Botryllus schlosseri Species Complex.

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    Marie L Nydam

    Full Text Available Human-induced global warming and species introductions are rapidly altering the composition and functioning of Earth's marine ecosystems. Ascidians (Phylum Chordata, Subphylum Tunicata, Class Ascidiacea are likely to play an increasingly greater role in marine communities. The colonial ascidian B. schlosseri is a cryptic species complex comprising five genetically divergent clades (A-E. Clade A is a global species, and Clade E has so far been identified in European waters only. Using the largest mitochondrial cytochrome oxidase I datasets yet assembled, we determine the origin and dispersal history of these species. Nucleotide diversity and Approximate Bayesian Computation analyses support a Pacific origin for Clade A, with two likely dispersal scenarios that both show the northwestern Atlantic populations establishing early in the history of the species. Both Discrete Phylogeographic Analysis and Approximate Bayesian Computation support an origin of Clade E on the French side of the English Channel. An unsampled lineage evolved from the French lineage, which reflects the conclusion from the median joining network that not all Clade E lineages have been sampled. This unsampled lineage gave rise to the haplotypes on the English side of the English Channel, which were the ancestors to the Mediterranean and Bay of Biscay populations. Clade E has a wider geographic range than previously thought, and shows evidence of recent range expansion. Both Clade A and Clade E should be considered widespread species: Clade A globally and Clade E within Europe.

  20. Decrypting the Hebeloma crustuliniforme complex: European species of Hebeloma section Denudata subsection Denudata (Agaricales).

    Science.gov (United States)

    Eberhardt, U; Beker, H J; Vesterholt, J

    2015-12-01

    Hebeloma subsection Denudata includes the type of H. section Denudata, Hebeloma crustuliniforme, as well as the majority of the taxa commonly included in the Hebeloma crustuliniforme complex. Complementing the work of D.K. Aanen and co-workers, and using refined morphological and molecular methods we were able to recognize further individual taxa within the section. Fifteen species occurring in Europe are assigned to H. subsect. Denudata. Of these, we describe eight species as new, namely H. aanenii, H. aurantioumbrinum, H. geminatum, H. louiseae, H. luteicystidiatum, H. pallidolabiatum, H. perexiguum and H. salicicola. Naucoria bellotiana, a species very similar to H. alpinum is recombined into Hebeloma. A key to Hebeloma subsect. Denudata is provided. We demonstrate that within this subsection there is good overall consistency between morphological, phylogenetic and biological species concepts. In contrast to current opinion, in this group there is little species overlap, particularly when also considering species frequencies, between arctic and alpine floras on one hand and temperate on the other.

  1. Origin and Dispersal History of Two Colonial Ascidian Clades in the Botryllus schlosseri Species Complex.

    Science.gov (United States)

    Nydam, Marie L; Giesbrecht, Kirsten B; Stephenson, Emily E

    2017-01-01

    Human-induced global warming and species introductions are rapidly altering the composition and functioning of Earth's marine ecosystems. Ascidians (Phylum Chordata, Subphylum Tunicata, Class Ascidiacea) are likely to play an increasingly greater role in marine communities. The colonial ascidian B. schlosseri is a cryptic species complex comprising five genetically divergent clades (A-E). Clade A is a global species, and Clade E has so far been identified in European waters only. Using the largest mitochondrial cytochrome oxidase I datasets yet assembled, we determine the origin and dispersal history of these species. Nucleotide diversity and Approximate Bayesian Computation analyses support a Pacific origin for Clade A, with two likely dispersal scenarios that both show the northwestern Atlantic populations establishing early in the history of the species. Both Discrete Phylogeographic Analysis and Approximate Bayesian Computation support an origin of Clade E on the French side of the English Channel. An unsampled lineage evolved from the French lineage, which reflects the conclusion from the median joining network that not all Clade E lineages have been sampled. This unsampled lineage gave rise to the haplotypes on the English side of the English Channel, which were the ancestors to the Mediterranean and Bay of Biscay populations. Clade E has a wider geographic range than previously thought, and shows evidence of recent range expansion. Both Clade A and Clade E should be considered widespread species: Clade A globally and Clade E within Europe.

  2. Biological and genetic aspects of experimental hybrids from species of the Phyllosoma complex (Hemiptera: Reduviidae: Triatominae).

    Science.gov (United States)

    Martínez-Ibarra, José Alejandro; Ventura-Rodríguez, Luz Verónica; Meillon-Isais, Karla; Barajas-Martínez, Héctor; Alejandre-Aguilar, Ricardo; Lupercio-Coronel, Patricia; Rocha-Chávez, Gonzalo; Nogueda-Torres, Benjamín

    2008-05-01

    The present work is a thorough investigation of the degree of reproductive isolation between Meccus mazzottii and Meccus longipennis, Meccus picturatus, Meccus pallidipennis and Meccus bassolsae, as well as between M. longipennis and M. picturatus. We examined fertility and segregation of morphological characteristics in two generations of hybrids derived from crosses between these species. The percentage of pairs with (fertile) offspring was highest in the set of crosses between M. longipennis and M. picturatus, and lowest between M. mazzottii and M. picturatus. Most first-generation (F1) individuals from crosses involving M. mazzottii were morphologically similar to this species, while only F1 x F1 progeny of parental crosses between M. mazzottii and M. longipennis had offspring second generation that looked like M. mazzottii. The results indicate that different degrees of reproductive isolation apparently exist among the species of the Phyllosoma complex examined in this study. The biological evidence obtained in this study does not support the proposal that M. longipennis and M. picturatus are full species. It could indicate on the contrary, that both could be considered as subspecies of a single polytypic species. On the other hand, biological evidence supports the proposal that M. mazzottii is a full species.

  3. Delimiting species in the Phacus longicauda complex (Euglenida) through morphological and molecular analyses.

    Science.gov (United States)

    Łukomska-Kowalczyk, Maja; Karnkowska, Anna; Milanowski, Rafał; Łach, Łukasz; Zakryś, Bożena

    2015-12-01

    Although Phacus longicauda is the type species of the genus Phacus and one of the most common species among autotrophic euglenids, its correct identification is nearly impossible. Over 30 morphologically similar taxa appear in the literature, but there are no good diagnostic features to distinguish them. Using environmental sampling and whole genome amplification, we delimited species within the Phacus longicauda complex. Morphological and molecular characters were analyzed for 36 strains isolated from environmental samples (mainly from Poland). DNA was obtained from a small number of cells (20-30) isolated with a micropipette from every sample (i.e., without setting up laboratory cultures), and phylogenetic analyses were based on variation in nSSU rDNA. Apart from Phacus longicauda, three other species (Phacus circumflexus, Phacus helikoides, and Phacus tortus) were distinguished. Phacus cordata comb. nov. Zakryś et M. Łukomska and Phacus rotunda comb. nov. Zakryś et M. Łukomska had their taxonomic ranks changed and two species new to science, Phacus cristatus sp. nov. Zakryś et M. Łukomska and Phacus crassus sp. nov. Zakryś et M. Łukomska, were described. For all verified species, diagnostic descriptions were amended and epitypes designated. © 2015 Phycological Society of America.

  4. Morphological and Molecular Phylogenetic Data Reveal a New Species of Primula (Primulaceae from Hunan, China.

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    Yuan Xu

    Full Text Available A new species of Primulaceae, Primula undulifolia, is described from the hilly area of Hunan province in south-central China. Its morphology and distributional range suggest that it is allied to P. kwangtungensis, both adapted to subtropical climate, having contiguous distribution and similar habitat, growing on shady and moist cliffs. Petioles, scapes and pedicels of them are densely covered with rusty multicellular hairs, but the new species can be easily distinguished by its smaller flowers and narrowly oblong leaves with undulate margins. Molecular phylogenetic analysis based on four DNA markers (ITS, matK, trnL-F and rps16 confirmed the new species as an independent lineage and constitutes a main clade together with P. kwangtungensis, P. kweichouensis, P. wangii and P. hunanensis of Primula sect. Carolinella.

  5. Genome wide analyses reveal little evidence for adaptive evolution in many plant species.

    Science.gov (United States)

    Gossmann, Toni I; Song, Bao-Hua; Windsor, Aaron J; Mitchell-Olds, Thomas; Dixon, Christopher J; Kapralov, Maxim V; Filatov, Dmitry A; Eyre-Walker, Adam

    2010-08-01

    The relative contribution of advantageous and neutral mutations to the evolutionary process is a central problem in evolutionary biology. Current estimates suggest that whereas Drosophila, mice, and bacteria have undergone extensive adaptive evolution, hominids show little or no evidence of adaptive evolution in protein-coding sequences. This may be a consequence of differences in effective population size. To study the matter further, we have investigated whether plants show evidence of adaptive evolution using an extension of the McDonald-Kreitman test that explicitly models slightly deleterious mutations by estimating the distribution of fitness effects of new mutations. We apply this method to data from nine pairs of species. Altogether more than 2,400 loci with an average length of approximately 280 nucleotides were analyzed. We observe very similar results in all species; we find little evidence of adaptive amino acid substitution in any comparison except sunflowers. This may be because many plant species have modest effective population sizes.

  6. Molecular study of Astyanax altiparanae (Osteichthyes, Characidae) as a probable species complex.

    Science.gov (United States)

    Deprá, I C; Gomes, V N; Deprá, G C; Oliveira, I J; Prioli, S M A P; Prioli, A J

    2014-08-07

    Astyanax altiparanae, belonging to the bimaculatus group, which includes species with similar colors and morphology, occurs in the upper Paraná River basin. As the use of mitochondrial DNA has made great strides in the diagnosis of species, in previous researches, two strains were detected in A. altiparanae with a high divergence in the D-loop region, provisionally called AltoPR and AltoPR-D. Evidence led to the hypothesis that the two strains did not belong to the same species. Phylogenetic hypotheses were produced by maximum-likelihood. Mean internal distances of the AltoPR and AltoPR-D groups were respectively 0.002 and 0.003, with the distance between them being 0.037. Sequences from GenBank of specimens collected from the Paraíba do Sul River basin were also divided into two groups, of which one may be identified as AltoPR. Since the other group provided an intermediate distance when compared to AltoPR-D, an in-depth investigation was required. The other species analyzed showed a greater distance and was revealed to be a monophyletic taxon. The results suggested that they are really two species and that neither corresponds to the other species used in the current study.

  7. Hybrid sterility in crosses between two Brazilian sibling species of the Anopheles albitarsis complex.

    Science.gov (United States)

    Fontoura, Nathalia Giglio; Araki, Alejandra Saori; Van Der Maas Azevedo, Renata; Galardo, Allan Kardec Ribeiro; Peixoto, Alexandre Afranio; Lima, José Bento Pereira

    2014-12-04

    Complexes of cryptic species are common in several taxa and this is also the case in the Anopheles genus, a group including all known human malaria vectors. The Anopheles albitarsis complex comprises at least nine cryptic species, some of which are implicated as vectors of human malaria. Several different types of data have been generated for this species complex such as cytogenetics, alloenzymes, morphological and feeding behavioral, hybridization experiments, RAPD-PCR and RFLP and mitochondrial and nuclear markers. Studies focused on its postzygotic isolation are still somewhat rare in the literature despite their importance to understand the speciation process and the level of gene flow potentially occurring among the different sibling species. Hybridization experiments between Anopheles albitarsis s.s. and Anopheles marajoara, as well as backcrosses between hybrids and Anopheles albitarsis s.s., were performed using the induced mating technique. Results were compared to intraspecific crosses. Larva-to-adult viability and sex ratio were also assessed. Male hybrids show very low insemination rates and nearly complete sterility, apparently due to abnormalities in their reproductive organs. Evidence of partial sterility among the hybrid females was also observed. Our data indicated that Anopheles albitarsis s.s. and Anopheles marajoara show a high level of postzygotic isolation with a strong hybrid male sterility. This result is consistent with the Haldane's rule which states that in interspecific crosses the heterogametic sex is the first to be affected. However, the fact that the females are not completely sterile raises the possibility of introgression between these two siblings species.

  8. Phenotypic differentiation in love song traits among sibling species of the Lutzomyia longipalpis complex in Brazil.

    Science.gov (United States)

    Vigoder, Felipe M; Souza, Nataly A; Brazil, Reginaldo P; Bruno, Rafaela V; Costa, Pietra L; Ritchie, Michael G; Klaczko, Louis B; Peixoto, Alexandre A

    2015-05-28

    Brazilian populations of Lutzomyia longipalpis may constitute a complex of cryptic species, and this report investigates the distribution and number of potential sibling species. One of the main differences observed among Brazilian populations is the type of acoustic signal produced by males during copulation. These copulation song differences seem to be evolving faster than neutral molecular markers and have been suggested to contribute to insemination failure observed in crosses between these sibling species. In previous studies, two main types of copulation songs were found, burst-type and pulse-type. The latter type can, in turn, be further subdivided into five different patterns. We recorded male song from 13 new populations of the L. longipalpis complex from Brazil and compared the songs with 12 already available. Out of these 25 populations, 16 produce burst-type and 9 produce pulse-type songs. We performed a principal component analysis in these two main groups separately and an additional discriminant analysis in the pulse-type group. The pulse-type populations showed a clear separation between the five known patterns with a high correspondence of individuals to their correct group, confirming the differentiation between them. The distinctiveness of the burst-type subgroups was much lower than that observed among the pulse-type groups and no clear population structure was observed. This suggests that the burst-type populations represent a single species. Overall, our results are consistent with the existence in Brazil of at least six species of the L. longipalpis complex, one with a wide distribution comprising all the populations with burst-type songs, and five more closely related allopatric siblings with different pulse-type song patterns and more restricted distribution ranges.

  9. Antibiotic resistance patterns of Acinetobacter calcoaceticus-A. baumannii complex species from Colombian hospitals.

    Science.gov (United States)

    Reguero, María Teresa; Medina, Olga Esther; Hernández, María Andrea; Flórez, Diana Vanessa; Valenzuela, Emilia María; Mantilla, José Ramón

    2013-03-01

    Only automated phenotypic methods are currently used in Colombian hospitals for identifying isolates of the Acinetobacter calcoaceticus-A. baumannii complex (ACB). The phenotypical similarities in these species mean that they cannot be differentiated by manual or automated methods, thereby leading to their identification as A. baumannii, or ACB complex in clinical settings. Our objective was to identify to the species level 60 isolates, from four hospitals, evaluate their antibiotic susceptibility, and detect resistance-related genes. 16S-23S rRNA internal transcribed spacer (ITS) region and rpoB gene partial sequences were amplified. Resistance genes for cephalosporin, carbapenem and aminoglycoside were detected by PCR. Possible mutations in the quinolone resistance-determining region (QRDR) were evaluated. The association of ISAba-1 with blaOXA and blaADC genes was determined by PCR. Amplification products of ITS region, rpoB gene and some resistance genes were sequenced and compared using the BLAST tool. 16S-23S rRNA ITS region and partial rpoB gene sequence analysis allowed 51isolates to be identified as A. baumannii, 8 as A. nosocomialis, and 1 isolate as A. pitti. A. baumannii isolates were highly resistant to all antibiotics tested, while the others were susceptible to ciprofloxacin and ampicillin/sulbactam. Quinolone resistance, found only in A. baumannii, was associated with mutations in the QRDR region of gyrA and parC genes. This is the first investigation in Colombia that has identified ACB complex species using molecular methods, and determined differences in antibiotic resistance and resistance genes among the species. It is of the highest importance to identify isolates to the species level for future resistance and epidemiology studies in our region. Copyright © 2012 Elsevier España, S.L. All rights reserved.

  10. Trichoderma Biodiversity of Agricultural Fields in East China Reveals a Gradient Distribution of Species.

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    Yuan Jiang

    Full Text Available We surveyed the Trichoderma (Hypocreales, Ascomycota biodiversity in agricultural fields in four major agricultural provinces of East China. Trichoderma strains were identified based on molecular approaches and morphological characteristics. In three sampled seasons (spring, summer and autumn, 2078 strains were isolated and identified to 17 known species: T. harzianum (429 isolates, T. asperellum (425, T. hamatum (397, T. virens (340, T. koningiopsis (248, T. brevicompactum (73, T. atroviride (73, T. fertile (26, T. longibrachiatum (22, T. pleuroticola (16, T. erinaceum (16, T. oblongisporum (2, T. polysporum (2, T. spirale (2, T. capillare (2, T. velutinum (2, and T. saturnisporum (1. T. harzianum, T. asperellum, T. hamatum, and T. virens were identified as the dominant species with dominance (Y values of 0.057, 0.052, 0.048, and 0.039, respectively. The species amount, isolate numbers and the dominant species of Trichoderma varied between provinces. Zhejiang Province has shown the highest diversity, which was reflected in the highest species amount (14 and the highest Shannon-Wiener diversity index of Trichoderma haplotypes (1.46. We observed that relative frequencies of T. hamatum and T. koningiopsis under rice soil were higher than those under wheat and maize soil, indicating the preference of Trichoderma to different crops. Remarkable seasonal variation was shown, with summer exhibiting the highest biodiversity of the studied seasons. These results show that Trichoderma biodiversity in agricultural fields varies by region, crop, and season. Zhejiang Province (the southernmost province in the investigated area had more T. hamatum than Shandong Province (the northernmost province, not only in isolate amounts but also in haplotype amounts. Furthermore, at haplotype level, only T. hamatum showed a gradient distribution from south to north in correspondence analysis among the four dominant species. The above results would contribute to the

  11. Species distribution of clinical Acinetobacter isolates revealed by different identification techniques.

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    Jianfeng Wang

    Full Text Available A total of 2582 non-duplicate clinical Acinetobacter spp. isolates were collected to evaluate the performance of four identification methods because it is important to identify Acinetobacter spp. accurately and survey the species distribution to determine the appropriate antimicrobial treatment. Phenotyping (VITEK 2 and VITEK MS and genotyping (16S rRNA and rpoB gene sequencing methods were applied for species identification, and antimicrobial susceptibility test of imipenem and meropenem was performed with a disk diffusion assay. Generally, the phenotypic identification results were quite different from the genotyping results, and their discrimination ability was unsatisfactory, whereas 16S rRNA and rpoB gene sequencing showed consistent typing results, with different resolution. Additionally, A. pittii, A. calcoaceticus and A. nosocomialis, which were phylogenetically close to A. baumannii, accounted for 85.5% of the non-A. baumannii isolates. One group, which could not be clustered with any reference strains, consisted of 11 isolates and constituted a novel Acinetobacter species that was entitled genomic species 33YU. None of the non-A. baumannii isolates harbored a blaOXA-51-like gene, and this gene was disrupted by ISAba19 in only one isolate; it continues to be appropriate as a genetic marker for A. baumannii identification. The resistance rate of non-A. baumannii isolates to imipenem and/or meropenem was only 2.6%, which was significantly lower than that of A. baumannii. Overall, rpoB gene sequencing was the most accurate identification method for Acinetobacter species. Except for A. baumannii, the most frequently isolated species from the nosocomial setting were A. pittii, A. calcoaceticus and A. nosocomialis.

  12. Species Distribution of Clinical Acinetobacter Isolates Revealed by Different Identification Techniques

    Science.gov (United States)

    Feng, Ye; Fu, Ying; Jiang, Yan; Wang, Haiping; Yu, Yunsong

    2014-01-01

    A total of 2582 non-duplicate clinical Acinetobacter spp. isolates were collected to evaluate the performance of four identification methods because it is important to identify Acinetobacter spp. accurately and survey the species distribution to determine the appropriate antimicrobial treatment. Phenotyping (VITEK 2 and VITEK MS) and genotyping (16S rRNA and rpoB gene sequencing) methods were applied for species identification, and antimicrobial susceptibility test of imipenem and meropenem was performed with a disk diffusion assay. Generally, the phenotypic identification results were quite different from the genotyping results, and their discrimination ability was unsatisfactory, whereas 16S rRNA and rpoB gene sequencing showed consistent typing results, with different resolution. Additionally, A. pittii, A. calcoaceticus and A. nosocomialis, which were phylogenetically close to A. baumannii, accounted for 85.5% of the non-A. baumannii isolates. One group, which could not be clustered with any reference strains, consisted of 11 isolates and constituted a novel Acinetobacter species that was entitled genomic species 33YU. None of the non-A. baumannii isolates harbored a bla OXA-51-like gene, and this gene was disrupted by ISAba19 in only one isolate; it continues to be appropriate as a genetic marker for A. baumannii identification. The resistance rate of non-A. baumannii isolates to imipenem and/or meropenem was only 2.6%, which was significantly lower than that of A. baumannii. Overall, rpoB gene sequencing was the most accurate identification method for Acinetobacter species. Except for A. baumannii, the most frequently isolated species from the nosocomial setting were A. pittii, A. calcoaceticus and A. nosocomialis. PMID:25120020

  13. Mitochondrial Genes Reveal Triatoma jatai as a Sister Species to Triatoma costalimai (Reduviidae: Triatominae).

    Science.gov (United States)

    Teves, Simone Caldas; Gardim, Sueli; Carbajal de la Fuente, Ana Laura; Lopes, Catarina Macedo; Gonçalves, Teresa Cristina Monte; dos Santos Mallet, Jacenir Reis; da Rosa, João Aristeu; Almeida, Carlos Eduardo

    2016-03-01

    Triatoma jatai was described using a set of morphological structures from specimens collected in Paranã municipality of Tocantins State, Brazil. Under a Bayesian framework and using two mitochondrial genes (16S and COI), phylogenetic analysis recovered T. jatai as a sister species to Triatoma costalimai with higher genetic distances than between other well-recognized species. Our results agree with previous suggestions based on morphometric analysis. In the light of the non-monophyly of Matogrossensis subcomplex, the inclusion of T. jatai shall be considered for reevaluating this group. © The American Society of Tropical Medicine and Hygiene.

  14. The rubber tree genome reveals new insights into rubber production and species adaptation

    OpenAIRE

    Tang, Chaorong; Yang, Meng; Fang, Yongjun; Luo, Yingfeng; Gao, Shenghan; Xiao, Xiaohu; An, Zewei; Zhou, Binhui; Zhang, Bing; Tan, Xinyu; Yeang, Hoong Yeet; Qin, Yunxia; Yang, Jianghua; Lin, Qiang; Mei, Hailiang

    2016-01-01

    The Para rubber tree (Hevea brasiliensis) is an economically important tropical tree species that produces natural rubber, an essential industrial raw material. Here we present a high-quality genome assembly of this species (1.37 Gb, scaffold N50 = 1.28 Mb) that covers 93.8% of the genome (1.47 Gb) and harbours 43,792 predicted protein-coding genes. A striking expansion of the REF/SRPP (rubber elongation factor/small rubber particle protein) gene family and its divergence into several laticif...

  15. Integrative Taxonomy of Southeast Asian Snail-Eating Turtles (Geoemydidae: Malayemys Reveals a New Species and Mitochondrial Introgression.

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    Flora Ihlow

    Full Text Available Based on an integrative taxonomic approach, we examine the differentiation of Southeast Asian snail-eating turtles using information from 1863 bp of mitochondrial DNA, 12 microsatellite loci, morphology and a correlative species distribution model. Our analyses reveal three genetically distinct groups with limited mitochondrial introgression in one group. All three groups exhibit distinct nuclear gene pools and distinct morphology. Two of these groups correspond to the previously recognized species Malayemys macrocephala (Chao Phraya Basin and M. subtrijuga (Lower Mekong Basin. The third and genetically most divergent group from the Khorat Basin represents a previously unrecognized species, which is described herein. Although Malayemys are extensively traded and used for religious release, only few studied turtles appear to be translocated by humans. Historic fluctuations in potential distributions were assessed using species distribution models (SDMs. The Last Glacial Maximum (LGM projection of the predictive SDMs suggests two distinct glacial distribution ranges, implying that the divergence of M. macrocephala and M. subtrijuga occurred in allopatry and was triggered by Pleistocene climate fluctuations. Only the projection derived from the global circulation model MIROC reveals a distinct third glacial distribution range for the newly discovered Malayemys species.

  16. Insights on the identities of sharks of the Rhizoprionodon acutus (Elasmobranchii: Carcharhiniformes) species complex based on three new species of Phoreiobothrium (Cestoda: Onchoproteocephalidea).

    Science.gov (United States)

    Caira, J N; Jensen, K

    2015-12-22

    Recent molecular work on milk sharks (Rhizoprionodon acutus [Rüppell]) suggests that, rather than a single widely distributed species, R. acutus represents a complex of four narrowly distributed cryptic species. Examination of the cestodes in three of the four members of that complex globally led to the discovery and description of three new species in the onchoproteocephalidean genus Phoreiobothrium Linton, 1889. The host associations and geographic distributions of the new species are fully congruent with the geographic distributions and species boundaries inferred for the sharks from molecular data: Phoreiobothrium jahki n. sp. parasitizes Rhizoprionodon cf. acutus 3 off Borneo, P. nadiae n. sp. parasitizes R. cf. acutus 1 off Senegal, and P. swaki n. sp. parasitizes R. cf. acutus 2 off northern Australia. The new cestodes differ from one another and from their 11 valid congeners in morphological features such as sublocular configuration and number, hook size, and testis number. Given the notoriously oioxenous nature of elasmobranch-hosted onchoproteocephalidean cestodes, these results provide further support for recognition of the milk shark species complex. This work also raises questions about the Phoreiobothrium species reported in cursory descriptions from India; further examination of these cestodes is key because they are potentially hosted by the fourth member of the R. acutus complex. To encourage future taxonomic work on the morphology of sharks in this complex, comparative photographs of representatives of the four potential host species are provided.

  17. Ecological and epidemiological status of species of the Phlebotomus perniciosus complex (Diptera: Psychodidae, Phlebotominae) in Morocco.

    Science.gov (United States)

    Zarrouk, Asmae; Kahime, Kholoud; Boussaa, Samia; Belqat, Boutaïna

    2016-03-01

    Leishmania infantum (Kinetoplastida: Trypanosomatidae) infection is transmitted by an infected female sand fly (Diptera: Psychodidae, Phlebotominae) of the subgenus Larroussius: Phlebotomus ariasi, Phlebotomus perniciosus, and Phlebotomus longicuspis in the Mediterranean basin. In Morocco, the vectorial role of P. ariasi was demonstrated, while that of P. longicuspis and P. perniciosus is not elucidated. In addition, Moroccan P. longicuspis and P. perniciosus populations present a higher morphologic and genetic variability. It was classified as P. perniciosus complex, including typical (PN) and atypical (PNA) morphs of P. perniciosus, P. longicuspis sensu stricto (LCss), and a sibling species of P. longicuspis (LCx). With the aim to study the ecological and epidemiological status of P. perniciosus complex species in Morocco, entomological surveys were carried out during three entomological seasons (2012, 2013, and 2014). We collected a total of 6298 specimens from 81 localities of northern, central, and southern Morocco. After describing the geographical distribution of P. perniciosus complex trough Morocco according to many variables (altitude, latitude, and longitude), we discuss the resulting epidemiological implications of its species. Our results highlight the geographical distribution of the two morphs of P. perniciosus through Morocco: PN is limited to the north, while PNA is widespread in northern, central, and southern Morocco. In terms of vectorial role, we hypothesize the potential involvement of PN, LCss, and LCx, at least, with P. ariasi, in the epidemiological cycle of L. infantum in Morocco.

  18. Post-Embryonic Development and Genital-Complex Formation in Three Species of Polyclad Flatworms.

    Science.gov (United States)

    Morita, Nozomi; Inaba, Kazuo; Saito, Yasunori

    2018-02-01

    Without the establishment of effective culturing systems, little can be known about the late developmental stages of polyclad flatworms. Here, we report a laboratory culturing system for three polyclad species: Comoplana pusilla, Notocomplana koreana, and Pseudostylochus obscurus, and we describe changes in their morphology from hatching to reproductive maturity. These species hatch out as lobe-less larvae with four eyespots, but the number of eyespots increases in later development. Cross-like and triangularly shaped larvae are observed in N. koreana and P. obscurus, respectively. After settlement, a pale area appears on the body of juveniles and then develops into the copulatory complexes. All three species could be successfully reared on brine shrimp, but only C. pusilla and N. koreana achieved reproductive maturation in such a culturing system. In P. obscurus, switching the food to the gastropod Monodonta labio induced sexual maturation.

  19. Clarifying the Dioscorea buchananii Benth. species complex: a new potentially extinct subspecies for South Africa

    Science.gov (United States)

    Wilkin, Paul; Muasya, A. Muthama

    2015-01-01

    Abstract The Dioscorea buchananii complex is shown to comprise three species, one of which is divided into two subspecies, based on morphological data. Two species, Dioscorea rupicola Kunth and Dioscorea multiloba Kunth, are endemic or subendemic to South Africa and of widespread occurrence in KwaZulu Natal. They differ markedly from each other in inflorescence and floral morphology and appear to be ecologically differentiated. The third species, Dioscorea buchananii Benth., is primarily found in southeastern tropical Africa, but a small number of specimens collected in South Africa in the late 19th and early 20th centuries are placed in an endemic subspecies, Dioscorea buchananii subsp. undatiloba (Baker) Wilkin. The latter taxon is a high priority in terms of rediscovery and conservation. Keys, descriptions, supporting information and illustrations are provided and made available online through eMonocot biodiversity informatics tools. Three nomenclatural acts are undertaken: two names are placed in synonymy and a new combination made. PMID:25931973

  20. Species and ecological diversity within the Cladosporium cladosporioides complex (Davidiellaceae, Capnodiales)

    DEFF Research Database (Denmark)

    Bensch, K.; Groenewald, J.Z.; Dijksterhuis, J.

    2010-01-01

    shape, width and arrangement. Many of the treated species, e.g., C. acalyphae, C. angustisporum, C. australiense, C. basiinflatum, C. chalastosporoides, C. colocasiae, C. cucumerinum, C. exasperatum, C. exile, C. flabelliforme, C. gamsianum, and C. globisporum are currently known only from specific......The genus Cladosporium is one of the largest genera of dematiaceous hyphomycetes, and is characterised by a coronate scar structure, conidia in acropetal chains and Davidiella teleomorphs. Based on morphology and DNA phylogeny, the species complexes of C. herbarum and C. sphaerospermum have been...... regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-α gene sequences. For the saprobic, widely distributed species Cladosporium cladosporioides, both a neotype and epitype are designated in order to specify a well established circumscription and concept...

  1. Implementing the European policies for alien species – networking, science, and partnership in a complex environment

    Directory of Open Access Journals (Sweden)

    Stelios Katsanevakis

    2013-02-01

    Full Text Available The European Commission has recognized the need for more stringent action to manage biological invasions and has committed to develop adedicated legislative instrument. Under this upcoming legislation, European countries and their relevant institutions will have additional obligations and commitments in respect to invasive alien species. In September 2012, the European Commission’s Joint Research Centre (JRC launched the European Alien Species Information Network (EASIN to facilitate the exploration of existing alien species information from distributed sources and to assist the implementation of European policies on biological invasions. Subsequent to the launching of EASIN, there was an evident need to define its niche within a complex environment of global, European, regional and national information systems. Herein we propose an organizational chart clearly defining the role of each actor in this framework, and we emphasize the need for collaboration in order to effectively support EU policies.

  2. Global population structure and taxonomy of the wandering albatross species complex.

    Science.gov (United States)

    Burg, T M; Croxall, J P

    2004-08-01

    A recent taxonomic revision of wandering albatross elevated each of the four subspecies to species. We used mitochondrial DNA and nine microsatellite markers to study the phylogenetic relationships of three species (Diomedea antipodensis, D. exulans and D. gibsoni) in the wandering albatross complex. A small number of samples from a fourth species, D. dabbenena, were analysed using mitochondrial DNA only. Mitochondrial DNA sequence analyses indicated the presence of three distinct groups within the wandering albatross complex: D. exulans, D. dabbenena and D. antipodensis/D. gibsoni. Although no fixed differences were found between D. antipodensis and D. gibsoni, a significant difference in the frequency of a single restriction site was detected using random fragment length polymorphism. Microsatellite analyses using nine variable loci, showed that D. exulans, D. antipodensis and D. gibsoni were genetically differentiated. Despite the widespread distribution of D. exulans, we did not detect any genetic differentiation among populations breeding on different island groups. The lower level of genetic differentiation between D. antipodensis and D. gibsoni should be reclassified as D. antipodensis. Within the context of the current taxonomy, these combined data support three species: D. dabbenena, D. exulans and D. antipodensis. Copyright 2004 Blackwell Publishing Ltd

  3. Using Google Earth Surface Metrics to Predict Plant Species Richness in a Complex Landscape

    Directory of Open Access Journals (Sweden)

    Sebastián Block

    2016-10-01

    Full Text Available Google Earth provides a freely available, global mosaic of high-resolution imagery from different sensors that has become popular in environmental and ecological studies. However, such imagery lacks the near-infrared band often used in studying vegetation, thus its potential for estimating vegetation properties remains unclear. In this study, we assess the potential of Google Earth imagery to describe and predict vegetation attributes. Further, we compare it to the potential of SPOT imagery, which has additional spectral information. We measured basal area, vegetation height, crown cover, density of individuals, and species richness in 60 plots in the oak forests of a complex volcanic landscape in central Mexico. We modelled each vegetation attribute as a function of surface metrics derived from Google Earth and SPOT images, and selected the best-supported linear models from each source. Total species richness was the best-described and predicted variable: the best Google Earth-based model explained nearly as much variation in species richness as its SPOT counterpart (R2 = 0.44 and 0.51, respectively. However, Google Earth metrics emerged as poor predictors of all remaining vegetation attributes, whilst SPOT metrics showed potential for predicting vegetation height. We conclude that Google Earth imagery can be used to estimate species richness in complex landscapes. As it is freely available, Google Earth can broaden the use of remote sensing by researchers and managers in low-income tropical countries where most biodiversity hotspots are found.

  4. Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis.

    Science.gov (United States)

    Gill, B A; Kondratieff, B C; Casner, K L; Encalada, A C; Flecker, A S; Gannon, D G; Ghalambor, C K; Guayasamin, J M; Poff, N L; Simmons, M P; Thomas, S A; Zamudio, K R; Funk, W C

    2016-06-15

    The 'mountain passes are higher in the tropics' (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may be largely cryptic, because physiological and dispersal traits isolating populations might not correspond to morphological differences. Yet previous tests of the MPHT hypothesis have not addressed cryptic diversity. We use integrative taxonomy, combining morphology (6136 specimens) and DNA barcoding (1832 specimens) to compare the species richness, cryptic diversity and elevational ranges of mayflies (Ephemeroptera) in the Rocky Mountains (Colorado; approx. 40°N) and the Andes (Ecuador; approx. 0°). We find higher species richness and smaller elevational ranges in Ecuador than Colorado, but only after quantifying and accounting for cryptic diversity. The opposite pattern is found when comparing diversity based on morphology alone, underscoring the importance of uncovering cryptic species to understand global biodiversity patterns. © 2016 The Author(s).

  5. Genetic relationships among some Pinus, Picea and Abies species revealed by RAPD markers

    Directory of Open Access Journals (Sweden)

    Kovačević Dragan

    2013-01-01

    Full Text Available Studies were undertaken to identify genetic relationships among ten different species of the family Pinaceae through randomly amplified polymorphic DNA (RAPD markers. Eighteen arbitrary RAPD primers produced 123 fragments of which 107 were polymorphic (87%. The similarity coefficient values varied from 0.34 to 0.67. The highest similarity coefficient was detected between Pinus wallichiana and P. strobus as well as between Picea abies and P. orientalis, and the lowest was detected between threePinus species (P. heldreichii, P. peuce and P. wallichiana and Picea omorika. The analysis of RAPD markers confirmed the genetic relationships among species. GenusPicea is clearly separated from genus Pinus and is closer to genus Abies (A. concolor than to genus Pinus, what confirms up-to-date numerous comparative-morphological, anatomical, chemotaxonomic and molecular results of these closely related genera. Furthermore, on the basis of our results, pine species from different subgenera -Pinus and Strobus are clearly separated. This statement is in agreement with contemporary intrageneric classification of the genus Pinus. [Projekat Ministarstva nauke Republike Srbije, br.173029

  6. Stable isotopes reveal the effect of trawl fisheries on the diet of commercially exploited species.

    Science.gov (United States)

    Hinz, Hilmar; Moranta, Joan; Balestrini, Stephen; Sciberras, Marija; Pantin, Julia R; Monnington, James; Zalewski, Alex; Kaiser, Michel J; Sköld, Mattias; Jonsson, Patrik; Bastardie, Francois; Hiddink, Jan Geert

    2017-07-24

    Bottom trawling can change food availability for benthivorous demersal species by (i) changing benthic prey composition through physical seabed impacts and (ii) by removing overall benthic consumer biomass increasing the net availability of benthic prey for remaining individuals. Thus trawling may both negatively and positively influence the quantity and quality of food available. Using δ 13 C and δ 15 N we investigated potential diet changes of three commercially exploited species across trawling gradients in the Kattegat (plaice, dab and Norway lobster (Nephrops)) and the Irish Sea (Nephrops). In the Kattegat, trawling affected primarily the biomass of benthic consumers, lowering competition. Nephrops showed significant positive relationships for δ 13 C and a domed relationship for δ 15 N with trawling. In the Irish Sea, intense trawling had a negative effect on benthic prey. δ 13 C and δ 15 N thus showed the inverse relationships to those observed in the Kattegat. Plaice from the Kattegat, showed a significant relationship with trawling intensity for δ 13 C, but not for δ 15 N. No relationship was found for dab. Changes of δ 13 C and δ 15 N correlated with changes in condition of species. The results show that the removal of demersal competitors and benthos by trawling can change the diets of commercial species, ultimately affecting their body condition.

  7. Stable isotopes reveal the effect of trawl fisheries on the diet of commercially exploited species

    DEFF Research Database (Denmark)

    Hinz, Hilmar; Moranta, Joan; Balestrini, Stephen

    2017-01-01

    Bottom trawling can change food availability for benthivorous demersal species by (i) changing benthic prey composition through physical seabed impacts and (ii) by removing overall benthic consumer biomass increasing the net availability of benthic prey for remaining individuals. Thus trawling ma...

  8. Thermal reactionomes reveal divergent responses to thermal extremes in warm and cool-climate ant species

    DEFF Research Database (Denmark)

    Stanton-Geddes, John; Nguyen, Andrew; Chick, Lacy

    2016-01-01

    The distributions of species and their responses to climate change are in part determined by their thermal tolerances. However, little is known about how thermal tolerance evolves. To test whether evolutionary extension of thermal limits is accomplished through enhanced cellular stress response...

  9. Updating rDNA restriction enzyme maps of Tetrahymena reveals four new intron-containing species

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Simon, E M; Engberg, J

    1985-01-01

    The extrachromosomal rDNA molecules from a number of Tetrahymena strains were characterized by restriction enzyme mapping using three different restriction enzymes combined with gel blotting and hybridization analysis. Strains from four out of six recently described species were found to contain...

  10. Reticulate evolution in the apogamous Dryopteris varia complex (Dryopteridaceae, subg. Erythrovariae, sect. Variae) and its related sexual species in Japan.

    Science.gov (United States)

    Hori, Kiyotaka; Tono, Akitaka; Fujimoto, Kazuto; Kato, Juntaro; Ebihara, Atsushi; Watano, Yasuyuki; Murakami, Noriaki

    2014-11-01

    Apogamous fern species are often difficult to distinguish from related species because of their continuous morphological variations. To clarify the genetic relationships among the members of the Dryopteris varia complex, we analyzed the nucleotide sequences of the plastid gene rbcL and the nuclear gene PgiC. We also analyzed the diploid sexual species D. caudipinna and D. chinensis, which have not been included in the complex, but were recently shown to be closely related to the complex in a molecular phylogenetic study. The PgiC sequences of the diploid sexual species, D. varia, D. saxifraga, D. sp. 'protobissetiana' (undescribed diploid sexual species), D. caudipinna, and D. chinensis, were well differentiated and hence designated A, B, C, D, and E, respectively. Thus, the PgiC constitution of apogamous species in the complex was as follows: D. bissetiana, B + C; D. kobayashii, B + C + E); D. pacifica, A + C, A + B + C, or A + C + D; D. sacrosancta, A + C + E; and D. saxifragivaria, B + C. These results suggest that these apogamous species are formed by hybridizations of species including not only the three diploid sexual species of the D. varia complex (A, B, and C) but also the two diploid sexual species D. caudipinna (D) and D. chinensis (E), which do not belong to the complex.

  11. Cross-species EST alignments reveal novel and conserved alternative splicing events in legumes

    Directory of Open Access Journals (Sweden)

    Brendel Volker

    2008-02-01

    Full Text Available Abstract Background Although originally thought to be less frequent in plants than in animals, alternative splicing (AS is now known to be widespread in plants. Here we report the characteristics of AS in legumes, one of the largest and most important plant families, based on EST alignments to the genome sequences of Medicago truncatula (Mt and Lotus japonicus (Lj. Results Based on cognate EST alignments alone, the observed frequency of alternatively spliced genes is lower in Mt (~10%, 1,107 genes and Lj (~3%, 92 genes than in Arabidopsis and rice (both around 20%. However, AS frequencies are comparable in all four species if EST levels are normalized. Intron retention is the most common form of AS in all four plant species (~50%, with slightly lower frequency in legumes compared to Arabidopsis and rice. This differs notably from vertebrates, where exon skipping is most common. To uncover additional AS events, we aligned ESTs from other legume species against the Mt genome sequence. In this way, 248 additional Mt genes were predicted to be alternatively spliced. We also identified 22 AS events completely conserved in two or more plant species. Conclusion This study extends the range of plant taxa shown to have high levels of AS, confirms the importance of intron retention in plants, and demonstrates the utility of using ESTs from related species in order to identify novel and conserved AS events. The results also indicate that the frequency of AS in plants is comparable to that observed in mammals. Finally, our results highlight the importance of normalizing EST levels when estimating the frequency of alternative splicing.

  12. Differential iridoid production as revealed by a diversity panel of 84 cultivated and wild blueberry species.

    Directory of Open Access Journals (Sweden)

    Courtney P Leisner

    Full Text Available Cultivated blueberry (Vaccinium corymbosum, Vaccinium angustifolium, Vaccinium darrowii, and Vaccinium virgatum is an economically important fruit crop native to North America and a member of the Ericaceae family. Several species in the Ericaceae family including cranberry, lignonberry, bilberry, and neotropical blueberry species have been shown to produce iridoids, a class of pharmacologically important compounds present in over 15 plant families demonstrated to have a wide range of biological activities in humans including anti-cancer, anti-bacterial, and anti-inflammatory. While the antioxidant capacity of cultivated blueberry has been well studied, surveys of iridoid production in blueberry have been restricted to fruit of a very limited number of accessions of V. corymbosum, V. angustifolium and V. virgatum; none of these analyses have detected iridoids. To provide a broader survey of iridoid biosynthesis in cultivated blueberry, we constructed a panel of 84 accessions representing a wide range of cultivated market classes, as well as wild blueberry species, and surveyed these for the presence of iridoids. We identified the iridoid glycoside monotropein in fruits and leaves of all 13 wild Vaccinium species, yet only five of the 71 cultivars. Monotropein positive cultivars all had recent introgressions from wild species, suggesting that iridoid production can be targeted through breeding efforts that incorporate wild germplasm. A series of diverse developmental tissues was also surveyed in the diversity panel, demonstrating a wide range in iridoid content across tissues. Taken together, this data provides the foundation to dissect the molecular and genetic basis of iridoid production in blueberry.

  13. The microgeographical patterns of morphological and molecular variation of a mixed ploidy population in the species complex Actinidia chinensis.

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    Yifei Liu

    Full Text Available Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%. Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.

  14. Phylogeography and DNA-based species delimitation provide insight into the taxonomy of the polymorphic rose chafer Protaetia (Potosia) cuprea species complex (Coleoptera: Scarabaeidae: Cetoniinae) in the Western Palearctic.

    Science.gov (United States)

    Vondráček, Dominik; Fuchsová, Aneta; Ahrens, Dirk; Král, David; Šípek, Petr

    2018-01-01

    The development of modern methods of species delimitation, unified under the "integrated taxonomy" approach, allows a critical examination and re-evaluation of complex taxonomic groups. The rose chafer Protaetia (Potosia) cuprea is a highly polymorphic species group with a large distribution range. Despite its overall commonness, its taxonomy is unclear and subject to conflicting hypotheses, most of which largely fail to account for its evolutionary history. Based on the sequences of two mitochondrial markers from 65 individuals collected across the species range, and a detailed analysis of morphological characters including a geometric morphometry approach, we infer the evolutionary history and phylogeography of the P. cuprea species complex. Our results demonstrate the existence of three separate lineages in the Western Palearctic region, presumably with a species status. However, these lineages are in conflict with current taxonomic concepts. None of the 29 analyzed morphological characters commonly used in the taxonomy of this group proved to be unambiguously species- or subspecies- specific. The geometric morphometry analysis reveals a large overlap in the shape of the analyzed structures (pronotum, meso-metaventral projection, elytra and aedeagus), failing to identify either the genetically detected clades or the classical species entities. Our results question the monophyly of P. cuprea in regard to P. cuprina, as well as the species status of P. metallica. On the other hand, we found support for the species status of the Sicilian P. hypocrita. Collectively, our findings provide a new and original insight into the taxonomy and phylogeny of the P. cuprea species complex. At the same time, the results represent the first attempt to elucidate the phylogeography of these polymorphic beetles.

  15. A stable gold(i)-enyne species obtained by alkyne carboauration in a complex rearrangement.

    Science.gov (United States)

    Cámara, Jéssica; Blanco, M Carmen; Laguna, Antonio; Naumov, Panče; Gimeno, M Concepción

    2017-08-15

    An unprecedented tetranuclear gold derivative with unusual gold-enyne moieties is prepared by a mild and neat rearrangement of a dinuclear gold complex with a bridging bis(diphenylphosphino)alkyne and terminal alkynyl ligands. The complex originates as a consequence of an intramolecular addition of the AuC[triple bond, length as m-dash]CTol fragment to the internal diphosphine triple bond Ph 2 PC[triple bond, length as m-dash]CPPh 2 . The crystal structure of the tetranuclear complex shows a dinuclear metallacycle with a very short AuAu bond interaction and bridging phosphino-enyne ligands. This disposition clearly stabilises the elusive vinyl gold species omnipresent as intermediates in gold-catalysed reactions.

  16. Using hand proportions to test taxonomic boundaries within the Tupaia glis species complex (Scandentia, Tupaiidae)

    Science.gov (United States)

    Sargos, Eric J.; Woodman, Neal; Reese, Aspen T.; Olson, Link E.

    2013-01-01

    Treeshrews (order Scandentia) comprise 2 families of squirrel-sized terrestrial, arboreal, and scansorial mammals distributed throughout much of tropical South and Southeast Asia. The last comprehensive taxonomic revision of treeshrews was published in 1913, and a well-supported phylogeny clarifying relationships among all currently recognized extant species within the order has only recently been published. Within the family Tupaiidae, 2 widely distributed species, the northern treeshrew, Tupaia belangeri (Wagner, 1841), and the common treeshrew, T. glis (Diard, 1820), represent a particularly vexing taxonomic complex. These 2 species are currently distinguished primarily based on their respective distributions north and south of the Isthmus of Kra on the Malay Peninsula and on their different mammae counts. This problematic species complex includes 54 published synonyms, many of which represent putative island endemics. The widespread T. glis and T. belangeri collectively comprise a monophyletic assemblage representing the sister lineage to a clade composed of the golden-bellied treeshrew, T. chrysogaster Miller, 1903 (Mentawai Islands), and the long-footed treeshrew, T. longipes (Thomas, 1893) (Borneo). As part of a morphological investigation of the T. glis–T. belangeri complex, we studied the proportions of hand bones, which have previously been shown to be useful in discriminating species of soricids (true shrews). We measured 38 variables from digital X-ray images of 148 museum study skins representing several subspecies of T. glis, T. belangeri, T. chrysogaster, and T. longipes and analyzed these data using principal components and cluster analyses. Manus proportions among these 4 species readily distinguish them, particularly in the cases of T. chrysogaster and T. longipes. We then tested the distinctiveness of several of the populations comprising T. glis and T. longipes. T. longipes longipes and T. l. salatana Lyon, 1913, are distinguishable from each

  17. Mating compatibility among four pest members of the Bactrocera dorsalis fruit fly species complex (Diptera: Tephritidae).

    Science.gov (United States)

    Schutze, M K; Jessup, A; Ul-Haq, I; Vreysen, M J B; Wornoayporn, V; Vera, M T; Clarke, A R

    2013-04-01

    Bactrocera dorsalis (Hendel), Bactrocera papayae Drew & Hancock, Bactrocera philippinensis Drew & Hancock, and Bactrocera carambolae Drew & Hancock are pest members within the B. dorsalis species complex of tropical fruit flies. The species status of these taxa is unclear and this confounds quarantine, pest management, and general research. Mating studies carried out under uniform experimental conditions are required as part of resolving their species limits. These four taxa were collected from the wild and established as laboratory cultures for which we subsequently determined levels of prezygotic compatibility, assessed by field cage mating trials for all pair-wise combinations. We demonstrate random mating among all pair-wise combinations involving B. dorsalis, B. papayae, and B. philippinensis. B. carambolae was relatively incompatible with each of these species as evidenced by nonrandom mating for all crosses. Reasons for incompatibility involving B. carambolae remain unclear; however, we observed differences in the location of couples in the field cage for some comparisons. Alongside other factors such as pheromone composition or other courtship signals, this may lead to reduced interspecific mating compatibility with B. carambolae. These data add to evidence that B. dorsalis, B. papayae, and B. philippinensis represent the same biological species, while B. carambolae remains sufficiently different to maintain its current taxonomic identity. This poses significant implications for this group's systematics, impacting on pest management, and international trade.

  18. Comparative proteomics of milk fat globule membrane in different species reveals variations in lactation and nutrition.

    Science.gov (United States)

    Lu, Jing; Wang, Xinyu; Zhang, Weiqing; Liu, Lu; Pang, Xiaoyang; Zhang, Shuwen; Lv, Jiaping

    2016-04-01

    In present study, 312, 554, 175 and 143 proteins were identified and quantified by label-free quantitative proteomics in human, cow, goat and yak milk fat globule membrane (MFGM), respectively. Fifty proteins involved in vesicle mediate transport and milk fat globule secretion were conserved among species. Moreover, proteins involved in lipid synthesis and secretion (xanthine dehydrogenase/oxidase, stomatin and CD36), showed different expression pattern and the host defense proteins exhibited various profiles within species. Notably, the content and activity of lipid catabolic enzymes were significantly higher in human MFGM, which could be indicative of the superior fat utilization in breast fed infants. Our findings unraveled the significant differences in protein composition of human milk and conventionally used substitutes of it. The in-depth study of lipid metabolic enzymes in human MFGM will probably contribute to the improvement of the fat utilization through modulation of lipid catabolic enzymes in infant formula. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Using mitochondrial and nuclear sequence data for disentangling population structure in complex pest species: a case study with Dermanyssus gallinae.

    Directory of Open Access Journals (Sweden)

    Lise Roy

    Full Text Available Among global changes induced by human activities, association of breakdown of geographical barriers and impoverishered biodiversity of agroecosystems may have a strong evolutionary impact on pest species. As a consequence of trade networks' expansion, secondary contacts between incipient species, if hybrid incompatibility is not yet reached, may result in hybrid swarms, even more when empty niches are available as usual in crop fields and farms. By providing important sources of genetic novelty for organisms to adapt in changing environments, hybridization may be strongly involved in the emergence of invasive populations. Because national and international trade networks offered multiple hybridization opportunities during the previous and current centuries, population structure of many pest species is expected to be the most intricate and its inference often blurred when using fast-evolving markers. Here we show that mito-nuclear sequence datasets may be the most helpful in disentangling successive layers of admixture in the composition of pest populations. As a model we used D. gallinae s. l., a mesostigmatid mite complex of two species primarily parasitizing birds, namely D. gallinae L1 and D. gallinae s. str. The latter is a pest species, considered invading layer farms in Brazil. The structure of the pest as represented by isolates from both wild and domestic birds, from European (with a focus on France, Australian and Brazilian farms, revealed past hybridization events and very recent contact between deeply divergent lineages. The role of wild birds in the dissemination of mites appears to be null in European and Australian farms, but not in Brazilian ones. In French farms, some recent secondary contact is obviously consecutive to trade flows. Scenarios of populations' history were established, showing five different combinations of more or less dramatic bottlenecks and founder events, nearly interspecific hybridizations and recent

  20. More of the same: a diminutive new species of the Limnonectes kuhlii complex from northern Vietnam (Anura: Dicroglossidae).

    Science.gov (United States)

    Mcleod, David S; Kurlbaum, Scuyler; Hoang, Ngoc Van

    2015-04-15

    A new species in the dicroglossid genus Limnonectes known only from Ha Giang province, Vietnam is described. Analysis of DNA sequence data from the mitochondrial 12S and 16S gene regions places the species within the Limnonectes kuhlii Complex and demonstrates it to be the sister taxon to an Indochinese clade containing L. isanensis, L. jarujini, L. megastomias, and L. taylori. The new species occurs in syntopy with L. bannaensis. Both molecular and morphological data support the recognition of this lineage as a new species. Notably, the relatively diminutive size of this species distinguishes Limnonectes nguyenorum sp. nov. from all other members of the L. kuhlii Complex.

  1. Two new species in the Matelea stenopetala complex (Apocynaceae, Asclepiadoideae) from the Guiana Shield and Amazonian Brazil

    Science.gov (United States)

    Krings, Alexander; Morillo, Gilberto

    2012-01-01

    Abstract Two new species in the Matelea stenopetala complex (Apocynaceae, Asclepiadoideae) are described from the Guiana Shield and Amazonian Brazil: Matelea brevistipitata Krings & Morillo, sp. nov. and Matelea trichopedicellataKrings & Morillo, sp. nov. The new species belong to a small group of adaxially-pubescent-flowered taxa within the complex, including Matelea hildegardiana and Matelea pakaraimensis. The new species are described and a dichotomous key is provided. PMID:23233816

  2. Multi locus sequence typing of Chlamydia reveals an association between Chlamydia psittaci genotypes and host species.

    Science.gov (United States)

    Pannekoek, Yvonne; Dickx, Veerle; Beeckman, Delphine S A; Jolley, Keith A; Keijzers, Wendy C; Vretou, Evangelia; Maiden, Martin C J; Vanrompay, Daisy; van der Ende, Arie

    2010-12-02

    Chlamydia comprises a group of obligate intracellular bacterial parasites responsible for a variety of diseases in humans and animals, including several zoonoses. Chlamydia trachomatis causes diseases such as trachoma, urogenital infection and lymphogranuloma venereum with severe morbidity. Chlamydia pneumoniae is a common cause of community-acquired respiratory tract infections. Chlamydia psittaci, causing zoonotic pneumonia in humans, is usually hosted by birds, while Chlamydia abortus, causing abortion and fetal death in mammals, including humans, is mainly hosted by goats and sheep. We used multi-locus sequence typing to asses the population structure of Chlamydia. In total, 132 Chlamydia isolates were analyzed, including 60 C. trachomatis, 18 C. pneumoniae, 16 C. abortus, 34 C. psittaci and one of each of C. pecorum, C. caviae, C. muridarum and C. felis. Cluster analyses utilizing the Neighbour-Joining algorithm with the maximum composite likelihood model of concatenated sequences of 7 housekeeping fragments showed that C. psittaci 84/2334 isolated from a parrot grouped together with the C. abortus isolates from goats and sheep. Cluster analyses of the individual alleles showed that in all instances C. psittaci 84/2334 formed one group with C. abortus. Moving 84/2334 from the C. psittaci group to the C. abortus group resulted in a significant increase in the number of fixed differences and elimination of the number of shared mutations between C. psittaci and C. abortus. C. psittaci M56 from a muskrat branched separately from the main group of C. psittaci isolates. C. psittaci genotypes appeared to be associated with host species. The phylogenetic tree of C. psittaci did not follow that of its host bird species, suggesting host species jumps. In conclusion, we report for the first time an association between C. psittaci genotypes with host species.

  3. Reconstructing past species assemblages reveals the changing patterns and drivers of extinction through time

    OpenAIRE

    Bromham, Lindell; Lanfear, Robert; Cassey, Phillip; Gibb, Gillian; Cardillo, Marcel

    2012-01-01

    Predicting future species extinctions from patterns of past extinctions or current threat status relies on the assumption that the taxonomic and biological selectivity of extinction is consistent through time. If the driving forces of extinction change through time, this assumption may be unrealistic. Testing the consistency of extinction patterns between the past and the present has been difficult, because the phylogenetically explicit methods used to model present-day extinction risk typica...

  4. Multi locus sequence typing of Chlamydia reveals an association between Chlamydia psittaci genotypes and host species.

    Directory of Open Access Journals (Sweden)

    Yvonne Pannekoek

    2010-12-01

    Full Text Available Chlamydia comprises a group of obligate intracellular bacterial parasites responsible for a variety of diseases in humans and animals, including several zoonoses. Chlamydia trachomatis causes diseases such as trachoma, urogenital infection and lymphogranuloma venereum with severe morbidity. Chlamydia pneumoniae is a common cause of community-acquired respiratory tract infections. Chlamydia psittaci, causing zoonotic pneumonia in humans, is usually hosted by birds, while Chlamydia abortus, causing abortion and fetal death in mammals, including humans, is mainly hosted by goats and sheep. We used multi-locus sequence typing to asses the population structure of Chlamydia. In total, 132 Chlamydia isolates were analyzed, including 60 C. trachomatis, 18 C. pneumoniae, 16 C. abortus, 34 C. psittaci and one of each of C. pecorum, C. caviae, C. muridarum and C. felis. Cluster analyses utilizing the Neighbour-Joining algorithm with the maximum composite likelihood model of concatenated sequences of 7 housekeeping fragments showed that C. psittaci 84/2334 isolated from a parrot grouped together with the C. abortus isolates from goats and sheep. Cluster analyses of the individual alleles showed that in all instances C. psittaci 84/2334 formed one group with C. abortus. Moving 84/2334 from the C. psittaci group to the C. abortus group resulted in a significant increase in the number of fixed differences and elimination of the number of shared mutations between C. psittaci and C. abortus. C. psittaci M56 from a muskrat branched separately from the main group of C. psittaci isolates. C. psittaci genotypes appeared to be associated with host species. The phylogenetic tree of C. psittaci did not follow that of its host bird species, suggesting host species jumps. In conclusion, we report for the first time an association between C. psittaci genotypes with host species.

  5. Differential reproductive responses to stress reveal the role of life-history strategies within a species.

    Science.gov (United States)

    Schultner, J; Kitaysky, A S; Gabrielsen, G W; Hatch, S A; Bech, C

    2013-11-22

    Life-history strategies describe that 'slow'- in contrast to 'fast'-living species allocate resources cautiously towards reproduction to enhance survival. Recent evidence suggests that variation in strategies exists not only among species but also among populations of the same species. Here, we examined the effect of experimentally induced stress on resource allocation of breeding seabirds in two populations with contrasting life-history strategies: slow-living Pacific and fast-living Atlantic black-legged kittiwakes. We tested the hypothesis that reproductive responses in kittiwakes under stress reflect their life-history strategies. We predicted that in response to stress, Pacific kittiwakes reduce investment in reproduction compared with Atlantic kittiwakes. We exposed chick-rearing kittiwakes to a short-term (3-day) period of increased exogenous corticosterone (CORT), a hormone that is released during food shortages. We examined changes in baseline CORT levels, parental care and effects on offspring. We found that kittiwakes from the two populations invested differently in offspring when facing stress. In response to elevated CORT, Pacific kittiwakes reduced nest attendance and deserted offspring more readily than Atlantic kittiwakes. We observed lower chick growth, a higher stress response in offspring and lower reproductive success in response to CORT implantation in Pacific kittiwakes, whereas the opposite occurred in the Atlantic. Our findings support the hypothesis that life-history strategies predict short-term responses of individuals to stress within a species. We conclude that behaviour and physiology under stress are consistent with trade-off priorities as predicted by life-history theory. We encourage future studies to consider the pivotal role of life-history strategies when interpreting inter-population differences of animal responses to stressful environmental events.

  6. Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance

    Directory of Open Access Journals (Sweden)

    Elliott Ferris

    2018-03-01

    Full Text Available The identity of most functional elements in the mammalian genome and the phenotypes they impact are unclear. Here, we perform a genome-wide comparative analysis of patterns of accelerated evolution in species with highly distinctive traits to discover candidate functional elements for clinically important phenotypes. We identify accelerated regions (ARs in the elephant, hibernating bat, orca, dolphin, naked mole rat, and thirteen-lined ground squirrel lineages in mammalian conserved regions, uncovering ∼33,000 elements that bind hundreds of different regulatory proteins in humans and mice. ARs in the elephant, the largest land mammal, are uniquely enriched near elephant DNA damage response genes. The genomic hotspot for elephant ARs is the E3 ligase subunit of the Fanconi anemia complex, a master regulator of DNA repair. Additionally, ARs in the six species are associated with specific human clinical phenotypes that have apparent concordance with overt traits in each species.

  7. Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences

    OpenAIRE

    Bunawan, Hamidun; Yen, Choong Chee; Yaakop, Salmah; Noor, Normah Mohd

    2017-01-01

    Background The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus. Results Phylogeny reconstruction was carried out using neighbor-joining, maximum parsimony and Bayesian analyses. All the trees revealed two major clusters, a lowland group consi...

  8. Indoor simulations reveal differences among plant species in capturing particulate matter

    Science.gov (United States)

    Chen, Jungang; Yu, Xinxiao; Bi, Huaxing; Fu, Yanlin

    2017-01-01

    A number of studies have focused on the capacity of urban trees and shrubs to serve as efficient biological filters to mitigate air pollution. In this study, five different tree species were assessed for this function. Kerria japonica, Sophora japonica, Philadelphus pekinensis, Gleditsia sinensis, and Prunus persica 'Atropurpurea' were tested in a deposition chamber using (NH4)2SO4 particles. We quantified and compared the capability of all tested trees to remove particles by assessing deposition velocity, a measure of the ability to remove particles. When placed in the deposition chamber, S. japonica had the greatest deposition velocity, followed by Philadelphus pekinensis, G. sinensis, Prunus persica 'Atropurpurea,' and K. japonica, in descending order. In addition, the comparison of deposition velocities among these species suggested that certain leaf geometries and surface characteristics of broadleaf trees, such as trichomes and grooves, increased particle capture. However, these results change under a different simulation condition using ambient air, suggesting that some trees actually increase pollutant number concentrations more than reduce particle concentration. This outcome can be explained by the aerodynamic effect of trees exceeding the filtering capacity of vegetation under some conditions. This highlights the difficulty of generalizing species selection criteria for practice use. Accordingly, our results indicate that using vegetation to reduce particle pollution and improve the air quality is not a universally advisable and viable solution. PMID:28520744

  9. Reconstructing past species assemblages reveals the changing patterns and drivers of extinction through time.

    Science.gov (United States)

    Bromham, Lindell; Lanfear, Robert; Cassey, Phillip; Gibb, Gillian; Cardillo, Marcel

    2012-10-07

    Predicting future species extinctions from patterns of past extinctions or current threat status relies on the assumption that the taxonomic and biological selectivity of extinction is consistent through time. If the driving forces of extinction change through time, this assumption may be unrealistic. Testing the consistency of extinction patterns between the past and the present has been difficult, because the phylogenetically explicit methods used to model present-day extinction risk typically cannot be applied to the data from the fossil record. However, the detailed historical and fossil records of the New Zealand avifauna provide a unique opportunity to reconstruct a complete, large faunal assemblage for different periods in the past. Using the first complete phylogeny of all known native New Zealand bird species, both extant and extinct, we show how the taxonomic and phylogenetic selectivity of extinction, and biological correlates of extinction, change from the pre-human period through Polynesian and European occupation, to the present. These changes can be explained both by changes in primary threatening processes, and by the operation of extinction filter effects. The variable patterns of extinction through time may confound attempts to identify risk factors that apply across time periods, and to infer future species declines from past extinction patterns and current threat status.

  10. Evolutionary history of Coleoptera revealed by extensive sampling of genes and species.

    Science.gov (United States)

    Zhang, Shao-Qian; Che, Li-Heng; Li, Yun; Dan Liang; Pang, Hong; Ślipiński, Adam; Zhang, Peng

    2018-01-15

    Beetles (Coleoptera) are the most diverse and species-rich group of insects, and a robust, time-calibrated phylogeny is fundamental to understanding macroevolutionary processes that underlie their diversity. Here we infer the phylogeny and divergence times of all major lineages of Coleoptera by analyzing 95 protein-coding genes in 373 beetle species, including ~67% of the currently recognized families. The subordinal relationships are strongly supported as Polyphaga (Adephaga (Archostemata, Myxophaga)). The series and superfamilies of Polyphaga are mostly monophyletic. The species-poor Nosodendridae is robustly recovered in a novel position sister to Staphyliniformia, Bostrichiformia, and Cucujiformia. Our divergence time analyses suggest that the crown group of extant beetles occurred ~297 million years ago (Mya) and that ~64% of families originated in the Cretaceous. Most of the herbivorous families experienced a significant increase in diversification rate during the Cretaceous, thus suggesting that the rise of angiosperms in the Cretaceous may have been an 'evolutionary impetus' driving the hyperdiversity of herbivorous beetles.

  11. A new species of Meligethes Stephens from China and additional data on members of the M. chinensis species-complex (Coleoptera: Nitidulidae, Meligethinae

    Directory of Open Access Journals (Sweden)

    Meike Liu

    2017-06-01

    Full Text Available Meligethes (Odontogethes inexpectatus sp. n. is described from China, Sichuan Province. The new species is based on a female specimen previously incorrectly referred to as Meligethes scrobescens Chen, Lin, Huang & Yang, 2015, which was recently described from a series of male specimens collected in the same area. Both species belong to the taxonomically difficult species-group related to M. chinensis Kirejtshuk, 1979, including a dozen closely related species distributed throughout Nepal and SW and Central China. The true female of Meligethes scrobescens is also described, based on recently collected material from China (Hubei and Chongqing, including a series of male and female specimens. Diagnostic characters distinguishing the new species from all other known members of the M. chinensis species-group and species-complex are discussed, and their overall range distribution are depicted. Additional data on geographic distribution and larval ecology of some of the closely related species are also reported.

  12. Demographic modelling with whole-genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization.

    Science.gov (United States)

    Meier, Joana I; Sousa, Vitor C; Marques, David A; Selz, Oliver M; Wagner, Catherine E; Excoffier, Laurent; Seehausen, Ole

    2017-01-01

    Modes and mechanisms of speciation are best studied in young species pairs. In older taxa, it is increasingly difficult to distinguish what happened during speciation from what happened after speciation. Lake Victoria cichlids in the genus Pundamilia encompass a complex of young species and polymorphic populations. One Pundamilia species pair, P. pundamilia and P. nyererei, is particularly well suited to study speciation because sympatric population pairs occur with different levels of phenotypic differentiation and reproductive isolation at different rocky islands within the lake. Genetic distances between allopatric island populations of the same nominal species often exceed those between the sympatric species. It thus remained unresolved whether speciation into P. nyererei and P. pundamilia occurred once, followed by geographical range expansion and interspecific gene flow in local sympatry, or if the species pair arose repeatedly by parallel speciation. Here, we use genomic data and demographic modelling to test these alternative evolutionary scenarios. We demonstrate that gene flow plays a strong role in shaping the observed patterns of genetic similarity, including both gene flow between sympatric species and gene flow between allopatric populations, as well as recent and early gene flow. The best supported model for the origin of P. pundamilia and P. nyererei population pairs at two different islands is one where speciation happened twice, whereby the second speciation event follows shortly after introgression from an allopatric P. nyererei population that arose earlier. Our findings support the hypothesis that very similar species may arise repeatedly, potentially facilitated by introgressed genetic variation. © 2016 John Wiley & Sons Ltd.

  13. DNA barcoding of Sri Lankan phlebotomine sand flies using cytochrome c oxidase subunit I reveals the presence of cryptic species.

    Science.gov (United States)

    Gajapathy, Kanapathy; Tharmasegaram, Tharmatha; Eswaramohan, Thampoe; Peries, Lalanthika B S L; Jayanetti, Raveendra; Surendran, Sinnathamby N

    2016-09-01

    Sri Lanka is known for high diversity of phlebotomine sand flies and prevalence of cutaneous and visceral leishmaniasis; a disease vectored by sand flies. The taxonomy of phlebotomine sand flies is complicated and often the diversity is over/underrated. The current study aims to use the cytochrome c oxidase gene subunit 1 (COI) sequence and formulate a barcode for the sand fly species in Sri Lanka. A total of 70 samples comprising seven species morphologically identified and collected from dry zone districts of Hambantota, Anuradhapura, Vavuniya, Trincomalee and Jaffna were processed. Neighbour-joining (NJ) tree created using the sequences revealed the species identity is compatible with the current morphology based identification. Further the analysis delineated morphologically identified Se. bailyi, Se babu babu and Se babu insularis into genetically distinct groups. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Comprehensive genetic analysis of OEIS complex reveals no evidence for a recurrent microdeletion or duplication

    NARCIS (Netherlands)

    Vlangos, C.N.; Siuniak, A.; Ackley, T.; Bokhoven, H. van; Veltman, J.A.; Iyer, R.; Park, J.M.; Keppler-Noreuil, K.; Keegan, C.E.

    2011-01-01

    Omphalocele-exstrophy of the bladder-imperforate anus-spinal defects (OEIS) complex, or cloacal exstrophy (EC), is a rare constellation of malformations in humans involving the urogenital, gastrointestinal, and skeletal systems, and less commonly the central nervous system. Although OEIS complex is

  15. Wolves, dogs, rearing and reinforcement: complex interactions underlying species differences in training and problem-solving performance.

    Science.gov (United States)

    Frank, Harry

    2011-11-01

    Frank and Frank et al. (1982-1987) administered a series of age-graded training and problem-solving tasks to samples of Eastern timber wolf (C. lupus lycaon) and Alaskan Malamute (C. familiaris) pups to test Frank's (Zeitschrift für Tierpsychologie 53:389-399, 1980) model of the evolution of information processing under conditions of natural and artificial selection. Results confirmed the model's prediction that wolves should perform better than dogs on problem-solving tasks and that dogs should perform better than wolves on training tasks. Further data collected at the University of Connecticut in 1983 revealed a more complex and refined picture, indicating that species differences can be mediated by a number of factors influencing wolf performance, including socialization regimen (hand-rearing vs. mother-rearing), interactive effects of socialization on the efficacy of both rewards and punishments, and the flexibility to select learning strategies that experimenters might not anticipate.

  16. Diversity and Distribution of Cryptic Species of the Bemisia tabaci (Hemiptera: Aleyrodidae) complex in Pakistan.

    Science.gov (United States)

    Masood, Mariyam; Amin, Imran; Hassan, Ishtiaq; Mansoor, Shahid; Brown, Judith K; Briddon, Rob W

    2017-12-05

    Bemisia tabaci (Gennadius; Hempitera: Aleyrodidae) is considered to be a cryptic (sibling) species complex, the members of which exhibit morphological invariability while being genetically and behaviorally distinct. Members of the complex are agricultural pests that cause direct damage by feeding on plants, and indirectly by transmitting viruses that cause diseases leading to reduced crop yield and quality. In Pakistan, cotton leaf curl disease, caused by multiple begomovirus species, is the most economically important viral disease of cotton. In the study outlined here, the diversity and geographic distribution of B. tabaci cryptic species was investigated by analyzing a taxonomically informative fragment of the mitochondrial cytochrome c oxidase 1 gene (mtCOI-3'). The mtCOI-3' sequence was determined for 285 adult whiteflies and found to represent six cryptic species, the most numerous being Asia II-1 and Middle East Asia Minor 1 (MEAM-1), the later also referred to as the B-biotype, which was previously thought to be confined to Sindh province but herein, was also found to be present in the Punjab province. The endemic Asia I was restricted to Sindh province, while an individual in the Asia II-8 was identified in Pakistan for the first time. Also for the first time, samples were collected from northwestern Pakistan and Asia II-1 was identified. Results indicate that in Pakistan the overall diversity of B. tabaci cryptic species is high and, based on comparisons with findings from previous studies, the distribution is dynamic. © The Author(s) 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  17. Multiple evolutionary processes drive the patterns of genetic differentiation in a forest tree species complex

    Science.gov (United States)

    Jones, Rebecca C; Steane, Dorothy A; Lavery, Martyn; Vaillancourt, René E; Potts, Brad M

    2013-01-01

    Forest trees frequently form species complexes, complicating taxonomic classification and gene pool management. This is certainly the case in Eucalyptus, and well exemplified by the Eucalyptus globulus complex. This ecologically and economically significant complex comprises four taxa (sspp. bicostata, globulus, maidenii, pseudoglobulus) that are geographically and morphologically distinct, but linked by extensive “intergrade” populations. To resolve their genetic affinities, nine microsatellites were used to genotype 1200 trees from throughout the natural range of the complex in Australia, representing 33 morphological core and intergrade populations. There was significant spatial genetic structure (FST = 0.10), but variation was continuous. High genetic diversity in southern ssp. maidenii indicates that this region is the center of origin. Genetic diversity decreases and population differentiation increases with distance from this area, suggesting that drift is a major evolutionary process. Many of the intergrade populations, along with other populations morphologically classified as ssp. pseudoglobulus or ssp. globulus, belong to a “cryptic genetic entity” that is genetically and geographically intermediate between core ssp. bicostata, ssp. maidenii, and ssp. globulus. Geography, rather than morphology, therefore, is the best predictor of overall genetic affinities within the complex and should be used to classify germplasm into management units for conservation and breeding purposes. PMID:23403692

  18. Species delimitation of the Hyphydrus ovatus complex in western Palaearctic with an update of species distributions (Coleoptera, Dytiscidae

    Directory of Open Access Journals (Sweden)

    Johannes Bergsten

    2017-06-01

    Full Text Available The species status of Hyphydrus anatolicus Guignot, 1957 and H. sanctus Sharp, 1882, previously often confused with the widespread H. ovatus (Linnaeus, 1760, are tested with molecular and morphological characters. Cytochrome c oxidase subunit 1 (CO1 was sequenced for 32 specimens of all three species. Gene-trees were inferred with parsimony, time-free bayesian and strict clock bayesian analyses. The GMYC model was used to estimate species limits. All three species were reciprocally monophyletic with CO1 and highly supported. The GMYC species delimitation analysis unequivocally delimited the three species with no other than the three species solution included in the confidence interval. A likelihood ratio test rejected the one-species null model. Important morphological characters distinguishing the species are provided and illustrated. New distributional data are given for the following species: Hyphydrus anatolicus from Slovakia and Ukraine, and H. aubei Ganglbauer, 1891, and H. sanctus from Turkey.

  19. Acinetobacter calcoaceticus-Acinetobacter baumannii complex species in clinical specimens in Singapore.

    Science.gov (United States)

    Koh, T H; Tan, T T; Khoo, C T; Ng, S Y; Tan, T Y; Hsu, L-Y; Ooi, E E; Van Der Reijden, T J K; Dijkshoorn, L

    2012-03-01

    This study was performed to determine the prevalence, distribution of specimen sources, and antimicrobial susceptibility of the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) species complex in Singapore. One hundred and ninety-three non-replicate Acb species complex clinical isolates were collected from six hospitals over a 1-month period in 2006. Of these, 152 (78·7%) were identified as A. baumannii, 18 (9·3%) as 'Acinetobacter pittii' [genomic species (gen. sp.) 3], and 23 (11·9%) as 'Acinetobacter nosocomialis' (gen. sp. 13TU). Carbapenem resistance was highest in A. baumannii (72·4%), followed by A. pittii (38·9%), and A. nosocomialis (34·8%). Most carbapenem-resistant A. baumannii and A. nosocomialis possessed the bla(OXA-23-like) gene whereas carbapenem-resistant A. pittii possessed the bla(OXA-58-like) gene. Two imipenem-resistant strains (A. baumannii and A. pittii) had the bla(IMP-like) gene. Representatives of carbapenem-resistant A. baumannii were related to European clones I and II.

  20. Oligonucleotide array-based identification of species in the Acinetobacter calcoaceticus-A. baumannii complex in isolates from blood cultures and antimicrobial susceptibility testing of the isolates.

    Science.gov (United States)

    Ko, Wen-Chien; Lee, Nan-Yao; Su, Siou Cing; Dijkshoorn, Lenie; Vaneechoutte, Mario; Wang, Li-Rong; Yan, Jin-Jou; Chang, Tsung Chain

    2008-06-01

    Acinetobacter calcoaceticus, A. baumannii, Acinetobacter genomic species (gen. sp.) 3, and Acinetobacter gen. sp. 13TU, which are included in the A. calcoaceticus-A. baumannii complex, are difficult to distinguish by phenotypic methods. An array with six oligonucleotide probes based on the 16S-23S rRNA gene intergenic spacer (ITS) region was developed to differentiate species in the A. calcoaceticus-A. baumannii complex. Validation of the array with a reference collection of 52 strains of the A. calcoaceticus-A. baumannii complex and 137 strains of other species resulted in an identification sensitivity and specificity of 100%. By using the array, the species distribution of 291 isolates of the A. calcoaceticus-A. baumannii complex from patients with bacteremia were determined to be A. baumannii (221 strains [75.9%]), Acinetobacter gen. sp. 3 (67 strains [23.0%]), Acinetobacter gen. sp. 13TU (2 strains [0.7%]), and unidentified Acinetobacter sp. (1 strain [0.3%]). The identification accuracy of the array for 12 randomly selected isolates from patients with bacteremia was further confirmed by sequence analyses of the ITS region and the 16S rRNA gene. Antimicrobial susceptibility testing of the 291 isolates from patients with bacteremia revealed that A. baumannii strains were less susceptible to antimicrobial agents than Acinetobacter gen. sp. 3. All Acinetobacter gen. sp. 3 strains were susceptible to ampicillin-sulbactam, imipenem, and meropenem; but only 67.4%, 90%, and 86% of the A. baumannii strains were susceptible to ampicillin-sulbactam, imipenem, and meropenem, respectively. The observed significant variations in antimicrobial susceptibility among different species in the A. calcoaceticus-A. baumannii complex emphasize that the differentiation of species within the complex is relevant from a clinical-epidemiological point of view.

  1. Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

    Directory of Open Access Journals (Sweden)

    Xiaorui Chen

    2017-10-01

    Full Text Available Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.

  2. Casting light on xylem vulnerability in an herbaceous species reveals a lack of segmentation.

    Science.gov (United States)

    Skelton, Robert P; Brodribb, Timothy J; Choat, Brendan

    2017-04-01

    Finding thresholds at which loss of plant functionality occurs during drought is critical for predicting future crop productivity and survival. Xylem resistance to embolism has been suggested as a key trait associated with water-stress tolerance. Although a substantial literature exists describing the vulnerability of woody stems to embolism, leaves and roots of herbaceous species remain under-represented. Also, little is known about vulnerability to embolism at a whole-plant scale or propagation of embolism within plants. New techniques to view the process of embolism formation provide opportunities to resolve long-standing questions. Here, we used multiple visual techniques, including X-ray micro-computed tomography and the optical vulnerability method, to investigate the spread of embolism within intact stems, leaves and roots of Solanum lycopersicum (common tomato). We found that roots, stems and leaves of tomato plants all exhibited similar vulnerability to embolism, suggesting that embolism rapidly propagates among tissues. Although we found scarce evidence for differentiation of xylem vulnerability among tissues at the scale of the whole plant, within a leaf the midrib embolized at higher water potentials than lower order veins. Substantial overlap between the onset of cavitation and incipient leaf damage suggests that cavitation represents a substantial damage to plants, but the point of lethal cavitation in this herbaceous species remains uncertain. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  3. Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.

    Science.gov (United States)

    Nielsen, Jens Christian; Grijseels, Sietske; Prigent, Sylvain; Ji, Boyang; Dainat, Jacques; Nielsen, Kristian Fog; Frisvad, Jens Christian; Workman, Mhairi; Nielsen, Jens

    2017-04-03

    Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we sequenced the genomes of 9 Penicillium species and, together with 15 published genomes, we investigated the secondary metabolism of Penicillium and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of 1,317 putative biosynthetic gene clusters (BGCs) were identified, and polyketide synthase and non-ribosomal peptide synthetase based BGCs were grouped into gene cluster families and mapped to known pathways. The grouping of BGCs allowed us to study the evolutionary trajectory of pathways based on 6-methylsalicylic acid (6-MSA) synthases. Finally, we cross-referenced the predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic diversity of Penicillia and highlights the potential of these species as a source of new antibiotics and other pharmaceuticals.

  4. Cross-species chromosome painting in bats from Madagascar: the contribution of Myzopodidae to revealing ancestral syntenies in Chiroptera.

    Science.gov (United States)

    Richards, Leigh R; Rambau, Ramugondo V; Lamb, Jennifer M; Taylor, Peter J; Yang, Fengtang; Schoeman, M Corrie; Goodman, Steven M

    2010-09-01

    The chiropteran fauna of Madagascar comprises eight of the 19 recognized families of bats, including the endemic Myzopodidae. While recent systematic studies of Malagasy bats have contributed to our understanding of the morphological and genetic diversity of the island's fauna, little is known about their cytosystematics. Here we investigate karyotypic relationships among four species, representing four families of Chiroptera endemic to the Malagasy region using cross-species chromosome painting with painting probes of Myotis myotis: Myzopodidae (Myzopoda aurita, 2n = 26), Molossidae (Mormopterus jugularis, 2n = 48), Miniopteridae (Miniopterus griveaudi, 2n = 46), and Vespertilionidae (Myotis goudoti, 2n = 44). This study represents the first time a member of the family Myzopodidae has been investigated using chromosome painting. Painting probes of M. myotis were used to delimit 29, 24, 23, and 22 homologous chromosomal segments in the genomes of M. aurita, M. jugularis, M. griveaudi, and M. goudoti, respectively. Comparison of GTG-banded homologous chromosomes/chromosomal segments among the four species revealed the genome of M. aurita has been structured through 14 fusions of chromosomes and chromosomal segments of M. myotis chromosomes leading to a karyotype consisting solely of bi-armed chromosomes. In addition, chromosome painting revealed a novel X-autosome translocation in M. aurita. Comparison of our results with published chromosome maps provided further evidence for karyotypic conservatism within the genera Mormopterus, Miniopterus, and Myotis. Mapping of chromosomal rearrangements onto a molecular consensus phylogeny revealed ancestral syntenies shared between Myzopoda and other bat species of the infraorders Pteropodiformes and Vespertilioniformes. Our study provides further evidence for the involvement of Robertsonian (Rb) translocations and fusions/fissions in chromosomal evolution within Chiroptera.

  5. Biology, ecology and control of the Penthaleus species complex (Acari: Penthaleidae).

    Science.gov (United States)

    Umina, Paul A; Hoffmann, Ary A; Weeks, Andrew R

    2004-01-01

    Blue oat mites, Penthaleus spp. (Acari: Penthaleidae), are major agricultural pests in southern Australia and other parts of the world, attacking various pasture, vegetable and crop plants. Management of these mites has been complicated by the recent discovery of three cryptic pest species of Penthaleus, whereas prior research had assumed a single species. The taxonomy, population genetics, ecology, biology and control of the Penthaleus spp. complex are reviewed. Adult Penthaleus have a dark blue-black body approximately 1 mm in length, and eight red-orange legs. Within Australia, they are winter pests completing two or three generations a season, depending on conditions. The summer is passed as diapausing eggs, when long-distance dispersal is thought to occur. The Penthaleus spp. reproduce by thelytokous parthenogenesis, with populations comprising clones that differ ecologically. The three pest Penthaleus spp. differ markedly in their distributions, plant hosts, timing of diapause egg production and response to pesticides, highlighting the need to develop control strategies that consider each species separately. Chemicals are the main weapons used in current control programs, however research continues into alternative more sustainable management options. Host plant resistance, crop rotations, conservation of natural enemies, and improved timing of pesticide application would improve the management of these pests. The most cost-effective and environmentally acceptable means of control will result from the integration of these practices combined with the development of a simple field-based kit to distinguish the different mite species.

  6. Integrative taxonomy and phylogeny-based species delimitation of Philippine water monitor lizards (Varanus salvator Complex) with descriptions of two new cryptic species.

    Science.gov (United States)

    Welton, Luke J; Travers, Scott L; Siler, Cameron D; Brown, Rafe M

    2014-11-05

    We describe two new species of morphologically cryptic monitor lizards (genus Varanus) from the Philippine Archipelago:  Varanus dalubhasa sp. nov. and V. bangonorum sp. nov. These two distinct evolutionary lineages are members of the V. salvator species complex, and historically have been considered conspecific with the widespread, northern Philippine V. marmoratus. However, the new species each share closer phylogenetic affinities with V. nuchalis (and potentially V. palawanensis), than either does to one another or to V. marmoratus. Divergent from other recognized species within the V. salvator Complex of water monitors by as much as 3.5% pairwise genetic distance, these lineages are also distinguished by unique gular coloration, metrics of body size and scalation, their non-monophyly with "true" V. marmoratus, and insular allopatric distributions, suggesting biogeographically distinct and unique evolutionary histories. We compare the new species with the most geographically proximate and phenotypically relevant lineages.  Although we show that these new taxa are nearly indistinguishable morphologically from V. marmoratus, both species can be readily distinguished from their closest relatives (each's respective sister taxon, V. palawanensis and V. nuchalis) by traditional morphological characters.  Our findings underscore the high herpetological diversity and biogeographical complexity of vertebrates in the Philippines, and further emphasize the need for detailed study of species-level diversity, mechanisms of reproductive isolation, gene flow, and biologically relevant boundaries between taxa within the V. salvator Complex.

  7. Antifungal susceptibilities and identification of species of the Sporothrix schenckii complex isolated in Brazil.

    Science.gov (United States)

    Ottonelli Stopiglia, Cheila Denise; Magagnin, Cibele Massotti; Castrillón, Mauricio Ramírez; Mendes, Sandra Denise Camargo; Heidrich, Daiane; Valente, Patricia; Scroferneker, Maria Lúcia

    2014-01-01

    Sporotrichosis is a subacute or chronic mycosis caused worldwide by the dimorphic species complex, Sporothrix schenckii. We studied 85 isolates recovered in Brazil to verify their identification and evaluate their in vitro antifungal susceptibility patterns. Based on phenotypic tests (microscopic features, ability to grow at 30°C and 37°C, colony diameters, as well as assimilation of sucrose and raffinose) and molecular assays (amplification of a fragment of the calmodulin gene), the strains were identified as S. schenckii, S. brasiliensis and S. globosa, with a predominance of S. schenckii isolates. There was 37.7% disagreement between the phenotypic and genotypic identification methodologies. In general, terbinafine was the most active drug, followed by ketoconazole and itraconazole, and the less active fluconazole and voriconazole. Five isolates (one S. globosa and four S. schenckii) were found to be itraconazole-resistant strains but, in general, there were no differences in the in vitro antifungal susceptibility profiles among the Sporothrix species.

  8. Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species

    DEFF Research Database (Denmark)

    Nielsen, Jens Christian; Grijseels, Sietske; Prigent, Sylvain

    2017-01-01

    -referenced the predicted pathways with published data on the production of secondary metabolites and experimentally validated the production of antibiotic yanuthones in Penicillia and identified a previously undescribed compound from the yanuthone pathway. This study is the first genus-wide analysis of the genomic......Filamentous fungi produce a wide range of bioactive compounds with important pharmaceutical applications, such as antibiotic penicillins and cholesterol-lowering statins. However, less attention has been paid to fungal secondary metabolites compared to those from bacteria. In this study, we...... sequenced the genomes of 9 Penicillium species and, together with 15 published genomes, we investigated the secondary metabolism of Penicillium and identified an immense, unexploited potential for producing secondary metabolites by this genus. A total of 1,317 putative biosynthetic gene clusters (BGCs) were...

  9. Bacterial Profiling Reveals Novel "Ca. Neoehrlichia", Ehrlichia, and Anaplasma Species in Australian Human-Biting Ticks.

    Directory of Open Access Journals (Sweden)

    Alexander W Gofton

    Full Text Available In Australia, a conclusive aetiology of Lyme disease-like illness in human patients remains elusive, despite growing numbers of people presenting with symptoms attributed to tick bites. In the present study, we surveyed the microbial communities harboured by human-biting ticks from across Australia to identify bacteria that may contribute to this syndrome. Universal PCR primers were used to amplify the V1-2 hyper-variable region of bacterial 16S rRNA genes in DNA samples from individual Ixodes holocyclus (n = 279, Amblyomma triguttatum (n = 167, Haemaphysalis bancrofti (n = 7, and H. longicornis (n = 7 ticks. The 16S amplicons were sequenced on the Illumina MiSeq platform and analysed in USEARCH, QIIME, and BLAST to assign genus and species-level taxonomies. Nested PCR and Sanger sequencing were used to confirm the NGS data and further analyse novel findings. All 460 ticks were negative for Borrelia spp. by both NGS and nested PCR analysis. Two novel "Candidatus Neoehrlichia" spp. were identified in 12.9% of I. holocyclus ticks. A novel Anaplasma sp. was identified in 1.8% of A. triguttatum ticks, and a novel Ehrlichia sp. was identified in both A. triguttatum (1.2% ticks and a single I. holocyclus (0.6% tick. Further phylogenetic analysis of novel "Ca. Neoehrlichia", Anaplasma and Ehrlichia based on 1,265 bp 16S rRNA gene sequences suggests that these are new species. Determining whether these newly discovered organisms cause disease in humans and animals, like closely related bacteria do abroad, is of public health importance and requires further investigation.

  10. Screening of complex fucoidans from four brown algae species as procoagulant agents.

    Science.gov (United States)

    Zhang, Zhenqing; Till, Susanne; Knappe, Sabine; Quinn, Catherine; Catarello, James; Ray, G Joseph; Scheiflinger, Friedrich; Szabo, Christina M; Dockal, Michael

    2015-01-22

    Fucoidans are complex sulfated polysaccharides extracted from brown algae. Depending on the concentration, they have been shown to stimulate and inhibit blood coagulation in vitro. Promotion of coagulation is mediated by blocking tissue factor pathway inhibitor (TFPI). We screened fucoidan extracts from four brown algae species in vitro with respect to their potential to improve coagulation in bleeding disorders. The fucoidans' pro- and anticoagulant activities were assessed by global hemostatic and standard clotting assays. Results showed that fucoidans improved coagulation parameters. Some fucoidans also activated the contact pathway of coagulation, an undesired property reported for sulfated glycosaminoglycans. Chemical evaluation of fucoidans' complex and variable structure included molecular weight (Mw), polydispersity (polyD), structural heterogeneity, and organic and inorganic impurities. Herewith, we describe a screening strategy that facilitates the identification of crude fucoidan extracts with desired biological and structural properties for improvement of compromised coagulation like in hemophilia. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Characterization and 454 pyrosequencing of Major Histocompatibility Complex class I genes in the great tit reveal complexity in a passerine system

    Directory of Open Access Journals (Sweden)

    Sepil Irem

    2012-05-01

    Full Text Available Abstract Background The critical role of Major Histocompatibility Complex (Mhc genes in disease resistance and their highly polymorphic nature make them exceptional candidates for studies investigating genetic effects on survival, mate choice and conservation. Species that harbor many Mhc loci and high allelic diversity are particularly intriguing as they are potentially under strong selection and studies of such species provide valuable information as to the mechanisms maintaining Mhc diversity. However comprehensive genotyping of complex multilocus systems has been a major challenge to date with the result that little is known about the consequences of this complexity in terms of fitness effects and disease resistance. Results In this study, we genotyped the Mhc class I exon 3 of the great tit (Parus major from two nest-box breeding populations near Oxford, UK that have been monitored for decades. Characterization of Mhc class I exon 3 was adopted and bidirectional sequencing was carried using the 454 sequencing platform. Full analysis of sequences through a stepwise variant validation procedure allowed reliable typing of more than 800 great tits based on 214,357 reads; from duplicates we estimated the repeatability of typing as 0.94. A total of 862 alleles were detected, and the presence of at least 16 functional loci was shown - the highest number characterized in a wild bird species. Finally, the functional alleles were grouped into 17 supertypes based on their antigen binding affinities. Conclusions We found extreme complexity at the Mhc class I of the great tit both in terms of allelic diversity and gene number. The presence of many functional loci was shown, together with a pseudogene family and putatively non-functional alleles; there was clear evidence that functional alleles were under strong balancing selection. This study is the first step towards an in-depth analysis of this gene complex in this species, which will help

  12. Survey of large protein complexes D. vulgaris reveals great structural diversity

    Energy Technology Data Exchange (ETDEWEB)

    Han, B.-G.; Dong, M.; Liu, H.; Camp, L.; Geller, J.; Singer, M.; Hazen, T. C.; Choi, M.; Witkowska, H. E.; Ball, D. A.; Typke, D.; Downing, K. H.; Shatsky, M.; Brenner, S. E.; Chandonia, J.-M.; Biggin, M. D.; Glaeser, R. M.

    2009-08-15

    An unbiased survey has been made of the stable, most abundant multi-protein complexes in Desulfovibrio vulgaris Hildenborough (DvH) that are larger than Mr {approx} 400 k. The quaternary structures for 8 of the 16 complexes purified during this work were determined by single-particle reconstruction of negatively stained specimens, a success rate {approx}10 times greater than that of previous 'proteomic' screens. In addition, the subunit compositions and stoichiometries of the remaining complexes were determined by biochemical methods. Our data show that the structures of only two of these large complexes, out of the 13 in this set that have recognizable functions, can be modeled with confidence based on the structures of known homologs. These results indicate that there is significantly greater variability in the way that homologous prokaryotic macromolecular complexes are assembled than has generally been appreciated. As a consequence, we suggest that relying solely on previously determined quaternary structures for homologous proteins may not be sufficient to properly understand their role in another cell of interest.

  13. Postantifungal Effect of Micafungin against the Species Complexes of Candida albicans and Candida parapsilosis.

    Science.gov (United States)

    Gil-Alonso, Sandra; Jauregizar, Nerea; Eraso, Elena; Quindós, Guillermo

    2015-01-01

    Micafungin is an effective antifungal agent useful for the therapy of invasive candidiasis. Candida albicans is the most common cause of invasive candidiasis; however, infections due to non-C. albicans species, such as Candida parapsilosis, are rising. Killing and postantifungal effects (PAFE) are important factors in both dose interval choice and infection outcome. The aim of this study was to determinate the micafungin PAFE against 7 C. albicans strains, 5 Candida dubliniensis, 2 Candida Africana, 3 C. parapsilosis, 2 Candida metapsilosis and 2 Candida orthopsilosis. For PAFE studies, cells were exposed to micafungin for 1 h at concentrations ranging from 0.12 to 8 μg/ml. Time-kill experiments (TK) were conducted at the same concentrations. Samples were removed at each time point (0-48 h) and viable counts determined. Micafungin (2 μg/ml) was fungicidal (≥ 3 log10 reduction) in TK against 5 out of 14 (36%) strains of C. albicans complex. In PAFE experiments, fungicidal endpoint was achieved against 2 out of 14 strains (14%). In TK against C. parapsilosis, 8 μg/ml of micafungin turned out to be fungicidal against 4 out 7 (57%) strains. Conversely, fungicidal endpoint was not achieved in PAFE studies. PAFE results for C. albicans complex (41.83 ± 2.18 h) differed from C. parapsilosis complex (8.07 ± 4.2 h) at the highest tested concentration of micafungin. In conclusion, micafungin showed significant differences in PAFE against C. albicans and C. parapsilosis complexes, being PAFE for the C. albicans complex longer than for the C. parapsilosis complex.

  14. Separation and Species Characterization of Complex Compound of Yttrium-90 and Strontium-90 by Paper Electrophoresis

    International Nuclear Information System (INIS)

    Sulaiman; Adang Hardi G; Noor Anis Kundari

    2007-01-01

    The research for species characterization of 90 Y and 90 Sr complex compound have been conducted using variation of buffer, concentration of HCl, electrophoresis operation voltage, time of electrophoresis, and electrophoresis migration media. From many trials, the conclusions are the applicable buffer are tartrate buffer and citrate buffer. These buffers can make a complex compound of 90 Y and there is migration to the anode. But, 90 Sr can’t make any complex compound and migration to the cathode. The optimum concentration of hydrochloride acid is 8 M with tartrate buffer but for citrate buffer, the concentration HCl is 2 M. The hydrochloric acid is used to dissolved the both elements as the mentioned above, but also for making complex ligand. The optimum electrophoresis operation voltage is 200 Volt for the both buffer solution and the duration of electrophoresis operation is 2.5 hours with using tartrate buffer but for citrate buffer the duration is 2 hours. The media of migration which can be used for replacing paper is silica. (author)

  15. Genomic Analysis of Two Phylogenetically DistinctNitrospiraSpecies Reveals Their Genomic Plasticity and Functional Diversity.

    Science.gov (United States)

    Ushiki, Norisuke; Fujitani, Hirotsugu; Shimada, Yu; Morohoshi, Tomohiro; Sekiguchi, Yuji; Tsuneda, Satoshi

    2017-01-01

    The genus Nitrospira represents a dominant group of nitrite-oxidizing bacteria in natural and engineered ecosystems. This genus is phylogenetically divided into six lineages, for which vast phylogenetic and functional diversity has been revealed by recent molecular ecophysiological analyses. However, the genetic basis underlying these phenotypic differences remains largely unknown because of the lack of genome sequences representing their diversity. To gain a more comprehensive understanding of Nitrospira , we performed genomic comparisons between two Nitrospira strains (ND1 and NJ1 belonging to lineages I and II, respectively) previously isolated from activated sludge. In addition, the genomes of these strains were systematically compared with previously reported six Nitrospira genomes to reveal their similarity and presence/absence of several functional genes/operons. Comparisons of Nitrospira genomes indicated that their genomic diversity reflects phenotypic differences and versatile nitrogen metabolisms. Although most genes involved in key metabolic pathways were conserved between strains ND1 and NJ1, assimilatory nitrite reduction pathways of the two Nitrospira strains were different. In addition, the genomes of both strains contain a phylogenetically different urease locus and we confirmed their ureolytic activity. During gene annotation of strain NJ1, we found a gene cluster encoding a quorum-sensing system. From the enriched supernatant of strain NJ1, we successfully identified seven types of acyl-homoserine lactones with a range of C10-C14. In addition, the genome of strain NJ1 lacks genes relevant to flagella and the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated genes) systems, whereas most nitrifying bacteria including strain ND1 possess these genomic elements. These findings enhance our understanding of genomic plasticity and functional diversity among members of the genus Nitrospira .

  16. Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera

    Science.gov (United States)

    Karpe, Snehal D.; Jain, Rikesh; Brockmann, Axel; Sowdhamini, Ramanathan

    2016-01-01

    Abstract We developed a computational pipeline for homology based identification of the complete repertoire of olfactory receptor (OR) genes in the Asian honey bee species, Apis florea. Apis florea is phylogenetically the most basal honey bee species and also the most distant sister species to the Western honey bee Apis mellifera, for which all OR genes had been identified before. Using our pipeline, we identified 180 OR genes in A. florea, which is very similar to the number of ORs identified in A. mellifera (177 ORs). Many characteristics of the ORs including gene structure, synteny of tandemly repeated ORs and basic phylogenetic clustering are highly conserved. The composite phylogenetic tree of A. florea and A. mellifera ORs could be divided into 21 clades which are in harmony with the existing Hymenopteran tree. However, we found a few nonorthologous OR relationships between both species as well as independent pseudogenization of ORs suggesting separate evolutionary changes. Particularly, a subgroup of the OR gene clade XI, which had been hypothesized to code cuticular hydrocarbon receptors showed a high number of species-specific ORs. RNAseq analysis detected a total number of 145 OR transcripts in male and 162 in female antennae. Most of the OR genes were highly expressed on the female antennae. However, we detected five distinct male-biased OR genes, out of which three genes (AfOr11, AfOr18, AfOr170P) were shown to be male-biased in A. mellifera, too, thus corroborating a behavioral function in sex-pheromone communication. PMID:27540087

  17. Proteomic profiles reveal age-related changes in coelomic fluid of sea urchin species with different life spans.

    Science.gov (United States)

    Bodnar, Andrea

    2013-05-01

    Sea urchins have a different life history from humans and traditional model organisms used to study the process of aging. Sea urchins grow indeterminately, reproduce throughout their life span and some species have been shown to exhibit negligible senescence with no increase in mortality rate at advanced ages. Despite these properties, different species of sea urchins are reported to have very different natural life spans providing a unique model to investigate cellular mechanisms underlying life span determination and negligible senescence. To gain insight into the biological changes that accompany aging in these animals, proteomic profiles were examined in coelomic fluid from young and old sea urchins of three species with different life spans: short-lived Lytechinus variegatus, long-lived Strongylocentrotus franciscanus and Strongylocentrotus purpuratus which has an intermediate life span. The proteomic profiles of cell-free coelomic fluid were complex with many proteins exhibiting different forms and extensive post-translational modifications. Approximately 20% of the protein spots on 2-D gels showed more than two-fold change with age in each of the species. Changes that are consistent with age in all three species may prove to be useful biomarkers for age-determination for these commercially fished marine invertebrates and also may provide clues to mechanisms of negligible senescence. Among the proteins that change with age, the ectodomain of low-density lipoprotein receptor-related protein 4 (LRP4) was significantly increased in the coelomic fluid of all three sea urchin species suggesting that the Wnt signaling pathway should be further investigated for its role in negligible senescence. Copyright © 2012 Elsevier Inc. All rights reserved.

  18. Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

    Directory of Open Access Journals (Sweden)

    Carolina M. Voloch

    2014-11-01

    Full Text Available Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G, RNA-dependent RNA polymerase (L and polymerase (P genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.

  19. Comparison of Phylogeny, Venom Composition and Neutralization by Antivenom in Diverse Species of Bothrops Complex

    Science.gov (United States)

    Peixoto, Pedro S.; Bernardoni, Juliana L.; Oliveira, Sâmella S.; Portes-Junior, José Antonio; Mourão, Rosa Helena V.; Lima-dos-Santos, Isa; Sano-Martins, Ida S.; Chalkidis, Hipócrates M.; Valente, Richard H.; Moura-da-Silva, Ana M.

    2013-01-01

    In Latin America, Bothrops snakes account for most snake bites in humans, and the recommended treatment is administration of multispecific Bothrops antivenom (SAB – soro antibotrópico). However, Bothrops snakes are very diverse with regard to their venom composition, which raises the issue of which venoms should be used as immunizing antigens for the production of pan-specific Bothrops antivenoms. In this study, we simultaneously compared the composition and reactivity with SAB of venoms collected from six species of snakes, distributed in pairs from three distinct phylogenetic clades: Bothrops, Bothropoides and Rhinocerophis. We also evaluated the neutralization of Bothrops atrox venom, which is the species responsible for most snake bites in the Amazon region, but not included in the immunization antigen mixture used to produce SAB. Using mass spectrometric and chromatographic approaches, we observed a lack of similarity in protein composition between the venoms from closely related snakes and a high similarity between the venoms of phylogenetically more distant snakes, suggesting little connection between taxonomic position and venom composition. P-III snake venom metalloproteinases (SVMPs) are the most antigenic toxins in the venoms of snakes from the Bothrops complex, whereas class P-I SVMPs, snake venom serine proteinases and phospholipases A2 reacted with antibodies in lower levels. Low molecular size toxins, such as disintegrins and bradykinin-potentiating peptides, were poorly antigenic. Toxins from the same protein family showed antigenic cross-reactivity among venoms from different species; SAB was efficient in neutralizing the B. atrox venom major toxins. Thus, we suggest that it is possible to obtain pan-specific effective antivenoms for Bothrops envenomations through immunization with venoms from only a few species of snakes, if these venoms contain protein classes that are representative of all species to which the antivenom is targeted. PMID

  20. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    KAUST Repository

    Lee, O. O.

    2012-08-03

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

  1. How Can We Explain Poverty? Case Study of Dee Reveals the Complexities

    Science.gov (United States)

    Seccombe, Karen

    2011-01-01

    Many theories have been offered to explain why people are impoverished. This article by Karen Seccombe uses the case study of "Dee," a newly single mother, to explore four of the most common: individualism, social structuralism, the culture of poverty, and fatalism. She concludes that poverty is a highly complex phenomenon, and it is likely that…

  2. Cilium transition zone proteome reveals compartmentalization and differential dynamics of ciliopathy complexes

    Czech Academy of Sciences Publication Activity Database

    Dean, S.; Moreira-Leite, F.; Varga, Vladimír; Gull, K.

    2016-01-01

    Roč. 113, č. 35 (2016), E5135-E5143 ISSN 0027-8424 Institutional support: RVO:68378050 Keywords : transition zone * cilium/flagellum * BBSome * MKS/B9 complex * trypanosome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.661, year: 2016

  3. Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning

    NARCIS (Netherlands)

    Taylor, D.W.; Zhu, Y.; Staals, R.H.J.; Kornfeld, J.E.; Shinkai, A.; Oost, van der J.; Nogales, E.; Doudna, J.A.

    2015-01-01

    Adaptive immunity in bacteria involves RNA-guided surveillance complexes that use CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR RNAs (crRNAs) to target invasive nucleic acids for degradation. Whereas type I and type II CRISPR-Cas

  4. 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).

  5. Genomic and phylogenetic characterization of viruses included in the Manzanilla and Oropouche species complexes of the genus Orthobunyavirus, family Bunyaviridae.

    Science.gov (United States)

    Ladner, Jason T; Savji, Nazir; Lofts, Loreen; Travassos da Rosa, Amelia; Wiley, Michael R; Gestole, Marie C; Rosen, Gail E; Guzman, Hilda; Vasconcelos, Pedro F C; Nunes, Marcio R T; J Kochel, Tadeusz; Lipkin, W Ian; Tesh, Robert B; Palacios, Gustavo

    2014-05-01

    A thorough characterization of the genetic diversity of viruses present in vector and vertebrate host populations is essential for the early detection of and response to emerging pathogenic viruses, yet genetic characterization of many important viral groups remains incomplete. The Simbu serogroup of the genus Orthobunyavirus, family Bunyaviridae, is an example. The Simbu serogroup currently consists of a highly diverse group of related arboviruses that infect both humans and economically important livestock species. Here, we report complete genome sequences for 11 viruses within this group, with a focus on the large and poorly characterized Manzanilla and Oropouche species complexes. Phylogenetic and pairwise divergence analyses indicated the presence of high levels of genetic diversity within these two species complexes, on a par with that seen among the five other species complexes in the Simbu serogroup. Based on previously reported divergence thresholds between species, the data suggested that these two complexes should actually be divided into at least five species. Together these five species formed a distinct phylogenetic clade apart from the rest of the Simbu serogroup. Pairwise sequence divergences among viruses of this clade and viruses in other Simbu serogroup species complexes were similar to levels of divergence among the other orthobunyavirus serogroups. The genetic data also suggested relatively high levels of natural reassortment, with three potential reassortment events present, including two well-supported events involving viruses known to infect humans.

  6. Comparative Proteomics of Human and Macaque Milk Reveals Species-Specific Nutrition during Postnatal Development.

    Science.gov (United States)

    Beck, Kristen L; Weber, Darren; Phinney, Brett S; Smilowitz, Jennifer T; Hinde, Katie; Lönnerdal, Bo; Korf, Ian; Lemay, Danielle G

    2015-05-01

    Milk has been well established as the optimal nutrition source for infants, yet there is still much to be understood about its molecular composition. Therefore, our objective was to develop and compare comprehensive milk proteomes for human and rhesus macaques to highlight differences in neonatal nutrition. We developed a milk proteomics technique that overcomes previous technical barriers including pervasive post-translational modifications and limited sample volume. We identified 1606 and 518 proteins in human and macaque milk, respectively. During analysis of detected protein orthologs, we identified 88 differentially abundant proteins. Of these, 93% exhibited increased abundance in human milk relative to macaque and include lactoferrin, polymeric immunoglobulin receptor, alpha-1 antichymotrypsin, vitamin D-binding protein, and haptocorrin. Furthermore, proteins more abundant in human milk compared with macaque are associated with development of the gastrointestinal tract, the immune system, and the brain. Overall, our novel proteomics method reveals the first comprehensive macaque milk proteome and 524 newly identified human milk proteins. The differentially abundant proteins observed are consistent with the perspective that human infants, compared with nonhuman primates, are born at a slightly earlier stage of somatic development and require additional support through higher quantities of specific proteins to nurture human infant maturation.

  7. Complex history of admixture during citrus domestication revealed by genome analysis

    Energy Technology Data Exchange (ETDEWEB)

    Wu, G. Albert; Prochnik, Simon; Jenkins, Jerry; Salse, Jerome; Hellsten, Uffe; Murat, Florent; Perrier, Xavier; Ruiz, Manuel; Scalabrin, Simone; Terol, Javier; Takita, Marco Aur& #233; lio,; Labadie, Karine; Poulain, Julie; Couloux, Arnaud; Jabbari, Kamel; Cattonaro, Federica; Fabbro, Cristian Del; Pinosio, Sara; Zuccolo, Andrea; Chapman, Jarrod; Grimwood, Jane; Tadeo, Francisco; Estornell, Leandro H.; Mu?oz-Sanz, Juan V.; Ibanez, Victoria; Herrero-Ortega, Amparo; Aleza, Pablo; P& #233; rez, Juli& #225; n P& #233; rez,; Ramon, Daniel; Brunel, Dominique; Luro, Francois; Chen, Chunxian; Farmerie, William G.; Desany, Brian; Kodira, Chinnappa; Mohiuddin, Mohammed; Harkins, Tim; Fredrikson, Karin; Burns, Paul; Lomsadze, Alexandre; Borodovsky, Mark; Reforgiato, Giuseppe; Freitas-Astua, Juliana; Quetier, Francis; Navarro, Luis; Roose, Mikeal; Wincker, Patrick; Schmutz, Jeremy; Morgante, Michele; Machado, Marcos Antonio; Talon, Manuel; Jaillon, Olivier; Ollitrault, Patrick; Gmitter, Frederick; Rokhsar, Daniel

    2014-06-30

    Although Citrus is the most globally significant tree fruit, its domestication history is poorly understood. Cultivated citrus types are believed to comprise selections from and/or hybrids of several wild progenitor species, but the identities of these progenitors, and their contribution to modern cultivars, remain controversial. Here we report the genomes of a collection of mandarins, pummelos, and oranges, including a high quality reference sequence from a haploid Clementine mandarin. By comparative genome analysis we show that these cultivated types can be derived from two progenitor species. Cultivated pummelos represent selections from a single progenitor species C. maxima. Unexpectedly, however, we find that cultivated mandarins are introgressions of C. maxima into a distinct second population that we identify with the ancestral wild mandarin species C. reticulata. Sweet and sour oranges are found to be interspecific hybrids. Sweet orange, the most widely cultivated citrus, arose as the offspring of previously admixed individuals. In contrast, sour (or Seville) orange is an F1 hybrid of pure C. maxima and C. reticulata parents, implying that wild mandarins were part of the early breeding germplasm. Surprisingly, we also find that a wild Chinese mandarin from Mangshan, China shows substantial sequence divergence from C. reticulata and appears to represent a distinct taxon. Understanding the relationships and phylogeny of cultivated citrus through genome analysis will clarify taxonomic relationships and enable previously inconceivable opportunities for sequence-directed genetic improvement. Citrus are widely consumed worldwide as juice or fresh fruit, providing important sources of vitamin C and other health-promoting compounds. Global production in 2012 exceeded 86 million metric tons, with an estimated value of US$9 billion (http://www.fas.usda.gov/psdonline/circulars/citrus.pdf). The very narrow genetic diversity of cultivated citrus makes it highly

  8. Revealing the Differences Between Free and Complexed Enzyme Mechanisms and Factors Contributing to Cell Wall Recalcitrance

    Energy Technology Data Exchange (ETDEWEB)

    Resch, Michael G.; Donohoe, Byron; Ciesielski, Peter; Nill, Jennifer; McKinney, Kellene; Mittal, Ashutosh; Katahira, Rui; Himmel, Michael; Biddy, Mary; Beckham, Gregg; Decker, Steve

    2014-09-08

    Enzymatic depolymerization of polysaccharides is a key step in the production of fuels and chemicals from lignocellulosic biomass, and discovery of synergistic biomass-degrading enzyme paradigms will enable improved conversion processes. Historically, revealing insights into enzymatic saccharification mechanisms on plant cell walls has been hindered by uncharacterized substrates and low resolution.

  9. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

    DEFF Research Database (Denmark)

    Zhang, Guojie; Guo, Guangwu; Hu, Xueda

    2010-01-01

    fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell...

  10. The oyster genome reveals stress adaptation and complexity of shell formation

    DEFF Research Database (Denmark)

    Zhang, Guofan; Fang, Xiaodong; Guo, Ximing

    2012-01-01

    The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress re...... and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa....

  11. MALDI-TOF MS and chemometric based identification of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species.

    Science.gov (United States)

    Sousa, Clara; Botelho, João; Silva, Liliana; Grosso, Filipa; Nemec, Alexandr; Lopes, João; Peixe, Luísa

    2014-07-01

    MALDI-TOF MS is becoming the technique of choice for rapid bacterial identification at species level in routine diagnostics. However, some drawbacks concerning the identification of closely related species such as those belonging to the Acinetobacter calcoaceticus-Acinetobacter baumannii (Acb) complex lead to high rates of misidentifications. In this work we successfully developed an approach that combines MALDI-TOF MS and chemometric tools to discriminate the six Acb complex species (A. baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, A. calcoaceticus, genomic species "Close to 13TU" and genomic species "Between 1 and 3"). Mass spectra of 83 taxonomically well characterized clinical strains, reflecting the breadth of currently known phenetic diversity within the Acb complex, were achieved from intact cells and cell extracts and analyzed with hierarchical cluster analysis (HCA) and partial least squares discriminant analysis (PLSDA). This combined approach lead to 100% of correct species identification using mass spectra obtained from intact cells. Moreover, it was possible to discriminate two Acb complex species (genomic species "Close to 13TU" and genomic species "Between 1 and 3") not included in the MALDI Biotyper database. Copyright © 2014 Elsevier GmbH. All rights reserved.

  12. Metabolomics Reveals Cryptic Interactive Effects of Species Interactions and Environmental Stress on Nitrogen and Sulfur Metabolism in Seagrass

    DEFF Research Database (Denmark)

    Hasler-Sheetal, Harald; Castorani, Max; Glud, Ronnie N.

    2016-01-01

    among foundational species and eventually affect ecosystem health. Here, we used metabolomics to assess the impact of light reductions on interactions between the seagrass Zostera marina, an important habitat-forming marine plant, and the abundant and commercially important blue mussel Mytilus edulis....... Plant performance varied with light availability but was unaffected by the presence of mussels. Metabolomic analysis, on the other hand, revealed an interaction between light availability and presence of M. edulis on seagrass metabolism. Under high light, mussels stimulated seagrass nitrogen and energy...... metabolism. Conversely, in low light mussels impeded nitrogen and energy metabolism, and enhanced responses against sulfide toxicity, causing inhibited oxidative energy metabolism and tissue degradation. Metabolomic analysis thereby revealed cryptic changes to seagrass condition that could not be detected...

  13. Phylogenetic analysis of phenotypically characterized Cryptococcus laurentii isolates reveals high frequency of cryptic species.

    Directory of Open Access Journals (Sweden)

    Kennio Ferreira-Paim

    Full Text Available Although Cryptococcus laurentii has been considered saprophytic and its taxonomy is still being described, several cases of human infections have already reported. This study aimed to evaluate molecular aspects of C. laurentii isolates from Brazil, Botswana, Canada, and the United States.In this study, 100 phenotypically identified C. laurentii isolates were evaluated by sequencing the 18S nuclear ribosomal small subunit rRNA gene (18S-SSU, D1/D2 region of 28S nuclear ribosomal large subunit rRNA gene (28S-LSU, and the internal transcribed spacer (ITS of the ribosomal region.BLAST searches using 550-bp, 650-bp, and 550-bp sequenced amplicons obtained from the 18S-SSU, 28S-LSU, and the ITS region led to the identification of 75 C. laurentii strains that shared 99-100% identity with C. laurentii CBS 139. A total of nine isolates shared 99% identity with both Bullera sp. VY-68 and C. laurentii RY1. One isolate shared 99% identity with Cryptococcus rajasthanensis CBS 10406, and eight isolates shared 100% identity with Cryptococcus sp. APSS 862 according to the 28S-LSU and ITS regions and designated as Cryptococcus aspenensis sp. nov. (CBS 13867. While 16 isolates shared 99% identity with Cryptococcus flavescens CBS 942 according to the 18S-SSU sequence, only six were confirmed using the 28S-LSU and ITS region sequences. The remaining 10 shared 99% identity with Cryptococcus terrestris CBS 10810, which was recently described in Brazil. Through concatenated sequence analyses, seven sequence types in C. laurentii, three in C. flavescens, one in C. terrestris, and one in the C. aspenensis sp. nov. were identified.Sequencing permitted the characterization of 75% of the environmental C. laurentii isolates from different geographical areas and the identification of seven haplotypes of this species. Among sequenced regions, the increased variability of the ITS region in comparison to the 18S-SSU and 28S-LSU regions reinforces its applicability as a DNA

  14. 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

  15. Molecular diagnosis of cryptococcal meningitis in cerebrospinal fluid: comparison of primer sets for Cryptococcus neoformans and Cryptococcus gattii species complex

    Directory of Open Access Journals (Sweden)

    Marilena dos Anjos Martins

    2015-01-01

    Conclusions: These data suggest that the CN4/CN5 primer set was highly sensitive for the identification of C. neoformans/C. gattii species complex in cerebrospinal fluid samples from patients with clinical suspicion of cryptococcal meningitis.

  16. Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

    Energy Technology Data Exchange (ETDEWEB)

    Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven (BMS)

    2014-10-02

    Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

  17. Visualization of PML nuclear import complexes reveals FG-repeat nucleoporins at cargo retrieval sites.

    Science.gov (United States)

    Lång, Anna; Eriksson, Jens; Schink, Kay Oliver; Lång, Emma; Blicher, Pernille; Połeć, Anna; Brech, Andreas; Dalhus, Bjørn; Bøe, Stig Ove

    2017-07-04

    Selective nuclear import in eukaryotic cells involves sequential interactions between nuclear import receptors and phenylalanine-glycine (FG)-repeat nucleoporins. Traditionally, binding of cargoes to import receptors is perceived as a nuclear pore complex independent event, while interactions between import complexes and nucleoporins are thought to take place at the nuclear pores. However, studies have shown that nucleoporins are mobile and not static within the nuclear pores, suggesting that they may become engaged in nuclear import before nuclear pore entry. Here we have studied post-mitotic nuclear import of the tumor suppressor protein PML. Since this protein forms nuclear compartments called PML bodies that persist during mitosis, the assembly of putative PML import complexes can be visualized on the surface of these protein aggregates as the cell progress from an import inactive state in mitosis to an import active state in G1. We show that these post-mitotic cytoplasmic PML bodies incorporate a multitude of peripheral nucleoporins, but not scaffold or nuclear basket nucleoporins, in a manner that depends on FG-repeats, the KPNB1 import receptor, and the PML nuclear localization signal. The study suggests that nucleoporins have the ability to target certain nuclear cargo proteins in a nuclear pore-uncoupled state, before nuclear pore entry.

  18. Transcriptomic analyses reveal species-specific light-induced anthocyanin biosynthesis in chrysanthemum.

    Science.gov (United States)

    Hong, Yan; Tang, Xingjiao; Huang, He; Zhang, Yuan; Dai, Silan

    2015-03-17

    The flower colour of agricultural products is very important for their commercial value, which is mainly attributed to the accumulation of anthocyanins. Light is one of the key environmental factors that affect the anthocyanin biosynthesis. However, the deep molecular mechanism remains elusive, and many problems regarding the phenotypic change and the corresponding gene regulation are still unclear. In the present study, Chrysanthemum × morifolium 'Purple Reagan', a light-responding pigmentation cultivar, was selected to investigate the mechanism of light-induced anthocyanin biosynthesis using transcriptomic analyses. Only cyanidin derivatives were identified based on the analyses of the pigmentation in ray florets. Shading experiments revealed that the capitulum was the key organ and that its bud stage was the key phase responding to light. These results were used to design five libraries for transcriptomic analyses, including three capitulum developmental stages and two light conditions. RNA sequences were de novo assembled into 103,517 unigenes, of which 60,712 were annotated against four public protein databases. As many as 2,135 unigenes were differentially expressed between the light and dark libraries with 923 up-regulated and 1,212 down-regulated unigenes in response to shading. Next, interactive pathway analysis showed that the anthocyanin biosynthetic pathway was the only complete metabolic pathway both modulated in response to light and related to capitulum development. Following the shading treatment, nearly all structural genes involved in the anthocyanin biosynthetic pathway were down-regulated. Moreover, three CmMYB genes and one CmbHLH gene were identified as key transcription factors that might participate in the regulation of anthocyanin biosynthesis under light conditions based on clustering analysis and validation by RT-qPCR. Finally, a light-induced anthocyanin biosynthesis pathway in chrysanthemums was inferred. The pigmentation of the ray

  19. Human head lice and pubic lice reveal the presence of several Acinetobacter species in Algiers, Algeria.

    Science.gov (United States)

    Mana, Nassima; Louni, Meriem; Parola, Philippe; Bitam, Idir

    2017-08-01

    There are two majorspecies of medically important lice that parasitize humans: Phthirus pubis, found in pubic hair, and Pediculus humanus. Pediculus humanus consists of two eco types that live in specific niches on the human host: body lice (Pediculus humanus humanus), found on the human body and clothing, and head lice (Pediculus humanus capitis), found on the scalp. To date, only body lice are known to be vectors of human disease; however, it has recently been reported that the DNA of several bacterial agents has been detected in head lice, raising questions about their role in the transmission of pathogens. This issue caught our attention, in addition to the fact that the pathogenic bacteria associated with P. pubis and P. humanus capitis have never been investigated in Algeria. To investigate this,molecular techniques (real-time PCR) were used to screen for the presence of Acinetobacter spp., Bartonella spp., Borrelia spp. and Rickettsia prowazekii DNA from P. humanus capitis (64 lice) collected from schoolchildren,and P. pubis (4 lice),collected from one adultman living in Algiers. Positive samples for Acinetobacter spp.were identified by sequencing therpoBgene. Conventional PCR targeting the partial Cytb gene was used to determine the phylogenetic clade of the collected lice. Of the 64 samples collected, Acinetobacter spp. DNA was detected in 17/64 (27%) of head lice, identified as: A. baumannii (14%), A. johnsonii (11%) and A. variabilis (2%). Of the four P. pubissamples, 2(50%) were positive for A. johnsonii. The phylogenetic tree based on the Cytb gene revealed that P. humanus capitis were grouped into clades A and B. In this study, we report andidentify for the first time Acinetobacter spp.in Algerian P. pubis and P. humanus capitis. The detection of the genus Acinetobacter in lice should not be underestimated, especially in P. humanus capitis, which is distributed worldwide. However, additional epidemiological data are required to determine if human lice

  20. The Precambrian Singo Igneous Complex (SIC), Uganda Revealed As a Mineralized Nested Ring Complex Using High Resolution Airborne Radiometric and Magnetic Data.

    Science.gov (United States)

    Atekwana, E. A.; LePera, A.; Abdelsalam, M. G.; Katumwehe, A. B.; Achang, M.

    2014-12-01

    We used high-resolution radiometrics and aeromagnetic data to investigate the Precambrian Singo Igneous Complex (SIC) in Uganda. The SIC covers an area of about 700 km² and is host to hydrothermally formed economic minerals such as Gold and Tungsten. The distribution of the ore deposits is not well known and current mine workings are limited to the western margins of the complex. Our objectives were to (1) provide a detailed geological map of the SIC and surrounding, (2) investigate relationships between preserved intrusive bodies and Precambrian tectonic structures to provide insight into emplacement of the complex, (3) examine links between magma emplacement, discontinuities and hydrothermal alteration (4) generate two-dimensional (2-D) and three-dimensional (3-D) models of the complex to understand its subsurface geometry, (5) investigate the relationship between the structure of the SIC and mineral occurrences as an aid to future exploration programs. Edge enhancement filters such as the analytical signal, vertical and tilt derivatives were applied to the magnetic data. In addition, 2-D and 3-D models were produced using Geosoft's GM-SYS 2-D and Voxi modules. The filtered data provided unprecedented structural details of the complex and revealed the following: (1) the edge of the SIC is characterized by higher magnetic susceptibility and Thorium content than its interior, (2) the SIC is characterized by eight to nine nested ring complexes with diameters ranging from 2.5 to 14 km, (3) the 3-D inversion suggests near vertical walls for the ring complexes extending to a depth of about 7 km, (4) the SIC was emplaced within a Precambrian folded basement and was traversed by numerous NW-trending dykes and (5) present day mining activities are concentrated within the folded basement units although occurrences of Tungsten and Gold are found associated with the highly magnetized edge of the ring complexes. We interpret the highly magnetized edges of the nested ring

  1. Sperm dimorphism in the Triatoma brasiliensis species complex and its applications.

    Science.gov (United States)

    Baffa, A F; Camara, D C P; Santos-Mallet, J R; DA Silva, E R; Costa, J; Freitas, S P C

    2017-06-01

    Morphological and structural features of the sperm of the Triatoma brasiliensis Neiva, 1911 (Hemiptera: Reduviidae) species complex were examined in this first study investigating the sperm of Heteroptera and the genus Triatoma. Males were dissected and their seminal vesicles removed. For measurement, seminal vesicles were squashed on glass slides, spread, fixed and observed under a photomicroscope. The images were analysed and measures of sperm were made. Data were analysed using one-way analysis of variance and Tukey's test to detect differentiation among taxa. Furthermore, seminal vesicles were prepared for studies of transmission electron microscopy. All taxa studied showed polymorphic (short and long) sperm. The sperm of Triatoma brasiliensis macromelasoma was significantly longer (in total length) than that of the other four members of the complex, which supports the hypothesis of hybrid speciation of this member of the complex as an increase in the size of typical hybrids under heterosis was previously shown. The sperm cells of the five taxa have similar ultrastructural morphology. The ultrastructural features observed confirm the hypothesis, raised by previous studies, that they are synapomorphic to the suborder Heteroptera. © 2017 The Royal Entomological Society.

  2. The influence of climatic niche preferences on the population genetic structure of a mistletoe species complex.

    Science.gov (United States)

    Ramírez-Barahona, Santiago; González, Clementina; González-Rodríguez, Antonio; Ornelas, Juan Francisco

    2017-06-01

    The prevalent view on genetic structuring in parasitic plants is that host-race formation is caused by varying degrees of host specificity. However, the relative importance of ecological niche divergence and host specificity to population differentiation remains poorly understood. We evaluated the factors associated with population differentiation in mistletoes of the Psittacanthus schiedeanus complex (Loranthaceae) in Mexico. We used genetic data from chloroplast sequences and nuclear microsatellites to study population genetic structure and tested its association with host preferences and climatic niche variables. Pairwise genetic differentiation was associated with environmental and host preferences, independent of geography. However, environmental predictors appeared to be more important than host preferences to explain genetic structure, supporting the hypothesis that the occurrence of the parasite is largely determined by its own climatic niche and, to a lesser degree, by host specificity. Genetic structure is significant within this mistletoe species complex, but the processes associated with this structure appear to be more complex than previously thought. Although host specificity was not supported as the major determinant of population differentiation, we consider this to be part of a more comprehensive ecological model of mistletoe host-race formation that incorporates the effects of climatic niche evolution. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  3. Susceptibility of species within the Sporothrix schenckii complex to a panel of killer yeasts.

    Science.gov (United States)

    Stopiglia, Cheila Denise Ottonelli; Heidrich, Daiane; Sorrentino, Julia Medeiros; Vieira, Fabiane Jamono; Landell, Melissa Fontes; Valente, Patrícia; Scroferneker, Maria Lúcia

    2014-06-01

    The Sporothrix schenckii complex is the etiologic agent of sporotrichosis, a subacute or chronic mycosis which can affect humans and animals. Killer yeasts have been used in the medical field for development of novel antimycotics and biotyping of pathogenic fungi. The action of 18 killer yeasts on the growth of 88 characterized S. schenckii, Sporothrix globosa, Sporothrix brasiliensis, and Sporothrix mexicana clinical and environmental isolates was evaluated. Killer studies were performed on Petri dishes containing cheese black starch agar. The yeasts Candida catenulata (QU26, QU31, QU127, LV102); Trichosporon faecale (QU100); Trichosporon japonicum (QU139); Kluyveromyces lactis (QU30, QU99, QU73); Kazachstania unispora (QU49), Trichosporon insectorum (QU89), and Kluyveromyces marxianus (QU103) showed activity against all strains of the S. schenckii complex tested. Observation by optical microscopy of S. brasiliensis 61 within the inhibition haloes around the colonies of the killer yeasts QU100, QU139, and LV102 showed that there was no conidiation, but there was hyphal proliferation. The toxins were fungistatic against S. brasiliensis 61. There was no difference in susceptibility to the toxins among the S. schenckii species complex. Further investigations are necessary to clearly establish the mechanism of action of the toxins. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. No Evidence for Temporal Variation in a Cryptic Species Community of Freshwater Amphipods of the Hyalella azteca Species Complex

    OpenAIRE

    Dionne, Kaven; Vergilino, Roland; Dufresne, France; Charles, François; Nozais, Christian

    2011-01-01

    The co-occurrence of cryptic species of Hyalella amphipods is a challenge to our traditional views of how species assemble. Since these species have similar morphologies, it is not evident that they have developed phenotypic differences that would allow them to occupy different ecological niches. We examined the structure of a community of Hyalella amphipods in the littoral zone of a boreal lake to verify if temporal variation was present in relative abundances. Morphological and molecular an...

  5. Conservation Below The Species Level: Suitable Evolutionarily Significant Units Among Mountain Vipers (The Montivipera Raddei Complex) in Iran.

    Science.gov (United States)

    Behrooz, Roozbeh; Kaboli, Mohammad; Arnal, Véronique; Nazarizadeh, Masoud; Asadi, Atefeh; Salmanian, Amin; Ahmadi, Mohsen; Montgelard, Claudine

    2018-02-01

    Northern and western mountains of Iran are among the most important biodiversity and endemism hot spots for reptiles in the Middle East. Among herpetofauna, the montivipers represent an emblematic and fragmented endemic group for which estimating their level of genetic differentiation and defining conservation priorities is urgently needed. Here, we present the most comprehensive phylogenetic study on the Montivipera raddei species group comprising all five known taxa, among which three are endemic to Iran. Based on two mitochondrial genes, phylogenetic and phylogeographic analyses revealed three major lineages each presenting very contrasting distribution area. The Iranian montivipers are highly structured in clades showing low genetic diversity and corresponding to high altitude summits. Molecular dating revealed the role of Quaternary paleo-climatic oscillations and altitudinal movements of montivipers in shaping genetic diversity and differentiation of these sky-island taxa. In addition, the best scenario of historical biogeography allowed identifying three possible refugial areas in Iran most likely arising by vicariance. Based on our mitochondrial results and pending additional data, we recognize three candidate species among the Montivipera raddei complex: M. raddei, M.latifii and M. kuhrangica that are coherent with their geographical distribution. We propose that the most appropriate Evolutionary Significant Units for conservation of the montivipers are represented by thirteen units among which six are recognized as high priority. Finally, we suggest some recommendations to the IUCN as well as to the Iranian conservation policies with respect to conservation prioritization. © The American Genetic Association 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Mycobacterium arupense, Mycobacterium heraklionense, and a Newly Proposed Species, "Mycobacterium virginiense" sp. nov., but Not Mycobacterium nonchromogenicum, as Species of the Mycobacterium terrae Complex Causing Tenosynovitis and Osteomyelitis.

    Science.gov (United States)

    Vasireddy, Ravikiran; Vasireddy, Sruthi; Brown-Elliott, Barbara A; Wengenack, Nancy L; Eke, Uzoamaka A; Benwill, Jeana L; Turenne, Christine; Wallace, Richard J

    2016-05-01

    Mycobacterium terrae complex has been recognized as a cause of tenosynovitis, with M. terrae and Mycobacterium nonchromogenicum reported as the primary etiologic pathogens. The molecular taxonomy of the M. terrae complex causing tenosynovitis has not been established despite approximately 50 previously reported cases. We evaluated 26 isolates of the M. terrae complex associated with tenosynovitis or osteomyelitis recovered between 1984 and 2014 from 13 states, including 5 isolates reported in 1991 as M. nonchromogenicum by nonmolecular methods. The isolates belonged to three validated species, one new proposed species, and two novel related strains. The majority of isolates (20/26, or 77%) belonged to two recently described species: Mycobacterium arupense (10 isolates, or 38%) and Mycobacterium heraklionense (10 isolates, or 38%). Three isolates (12%) had 100% sequence identity to each other by 16S rRNA and 99.3 to 100% identity by rpoB gene region V sequencing and represent a previously undescribed species within the M. terrae complex. There were no isolates of M. terrae or M. nonchromogenicum, including among the five isolates reported in 1991. The 26 isolates were susceptible to clarithromycin (100%), rifabutin (100%), ethambutol (92%), and sulfamethoxazole or trimethoprim-sulfamethoxazole (70%). The current study suggests that M. arupense, M. heraklionense, and a newly proposed species ("M. virginiense" sp. nov.; proposed type strain MO-233 [DSM 100883, CIP 110918]) within the M. terrae complex are the major causes of tenosynovitis and osteomyelitis in the United States, with little change over 20 years. Species identification within this complex requires sequencing methods. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  7. Three routes to crypsis: Stasis, convergence, and parallelism in the Mastigias species complex (Scyphozoa, Rhizostomeae).

    Science.gov (United States)

    Swift, H F; Gómez Daglio, L; Dawson, M N

    2016-06-01

    Evolutionary inference can be complicated by morphological crypsis, particularly in open marine systems that may rapidly dissipate signals of evolutionary processes. These complications may be alleviated by studying systems with simpler histories and clearer boundaries, such as marine lakes-small bodies of seawater entirely surrounded by land. As an example, we consider the jellyfish Mastigias spp. which occurs in two ecotypes, one in marine lakes and one in coastal oceanic habitats, throughout the Indo-West Pacific (IWP). We tested three evolutionary hypotheses to explain the current distribution of the ecotypes: (H1) the ecotypes originated from an ancient divergence; (H2) the lake ecotype was derived recently from the ocean ecotype during a single divergence event; and (H3) the lake ecotype was derived from multiple, recent, independent, divergences. We collected specimens from 21 locations throughout the IWP, reconstructed multilocus phylogenetic and intraspecific relationships, and measured variation in up to 40 morphological characters. The species tree reveals three reciprocally monophyletic regional clades, two of which contain ocean and lake ecotypes, suggesting repeated, independent evolution of coastal ancestors into marine lake ecotypes, consistent with H3; hypothesis testing and an intraspecific haplotype network analysis of samples from Palau reaffirms this result. Phylogenetic character mapping strongly correlates morphology to environment rather than lineage (r=0.7512, pmorphological similarity in Mastigias spp. clearly results from three separate patterns of evolution: morphological stasis in ocean medusae, convergence of lake morphology across distinct species and parallelism between lake morphologies within species. That three evolutionary routes each result in crypsis illustrates the challenges of interpreting evolutionary processes from patterns of biogeography and diversity in the seas. Identifying cryptic species is only the first step in

  8. Strong Genomic and Phenotypic Heterogeneity in the Aeromonas sobria Species Complex

    Directory of Open Access Journals (Sweden)

    Jeff Gauthier

    2017-12-01

    Full Text Available Aeromonas sobria is a mesophilic motile aeromonad currently depicted as an opportunistic pathogen, despite increasing evidence of mutualistic interactions in salmonid fish. However, the determinants of its host-microbe associations, either mutualistic or pathogenic, remain less understood than for other aeromonad species. On one side, there is an over-representation of pathogenic interactions in the A. sobria literature, of which only three articles to date report mutualistic interactions; on the other side, genomic characterization of this species is still fairly incomplete as only two draft genomes were published prior to the present work. Consequently, no study specifically investigated the biodiversity of A. sobria. In fact, the investigation of A. sobria as a species complex may have been clouded by: (i confusion with A. veronii biovar sobria because of their similar biochemical profiles, and (ii the intrinsic low resolution of previous studies based on 16S rRNA gene sequences and multilocus sequence typing. So far, the only high-resolution, phylogenomic studies of the genus Aeromonas included one A. sobria strain (CECT 4245 / Popoff 208, making it impossible to robustly conclude on the phylogenetic intra-species diversity and the positioning among other Aeromonas species. To further understand the biodiversity and the spectrum of host-microbe interactions in A. sobria as well as its potential genomic diversity, we assessed the genomic and phenotypic heterogeneity among five A. sobria strains: two clinical isolates recovered from infected fish (JF2635 and CECT 4245, one from an infected amphibian (08005 and two recently isolated brook charr probionts (TM12 and TM18 which inhibit in vitro growth of A. salmonicida subsp. salmonicida (a salmonid fish pathogen. A phylogenomic assessment including 2,154 softcore genes corresponding to 946,687 variable sites from 33 Aeromonas genomes confirms the status of A. sobria as a distinct species divided