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Sample records for harbour cryptic genetic

  1. Population genetics and cryptic species

    International Nuclear Information System (INIS)

    McPheron, Bruce A.

    2000-01-01

    Does the definition of a species matter for pest management purposes? Taxonomists provide us with tools - usually morphological characters - to identify a group of organisms that we call a species. The implication of this identification is that all of the individuals that fit the provided description are members of the species in question. The taxonomists have considered the range of variation among individuals in defining the species, but this variation is often forgotten when we take the concept of species to the level of management. Just as there is morphological variation among individuals, there is also variation in practically any character we might imagine, which has implications for the short and long term success of our management tactics. The rich literature on insecticide resistance should be a constant reminder of the fact that the pressure on pest survival and reproduction applied by our management approaches frequently leads to evolutionary changes within the pest species. The degree of variation within a particular species is a defining characteristic of that species. This level of variability may have very important implications for successful management, so it is very important to measure variation and, whenever possible, the genetic basis of that variation, in a target species. Population genetic approaches can provide evidence of genetic structure (or lack thereof) among populations of a species. These types of data can be used to discuss the movement of pest populations on a local or global scale. In other cases, we may have a complex of species that share some, but not all, characteristics. Species complexes that share morphological characters (i.e., cannot be easily distinguished) but not biological characters are referred to as sibling or cryptic species

  2. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    Directory of Open Access Journals (Sweden)

    Annalise B. Paaby

    2016-06-01

    Full Text Available Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits.

  3. Towards a genetic architecture of cryptic genetic variation

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 84; Issue 3. Towards a genetic architecture of cryptic genetic variation and genetic assimilation: the contribution of K. G. Bateman. Ian Dworkin. Commentary on J. Genet. Classic Volume 84 Issue 3 December 2005 pp 223-226 ...

  4. Towards a genetic architecture of cryptic genetic variation and ...

    Indian Academy of Sciences (India)

    Unknown

    reprinted in this issue as a J. Genet. classic, pages 227–257). IAN DWORKIN* ... In this commentary, I will discuss the context of this work examining the genetic ... mental buffering where development was channelled in one of several ...

  5. Genetic variation in Phoca vitulina (the harbour seal) revealed by DNA fingerprinting and RAPDs

    NARCIS (Netherlands)

    Kappe, A.L.; van de Zande, L.; Vedder, E.J.; Bijlsma, R.; van Delden, Wilke

    Genetic variation in two harbour seal (Phoca vitulina) populations from the Dutch Wadden Sea and Scotland was examined by RAPD analysis and DNA fingerprinting. For comparison a population of grey seals (Halichoerus grypus) was studied. The RAPD method revealed a very low number of polymorphic bands.

  6. Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development.

    Directory of Open Access Journals (Sweden)

    Nuno D Pires

    2016-01-01

    Full Text Available Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship theory proposes that imprinting can evolve due to a conflict between maternal and paternal alleles over resource allocation during seed development. One assumption of this theory is that paternal alleles can regulate seed growth; however, paternal effects on seed size are often very low or non-existent. We demonstrate that there is a pool of cryptic genetic variation in the paternal control of Arabidopsis thaliana seed development. Such cryptic variation can be exposed in seeds that maternally inherit a medea mutation, suggesting that MEA acts as a maternal buffer of paternal effects. Genetic mapping using recombinant inbred lines, and a novel method for the mapping of parent-of-origin effects using whole-genome sequencing of segregant bulks, indicate that there are at least six loci with small, paternal effects on seed development. Together, our analyses reveal the existence of a pool of hidden genetic variation on the paternal control of seed development that is likely shaped by parental conflict.

  7. Cryptic within cryptic: genetics, morphometrics, and bioacoustics delimitate a new species of Eleutherodactylus (Anura: Eleutherodactylidae) from Eastern Cuba.

    Science.gov (United States)

    Rodríguez, Ariel; Dugo-Cota, Álvaro; Montero-Mendieta, Santiago; Gonzalez-Voyer, Alejandro; Bosch, Roberto Alonso; Vences, Miguel; Vilà, Carles

    2017-01-20

    We studied the variation in genetics, bioacustics, and morphology in Eleutherodactylus glamyrus, a regionally endemic frog species restricted to high elevations in the Sierra Maestra Massif, Western Cuba that was originally described as a cryptic species hidden under the name E. auriculatus. Genetic analysis of mtDNA sequences of the 16S and cob genes identify two allopatric and strongly supported mitochondrial clades (phylogroups) which also showed no haplotype sharing in the nuclear Rag-1 gene. Bioacustic, and morphological comparisons concordantly identify these two phylogroups as independent evolutionary lineages. Therefore, we herein restrict the name Eleutherodactylus glamyrus Estrada and Hedges to populations represented in our analyses as the western phylogroup (Cordillera del Turquino to Pico La Bayamesa) and consider specimens from the eastern phylogroup (Sierra del Cobre) to represent a new species described and named as Eleutherodactylus cattus. Our results add to the growing list of Eleutherodactylus species endemic to Cuba and highlight the importance of combining different sources of evidence for obtaining robust assessments of species limits in amphibians.

  8. Integrating genetic data and population viability analyses for the identification of harbour seal (Phoca vitulina) populations and management units

    DEFF Research Database (Denmark)

    Olsen, Morten Tange; Andersen, Liselotte Wesley; Dietz, Rune

    2014-01-01

    present a novel approach, integrating genetic, life-history and demographic data to identify populations and management units in southern Scandinavian harbour seals. First, 15 microsatellite markers and model- and distance-based genetic clustering methods were used to determine the population genetic...... structure in harbour seals. Second, we used harbour seal demographic and life-history data to conduct population viability analyses (PVAs) in the VORTEX simulation model in order to determine whether the inferred genetic units could be classified as management units according to Lowe and Allendorf's (2010......, and that the combined use of genetic data and PVAs constitute a promising approach for delineating populations and management units. This article is protected by copyright. All rights reserved....

  9. A population on the edge: genetic diversity and population structure of the world's northernmost harbour seals (Phoca vitulina)

    DEFF Research Database (Denmark)

    Andersen, Liselotte Wesley; Lydersen, Christian; Frie, Anne Kirstine

    2011-01-01

    insight into consequences of population declines in a broader conservation context. The harbour seal population at Svalbard is the world's northernmost harbour seal population. Nothing is known about the genetic diversity, distinctiveness or origin of this small, marginalized mammalian population. Thus......  It is crucial to examine the genetic diversity and structure of small, isolated populations, especially those at the edge of their distribution range, because they are vulnerable to stochastic processes if genetic diversity is low and isolation level high, and because such populations provide...... microsatellites and variation in the D-loop. Each of the four locations was a genetically distinct population. The Svalbard population was highly genetically distinct, had reduced genetic diversity, received limited gene flow, had a rather low effective population size and showed an indication of having...

  10. Structure and amount of genetic variation at minisatellite loci within the subspecies complex of Phoca vitulina (the harbour seal)

    NARCIS (Netherlands)

    Kappe, A.L.; Bijlsma, R.; Osterhaus, ADME; van Delden, W.; van de Zande, L.

    The structure and amount of genetic variation within and between three subspecies of the harbour seal Phoca vitulina was assessed by multilocus DNA fingerprinting. Bandsharing similarity indicates that the subspecies Phoca vitulina richarhsi (Alaska, East Pacific) is clearly separated from the other

  11. Genetics, morphology and ecology reveal a cryptic pika lineage in the Sikkim Himalaya.

    Science.gov (United States)

    Dahal, Nishma; Lissovsky, Andrey A; Lin, Zhenzhen; Solari, Katherine; Hadly, Elizabeth A; Zhan, Xiangjiang; Ramakrishnan, Uma

    2017-01-01

    Asian pika species are morphologically ∼similar and have overlapping ranges. This leads to uncertainty and species misidentification in the field. Phylogenetic analyses of such misidentified samples leads to taxonomic ambiguity. The ecology of many pika species remains understudied, particularly in the Himalaya, where sympatric species could be separated by elevation and/or substrate. We sampled, measured, and acquired genetic data from pikas in the Sikkim Himalaya. Our analyses revealed a cryptic lineage, Ochotona sikimaria, previously reported as a subspecies of O. thibetana. The results support the elevation of this lineage to the species level, as it is genetically divergent from O. thibetana, as well as sister species, O. cansus (endemic to central China) and O. curzoniae (endemic to the Tibetan plateau). The Sikkim lineage diverged from its sister species' about 1.7-0.8myrago, coincident with uplift events in the Himalaya. Our results add to the recent spate of cryptic diversity identified from the eastern Himalaya and highlight the need for further study within the Ochotonidae. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. DNA barcoding applied to ex situ tropical amphibian conservation programme reveals cryptic diversity in captive populations.

    Science.gov (United States)

    Crawford, Andrew J; Cruz, Catalina; Griffith, Edgardo; Ross, Heidi; Ibáñez, Roberto; Lips, Karen R; Driskell, Amy C; Bermingham, Eldredge; Crump, Paul

    2013-11-01

    Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community. © 2012 John Wiley & Sons Ltd.

  13. Clinical and genetic features of dyskeratosis congenita, cryptic dyskeratosis congenita, and Hoyeraal-Hreidarsson syndrome in Japan.

    Science.gov (United States)

    Yamaguchi, Hiroki; Sakaguchi, Hirotoshi; Yoshida, Kenichi; Yabe, Miharu; Yabe, Hiromasa; Okuno, Yusuke; Muramatsu, Hideki; Takahashi, Yoshiyuki; Yui, Shunsuke; Shiraishi, Yuichi; Chiba, Kenichi; Tanaka, Hiroko; Miyano, Satoru; Inokuchi, Koiti; Ito, Etsuro; Ogawa, Seishi; Kojima, Seiji

    2015-11-01

    Dyskeratosis congenita (DKC) is an inherited bone marrow failure (BMF) syndrome typified by reticulated skin pigmentation, nail dystrophy, and mucosal leukoplakia. Hoyeraal-Hreidarsson syndrome (HHS) is considered to be a severe form of DKC. Unconventional forms of DKC, which develop slowly in adulthood but without the physical anomalies characteristic of DKC (cryptic DKC), have been reported. Clinical and genetic features of DKC have been investigated in Caucasian, Black, and Hispanic populations, but not in Asian populations. The present study aimed to determine the clinical and genetic features of DKC, HHS, and cryptic DKC among Japanese patients. We analyzed 16 patients diagnosed with DKC, three patients with HHS, and 15 patients with cryptic DKC. We found that platelet count was significantly more depressed than neutrophil count or hemoglobin value in DKC patients, and identified DKC patients with large deletions in the telomerase reverse transcriptase and cryptic DKC patients with RTEL1 mutations on both alleles. This led to some patients previously considered to have unclassifiable BMF being diagnosed with cDKC through identification of new gene mutations. It thus seems important from a clinical viewpoint to re-examine the clinical characteristics, frequency of genetic mutations, and treatment efficacy in DKC, HHS, and cDKC.

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

    Directory of Open Access Journals (Sweden)

    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

  15. Molecular analysis of echinostome metacercariae from their second intermediate host found in a localised geographic region reveals genetic heterogeneity and possible cryptic speciation.

    Directory of Open Access Journals (Sweden)

    Waraporn Noikong

    2014-04-01

    Full Text Available Echinostome metacercariae are the infective stage for humans and animals. The identification of echinostomes has been based until recently on morphology but molecular techniques using sequences of ribosomal RNA and mitochondrial DNA have indicated major clades within the group. In this study we have used the ITS2 region of ribosomal RNA and the ND1 region of mitochondrial DNA to identify metacercariae from snails collected from eight well-separated sites from an area of 4000 km2 in Lamphun Province, Thailand. The derived sequences have been compared to those collected from elsewhere and have been deposited in the nucleotide databases. There were two aims of this study; firstly, to determine the species of echinostome present in an endemic area, and secondly, to assess the intra-specific genetic diversity, as this may be informative with regard to the potential for the development of anthelmintic resistance and with regard to the spread of infection by the definitive hosts. Our results indicate that the most prevalent species are most closely related to E. revolutum, E. trivolvis, E. robustum, E. malayanum and Euparyphium albuferensis. Some sites harbour several species and within a site there could be considerable intra-species genetic diversity. There is no significant geographical structuring within this area. Although the molecular techniques used in this study allowed the assignment of the samples to clades within defined species, however, within these groupings there were significant differences indicating that cryptic speciation may have occurred. The degree of genetic diversity present would suggest the use of targeted regimes designed to minimise the selection of anthelmintic resistance. The apparent lack of geographic structuring is consistent with the transmission of the parasites by the avian hosts.

  16. Pinpointing cryptic borders: Fine-scale phylogeography and genetic landscape analysis of the Hormogaster elisae complex (Oligochaeta, Hormogastridae).

    Science.gov (United States)

    Marchán, Daniel F; Fernández, Rosa; de Sosa, Irene; Díaz Cosín, Darío J; Novo, Marta

    2017-07-01

    Spatial and temporal aspects of the evolution of cryptic species complexes have received less attention than species delimitation within them. The phylogeography of the cryptic complex Hormogaster elisae (Oligochaeta, Hormogastridae) lacks knowledge on several aspects, including the small-scale distribution of its lineages or the palaeogeographic context of their diversification. To shed light on these topics, a dense specimen collection was performed in the center of the Iberian Peninsula - resulting in 28 new H. elisae collecting points, some of them as close as 760m from each other- for a higher resolution of the distribution of the cryptic lineages and the relationships between the populations. Seven molecular regions were amplified: mitochondrial subunit 1 of cytochrome c oxidase (COI), 16S rRNA and tRNA Leu, Ala, and Ser (16S t-RNAs), one nuclear ribosomal gene (a fragment of 28S rRNA) and one nuclear protein-encoding gene (histone H3) in order to infer their phylogenetic relationships. Different representation methods of the pairwise divergence in the cytochrome oxidase I sequence (heatmap and genetic landscape graphs) were used to visualize the genetic structure of H. elisae. A nested approach sensu Mairal et al. (2015) (connecting the evolutionary rates of two datasets of different taxonomic coverage) was used to obtain one approximation to a time-calibrated phylogenetic tree based on external Clitellata fossils and a wide molecular dataset. Our results indicate that limited active dispersal ability and ecological or biotic barriers could explain the isolation of the different cryptic lineages, which never co-occur. Rare events of long distance dispersal through hydrochory appear as one of the possible causes of range expansion. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Proliferation and survival molecules implicated in the inhibition of BRAF pathway in thyroid cancer cells harbouring different genetic mutations

    International Nuclear Information System (INIS)

    Preto, Ana; Soares, Paula; Sobrinho-Simões, Manuel; Gonçalves, Joana; Rebocho, Ana P; Figueiredo, Joana; Meireles, Ana M; Rocha, Ana S; Vasconcelos, Helena M; Seca, Hugo; Seruca, Raquel

    2009-01-01

    Thyroid carcinomas show a high prevalence of mutations in the oncogene BRAF which are inversely associated with RAS or RET/PTC oncogenic activation. The possibility of using inhibitors on the BRAF pathway as became an interesting therapeutic approach. In thyroid cancer cells the target molecules, implicated on the cellular effects, mediated by inhibition of BRAF are not well established. In order to fill this lack of knowledge we studied the proliferation and survival pathways and associated molecules induced by BRAF inhibition in thyroid carcinoma cell lines harbouring distinct genetic backgrounds. Suppression of BRAF pathway in thyroid cancer cell lines (8505C, TPC1 and C643) was achieved using RNA interference (RNAi) for BRAF and the kinase inhibitor, sorafenib. Proliferation analysis was performed by BrdU incorporation and apoptosis was accessed by TUNEL assay. Levels of protein expression were analysed by western-blot. Both BRAF RNAi and sorafenib inhibited proliferation in all the cell lines independently of the genetic background, mostly in cells with BRAF V600E mutation. In BRAF V600E mutated cells inhibition of BRAF pathway lead to a decrease in ERK1/2 phosphorylation and cyclin D1 levels and an increase in p27 Kip1 . Specific inhibition of BRAF by RNAi in cells with BRAF V600E mutation had no effect on apoptosis. In the case of sorafenib treatment, cells harbouring BRAF V600E mutation showed increase levels of apoptosis due to a balance of the anti-apoptotic proteins Mcl-1 and Bcl-2. Our results in thyroid cancer cells, namely those harbouring BRAF V600E mutation showed that BRAF signalling pathway provides important proliferation signals. We have shown that in thyroid cancer cells sorafenib induces apoptosis by affecting Mcl-1 and Bcl-2 in BRAF V600E mutated cells which was independent of BRAF. These results suggest that sorafenib may prove useful in the treatment of thyroid carcinomas, particularly those refractory to conventional treatment and

  18. Quantitative Genetics Identifies Cryptic Genetic Variation Involved in the Paternal Regulation of Seed Development

    NARCIS (Netherlands)

    Pires, Nuno D.; Bemer, Marian; Müller, Lena M.; Baroux, Célia; Spillane, Charles; Grossniklaus, Ueli

    2016-01-01

    Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can

  19. Cryptic diversity and population genetic structure in the rare, endemic, forest-obligate, slender geckos of the Philippines.

    Science.gov (United States)

    Siler, Cameron D; Dececchi, T Alex; Merkord, Chris L; Davis, Drew R; Christiani, Tony J; Brown, Rafe M

    2014-01-01

    Recent studies of forest lizards in Southeast Asia have highlighted spectacular morphological and cryptic genetic diversity in several poorly known clades. Unfortunately, many of the included species have microhabitat preferences for forested environments, and therefore they are threatened by extensive forest destruction throughout the region. This is particularly true in the Philippines, an archipelago with a strikingly high proportion (84%) of endemic geckos. Abundances inferred from historical museum collections suggests that we are in a critical period where apparent declines in population viability and species' abundance have taken place faster than the growth in our understanding of alpha diversity. This phenomenon is exemplified in the exceedingly rare Philippine slender forest geckos of the genus Pseudogekko. Most of the known species are rarely encountered by field biologists, and species boundaries are unclear; this poor state of knowledge impedes effective conservation measures. Using the first multilocus phylogeny for these taxa, and phylogenetic and population genetic approaches, we elucidate evolutionary lineages and delimit species-level conservation targets in this unique radiation of endemic Philippine geckos. The results support the presence of widespread cryptic diversity in the genus, providing a framework for the re-evaluation of conservation priorities aimed at protecting these rare, forest-obligate species. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis

    NARCIS (Netherlands)

    Festen, E. A. M.; Goyette, P.; Scott, R.; Annese, V.; Zhernakova, A.; Lian, J.; Lefebvre, C.; Brant, S. R.; Cho, J. H.; Silverberg, M. S.; Taylor, K. D.; de Jong, D. J.; Stokkers, P. C.; Mcgovern, D.; Palmieri, O.; Achkar, J-P; Xavier, R. J.; Daly, M. J.; Duerr, R. H.; Wijmenga, C.; Weersma, R. K.; Rioux, J. D.

    Objectives: Genetic susceptibility is known to play a large part in the predisposition to the inflammatory bowel diseases (IBDs) known as Crohn's disease (CD) and ulcerative colitis (UC). The IL2/IL21 locus on 4q27 is known to be a common risk locus for inflammatory disease (shown in coeliac

  1. Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis

    NARCIS (Netherlands)

    Festen, E.A.M.; Goyette, P.; Scott, R.; Annese, V.; Zhernakova, A.; Lian, J.; Lefèbvre, C.; Brant, S.R.; Cho, J.H.; Silverberg, M.S.; Taylor, K.D.; de Jong, D.J.; Stokkers, P.C.; Mcgovern, D.; Palmieri, O.; Achkar, J.P.; Xavier, R.J.; Daly, M.J.; Duerr, R.H.; Wijmenga, C.; Weersma, R.K.; Rioux, J.D.

    2009-01-01

    Objectives: Genetic susceptibility is known to play a large part in the predisposition to the inflammatory bowel diseases (IBDs) known as Crohn's disease (CD) and ulcerative colitis (UC). The IL2/IL21 locus on 4q27 is known to be a common risk locus for inflammatory disease (shown in coeliac

  2. Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis

    NARCIS (Netherlands)

    Festen, E. A. M.; Goyette, P.; Scott, R.; Annese, V.; Zhernakova, A.; Lian, J.; Lefèbvre, C.; Brant, S. R.; Cho, J. H.; Silverberg, M. S.; Taylor, K. D.; de Jong, D. J.; Stokkers, P. C.; Mcgovern, D.; Palmieri, O.; Achkar, J.-P.; Xavier, R. J.; Daly, M. J.; Duerr, R. H.; Wijmenga, C.; Weersma, R. K.; Rioux, J. D.

    2009-01-01

    Genetic susceptibility is known to play a large part in the predisposition to the inflammatory bowel diseases (IBDs) known as Crohn's disease (CD) and ulcerative colitis (UC). The IL2/IL21 locus on 4q27 is known to be a common risk locus for inflammatory disease (shown in coeliac disease, type 1

  3. Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis.

    NARCIS (Netherlands)

    Festen, E.A.; Goyette, P.; Scott, R.; Annese, V.; Zhernakova, A.; Lian, J.; Lefebvre, C.; Brant, S.R.; Cho, J.H.; Silverberg, M.S.; Taylor, K.D.; Jong, D.J. de; Stokkers, P.C.; Mcgovern, D.; Palmieri, O.; Achkar, J.P.; Xavier, R.J.; Daly, M.J.; Duerr, R.H.; Wijmenga, C.; Weersma, R.K.; Rioux, J.D.

    2009-01-01

    OBJECTIVES: Genetic susceptibility is known to play a large part in the predisposition to the inflammatory bowel diseases (IBDs) known as Crohn's disease (CD) and ulcerative colitis (UC). The IL2/IL21 locus on 4q27 is known to be a common risk locus for inflammatory disease (shown in coeliac

  4. Nuclear and mitochondrial markers reveal evidence for genetically segregated cryptic speciation in giant Pacific octopuses from Prince William Sound, Alaska

    Science.gov (United States)

    Toussaint, Rebecca K.; Scheel, David; Sage, G.K.; Talbot, S.L.

    2012-01-01

    Multiple species of large octopus are known from the north Pacific waters around Japan, however only one large species is known in the Gulf of Alaska (the giant Pacific octopus, Enteroctopus dofleini). Current taxonomy of E. dofleini is based on geographic and morphological characteristics, although with advances in genetic technology that is changing. Here, we used two mitochondrial genes (cytochrome b and cytochrome oxidase I), three nuclear genes (rhodopsin, octopine dehydrogenase, and paired-box 6), and 18 microsatellite loci for phylogeographic and phylogenetic analyses of octopuses collected from across southcentral and the eastern Aleutian Islands (Dutch Harbor), Alaska. Our results suggest the presence of a cryptic Enteroctopus species that is allied to, but distinguished from E. dofleini in Prince William Sound, Alaska. Existence of an undescribed and previously unrecognized taxon raises important questions about the taxonomy of octopus in southcentral Alaska waters.

  5. Cryptic speciation in the recently discovered American cycliophoran Symbion americanus; genetic structure and population expansion

    DEFF Research Database (Denmark)

    Baker, J.M.; Funch, Peter; Giribet, G.

    2007-01-01

      Symbion americanus was recently described as the second species in the phylum Cycliophora, living commensally on the American commercial lobster Homarus americanus. A previous genetic analysis of American and European populations of cycliophorans suggested that haplotype divergence in S....... americanus was much greater than in its European counterpart S. pandora. This study examined the population structure and demographics of 169 individuals thought to belong to S. americanus collected from lobsters over 13 North American localities (Nova Scotia, Canada to Maryland, USA) between October 2003...... and January 2006. Cytochrome c oxidase subunit I sequence data clearly suggested the presence of three cryptic lineages in a species complex, often co-occurring in the same lobster specimens. One of these lineages, named the "G" lineage, was represented by very few individuals and therefore was excluded from...

  6. Cryptic changes in the genetic structure of a highly clonal coral population and the relationship with ecological performance

    Science.gov (United States)

    Williams, Dana E.; Miller, M. W.; Baums, I. B.

    2014-09-01

    Elkhorn coral , Acropora palmata, relies heavily on clonal propagation and often displays low genotypic (clonal) diversity. Populations in the Florida Keys experienced rapid declines in tissue cover between 2004 and 2006, largely due to hurricanes and disease, but remained stable from 2006 to 2010. All elkhorn colonies in 150 m2 permanent study plots were genotyped in 2006 ( n = 15 plots) and 2010 ( n = 24 plots), and plots sampled in both years were examined for changes in allelic and genotypic diversity during this period of stable ecological abundance. Overall, genetic diversity of Florida plots was low and declined further over the 4-yr period; seven of the 36 original genets and two of 67 alleles (among five microsatellite loci) were lost completely from the sampled population, and an additional 15 alleles were lost from individual reefs. In 2010, Florida plots (~19 colonies) contained an average of 2.2 ± 1.38 (mean ± SD) genets with a significant negative correlation between colony abundance and genotypic diversity. When scaled to total tissue abundance, genotypic diversity is even lower, with 43 % of genets below the size of sexual maturity. We examined the hypothesized positive relationship of local genotypic diversity with ecological performance measures. In Florida plots ( n = 15), genotypic diversity was not significantly correlated with tissue loss associated with chronic predation, nor with acute disease and storm-fragmentation events, though this relationship may be obscured by the low range of observed diversity and potential confounding with abundance. When more diverse plots in Curaçao ( n = 9) were examined, genotypic diversity was not significantly correlated with resistance during an acute storm disturbance or rate of recovery following disturbance. Cryptic loss of genetic diversity occurred in the apparently stable Florida population and confirms that stable or even increasing abundance does not necessarily indicate genetic stability.

  7. Genetic Structure and Antimicrobial Resistance of Escherichia coli and Cryptic Clades in Birds with Diverse Human Associations.

    Science.gov (United States)

    Blyton, Michaela D J; Pi, Hongfei; Vangchhia, Belinda; Abraham, Sam; Trott, Darren J; Johnson, James R; Gordon, David M

    2015-08-01

    The manner and extent to which birds associate with humans may influence the genetic attributes and antimicrobial resistance of their commensal Escherichia communities through strain transmission and altered selection pressures. In this study, we determined whether the distribution of the different Escherichia coli phylogenetic groups and cryptic clades, the occurrence of 49 virulence associated genes, and/or the prevalence of resistance to 12 antimicrobials differed between four groups of birds from Australia with contrasting types of human association. We found that birds sampled in suburban and wilderness areas had similar Escherichia communities. The Escherichia communities of backyard domestic poultry were phylogenetically distinct from the Escherichia communities sourced from all other birds, with a large proportion (46%) of poultry strains belonging to phylogenetic group A and a significant minority (17%) belonging to the cryptic clades. Wild birds sampled from veterinary and wildlife rehabilitation centers (in-care birds) carried Escherichia isolates that possessed particular virulence-associated genes more often than Escherichia isolates from birds sampled in suburban and wilderness areas. The Escherichia isolates from both the backyard poultry and in-care birds were more likely to be multidrug resistant than the Escherichia isolates from wild birds. We also detected a multidrug-resistant E. coli strain circulating in a wildlife rehabilitation center, reinforcing the importance of adequate hygiene practices when handling and caring for wildlife. We suggest that the relatively high frequency of antimicrobial resistance in the in-care birds and backyard poultry is due primarily to the use of antimicrobials in these animals, and we recommend that the treatment protocols used for these birds be reviewed. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  8. Genetic structure, nestmate recognition and behaviour of two cryptic species of the invasive big-headed ant Pheidole megacephala.

    Directory of Open Access Journals (Sweden)

    Denis Fournier

    Full Text Available Biological invasions are recognized as a major cause of biodiversity decline and have considerable impact on the economy and human health. The African big-headed ant Pheidole megacephala is considered one of the world's most harmful invasive species.To better understand its ecological and demographic features, we combined behavioural (aggression tests, chemical (quantitative and qualitative analyses of cuticular lipids and genetic (mitochondrial divergence and polymorphism of DNA microsatellite markers data obtained for eight populations in Cameroon. Molecular data revealed two cryptic species of P. megacephala, one inhabiting urban areas and the other rainforests. Urban populations belong to the same phylogenetic group than those introduced in Australia and in other parts of the world. Behavioural analyses show that the eight populations sampled make up four mutually aggressive supercolonies. The maximum distance between nests from the same supercolony was 49 km and the closest distance between two nests belonging to two different supercolonies was 46 m. The genetic data and chemical analyses confirmed the behavioural tests as all of the nests were correctly assigned to their supercolony. Genetic diversity appears significantly greater in Africa than in introduced populations in Australia; by contrast, urban and Australian populations are characterized by a higher chemical diversity than rainforest ones.Overall, our study shows that populations of P. megacephala in Cameroon adopt a unicolonial social structure, like invasive populations in Australia. However, the size of the supercolonies appears several orders of magnitude smaller in Africa. This implies competition between African supercolonies and explains why they persist over evolutionary time scales.

  9. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

    Science.gov (United States)

    Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

    2011-12-01

    Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

  10. Detection of cryptic species

    International Nuclear Information System (INIS)

    Cockburn, A.F.; Jensen, T.; Seawright, J.A.

    1998-01-01

    Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insect were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keen the individual genes homogeneous within a species. (author)

  11. Detection of cryptic species

    Energy Technology Data Exchange (ETDEWEB)

    Cockburn, A F; Jensen, T; Seawright, J A [United States Dept. of Agriculture, Agricultural Research Service, Medical and Veterinary Entomology Research Lab., Gainesville, FL (United States)

    1998-01-01

    Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insect were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keen the individual genes homogeneous within a species. (author). 11 refs, 2 figs, 2 tabs.

  12. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

    Directory of Open Access Journals (Sweden)

    Michel Tibayrenc

    2014-04-01

    Full Text Available An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination, are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately ("Russian doll pattern". Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections ("starving sex hypothesis". We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

  13. Cryptic distant relatives are common in both isolated and cosmopolitan genetic samples.

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    Brenna M Henn

    Full Text Available Although a few hundred single nucleotide polymorphisms (SNPs suffice to infer close familial relationships, high density genome-wide SNP data make possible the inference of more distant relationships such as 2(nd to 9(th cousinships. In order to characterize the relationship between genetic similarity and degree of kinship given a timeframe of 100-300 years, we analyzed the sharing of DNA inferred to be identical by descent (IBD in a subset of individuals from the 23andMe customer database (n = 22,757 and from the Human Genome Diversity Panel (HGDP-CEPH, n = 952. With data from 121 populations, we show that the average amount of DNA shared IBD in most ethnolinguistically-defined populations, for example Native American groups, Finns and Ashkenazi Jews, differs from continentally-defined populations by several orders of magnitude. Via extensive pedigree-based simulations, we determined bounds for predicted degrees of relationship given the amount of genomic IBD sharing in both endogamous and 'unrelated' population samples. Using these bounds as a guide, we detected tens of thousands of 2(nd to 9(th degree cousin pairs within a heterogenous set of 5,000 Europeans. The ubiquity of distant relatives, detected via IBD segments, in both ethnolinguistic populations and in large 'unrelated' populations samples has important implications for genetic genealogy, forensics and genotype/phenotype mapping studies.

  14. Contradictory genetic make-up of Dutch harbour porpoises: Response to van der Plas-Duivesteijn et al.

    Science.gov (United States)

    Kopps, Anna M.; Palsbøll, Per J.

    2016-02-01

    The assessment of the status of endangered species or populations typically draw generously on the plethora of population genetic software available to detect population genetic structuring. However, despite the many available analytical approaches, population genetic inference methods [of neutral genetic variation] essentially capture three basic processes; migration, random genetic drift and mutation. Consequently, different analytical approaches essentially capture the same basic process, and should yield consistent results.

  15. Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in south Africa

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    van Hooft Pim

    2011-02-01

    Full Text Available Abstract Background South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present. Results To this end, intensified sampling at 28 South African localities and at one site in Swaziland, identified 149 Rattus specimens. Cytochrome b gene sequencing revealed the presence of two R. tanezumi, seven Rattus rattus and five Rattus norvegicus haplotypes in south Africa. Phylogenetic results were consistent with a single, recent R. tanezumi introduction and indicated that R. norvegicus and R. rattus probably became established following at least two and three independent introductions, respectively. Intra- and inter-specific diversity was highest in informal human settlements, with all three species occurring at a single metropolitan township site. Rattus norvegicus and R. rattus each occurred sympatrically with Rattus tanezumi at one and five sites, respectively. Karyotyping of selected R. rattus and R. tanezumi individuals identified diploid numbers consistent with those reported previously for these cryptic species. Ordination of bioclimatic variables and MaxEnt ecological niche modelling confirmed that the bioclimatic niche occupied by R. tanezumi in south Africa was distinct from that occupied in its naturalised range in south-east Asia suggesting that factors other than climate may influence the distribution of this species. Conclusions This study has highlighted the value of genetic typing for detecting cryptic invasive species, providing

  16. Cryptic genetic diversity in the mottled rabbitfish Siganus fuscescens with mitochondrial introgression at a contact zone in the South China Sea.

    Science.gov (United States)

    Ravago-Gotanco, Rachel; de la Cruz, Talna Lorena; Pante, Ma Josefa; Borsa, Philippe

    2018-01-01

    The taxonomy of the mottled rabbitfish Siganus fuscescens species complex has long been challenging. In this study, we analyzed microsatellite genotypes, mitochondrial lineages, and morphometric data from 373 S. fuscescens individuals sampled from the northern Philippines and Hong Kong (South China Sea, Philippine Sea and Sulu Sea basins), to examine putative species boundaries in samples comprising three co-occurring mitochondrial lineages previously reported to characterize S. fuscescens (Clade A and Clade B) or S. canaliculatus (Clade C). We report the existence of two cryptic species within S. fuscescens in the northeast region of the South China Sea and northern Philippine Sea, supported by genetic and morphological differences. Individual-based assignment methods recovered concordant groupings of individuals into two nuclear genotype clusters (Cluster 1, Cluster 2) with (1) limited gene flow, if any, between them (FST = 0.241; P South China Sea. Mitonuclear discordance due to introgression obscures phylogenetic relationships for recently-diverged lineages, and cautions against the use of mitochondrial markers alone for species identification within the mottled rabbitfish species complex in the South China Sea region.

  17. Cryptic genetic diversity is paramount in small-bodied amphibians of the genus Euparkerella (Anura: Craugastoridae endemic to the Brazilian Atlantic forest.

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    Luciana A Fusinatto

    Full Text Available Morphological similarity associated to restricted distributions and low dispersal abilities make the direct developing "Terrarana" frogs of the genus Euparkerella a good model for examining diversification processes. We here infer phylogenetic relationships within the genus Euparkerella, using DNA sequence data from one mitochondrial and four nuclear genes coupled with traditional Bayesian phylogenetic reconstruction approaches and more recent coalescent methods of species tree inference. We also used Bayesian clustering analysis and a recent Bayesian coalescent-based approach specifically to infer species delimitation. The analysis of 39 individuals from the four known Euparkerella species uncovered high levels of genetic diversity, especially within the two previously morphologically-defined E. cochranae and E. brasiliensis. Within these species, the gene trees at five independent loci and trees from combined data (concatenated dataset and the species tree uncovered six deeply diverged and geographically coherent evolutionary units, which may have diverged between the Miocene and the Pleistocene. These six units were also uncovered in the Bayesian clustering analysis, and supported by the Bayesian coalescent-based species delimitation (BPP, and Genealogical Sorting Index (GSI, providing thus strong evidence for underestimation of the current levels of diversity within Euparkerella. The cryptic diversity now uncovered opens new opportunities to examine the origins and maintenance of microendemism in the context of spatial heterogeneity and/or human induced fragmentation of the highly threatened Brazilian Atlantic forest hotspot.

  18. Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

    Directory of Open Access Journals (Sweden)

    Stephanie G Schuttler

    Full Text Available Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana and Asian (Elephas maximus species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and

  19. Fine-scale genetic structure and cryptic associations reveal evidence of kin-based sociality in the African forest elephant.

    Science.gov (United States)

    Schuttler, Stephanie G; Philbrick, Jessica A; Jeffery, Kathryn J; Eggert, Lori S

    2014-01-01

    Spatial patterns of relatedness within animal populations are important in the evolution of mating and social systems, and have the potential to reveal information on species that are difficult to observe in the wild. This study examines the fine-scale genetic structure and connectivity of groups within African forest elephants, Loxodonta cyclotis, which are often difficult to observe due to forest habitat. We tested the hypothesis that genetic similarity will decline with increasing geographic distance, as we expect kin to be in closer proximity, using spatial autocorrelation analyses and Tau K(r) tests. Associations between individuals were investigated through a non-invasive genetic capture-recapture approach using network models, and were predicted to be more extensive than the small groups found in observational studies, similar to fission-fusion sociality found in African savanna (Loxodonta africana) and Asian (Elephas maximus) species. Dung samples were collected in Lopé National Park, Gabon in 2008 and 2010 and genotyped at 10 microsatellite loci, genetically sexed, and sequenced at the mitochondrial DNA control region. We conducted analyses on samples collected at three different temporal scales: a day, within six-day sampling sessions, and within each year. Spatial autocorrelation and Tau K(r) tests revealed genetic structure, but results were weak and inconsistent between sampling sessions. Positive spatial autocorrelation was found in distance classes of 0-5 km, and was strongest for the single day session. Despite weak genetic structure, individuals within groups were significantly more related to each other than to individuals between groups. Social networks revealed some components to have large, extensive groups of up to 22 individuals, and most groups were composed of individuals of the same matriline. Although fine-scale population genetic structure was weak, forest elephants are typically found in groups consisting of kin and based on matrilines

  20. Genes Left Behind: Climate Change Threatens Cryptic Genetic Diversity in the Canopy-Forming Seaweed Bifurcaria bifurcata.

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    João Neiva

    Full Text Available The global redistribution of biodiversity will intensify in the coming decades of climate change, making projections of species range shifts and of associated genetic losses important components of conservation planning. Highly-structured marine species, notably brown seaweeds, often harbor unique genetic variation at warmer low-latitude rear edges and thus are of particular concern. Here, a combination of Ecological Niche Models (ENMs and molecular data is used to forecast the potential near-future impacts of climate change for a warm-temperate, canopy forming seaweed, Bifurcaria bifurcata. ENMs for B. bifurcata were developed using marine and terrestrial climatic variables, and its range projected for 2040-50 and 2090-2100 under two greenhouse emission scenarios. Geographical patterns of genetic diversity were assessed by screening 18 populations spawning the entire distribution for two organelle genes and 6 microsatellite markers. The southern limit of B. bifurcata was predicted to shift northwards to central Morocco by the mid-century. By 2090-2100, depending on the emission scenario, it could either retreat further north to western Iberia or be relocated back to Western Sahara. At the opposing margin, B. bifurcata was predicted to expand its range to Scotland or even Norway. Microsatellite diversity and endemism were highest in Morocco, where a unique and very restricted lineage was also identified. Our results imply that B. bifurcata will maintain a relatively broad latitudinal distribution. Although its persistence is not threatened, the predicted extirpation of a unique southern lineage or even the entire Moroccan diversity hotspot will erase a rich evolutionary legacy and shrink global diversity to current (low European levels. NW Africa and similarly understudied southern regions should receive added attention if expected range changes and diversity loss of warm-temperate species is not to occur unnoticed.

  1. Cryptic sexual populations account for genetic diversity and ecological success in a widely distributed, asexual fungus-growing ant.

    Science.gov (United States)

    Rabeling, Christian; Gonzales, Omar; Schultz, Ted R; Bacci, Maurício; Garcia, Marcos V B; Verhaagh, Manfred; Ishak, Heather D; Mueller, Ulrich G

    2011-07-26

    Sex and recombination are central processes in life generating genetic diversity. Organisms that rely on asexual propagation risk extinction due to the loss of genetic diversity and the inability to adapt to changing environmental conditions. The fungus-growing ant species Mycocepurus smithii was thought to be obligately asexual because only parthenogenetic populations have been collected from widely separated geographic localities. Nonetheless, M. smithii is ecologically successful, with the most extensive distribution and the highest population densities of any fungus-growing ant. Here we report that M. smithii actually consists of a mosaic of asexual and sexual populations that are nonrandomly distributed geographically. The sexual populations cluster along the Rio Amazonas and the Rio Negro and appear to be the source of independently evolved and widely distributed asexual lineages, or clones. Either apomixis or automixis with central fusion and low recombination rates is inferred to be the cytogenetic mechanism underlying parthenogenesis in M. smithii. Males appear to be entirely absent from asexual populations, but their existence in sexual populations is indicated by the presence of sperm in the reproductive tracts of queens. A phylogenetic analysis of the genus suggests that M. smithii is monophyletic, rendering a hybrid origin of asexuality unlikely. Instead, a mitochondrial phylogeny of sexual and asexual populations suggests multiple independent origins of asexual reproduction, and a divergence-dating analysis indicates that M. smithii evolved 0.5-1.65 million years ago. Understanding the evolutionary origin and maintenance of asexual reproduction in this species contributes to a general understanding of the adaptive significance of sex.

  2. Serratia marcescens harbouring SME-type class A carbapenemases in Canada and the presence of blaSME on a novel genomic island, SmarGI1-1.

    Science.gov (United States)

    Mataseje, L F; Boyd, D A; Delport, J; Hoang, L; Imperial, M; Lefebvre, B; Kuhn, M; Van Caeseele, P; Willey, B M; Mulvey, M R

    2014-07-01

    An increasing prevalence since 2010 of Serratia marcescens harbouring the Ambler class A carbapenemase SME prompted us to further characterize these isolates. Isolates harbouring bla(SME) were identified by PCR and sequencing. Phenotypic analysis for carbapenemase activity was carried out by a modified Hodge test and a modified Carba NP test. Antimicrobial susceptibilities were determined by Etest and Vitek 2. Typing was by PFGE of macrorestriction digests. Whole-genome sequencing of three isolates was carried out to characterize the genomic region harbouring the bla(SME)-type genes. All S. marcescens harbouring SME-type enzymes could be detected using a modified Carba NP test. Isolates harbouring bla(SME) were resistant to penicillins and carbapenems, but remained susceptible to third-generation cephalosporins, as well as fluoroquinolones and trimethoprim/sulfamethoxazole. Isolates exhibited diverse genetic backgrounds, though 57% of isolates were found in three clusters. Analysis of whole-genome sequence data from three isolates revealed that the bla(SME) gene occurred in a novel cryptic prophage genomic island, SmarGI1-1. There has been an increasing occurrence of S. marcescens harbouring bla(SME) in Canada since 2010. The bla(SME) gene was found on a genomic island, SmarGI1-1, that can be excised and circularized, which probably contributes to its dissemination amongst S. marcescens. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Firefly luciferase gene contains a cryptic promoter

    Czech Academy of Sciences Publication Activity Database

    Vopálenský, V.; Mašek, T.; Horváth, Ondřej; Vicenová, B.; Mokrejš, M.; Pospíšek, M.

    2008-01-01

    Roč. 14, č. 9 (2008), s. 1720-1729 ISSN 1355-8382 Grant - others:GAČR(CZ) GA204/03/1487; GAČR(CZ) GA301/07/0607; Mšk(CZ) LC06066 Program:LC Institutional research plan: CEZ:AV0Z50520514 Keywords : luciferase * cryptic promoter * hepatitis C virus Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.018, year: 2008

  4. Information accessibility and cryptic processes

    Energy Technology Data Exchange (ETDEWEB)

    Mahoney, John R; Ellison, Christopher J; Crutchfield, James P [Complexity Sciences Center and Physics Department, University of California at Davis, One Shields Avenue, Davis, CA 95616 (United States)], E-mail: jrmahoney@ucdavis.edu, E-mail: cellison@cse.ucdavis.edu, E-mail: chaos@cse.ucdavis.edu

    2009-09-11

    We give a systematic expansion of the crypticity-a recently introduced measure of the inaccessibility of a stationary process's internal state information. This leads to a hierarchy of k-cryptic processes and allows us to identify finite-state processes that have infinite cryptic order-the internal state information is present across arbitrarily long, observed sequences. The crypticity expansion is exact in both the finite- and infinite-order cases. It turns out that k-crypticity is complementary to the Markovian finite-order property that describes state information in processes. One application of these results is an efficient expansion of the excess entropy-the mutual information between a process's infinite past and infinite future-that is finite and exact for finite-order cryptic processes. (fast track communication)

  5. Molecular phylogeny of the genus Lolliguncula steenstrup, 1881 based on nuclear and mitochondrial DNA sequences indicates genetic isolation of populations from north and South atlantic, and the possible presence of further cryptic species.

    Directory of Open Access Journals (Sweden)

    João Bráullio L Sales

    Full Text Available Squid of the genus Lolliguncula Steenstrup, 1881 are small bodied, coastal species capable of tolerating low salinity. Lolliguncula sp. are found exclusively in the New World, although only one of the four recognized species (Lolliguncula brevis occurs in the Atlantic Ocean. Preliminary morphological analyses suggest that Lolliguncula brevis populations in the North and South Atlantic may represent distinct species. The principal objective of the present study was to verify the phylogenetic relationships within the genus and test for the presence of possible cryptic species. Both gene and species tree topologies indicated that Lolliguncula brevis specimens from the North and South Atlantic represent distinct phylogenetic clades. In contrast with previous studies, L. panamensis was identified as the basal species of the genus. Our results provide important insights into the phylogenetic relationships among the Lolliguncula specimens analyzed, and confirm the genetic separation of Lolliguncula brevis populations of the North and South Atlantic at the level of sister species.

  6. KINETIC ALGORITHMS FOR HARBOUR MANAGEMENT

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    C. M. Gold

    2012-07-01

    Full Text Available Modern harbour management for a busy port needs to resolve a variety of simultaneous problems. Harbour traffic may be busy and the waterways congested, both by the major shipping and by the attendant harbour tugs. The harbour channel may be narrow and tortuous, and rapidly changing tides may require frequent course adjustments. Navigation aids must be clearly specified and immediately identifiable, in order to permit safe passage for the vessels. This requires a GIS with attributes not easily available with traditional products. The GeoVS system is a kinetic GIS with full three-dimensional visualisation, so that ships, bathymetry and landscape may be viewed in a form that is immediately understandable to both harbour pilots and the harbour authority. The system is kinetic because the data structures used to preserve the topological relationships between ships, seafloor and coastline are able to be maintained on a real-time basis, taking account of ship movement recorded on the compulsory AIS (Automatic Information System beacons. Maintenance of this real-time topology allows for easy detection of potential collisions, as well as real-time bathymetric estimations, necessary to prevent ship grounding in highly tidal environments. The system, based on previous research into kinetic Voronoi diagrams, as well as development of a completely new graphical engine, is now in commercial production, where its advantages over simpler twodimensional models without automatic collision and grounding detection are becoming evident. Other applications are readily envisaged, and will be addressed in the near future.

  7. Muddy waters and the Wadden Sea harbours

    NARCIS (Netherlands)

    Eekelen, van E.; Baptist, M.J.; Dankers, P.; Grasmeijer, B.T.; Kessel, van T.; Maren, van D.S.

    2016-01-01

    Several harbours along the Dutch Wadden Sea deal with large siltation rates and limited possibilities for developments. However, development of new harbour activities is needed for these harbours to be able to survive in the long run. As these harbours lie in or close to areas with a protected

  8. Cryptic relatedness in epidemiologic collections accessed for genetic association studies: experiences from the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study and the National Health and Nutrition Examination Surveys (NHANES).

    Science.gov (United States)

    Malinowski, Jennifer; Goodloe, Robert; Brown-Gentry, Kristin; Crawford, Dana C

    2015-01-01

    Epidemiologic collections have been a major resource for genotype-phenotype studies of complex disease given their large sample size, racial/ethnic diversity, and breadth and depth of phenotypes, traits, and exposures. A major disadvantage of these collections is they often survey households and communities without collecting extensive pedigree data. Failure to account for substantial relatedness can lead to inflated estimates and spurious associations. To examine the extent of cryptic relatedness in an epidemiologic collection, we as the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study accessed the National Health and Nutrition Examination Surveys (NHANES) linked to DNA samples ("Genetic NHANES") from NHANES III and NHANES 1999-2002. NHANES are population-based cross-sectional surveys conducted by the National Center for Health Statistics at the Centers for Disease Control and Prevention. Genome-wide genetic data is not yet available in NHANES, and current data use agreements prohibit the generation of GWAS-level data in NHANES samples due issues in maintaining confidentiality among other ethical concerns. To date, only hundreds of single nucleotide polymorphisms (SNPs) genotyped in a variety of candidate genes are available for analysis in NHANES. We performed identity-by-descent (IBD) estimates in three self-identified subpopulations of Genetic NHANES (non-Hispanic white, non- Hispanic black, and Mexican American) using PLINK software to identify potential familial relationships from presumed unrelated subjects. We then compared the PLINKidentified relationships to those identified by an alternative method implemented in Kinship-based INference for Genome-wide association studies (KING). Overall, both methods identified familial relationships in NHANES III and NHANES 1999-2002 for all three subpopulations, but little concordance was observed between the two methods due in major part to the limited SNP data available in Genetic NHANES

  9. Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods

    Directory of Open Access Journals (Sweden)

    Carlos A. Santamaria

    2017-10-01

    Full Text Available Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.

  10. SECURITY SYSTEMS FOR MARITIME HARBOUR

    Directory of Open Access Journals (Sweden)

    Georgică SLĂMNOIU

    2010-11-01

    Full Text Available Infrastructure protection objectives are at the top of the agenda of those responsible in the European Union. Currently Romania is one of the countries on its eastern border of the Union and this has special implications in terms of security measures that are required to be implemented. Ships and harbours are important current conflict stage. An integrated system of protection of harbours must be prepared in advance in order to continuously provide information that will increase the overall performance of the intervention forces.

  11. The birds of Blyth Harbour

    International Nuclear Information System (INIS)

    Still, D.; Carver, H.; Little, B.; Lawrence, S.G.

    1995-01-01

    Blyth Harbour Wind Farm, constructed upon an exposed pier, is not a Site of Special Scientific Interest and is designated to become a RAMSAR location because of the presence of a significant population of the Purple Sandpiper. A study of the effect of the wind farm on the birds was started before the wind farm was constructed and is ongoing. Initial evidence of how the wind turbines have affected the 110 varieties of birds recorded within the harbour will be presented and compared to previous research carried out in Europe and the USA. Methodology has included intensive beach surveys, visits to wind farms in the UK and USA and consultations with wildlife advisory bodies. The study will continue until 1996. (Author)

  12. Transfer pricing and safe harbours

    Directory of Open Access Journals (Sweden)

    Veronika Solilová

    2013-01-01

    Full Text Available Transfer prices are significant for both taxpayers and tax administrations because they determine in large part taxable profits of associated enterprises in different tax jurisdictions. Moreover, in the context of taxation, transfer prices must be complied with the arm’s length principle. However, Multinational Enterprises have been faced daily by conflicting rules and approaches to applying the arm’s length principle, burdensome documentation requirements, inconsistent audit standards and unpredictable competent authority outcomes. Therefore, the Committee on Fiscal Affairs launched another project on the administrative aspects of transfer pricing in 2010. On 16 May 2013 as a partial solution of this project was approved by the OECD Council the Revised Section E on Safe Harbours in Chapter IV of the Transfer Pricing Guidelines for Multinational Enterprises and Tax Authorities. The paper is focused on significant changes of newly approved chapter IV of the Transfer Pricing Guidelines for Multinational Enterprises and Tax Authorities, further on analysis of practice in this area, on advantages and disadvantages of safe harbours for taxpayers and competent authorities with aim to suggest recommendations on use of safe harbours in the Czech Republic.

  13. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

    Directory of Open Access Journals (Sweden)

    Maris Hindrikson

    Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  14. Benthic ecological status of Algerian harbours.

    Science.gov (United States)

    Dauvin, J C; Bakalem, A; Baffreau, A; Grimes, S

    2017-12-15

    This work is an overview of all available benthic data collected in the Algerian harbours between 1983 and 2001. So, total of 571 stations were reported in the 10 major Algerian harbours along the Algerian coast (1200km). Two main categories of harbours were distinguished according to their hydrodynamic regime and volume of water exchange between inner harbour basins and the entrance of the harbours. Univariate, multivariate, benthic indices and Biological Traits of Life approaches were applied on stations sampled in the late 1990s and long-term observations in six out of these ten harbours. These approaches assessed the main characteristics and ecological statuses from these south Mediterranean harbours. One of the main characteristics of the Algerian harbours was the very high species diversity (847 species). Although all the fauna was dominated by pollution-tolerant species; some harbours such as Bethioua and Djendjen hosted normal benthic communities as found in the open sea, but also included some pollution indicator species typical of a slight polluted system. On the contrary, the newly constructed port of Skikda showed perturbed benthic communities in relation to hydrocarbon pollution. Biological Traits of Life analysis reinforced the separation of benthic species along a gradient reflecting their sensitivity or tolerance to pollution. This response was related to an increase in organic matter content, probably associated with a general organic and metal contamination, from the entrance of the harbour to the innermost basins in areas with weak circulation, high sedimentation rate and concentrations of pollutants. Except for Oran harbour, where the poor to moderate ecological status remained unchanged with time, the other harbours showed an improvement or a slight degradation. A strategy of long-term monitoring should be promoted, based on a restricted and selected number of stations characteristic of the different basins and water masses occupying the

  15. Balancing selection maintains cryptic colour morphs.

    Science.gov (United States)

    Wellenreuther, Maren

    2017-11-01

    Animals display incredibly diverse colour patterns, a testament to evolution's endless innovation in shaping life. In many species, the interplay between males and females in the pursuit of mates has driven the evolution of a myriad of colour forms, from the flashy peacock tail feathers to the tiniest colour markings in damselflies. In others, colour provides crypsis by allowing to blend into the background and to escape the eyes of predators. While the obvious benefits of this dazzling diversity for reproduction and survival seem straightforward, its maintenance is not. Theory predicts that genetic drift and various forms of selection reduce variation over time, making the persistence of colour variants over generations a puzzle. In this issue of Molecular Ecology, Lindtke et al. () study the cryptic colour morphs of Timema cristinae walking sticks to shed light on the genetic architecture and mechanisms that allow colour polymorphism maintenance over long timescales. By combining genome-wide data with phenotyping information from natural populations, they were able to map the green and melanistic colour to one genomic region with highly reduced effective recombination rate between two main chromosomal variants, consistent with an inversion polymorphism. These two main chromosomal variants showed geographically widespread heterozygote excess, and genomic signatures consistent with long-term balancing selection. A younger chromosomal variant was detected for the third morph, the green-striped colour morphs, in the same genomic regions as the melanistic and the green-unstriped morphs. Together, these results suggest that the genetic architecture of cryptic T. cristinae morphs is caused by nonrecombining genomic blocks that have been maintained over extended time periods by balancing selection making this study one of the few available empirical examples documenting that balancing selection of various forms may play an important role in maintaining adaptive genetic

  16. Source of Aegean Sea harbour porpoises

    DEFF Research Database (Denmark)

    Lockyer, Christina; Rosel, P. E.; Frantzis, A.

    2003-01-01

    Documented sightings of harbour porpoises in the Mediterranean are rare, although the species is common in the neighbouring North Atlantic and Black Sea. However, in the past 2 decades, 4 harbour porpoises Phocoena phocoena have been recorded in the northern Aegean Sea in the eastern Mediterranea...

  17. The structure of the transposable genetic element ISBsu2 from the cryptic plasmid p1516 of a soil Bacillus subtilis strain and the presence of homologues of this element in the chromosomes of various Bacillus subtilis strains

    NARCIS (Netherlands)

    Holsappel, S; Gagarina, EY; Poluektova, EU; Nezametdinova, VZ; Gel'fand, MS; Prozorov, AA; Bron, S

    2003-01-01

    A cryptic plasmid from a soil strain of Bacillus subtilis was found to contain a sequence having features of an IS element. Homologous sequences were also found in the chromosome of this strain and in the chromosomes of some other B. subtilis strains.

  18. Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex

    Science.gov (United States)

    Lajus, Dmitry; Sukhikh, Natalia; Alekseev, Victor

    2015-01-01

    Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the “cryptic or pseudocryptic” dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in-depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species

  19. Mercury in Thana creek, Bombay harbour

    Digital Repository Service at National Institute of Oceanography (India)

    Zingde, M.D.; Desai, B.N.

    weight) with marked increased from harbour to the creek region suggests substantial mercury input in the head region. Chemical extraction by hydrogen peroxide indicated that more than 70% of mercury was leachable and probably organically bound...

  20. Widespread prevalence of cryptic Symbiodinium D in the key Caribbean reef builder, Orbicella annularis

    Science.gov (United States)

    Kennedy, Emma V.; Foster, Nicola L.; Mumby, Peter J.; Stevens, Jamie R.

    2015-06-01

    Symbiodinium D, a relatively rare clade of algal endosymbiont with a global distribution, has attracted interest as some of its sub-cladal types induce increased thermal tolerance and associated trade-offs, including reduced growth rate in its coral hosts. Members of Symbiodinium D are increasingly reported to comprise low-abundance `cryptic' (30 % of corals per site found to harbour the symbiont. When the same samples were analysed using the conventional screening technique, denaturing gradient gel electrophoresis, Symbiodinium D1 was only detected in 12 populations and appeared to be hosted by agreement with other reported low prevalence/absences in O. annularis). Cryptic Symbiodinium D1 showed a mainly uniform distribution across the wider Caribbean region, although significantly more Mesoamerican Barrier Reef corals hosted cryptic Symbiodinium D1 than might be expected by chance, possibly as a consequence of intense warming in the region in 1998. Widespread prevalence of thermally tolerant Symbiodinium in O. annularis may potentially reflect a capacity for the coral to temporarily respond to warming events through symbiont shuffling. However, association with reduced coral calcification means that the ubiquitous nature of Symbiodinium D1 in O. annularis populations is unlikely to prevent long-term declines in reef health, at a time when maintaining reef growth is vital to sustain reef ecosystem function.

  1. Cryptic diversity and deep divergence in an upper Amazonian leaflitter frog, Eleutherodactylus ockendeni

    Directory of Open Access Journals (Sweden)

    Dávila José A

    2007-12-01

    Full Text Available Abstract Background The forests of the upper Amazon basin harbour some of the world's highest anuran species richness, but to date we have only the sparsest understanding of the distribution of genetic diversity within and among species in this region. To quantify region-wide genealogical patterns and to test for the presence of deep intraspecific divergences that have been documented in some other neotropical anurans, we developed a molecular phylogeny of the wide-spread terrestrial leaflitter frog Eleutherodactylus ockendeni (Leptodactylidae from 13 localities throughout its range in Ecuador using data from two mitochondrial genes (16S and cyt b; 1246 base pairs. We examined the relation between divergence of mtDNA and the nuclear genome, as sampled by five species-specific microsatellite loci, to evaluate indirectly whether lineages are reproductively isolated where they co-occur. Our extensive phylogeographic survey thus assesses the spatial distribution of E. ockendeni genetic diversity across eastern Ecuador. Results We identified three distinct and well-supported clades within the Ecuadorean range of E. ockendeni: an uplands clade spanning north to south, a northeastern and central lowlands clade, and a central and southeastern clade, which is basal. Clades are separated by 12% to 15% net corrected p-distance for cytochrome b, with comparatively low sequence divergence within clades. Clades marginally overlap in some geographic areas (e.g., Napo River basin but are reproductively isolated, evidenced by diagnostic differences in microsatellite PCR amplification profiles or DNA repeat number and coalescent analyses (in MDIV best modelled without migration. Using Bayesian (BEAST and net phylogenetic estimates, the Southeastern Clade diverged from the Upland/Lowland clades in the mid-Miocene or late Oligocene. Lowland and Upland clades speciated more recently, in the early or late Miocene. Conclusion Our findings uncover previously

  2. Ab initio prediction of mutation-induced cryptic splice-site activation and exon skipping

    Czech Academy of Sciences Publication Activity Database

    Divina, Petr; Kvitkovicova, Andrea; Buratti, E.; Vorechovsky, I.

    2009-01-01

    Roč. 17, č. 6 (2009), s. 759-765 ISSN 1018-4813 Institutional research plan: CEZ:AV0Z50520514 Keywords : mutation * cryptic splice site * exon skipping Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.564, year: 2009

  3. Earlier pupping in harbour seals, Phoca vitulina

    NARCIS (Netherlands)

    Reijnders, P.J.H.; Brasseur, S.M.J.M.; Meesters, H.W.G.

    2010-01-01

    The annual reproductive cycle of most seal species is characterized by a tight synchrony of births. Typically, timing of birth shows little inter-annual variation. Here, however we show that harbour seals Phoca vitulina from the Wadden Sea (southeast North Sea) have shortened their yearly cycle,

  4. Subsurface geology of the Bombay Harbour

    Digital Repository Service at National Institute of Oceanography (India)

    Almeida, F.; Ramana, M.V.; Vora, K.H.; Bhattacharya, G.C.; Subrahmanyam, V.

    As part of engineering pre-design investigations, high resolution geophysical surveys were carried out in and around Bombay harbour, India. The depth in the area varies from dries over the mudflats to about 14m towards the offshore end. The seabed...

  5. Phytoremediation of TBT-contaminated Harbour Sediment

    DEFF Research Database (Denmark)

    Trapp, Stefan; Novak, Jana; DeClercq, Bartel

    This sub-project of the TBT CLEAN project investigated the feasibility of growing plants on dredged harbour sediments and the influence of vegetation on TBT degradation. The toxicity of TBT to vascular plants was determined with the willow tree transpiration test. Compared to other species, the t...

  6. Harborsim, a generally applicable harbour simulation model

    NARCIS (Netherlands)

    Groenveld, R.

    1983-01-01

    Every planning of a port development or design of a new harbour is confronted with the unique physical properties and related problems to be solved. On the other hand every port can be defined as a link in the transport chain involved in the transfer of cargo from one medium of transport to another.

  7. Seabed surveys of Victoria harbour, Mahe, Seychelles

    Digital Repository Service at National Institute of Oceanography (India)

    Hashimi, N.H.; Wagle, B.G.

    The seabed surveys in the Victoria Harbour, Mahe, Seychelles shows that the prominent feature is the navigational channel aligned in the northeast-southwest direction with a width varying from 300 to 450m. The depth in the channel ranges from 14...

  8. Pollution characteristics and water quality in the Visakhapatnam harbour

    Digital Repository Service at National Institute of Oceanography (India)

    Sarma, V.V.; Raju, G.R.K.; Babu, T.B.

    The impact of organic pollution on the quality of waters in the Visakhapatnam harbour has been studied over a year at 8 stations. The enrichment of nutrients in these waters enhances the eutrophication. The construction of outer harbour retards...

  9. Impact investigations of access channel modifications of Cochin harbour, India

    Digital Repository Service at National Institute of Oceanography (India)

    DineshKumar, P.K.

    Though the modernization projects over the decades for harbour development also brought about several severe environmental modifications in Cochin harbour, along the west coast of India, so far, the physical processes involved are seldom...

  10. Postglacial climate changes and rise of three ecotypes of harbour porpoises, Phocoena phocoena, in western Palearctic waters

    NARCIS (Netherlands)

    Fontaine, Michaël C; Roland, Kathleen; Calves, Isabelle; Austerlitz, Frederic; Palstra, Friso P; Tolley, Krystal A; Ryan, Sean; Ferreira, Marisa; Jauniaux, Thierry; Llavona, Angela; Öztürk, Bayram; Öztürk, Ayaka A; Ridoux, Vincent; Rogan, Emer; Sequeira, Marina; Siebert, Ursula; Vikingsson, Gísli A; Borrell, Asunción; Michaux, Johan R; Aguilar, Alex

    Despite no obvious barriers to gene flow in the marine realm, environmental variation and ecological specializations can lead to genetic differentiation in highly mobile predators. Here, we investigated the genetic structure of the harbour porpoise over the entire species distribution range in

  11. Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae, Rhodophyta) from New Zealand.

    Science.gov (United States)

    Muangmai, Narongrit; Fraser, Ceridwen I; Zuccarello, Giuseppe C

    2015-06-01

    Spatial patterns of genetic diversity provide insight into the demography and history of species. Morphologically similar but genetically distinct "cryptic" species are increasingly being recognized in marine organisms through molecular analyses. Such species are, on closer inspection, often discovered to display contrasting life histories or occasionally minor morphological differences; molecular tools can thus be useful indicators of diversity. Bostrychia intricata, a marine red alga, is widely distributed throughout the Southern Hemisphere and comprises many cryptic species. We used mitochondrial cytochrome c oxidase I gene sequences to assess the genetic variation, population genetic structure, and demographic history of B. intricata in New Zealand. Our results supported the existence of three cryptic species of B. intricata (N2, N4, and N5) in New Zealand. Cryptic species N4, which was found throughout New Zealand, showed a higher genetic diversity and wider distribution than the other two species, which were only found in the North Island and northern South Island. Our analyses showed low to moderate genetic differentiation among eastern North Island populations for cryptic species N2, but high differentiation among North and South Island populations for N4, suggesting different population structure between these cryptic species. Data also indicated that N2 has recently undergone population expansion, probably since the Last Glacial Maximum (LGM), while the higher genetic diversity in N4 populations suggests persistence in situ through the LGM. The contrasting population structures and inferred demographic histories of these species highlight that life history can vary greatly even among morphologically indistinguishable taxa. © 2015 Phycological Society of America.

  12. 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...

  13. Journal of Genetics | Indian Academy of Sciences

    Indian Academy of Sciences (India)

    pp 223-226 Commentary on J. Genet. Classic. Towards a genetic architecture of cryptic genetic variation and genetic assimilation: the contribution of K. G. Bateman · Ian Dworkin · More Details Fulltext PDF. pp 227-257 J. Genet. Classic. The Genetic Assimilation of Four Venation Phenocopies (Published on 1959 J. Genet.

  14. Uranium isotopes in El hamraween harbour sediments

    International Nuclear Information System (INIS)

    Salahel Din, K.

    2009-01-01

    Isotopes of uranium in marine sediments collected from El Hamraween harbour and Ras El-Bhar areas on the Egyptian coast of the Red Sea have been studied using radiochemical separation procedures and alpha-particle spectrometry. Activity concentrations of 238 U, 235 U, 234 U were calculated. The activities observed indicating the enhancement of radioactivity level in El Hamraween harbor area due to the activities of phosphate shipment operation. Secular equilibrium between 234 U and 238 U was found in the analyzed samples. The average activity ratio of 235 U/ 238 U was close to the value 0.046 for uranium in nature

  15. Estimation of Wave Disturbance in Harbours

    DEFF Research Database (Denmark)

    Helm-Petersen, Jacob

    . Information on how the sponge layers perform with respect to reflection of short-crested waves are presented mainly in terms of overall reflection coefficients and main directions as functions of incident main direction relative to the structure. The influence of a irregular structure front has also been......The motivation for the present study has been to improve the reliability in using numerical wave propagation models as a tool for estimating wave disturbance in harbours. Attention has been directed towards the importance of the modelling of reflection in the applied mild-slope model. Methods have...... been presented for the analysis of reflected wave fields in 2D and 3D. The Bayesian Directional Wave Spectrum Estimation Method has been applied throughout the study. Reflection characteristics have been investigated by use of physical models for three types of coastal structures with vertical fronts...

  16. Reuse of harbour sediments in the Greenlandic construction industry

    DEFF Research Database (Denmark)

    Belmonte, Louise Josefine; Kirkelund, Gunvor Marie; Ottosen, Lisbeth M.

    2010-01-01

    The purpose of this study is to investigate possibilities of using harbour sediments from the Greenlandic harbours as substitutes in the Greenlandic construction industry, mainly for concrete production and road construction. Materials for use in the Greenlandic construction industry are shipped...

  17. Cryptic diversity in the Japanese mantis shrimp Oratosquilla oratoria (Crustacea: Squillidae): Allopatric diversification, secondary contact and hybridization.

    Science.gov (United States)

    Cheng, Jiao; Sha, Zhong-Li

    2017-05-16

    Mounting evidence of cryptic species in the marine realm emphasizes the necessity to thoroughly revise our current perceptions of marine biodiversity and species distributions. Here, we used mitochondrial cytochrome oxidase subunit I (mtDNA COI) and nuclear ribosomal internal transcribed spacer (nrDNA ITS) to investigate cryptic diversity and potential hybridization in the Japanese mantis shrimp Oratosquilla oratoria in the Northwestern (NW) Pacific. Both mitochondrial and nuclear gene genealogies revealed two cryptic species in this morphotaxon, which was further confirmed by extensive population-level analyses. One cryptic species is restricted to cold waters with a distribution range corresponding to temperate affinities, while the other dwelled warm waters influenced by the Kuroshio Current. Their divergence was postulated to be attributable to the vicariant event which resulted from the isolation of the Sea of Japan during the middle Pliocene (c. 3.85 Mya, 95% HPD 2.23-6.07 Mya). Allopatric speciation was maintained by limited genetic exchange due to their habitat preferences. Furthermore, the observation of recombinant nrDNA ITS sequence and intra-individual ITS polymorphism suggested recent hybridization event of the two cryptic species occurred in sympatric areas. Our study also illustrated that the Changjiang River outflow might act as an oceanic barrier to gene flow and promoted allopatric diversification in O. oratoria species complex.

  18. Phylogeographic insights into cryptic glacial refugia.

    Science.gov (United States)

    Provan, Jim; Bennett, K D

    2008-10-01

    The glacial episodes of the Quaternary (2.6 million years ago-present) were a major factor in shaping the present-day distributions of extant flora and fauna, with expansions and contractions of the ice sheets rendering large areas uninhabitable for most species. Fossil records suggest that many species survived glacial maxima by retreating to refugia, usually at lower latitudes. Recently, phylogeographic studies have given support to the existence of previously unknown, or cryptic, refugia. Here we summarise many of these insights into the glacial histories of species in cryptic refugia gained through phylogeographic approaches. Understanding such refugia might be important as the Earth heads into another period of climate change, in terms of predicting the effects on species distribution and survival.

  19. Characterization of the novel In1059 harbouring VIM gene cassette

    Directory of Open Access Journals (Sweden)

    Dongguo Wang

    2017-05-01

    Full Text Available Abstract Background VIM-type enzyme encodes the most widely acquired metallo-β-lactamases in Gram- negative bacteria. To obtain current epidemiological data for integrons from enterobacteriae in hospital, the study characterizes the genetic structure in In1059 by comparison with In846 integrons harbouring VIM gene and other class 1 integrons including In37, In62, In843 and In1021 with the aim of identifying the putative mechanisms involved integron mobilization and infer evolution of relevant integrons. Methods Six of 69 recombinant plasmids from clinical strains were found to be class 1 integrons by digestion with BamHI, drug susceptibility testing, conjugation experiments, PCR amplification, integron cloning and sequencing, genome comparison, and detection of carbapenemase activity. Results The sequences of the six recombinant plasmids encoding In1021, In843, In846, In37, In62, and the novel In1059 integron had approximate lengths of ~4.8-, 4.1-, 5.1-, 5.3-, 5.3- and 6.6- kb, respectively. The genetic structures of these integrons were mapped and characterized, and the carbapenemase activities of their parental strains were assessed. Conclusions Our results suggest that the six variable integron structures and regular variations that exist in the gene cassettes provide a putative mechanism for the integron changes. Our study has also shown that the genetic features in the integrons named above fall within a scheme involving the stepwise and parallel evolution of class 1 integron variation likely under antibiotic selection pressure in clinical settings.

  20. Introduced cryptic species of parasites exhibit different invasion pathways.

    Science.gov (United States)

    Miura, Osamu; Torchin, Mark E; Kuris, Armand M; Hechinger, Ryan F; Chiba, Satoshi

    2006-12-26

    Sometimes infectious agents invade and become established in new geographic regions. Others may be introduced yet never become established because of the absence of suitable hosts in the new region. This phenomenon may be particularly true for the many parasites with complex life cycles, where various life stages require different host species. Homogenization of the world's biota through human-mediated invasions may reunite hosts and parasites, resulting in disease outbreaks in novel regions. Here we use molecular genetics to differentiate invasion pathways for two digenean trematode parasites and their exotic host, the Asian mud snail, Batillaria attramentaria. All of the snail haplotypes found in introduced populations in North America were identical to haplotypes common in the areas of Japan that provided oysters for cultivation in North America, supporting the hypothesis that the snails were introduced from Japan with seed oysters. Two cryptic trematode species were introduced to North American populations in high frequencies. We found a marked reduction of genetic variation in one of these species, suggesting it experienced a bottleneck or founder event comparable to that of the host snail. In contrast, no genetic variation was lost in the other parasite species. We hypothesize that this parasite was and is dispersed naturally by migratory shorebirds and was able to establish only after the host snail, B. attramentaria, was introduced to North America. Evaluation of the nature of invasion pathways and postinvasion consequences will aid mitigation of spreading diseases of humans, livestock, and wildlife in an increasingly globalized world.

  1. Fate and transport modelling of uranium in Port Hope Harbour

    International Nuclear Information System (INIS)

    Pinilla, C.E.; Garisto, N.; Peters, R.

    2010-01-01

    Fate and transport modelling of contaminants in Port Hope Harbour and near-shore Lake Ontario was undertaken in support of an ecological and human health risk assessment. Uranium concentrations in the Harbour and near-shore Lake Ontario due to groundwater and storm water loadings were estimated with a state-of-the-art 3D hydrodynamic and contaminant transport model (ECOMSED). The hydrodynamic model was simplified to obtain a first estimate of the flow pattern in the Harbour. The model was verified with field data using a tracer (fluoride). The modelling results generally showed good agreement with the tracer field data. (author)

  2. Biofluorescence as a survey tool for cryptic marine species.

    Science.gov (United States)

    De Brauwer, Maarten; Hobbs, Jean-Paul A; Ambo-Rappe, Rohani; Jompa, Jamaluddin; Harvey, Euan S; McIlwain, Jennifer L

    2017-10-06

    As ecosystems come under increasing anthropogenic pressure, rare species face the highest risk of extinction. Paradoxically, data necessary to evaluate the conservation status of rare species are often lacking because of the challenges of detecting species with low abundance. One group of fishes subject to this undersampling bias are those with cryptic body patterns. Twenty-one percent of cryptic fish species assessed for their extinction risk (International Union for Conservation of Nature [IUCN]) are data deficient. We developed a nondestructive method for surveying cryptically patterned marine fishes based on the presence of biofluorescence (underwater biofluorescence census, UBC). Blue LED torches were used to investigate how widespread biofluorescence was in cryptic reef fishes in the Coral Triangle region. The effectiveness of UBC to generate abundance data was tested on a data-deficient pygmy seahorse species (Hippocampus bargibanti) and compared with data obtained from standard underwater visual census (UVC) surveys. We recorded 95 reef fish species displaying biofluorescence, 73 of which had not been previously described as biofluorescent. Of those fish with cryptic patterns, 87% were biofluorescent compared with 9% for noncryptic fishes. The probability of species displaying biofluorescence was 70.9 times greater for cryptic species than for noncryptic species. Almost twice the number of H. bargibanti was counted using the UBC compared with UVC. For 2 triplefin species (Ucla xenogrammus, Enneapterygius tutuilae), the abundance detected with UBC was triple that detected with UVC. The UBC method was effective at finding cryptic species that would otherwise be difficult to detect and thus will reduce interobserver variability inherent to UVC surveys. Biofluorescence is ubiquitous in cryptic fishes, making this method applicable across a wide range of species. Data collected using UBC could be used with multiple IUCN criteria to assess the extinction risk of

  3. Particular intervention plan of Cherbourg's military harbour

    International Nuclear Information System (INIS)

    2014-01-01

    The Particular intervention plan (PPI in French) is an emergency plan which foresees the measures and means to be implemented to address the potential risks of the presence and operation of a nuclear facility. This plan is implemented and developed by the Prefect in case of nuclear accident (or incident leading to a potential accident), the impact of which extending beyond the facility perimeter. It represents a special section of the organisation plan for civil protection response (ORSEC plan). The PPI foresees the necessary measures and means for crisis management during the first hours following the accident and is triggered by the Department Prefect according to the information provided by the facility operator. Its aim is to protect the populations leaving within 10 km of the facility against a potential radiological hazard. The PPI describes: the facility, the intervention area, the protection measures for the population, the conditions of emergency plan triggering, the crisis organisation, the action forms of the different services, and the post-accident stage. This document is the public version of the Particular intervention plan of the military harbour of Cherbourg (Manche, France) which hosts several nuclear facilities devoted to the construction and dismantling of nuclear submarines (without weapons)

  4. n-Alkanes in surficial sediments of Visakhapatnam harbour, east ...

    Indian Academy of Sciences (India)

    Visakhapatnam harbour, a semi-enclosed water body is one of the .... PDB − 1. } × 1000. 2.5 Extraction of lipids. Total lipids (TL) were extracted from lyophilized sediments following ..... 2010 Sources of OM and microbial community structure.

  5. Mumbai harbour, India: Gateway for introduction of marine organisms

    Digital Repository Service at National Institute of Oceanography (India)

    Gaonkar, C.; Sawant, S.S.; Anil, A; Venkat, K.; Harkantra, S.N.

    Ships have been identified as one of the important vectors in the translocation of organisms from one bioregion to another leading to bioinvasion. In this context, harbours serve as a gateway for the introduction of alien species. Surveys were...

  6. Seabed surveys of Mormugao Harbour, Central west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Wagle, B.G.; Gujar, A.R.; Subrahmanyam, V.; Mislankar, P.G.

    Detailed echosounding, side scan sonar and shallow seismics (125 line km) covering an area of 6.2 km2 in the Mormugao harbour provided information on seabed topography, surficial distribution of sediments, their thickness and rock outcrops along...

  7. Characterisation of dust material emitted during harbour operations (HADA Project)

    Energy Technology Data Exchange (ETDEWEB)

    Moreno, N.; Alastuey, A.; Querol, X.; Artinano, B.; Guerra, A.; Luaces, J.A.; Lorente, A.; Basora, J. [CSIC, Institute of Earth Science ' Jaume Almera' , Barcelona (Spain)

    2007-09-15

    The aim of this work is to compile an inventory of the main characteristics (chemical, morphological, mineralogical and grain size parameters) of the bulk cargo materials and of the material emitted during different port operations for possible use as tracers of the fugitive PM emission sources. For all cases, the tracer characteristics determined for each bulk material were also identified in the corresponding PM material emitted. This inventory could assist the harbour authorities to identify the origin of high PM events recorded by air quality monitoring networks in harbour areas, and could also help modellers to predict the impact of harbour activities on ambient PM levels. The harbour of Tarragona (north-east Spain) was selected for this study given the high volume of solids in bulk handled. To this end, 12 handling operations of selected materials (clinker, phosphate, pyrite ash, Mn mineral, fine Si-Mn, coke (coal), bituminous coal, tapioca, soybean, alfalfa, corn, andalusite) were selected for the characterisation of suspended and deposited PM. In spite of the coarse grain size distribution of these bulk cargo materials, with a very low % in the fraction {lt}10 {mu}m, manipulation of these materials during harbour operations may result in high emissions of PM 10 with relatively high levels of potential toxic elements. Furthermore, ambient PM 10 in the area with the highest traffic density of the harbour was also sampled and characterised.

  8. Familial cryptic translocation in Angelman syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Weyerts, L.K.; Wiley, J.E.; Loud, K.M. [ECU School of Medicine, Greenville, NC (United States)] [and others

    1994-09-01

    The majority of patients with Angelman syndrome have been shown to have a cytogenetic or molecular deletion on the maternally derived chromosome 15. We report on a case of Angelman syndrome in which this deletion occurs as an unbalanced cryptic translocation involving chromosomes 14 and 15. The proband was diagnosed clinically as having Angelman syndrome. Multiple cytogenetic studies were done without detecting any deletion. When DNA probes (Oncor) specific for the Prader Willi/Angelman locus became available, the patient was restudied and found to be deleted for {open_quotes}region A{close_quotes} (D15S11) but not for {open_quotes}region B{close_quotes} (GABRB3). No other abnormality was detected. The proband`s mother was then studied. The chromosome 15 marker probe and D15S11 were detected on different chromosomes. Using alpha-satellite probes, a cryptic 14;15 translocation was uncovered. This balanced translocation was also found to be carried by the sister of the proband. This case, along with a case presented at the 1993 ASHG meeting, illustrates the need for using acrocentric probes when studying Angelman syndrome patients. The proband was studied using additional probes specific for this region and found to be deleted for SNRPN but not for D15S10. The breakpoint of the translocation in this patient delineates the smallest deletion of the Angelman syndrome region reported to date and therefore may represent the specific gene involved.

  9. 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.

  10. Hidden in plain view: Cryptic diversity in the emblematic Araucaria of New Caledonia.

    Science.gov (United States)

    Ruhsam, Markus; Clark, Alexandra; Finger, Aline; Wulff, Adrien S; Mill, Robert R; Thomas, Philip I; Gardner, Martin F; Gaudeul, Myriam; Ennos, Richard A; Hollingsworth, Peter M

    2016-05-01

    Cryptic species represent a conservation challenge, because distributions and threats cannot be accurately assessed until species are recognized and defined. Cryptic species are common in diminutive and morphologically simple organisms, but are rare in charismatic and/or highly visible groups such as conifers. New Caledonia, a small island in the southern Pacific is a hotspot of diversity for the emblematic conifer genus Araucaria (Araucariaceae, Monkey Puzzle trees) where 13 of the 19 recognized species are endemic. We sampled across the entire geographical distribution of two closely related species (Araucaria rulei and A. muelleri) and screened them for genetic variation at 12 nuclear and 14 plastid microsatellites and one plastid minisatellite; a subset of the samples was also examined using leaf morphometrics. The genetic data show that populations of the endangered A. muelleri fall into two clearly distinct genetic groups: one corresponding to montane populations, the other corresponding to trees from lower elevation populations from around the Goro plateau. These Goro plateau populations are more closely related to A. rulei, but are sufficiently genetically and morphological distinct to warrant recognition as a new species. Our study shows the presence of a previously unrecognized species in this flagship group, and that A. muelleri has 30% fewer individuals than previously thought. Combined, this clarification of species diversity and distributions provides important information to aid conservation planning for New Caledonian Araucaria. © 2016 Botanical Society of America.

  11. DNA barcode reference library for Iberian butterflies enables a continental-scale preview of potential cryptic diversity

    Science.gov (United States)

    Dincă, Vlad; Montagud, Sergio; Talavera, Gerard; Hernández-Roldán, Juan; Munguira, Miguel L.; García-Barros, Enrique; Hebert, Paul D. N.; Vila, Roger

    2015-01-01

    How common are cryptic species - those overlooked because of their morphological similarity? Despite its wide-ranging implications for biology and conservation, the answer remains open to debate. Butterflies constitute the best-studied invertebrates, playing a similar role as birds do in providing models for vertebrate biology. An accurate assessment of cryptic diversity in this emblematic group requires meticulous case-by-case assessments, but a preview to highlight cases of particular interest will help to direct future studies. We present a survey of mitochondrial genetic diversity for the butterfly fauna of the Iberian Peninsula with unprecedented resolution (3502 DNA barcodes for all 228 species), creating a reliable system for DNA-based identification and for the detection of overlooked diversity. After compiling available data for European butterflies (5782 sequences, 299 species), we applied the Generalized Mixed Yule-Coalescent model to explore potential cryptic diversity at a continental scale. The results indicate that 27.7% of these species include from two to four evolutionary significant units (ESUs), suggesting that cryptic biodiversity may be higher than expected for one of the best-studied invertebrate groups and regions. The ESUs represent important units for conservation, models for studies of evolutionary and speciation processes, and sentinels for future research to unveil hidden diversity. PMID:26205828

  12. Cryptic species? Patterns of maternal and paternal gene flow in eight neotropical bats.

    Directory of Open Access Journals (Sweden)

    Elizabeth L Clare

    Full Text Available Levels of sequence divergence at mitochondrial loci are frequently used in phylogeographic analysis and species delimitation though single marker systems cannot assess bi-parental gene flow. In this investigation I compare the phylogeographic patterns revealed through the maternally inherited mitochondrial COI region and the paternally inherited 7(th intron region of the Dby gene on the Y-chromosome in eight common Neotropical bat species. These species are diverse and include members of two families from the feeding guilds of sanguivores, nectarivores, frugivores, carnivores and insectivores. In each case, the currently recognized taxon is comprised of distinct, substantially divergent intraspecific mitochondrial lineages suggesting cryptic species complexes. In Chrotopterus auritus, and Saccopteryx bilineata I observed congruent patterns of divergence in both genetic regions suggesting a cessation of gene flow between intraspecific groups. This evidence supports the existence of cryptic species complexes which meet the criteria of the genetic species concept. In Glossophaga soricina two intraspecific groups with largely sympatric South American ranges show evidence for incomplete lineage sorting or frequent hybridization while a third group with a Central American distribution appears to diverge congruently at both loci suggesting speciation. Within Desmodus rotundus and Trachops cirrhosus the paternally inherited region was monomorphic and thus does not support or refute the potential for cryptic speciation. In Uroderma bilobatum, Micronycteris megalotis and Platyrrhinus helleri the gene regions show conflicting patterns of divergence and I cannot exclude ongoing gene flow between intraspecific groups. This analysis provides a comprehensive comparison across taxa and employs both maternally and paternally inherited gene regions to validate patterns of gene flow. I present evidence for previously unrecognized species meeting the criteria of

  13. Water Quality Observations in the Dekhaila Harbour, Alexandria, Egypt

    International Nuclear Information System (INIS)

    Fahmy, M.A.; Abdel-Aziz, N.E.; Dorgham, M.M.

    2004-01-01

    The Dekhaila Harbour, which was recently constructed in Alexandria, had become a highly eutrophied areas due to intensive maritime activities, and the effect of a mixture of nutrients and different pollutants reaching the harbour through land-based effluent. Environmental observations which were carried monthly from April 1998 to March 1999 demonstrated extremely high nutrient level and productive phytoplankton, showing wide temporal and spatial variations. The variability of surface salinity was one of the characteristic features of the harbour, falling within the range of 17.3-39.2 ppt. Nutrients sustained pronouncedly high values, with annual average of 19.22uM for nitrate, 4.16um for nitrite, 38.69uM for ammonia, 6.44uM for phosphate and 49.52 for silicate. Chlorophyll a was exceptionally high (up to 13.23ug/1), having an annual average of 107.5ug/1. The harbour water was relatively turbid most of the year. The concentrations of dissolved oxygen revealed the alternations of good (5-10ml/1) aeration conditions. Consequently, low zooplankton abundance was found in the Dekhalia Harbour (annual average: 22,640 ind./m3). Statistical analysis showed that the envirnomental factors controlling both phyplankton and zooplankton biomass had different seasonal patterns. (author)

  14. Is Eucalyptus Cryptically Self-incompatible?

    Science.gov (United States)

    Horsley, Tasmien N; Johnson, Steven D

    2007-12-01

    The probability that seeds will be fertilized from self- versus cross-pollen depends strongly on whether plants have self-incompatibility systems, and how these systems influence the fate of pollen tubes. In this study of breeding systems in Eucalyptus urophylla and Eucalyptus grandis, epifluorescence microscopy was used to study pollen tube growth in styles following self- and cross-pollinations. Pollen tubes from self-pollen took significantly longer than those from cross-pollen to grow to the base of the style in both E. urophylla (120 h vs. 96 h) and E. grandis (96 h vs. 72 h). In addition, both species exhibited reduced seed yields following self-pollination compared with cross-pollination. The present observations suggest that, in addition to a late-acting self-incompatibility barrier, cryptic self-incompatibility could be a mechanism responsible for the preferential out-crossing system in these two eucalypt species.

  15. A bridge too far: dispersal barriers and cryptic speciation in an Arabian Peninsula grouper (Cephalopholis hemistiktos)

    KAUST Repository

    Priest, Mark; DiBattista, Joseph; McIlwain, Jennifer L.; Taylor, Brett M.; Hussey, Nigel E.; Berumen, Michael L.

    2015-01-01

    Aim: We use genetic and age-based analyses to assess the evidence for a biogeographical barrier to larval dispersal in the yellowfin hind, Cephalopholis hemistiktos, a commercially important species found across the Arabian Peninsula. Location: Red Sea, Gulf of Aden, Gulf of Oman and Arabian Gulf. Methods: Mitochondrial DNA cytochrome-c oxidase subunit-I and nuclear DNA (S7) sequences were obtained for C. hemistiktos sampled throughout its distributional range. Phylogeographical and population-level analyses were used to assess patterns of genetic structure and to identify barriers to dispersal. Concurrently, age-based demographic analyses using otoliths determined differences in growth and longevity between regions. Results: Our analyses revealed significant genetic structure congruent with growth parameter differences observed across sampling sites, suggesting cryptic speciation between populations in the Red Sea and Gulf of Aden versus the Gulf of Oman and Arabian Gulf. Coalescence analyses indicated these two regions have been isolated for > 800,000 years. Main conclusions: Our results indicate historical disruption to gene flow and a contemporary dispersal barrier in the Arabian Sea, which C. hemistiktos larvae are unable to effectively traverse. This provides yet another example of a (cryptic) species with high dispersive potential whose range is delimited by a lack of suitable habitat between locations or an inability to successfully recruit at the range edge. © 2015 John Wiley & Sons Ltd.

  16. A bridge too far: dispersal barriers and cryptic speciation in an Arabian Peninsula grouper (Cephalopholis hemistiktos)

    KAUST Repository

    Priest, Mark

    2015-12-12

    Aim: We use genetic and age-based analyses to assess the evidence for a biogeographical barrier to larval dispersal in the yellowfin hind, Cephalopholis hemistiktos, a commercially important species found across the Arabian Peninsula. Location: Red Sea, Gulf of Aden, Gulf of Oman and Arabian Gulf. Methods: Mitochondrial DNA cytochrome-c oxidase subunit-I and nuclear DNA (S7) sequences were obtained for C. hemistiktos sampled throughout its distributional range. Phylogeographical and population-level analyses were used to assess patterns of genetic structure and to identify barriers to dispersal. Concurrently, age-based demographic analyses using otoliths determined differences in growth and longevity between regions. Results: Our analyses revealed significant genetic structure congruent with growth parameter differences observed across sampling sites, suggesting cryptic speciation between populations in the Red Sea and Gulf of Aden versus the Gulf of Oman and Arabian Gulf. Coalescence analyses indicated these two regions have been isolated for > 800,000 years. Main conclusions: Our results indicate historical disruption to gene flow and a contemporary dispersal barrier in the Arabian Sea, which C. hemistiktos larvae are unable to effectively traverse. This provides yet another example of a (cryptic) species with high dispersive potential whose range is delimited by a lack of suitable habitat between locations or an inability to successfully recruit at the range edge. © 2015 John Wiley & Sons Ltd.

  17. Fouling Bryozoa from some Alexandria harbours, EGYPT. (I Erect species

    Directory of Open Access Journals (Sweden)

    KH.M. ABDEL-SALAM

    2008-05-01

    Full Text Available The fouling erect Bryozoa settled on polystyrene test panels immersed half a meter deep in the water of Abu Qir Harbour, the Eastern Harbour and El-Dekheila Harbour were studied. The present study yields 5 species of erect bryozoa. These areAmathia pruvoti, Zoobotryon verticillatum, Bowerbankia gracilis,Bugula neritina and Bugula stolonifera. The first three ones pertain to 3 genera of the family Vesiculariidae belonging to suborder the Stolonifera; while the other two species affiliate to the genus Bugula belonging to the family Bugulidae of suborder Anasca. The present record of Amathia pruvoti is the first from the Egyptian Mediterranean waters. A re-description, supplied with full structural illustrations of the recorded species is given. Moreover, the temporal and spatial distributions of the species recorded are encountered.

  18. Survey of research on the optimal design of sea harbours

    Directory of Open Access Journals (Sweden)

    Hassan Diab

    2017-07-01

    Full Text Available The design of harbours, as with any other system design, must be an optimization process. In this study, a global examination of the different constraints in coastal engineering was performed and an optimization problem was defined. The problem has multiple objectives, and the criteria to be minimized are the structure cost and wave height disturbance inside a harbour. As concluded in this survey, the constraints are predefined parameters, mandatory constraints or optional constraints. All of these constraints are categorized into four categories: environmental, fluid mechanical, structural and manoeuvring.

  19. Phylogeny and cryptic diversification in Southeast Asian flying geckos.

    Science.gov (United States)

    Brown, Rafe M; Siler, Cameron D; Lee Grismer, L; Das, Indraneil; McGuire, Jimmy A

    2012-11-01

    The closed-canopy forests of Southeast Asia are home to an impressive number of vertebrates that have independently evolved morphologies that enhance directed aerial descent (gliding, parachuting). These assemblages include numerous mammal, frog, snake, and lizard clades. Several genera of gekkonid lizards, in particular, have evolved specialized structures such as cutaneous expansions, flaps, and midbody patagia, that enhance lift generation in the context of unique gliding and parachuting locomotion. The genus Ptychozoon represents arguably the most morphologically extreme, highly specialized clade of gliding geckos. Despite their notoriety and celebrated locomotor ability, members of the genus Ptychozoon have never been the subject of a species-level molecular phylogenetic analysis. In this paper, we utilize molecular sequence data from mitochondrial and nuclear gene fragments to estimate the evolutionary relationships of this unique group of flying geckos. Capitalizing on the recent availability of genetic samples for even the rarest of known species, we include the majority of known taxa and use model-based phylogenetic methods to reconstruct their evolutionary history. Because one species, P. kuhli, exhibits an unusually wide distribution coupled with an impressive range of morphological variation, we additionally use intensive phylogeographic/population genetic sampling, phylogenetic network analyses, and Bayesian species delimitation procedures to evaluate this taxon for the possible presence of cryptic evolutionary lineages. Our results suggest that P. kuhli may consist of between five and nine unrecognized, distinct species. Although we do not elevate these lineages to species status here, our findings suggest that lineage diversity in Ptychozoon is likely dramatically underestimated. Copyright © 2012 Elsevier Inc. All rights reserved.

  20. Coalescent Modelling Suggests Recent Secondary-Contact of Cryptic Penguin Species.

    Science.gov (United States)

    Grosser, Stefanie; Burridge, Christopher P; Peucker, Amanda J; Waters, Jonathan M

    2015-01-01

    Molecular genetic analyses present powerful tools for elucidating demographic and biogeographic histories of taxa. Here we present genetic evidence showing a dynamic history for two cryptic lineages within Eudyptula, the world's smallest penguin. Specifically, we use a suite of genetic markers to reveal that two congeneric taxa ('Australia' and 'New Zealand') co-occur in southern New Zealand, with only low levels of hybridization. Coalescent modelling suggests that the Australian little penguin only recently expanded into southern New Zealand. Analyses conducted under time-dependent molecular evolutionary rates lend support to the hypothesis of recent anthropogenic turnover, consistent with shifts detected in several other New Zealand coastal vertebrate taxa. This apparent turnover event highlights the dynamic nature of the region's coastal ecosystem.

  1. Genetics of cryptic speciation within an Arctic mustard, Draba nivalis.

    Directory of Open Access Journals (Sweden)

    A Lovisa S Gustafsson

    Full Text Available Crossing experiments indicate that hybrid sterility barriers frequently have developed within diploid, circumpolar plant species of the genus Draba. To gain insight into the rapid evolution of postzygotic reproductive isolation in this system, we augmented the linkage map of one of these species, D. nivalis, and searched for quantitative trait loci (QTLs associated with reproductive isolation. The map adds 63 new dominant markers to a previously published dataset of 31 co-dominant microsatellites. These markers include 52 amplified fragment length polymorphisms (AFLPs and 11 sequence-specific amplified polymorphisms (SSAPs based on retrotransposon sequence. 22 markers displaying transmission ratio distortion were further included in the map. We resolved eight linkage groups with a total map length of 894 cM. Significant genotype-trait associations, or quantitative trait loci (QTL, were detected for reproductive phenotypes including pollen fertility (4 QTLs, seed set (3 QTLs, flowering time (3 QTLs and number of flowers (4 QTLs. Observed patterns of inheritance were consistent with the influence of both nuclear-nuclear interactions and chromosomal changes on these traits. All seed set QTLs and one pollen fertility QTL displayed underdominant effects suggestive of the involvement of chromosomal rearrangements in hybrid sterility. Interestingly, D. nivalis is predominantly self-fertilizing, which may facilitate the establishment of underdominant loci and contribute to reproductive isolation.

  2. The world's northernmost harbour seal population-how many are there?

    Directory of Open Access Journals (Sweden)

    Benjamin Merkel

    Full Text Available This study presents the first abundance estimate for the world's northernmost harbour seal (Phoca vitulina population, which resides in Svalbard, Norway, based on three digital stereoscopic photographic surveys conducted in 2009 and 2010. The counts from these high resolution 3D images were combined with a novel method for estimating correction factors for animals that were in the water at the time of the surveys, in which extensive behavioural data from radio-tagged harbour seals were used together with age distribution data to estimate the proportion of seals of various age and sex classes hauled out at the times of the surveys. To detect possible seasonal shifts in age distribution between surveys, lengths of hauled out seals were measured from the stereoscopic images. No body-length differences were detected between the surveys; but, this may be due to a high degree of sexual dimorphism exhibited in this population. Applying the modelled correction factors, a total of 1888 (95% CI: 1660-3023, 1742 (1381-3549 and 1812 (1656-4418 harbour seals were estimated for the surveys flown on 01 August 2009, 01 August 2010 and 19 August 2010, respectively. The similarity between the three survey estimates (despite significant differences in the number of animals actually counted on the photos from each survey effort suggests that the variation in numbers of hauled out seals is reasonably accurately adjusted for by the haul-out probability model. The low population size, the limited spatial distribution of the population and its reduced genetic diversity make this population vulnerable to chance events, such as disease epidemics.

  3. Epizootics in harbour seals (Phoca vitulina: clinical aspects

    Directory of Open Access Journals (Sweden)

    Ursula Siebert

    2010-09-01

    Full Text Available Epizootic diseases causing considerable mortality in harbour seal populations have mainly been reported from the waters of the United States and Europe. Such die-offs were largely attributable to viral infections. Several hundred individuals died from respiratory infections caused by Influenza A viruses at the coast of New England, USA, in 1979, 1980 and 1982. More than 53,000 harbour seals were killed in European waters by Phocine Distemper Virus (PDV, a morbillivirus,in two outbreaks in 1988 and 2002. For several other epizootics of smaller scale in the waters of the Atlantic and Pacific coast of the USA and, most recently, in Danish and Swedish waters in 2007 the causes remain unclear, although characteristic respiratory symptoms and interstitial pneumonia suspicious of viral etiology were detected as well as occasionally bacterial infections caused by Erysipelothrix rhusiopathiae and Pseudomonas aeruginosa. Mass mortalities caused by biotoxins, direct human interactions or changes in oceanographic conditions have so far not been described for harbour seals. However, high organochlorine loads detected in European harbour seal populations and suspected to impede immune functions, were considered an aggravating factor in the 1988 morbillivirus epizootic. Establishing supranational stranding networks is a key prerequisite for the detection of future unusual die-offs in marine mammals. Detailed post-mortem investigations of all organ systems are essential for targeted etiological studies towards the causes of mass mortalities in seals.

  4. Pollution studies on harbours and jetties in Nigeria | Agbagwa ...

    African Journals Online (AJOL)

    The distribution of bacteria in the surface waters and sediment of selected harbours and landing jetties in the city of Port Harcourt was investigated. Nine water and sediments samples were allocated on each trip and cultured for various organisms on the rainy and dry season. The total heterotrophic count of the water ...

  5. Water quality effects of harbour activities assessed with integrated ...

    African Journals Online (AJOL)

    Ecological tools were developed to study the water quality in Cochin harbour, a complex aquatic ecosystems, through the integration of microbiological monitoring (faecal coliforms and Pseudomonas species) and heavy metal contamination (lead, cadmium and mercury). One way ANOVA indicates statistically significant ...

  6. Plastic ingestion by harbour seal (Phoca vitulina) in the Netherlands

    NARCIS (Netherlands)

    Bravo Rebolledo, E.; Franeker, van J.A.; Jansen, O.E.; Brasseur, S.M.J.M.

    2013-01-01

    Abundance of ingested debris by seals has been mentioned as a potential indicator of marine litter in the European Marine Strategy Framework Directive (MSFD). A sample of 107 stomachs, 100 intestines and 125 scats of harbour seals from the Netherlands was analysed for the presence of plastics.

  7. Status of harbour seals (Phoca vitulina in Atlantic Canada

    Directory of Open Access Journals (Sweden)

    Mike O Hammill

    2010-09-01

    Full Text Available Harbour seals are associated with small islets, reefs and rocks exposed at low tide and estuarine habitats throughout eastern Canada. Evidence of harvesting by indigenous people has been found in pre-European contact archaeological excavations. A bounty harvest as well as subsistence and commercial hunting probably lead to a decline in the population from 1949 to the early 1970s. The bounty was removed in 1976, and harbour seals, in the southern parts of their range have been protected since then. There is little information available on total abundance and current population trend. Mitochondrial and microsatellite DNA research has shown separation between Northeast and Northwest Atlantic harbour seals. Within Canada, the subspecies Phoca vitulina concolor shows some population sub-structure with three distinct units that could be separated into Hudson Bay, Gulf of St. Lawrence and Sable Island. Urban development resulting in habitat degradation is probably the most important factor affecting harbour seal populations in AtlanticCanada, although other factors such as incidental catches in commercial fisheries and competition with grey seals may also be important.

  8. Harbour porpoise occurrence in relation to the Prinses Amaliawindpark

    NARCIS (Netherlands)

    Polanen Petel, van T.; Geelhoed, S.C.V.; Meesters, H.W.G.

    2012-01-01

    The potential effects of the construction and operation of wind farms at sea on marine life is a pertinent question in today’s world. Although for this report we focus on harbour porpoises (Phocoena phocoena), wind farms have the potential to affect all marine life, including marine mammals, fish,

  9. Water quality effects of harbour activities assessed with integrated ...

    African Journals Online (AJOL)

    moes2

    Ecological tools were developed to study the water quality in Cochin harbour, a complex aquatic ecosystems ... contamination index is another important factor to assess ... Nutrient agar with the ... yeast extract 3.0 g; beef extract 2.0 g; agar 15.0 g; aged sea water .... ability to be incorporated into food chains (Kishe and.

  10. Shoreline stability in the vicinity of Cochin Harbour

    Digital Repository Service at National Institute of Oceanography (India)

    PrasannaKumar, S.; Vethamony, P.

    , showing stability over a period of one year. The growth of shoreline north of Cochin harbour channel takes place at the cost of sediment that should have otherwise by-passed the estuarine mouth. During the southwest monsoon the development of opposing...

  11. Status of the harbour seal (Phoca vitulina in Southern Scandinavia

    Directory of Open Access Journals (Sweden)

    Morten Tange Olsen

    2013-09-01

    Full Text Available The harbour seal population in Southern Scandinavia has experienced repeated declines caused by hunting and epizootics. These events have shaped the current distribution and abundance of the population. This paper assesses the current status of the population. We estimate trends in abundance of harbour seals from long term survey data, compare these with historic trends inferred from previously published material, and discuss past and potential threats to the harbour seal population of Southern Scandinavia. It is evident that harbour seals have disappeared from haulout areas along the Danish shores of Kattegat and in the westernmost part of the Baltic Sea, where they were previously numerous. In the 1920-30s, when abundance was at its lowest, the population is estimated to have been only a fraction of its original size. Following 30 years of protection the population is currently approaching historic abundance and might have reached the carrying capacity in some areas. Further development depends largely on effects of future epizootics, anthropogenic disturbance, and availability of suitable haulout sites.

  12. Determining optimal pinger spacing for harbour porpoise bycatch mitigation

    DEFF Research Database (Denmark)

    Larsen, Finn; Krog, Carsten; Eigaard, Ole Ritzau

    2013-01-01

    A trial was conducted in the Danish North Sea hake gillnet fishery in July to September 2006 to determine whether the spacing of the Aquatec AQUAmark100 pinger could be increased without reducing the effectiveness of the pinger in mitigating harbour porpoise bycatch. The trial was designed as a c...

  13. Numerical simulation of ship motion in offshore and harbour areas

    DEFF Research Database (Denmark)

    Christensen, Erik Damgaard; Jensen, Bjarne; Mortensen, Simon Brandi

    2008-01-01

    A method for simulating the motions and mooring forces of a moored ship subject to wave forcing has been further developed and validated for both the open water case and inside harbour areas. The method was originally developed and reported in Bingham (2000). The simulation tool is named WAMSIM...

  14. Integrative taxonomy detects cryptic and overlooked fish species in a neotropical river basin.

    Science.gov (United States)

    Gomes, Laís Carvalho; Pessali, Tiago Casarim; Sales, Naiara Guimarães; Pompeu, Paulo Santos; Carvalho, Daniel Cardoso

    2015-10-01

    The great freshwater fish diversity found in the neotropical region makes management and conservation actions challenging. Due to shortage of taxonomists and insufficient infrastructure to deal with such great biodiversity (i.e. taxonomic impediment), proposed remedies to accelerate species identification and descriptions include techniques that combine DNA-based identification and concise morphological description. The building of a DNA barcode reference database correlating meristic and genetic data was developed for 75 % of the Mucuri River basin's freshwater fish. We obtained a total of 141 DNA barcode sequences from 37 species belonging to 30 genera, 19 families, and 5 orders. Genetic distances within species, genera, and families were 0.74, 9.5, and 18.86 %, respectively. All species could be clearly identified by the DNA barcodes. Divergences between meristic morphological characteristics and DNA barcodes revealed two cryptic species among the Cyphocharax gilbert and Astyanax gr. bimaculatus specimens, and helped to identify two overlooked species within the Gymnotus and Astyanax taxa. Therefore, using a simplified model of neotropical biodiversity, we tested the efficiency of an integrative taxonomy approach for species discovery, identification of cryptic diversity, and accelerating biodiversity descriptions.

  15. 75 FR 4783 - Federal Consistency Appeal by Villa Marina Yacht Harbour, Inc.

    Science.gov (United States)

    2010-01-29

    ... DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration Federal Consistency Appeal by Villa Marina Yacht Harbour, Inc. AGENCY: National Oceanic and Atmospheric Administration (NOAA... days, closure of the decision record in an administrative appeal filed by Villa Marina Yacht Harbour...

  16. A systematic study of wave conditions and sediment transport near Mormugao harbour

    Digital Repository Service at National Institute of Oceanography (India)

    Reddy, M.P.M.

    Wave conditions and the nature of sediment transport in the Mormugao Harbour area have been evaluated in view of the proposed development project of this harbour It has been found from this study that generally high waves will be experienced...

  17. Comparison of tropical nematode communities from three harbours, west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Nanajkar, M.; Ingole, B.S.

    The three major harbours from the central west coast of India were investigated for their benthic environmental status using nematodes as surrogate community. As these three harbours have shown deteriorated conditions revealed from macrobenthic...

  18. Third Indian National Conference on Harbour and Ocean Engineering (INCHOE - 2004). Proceedings

    Digital Repository Service at National Institute of Oceanography (India)

    Mandal, S.; SanilKumar, V.; Jayakumar, S.

    The two volumes contain 103 scientific papers in the field of harbour and ocean engineering, presented at the Third Indian National Conference on Harbour and Ocean Engineering (INCHOE - 2004), held at National Institute of Oceanography (NIO), Dona...

  19. Identification of a cryptic prokaryotic promoter within the cDNA encoding the 5' end of dengue virus RNA genome.

    Directory of Open Access Journals (Sweden)

    Dongsheng Li

    Full Text Available Infectious cDNA clones of RNA viruses are important research tools, but flavivirus cDNA clones have proven difficult to assemble and propagate in bacteria. This has been attributed to genetic instability and/or host cell toxicity, however the mechanism leading to these difficulties has not been fully elucidated. Here we identify and characterize an efficient cryptic bacterial promoter in the cDNA encoding the dengue virus (DENV 5' UTR. Following cryptic transcription in E. coli, protein expression initiated at a conserved in-frame AUG that is downstream from the authentic DENV initiation codon, yielding a DENV polyprotein fragment that was truncated at the N-terminus. A more complete understanding of constitutive viral protein expression in E. coli might help explain the cloning and propagation difficulties generally observed with flavivirus cDNA.

  20. Cryptic cuckoo eggs hide from competing cuckoos

    Science.gov (United States)

    Gloag, Ros; Keller, Laurie-Anne; Langmore, Naomi E.

    2014-01-01

    Interspecific arms races between cuckoos and their hosts have produced remarkable examples of mimicry, with parasite eggs evolving to match host egg appearance and so evade removal by hosts. Certain bronze-cuckoo species, however, lay eggs that are cryptic rather than mimetic. These eggs are coated in a low luminance pigment that camouflages them within the dark interiors of hosts' nests. We investigated whether cuckoo egg crypsis is likely to have arisen from the same coevolutionary processes known to favour egg mimicry. We added high and low luminance-painted eggs to the nests of large-billed gerygones (Gerygone magnirostris), a host of the little bronze-cuckoo (Chalcites minutillus). Gerygones rarely rejected either egg type, and did not reject natural cuckoo eggs. Cuckoos, by contrast, regularly removed an egg from clutches before laying their own and were five times more likely to remove a high luminance model than its low luminance counterpart. Given that we found one-third of all parasitized nests were exploited by multiple cuckoos, our results suggest that competition between cuckoos has been the key selective agent for egg crypsis. In such intraspecific arms races, crypsis may be favoured over mimicry because it can reduce the risk of egg removal to levels below chance. PMID:25122227

  1. Vuosaari Harbour Road Tunnel Traffic Management and Incident Detection System Design Issues

    Directory of Open Access Journals (Sweden)

    Caj Holm

    2006-11-01

    Full Text Available Helsinki is constructing in Vuosaari a new modem and effectivecargo harbour. All cargo harbour activities will be concentratedthere. The total project includes the harbour, a logisticsarea, traffic connections (road, railway and fairway and aBusiness Park. The road connection goes through the Porvarinlahtiroad tunnel. The harbour will commence operatingin 2008. This paper gives an oveTView of the tunnel design phasefunctional studies and risk analysis tunnel incident detectionsystem design issues and some specific environmental featuresof the tunnel.

  2. Diversification and reproductive isolation: cryptic species in the only New World high-duty cycle bat, Pteronotus parnellii

    Directory of Open Access Journals (Sweden)

    Clare Elizabeth L

    2013-01-01

    Full Text Available Abstract Background Molecular techniques are increasingly employed to recognize the presence of cryptic species, even among commonly observed taxa. Previous studies have demonstrated that bats using high-duty cycle echolocation may be more likely to speciate quickly. Pteronotus parnellii is a widespread Neotropical bat and the only New World species to use high-duty cycle echolocation, a trait otherwise restricted to Old World taxa. Here we analyze morphological and acoustic variation and genetic divergence at the mitochondrial COI gene, the 7th intron region of the y-linked Dby gene and the nuclear recombination-activating gene 2, and provide extensive evidence that P. parnellii is actually a cryptic species complex. Results Central American populations form a single species while three additional species exist in northern South America: one in Venezuela, Trinidad and western Guyana and two occupying sympatric ranges in Guyana and Suriname. Reproductive isolation appears nearly complete (only one potential hybrid individual found. The complex likely arose within the last ~6 million years with all taxa diverging quickly within the last ~1-2 million years, following a pattern consistent with the geological history of Central and northern South America. Significant variation in cranial measures and forearm length exists between three of the four groups, although no individual morphological character can discriminate these in the field. Acoustic analysis reveals small differences (5–10 kHz in echolocation calls between allopatric cryptic taxa that are unlikely to provide access to different prey resources but are consistent with divergence by drift in allopatric species or through selection for social recognition. Conclusions This unique approach, considering morphological, acoustic and multi-locus genetic information inherited maternally, paternally and bi-parentally, provides strong support to conclusions about the cessation of gene flow and

  3. The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis in the grasslands of Queensland, Australia.

    Directory of Open Access Journals (Sweden)

    Jane Melville

    Full Text Available Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora, which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1 revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

  4. The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

    Science.gov (United States)

    Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

    2014-01-01

    Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

  5. Cryptic Methane Emissions from Upland Forest Ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Megonigal, Patrick [Smithsonian Institution, Washington, DC (United States); Pitz, Scott [Johns Hopkins Univ., Baltimore, MD (United States); Smithsonian Institution, Washington, DC (United States)

    2016-04-19

    This exploratory research on Cryptic Methane Emissions from Upland Forest Ecosystems was motivated by evidence that upland ecosystems emit 36% as much methane to the atmosphere as global wetlands, yet we knew almost nothing about this source. The long-term objective was to refine Earth system models by quantifying methane emissions from upland forests, and elucidate the biogeochemical processes that govern upland methane emissions. The immediate objectives of the grant were to: (i) test the emerging paradigm that upland trees unexpectedly transpire methane, (ii) test the basic biogeochemical assumptions of an existing global model of upland methane emissions, and (iii) develop the suite of biogeochemical approaches that will be needed to advance research on upland methane emissions. We instrumented a temperate forest system in order to explore the processes that govern upland methane emissions. We demonstrated that methane is emitted from the stems of dominant tree species in temperate upland forests. Tree emissions occurred throughout the growing season, while soils adjacent to the trees consumed methane simultaneously, challenging the concept that forests are uniform sinks of methane. High frequency measurements revealed diurnal cycling in the rate of methane emissions, pointing to soils as the methane source and transpiration as the most likely pathway for methane transport. We propose the forests are smaller methane sinks than previously estimated due to stem emissions. Stem emissions may be particularly important in upland tropical forests characterized by high rainfall and transpiration, resolving differences between models and measurements. The methods we used can be effectively implemented in order to determine if the phenomenon is widespread.

  6. Echolocation by the harbour porpoise: Life in coastal waters

    Directory of Open Access Journals (Sweden)

    Lee Anton Miller

    2013-04-01

    Full Text Available The harbour porpoise is one of the smallest and most widely spread of all toothed whales. They are found abundantly in coastal waters all around the northern hemisphere. They are among the 11 species known to use high frequency sonar of relative narrow bandwidth. Their narrow biosonar beam helps isolate echoes from prey among those from unwanted items and noise. Obtaining echoes from small objects like net mesh, net floats and small prey is facilitated by the very high peak frequency around 130 kHz with a wavelength of about 12 mm. We argue that such echolocation signals and narrow band auditory filters give the harbour porpoise a selective advantage in a coastal environment. Predation by killer whales and a minimum noise region in the ocean around 130 kHz may have provided selection pressures for using this frequency band for biosonar signals.

  7. Sexually dimorphic proportions of the harbour porpoise (Phocoena phocoena) skeleton

    DEFF Research Database (Denmark)

    Galatius, Anders

    2005-01-01

    Sexual differences in growth, allometric growth patterns and skeletal proportions were investigated by linear measurements of skeletal parts on 225 harbour porpoises (Phocoena phocoena) from the inner Danish and adjacent waters. Females show larger asymptotic sizes and extended period of growth...... to females is also found in the vertebral epiphyses that mature later in males than females, although the males finish growth at a younger age....

  8. Status of harbour seals (Phoca vitulina in mainland Norway

    Directory of Open Access Journals (Sweden)

    Kjell Tormod Nilssen

    2010-09-01

    Full Text Available Harbour seals were counted along the entire Norwegian coast at known moulting haulout sites in the period mid-August to early September 2003-2006. In 2003-2005, almost all known moulting areas from Finnmark to Vestfold counties were covered by aerial photo surveys flown at altitudes of approximately 800-900 ft (243-274m, and at low tide (± 2 hours. Surveys in the Østfold County were flown in 2003-2006 at 300 ft (91m, and the small tidal amplitudes permitted counts to be carried out irrespective of the tidal cycle. In some sub-areas, two or three independent surveys were conducted. Visual counts using binoculars from smaller boats and islands were carried out in some selected areas. The surveys revealed a total minimum population of 6,705 harbour seals in Norwegian waters. Harbour seals were most abundant in the Nordland and Sør-Trøndelag counties with minimum estimates of approximately 2,500 and 1,500 seals, respectively. The presented minimum estimate is approximately 800 seals lower than an estimate obtained in a comparable study carried out during the moult in 1996-1999. Increased anthropogenic removals, and the phocine distemper virus (PDV epidemic in the Skagerrak region in 2002, may have contributed to the current lower estimate.

  9. Pilot remediation of sediment from the Petroleum harbour in Amsterdam

    International Nuclear Information System (INIS)

    Hakstege, A.L.; Geldermalsen, L.A. van

    1998-01-01

    The Petroleum Harbour project is the third pilot remediation, which was carried out within the framework of POSW (the national development programme for treatment processes of polluted sediments). The main objectives of the pilot remediation are: to demonstrate the biological treatment of dredged materials on a practical scale; and to gain knowledge and experience for the future remediation of the total Petroleum harbour. A strict tender procedure was carefully executed in order to select the most effective and 'state of the art' biodegradation technology. The selected remediation chain was a combination of 'standard' soil treatment technology and newly developed biotechnology. Dredging, biotechnological treatment and the effects of the remediation on the environment were monitored in detail. The quality of the treated sand fraction complied with the Dutch standards for re-use and was actually applied in a project of Rijkswaterstaat. Biodegradation resulted in a substantial decrease of the oil and PAH's contents, but due to the lack of breakdown of a few high-molecular PAH's, the quality requirements of the contract were not achieved. It is concluded that the two main objectives of the project have been attained. Finally some recommendations for the future clean-up of the Petroleum harbour are given. (author)

  10. Molecular characterization of a novel cryptic virus infecting pigeonpea plants.

    Directory of Open Access Journals (Sweden)

    Surender Kumar

    Full Text Available A new member of the genus Deltapartitivirus was identified containing three dsRNAs with an estimated size of 1.71, 1.49 and 1.43 kb. The dsRNAs were extracted from symptomless pigeonpea [Cajanus cajan (L. Millspaugh] plants cv. Erra Kandulu. This new virus with 4.64 kb genome was tentatively named Arhar cryptic virus-1 (ArCV-1. The genomic RNAs were amplified and characterized by sequence independent single primer amplification. The dsRNAs shared a highly conserved 16 nt 5' non-coding region (5'-GATAATGATCCAAGGA-3'. The largest dsRNA (dsRNA-1 was identified as the viral RNA dependent RNA polymerase (replicase, predicted to encode a putative 55.34 kDa protein (P1. The two other smaller dsRNAs (dsRNA-2 and dsRNA-3 predicted to encode for putative capsid proteins of 38.50kDa (P2 and 38.51kDa (P3, respectively. Phylogenetic analysis indicated that ArCV-1 formed a clade together with Fragaria chiloensis cryptic virus, Rosa multiflora cryptic virus and Rose cryptic virus-1, indicating that ArCV-1 could be a new member of the genus Deltapartitivirus. ArCV-1 3Dpol structure revealed several interesting features. The 3Dpol in its full-length shares structural similarities with members of the family Caliciviridaeand family Picornaviridae. In addition, fourth dsRNA molecule (dsRNA-2A, not related to ArCV-1 genome, was found in the same plant tissue. The dsRNA-2A (1.6 kb encodes a protein (P4, with a predicted size of 44.5 kDa. P4 shares similarity with coat protein genes of several cryptic viruses, in particular the bipartite cryptic viruses including Raphanus sativus cryptic virus-3. This is the first report of occurrence of a cryptic virus in pigeonpea plants.

  11. Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization?

    Science.gov (United States)

    Ravinet, Mark; Harrod, Chris; Eizaguirre, Christophe; Prodöhl, Paulo A

    2014-06-01

    Repeated recolonization of freshwater environments following Pleistocene glaciations has played a major role in the evolution and adaptation of anadromous taxa. Located at the western fringe of Europe, Ireland and Britain were likely recolonized rapidly by anadromous fishes from the North Atlantic following the last glacial maximum (LGM). While the presence of unique mitochondrial haplotypes in Ireland suggests that a cryptic northern refugium may have played a role in recolonization, no explicit test of this hypothesis has been conducted. The three-spined stickleback is native and ubiquitous to aquatic ecosystems throughout Ireland, making it an excellent model species with which to examine the biogeographical history of anadromous fishes in the region. We used mitochondrial and microsatellite markers to examine the presence of divergent evolutionary lineages and to assess broad-scale patterns of geographical clustering among postglacially isolated populations. Our results confirm that Ireland is a region of secondary contact for divergent mitochondrial lineages and that endemic haplotypes occur in populations in Central and Southern Ireland. To test whether a putative Irish lineage arose from a cryptic Irish refugium, we used approximate Bayesian computation (ABC). However, we found no support for this hypothesis. Instead, the Irish lineage likely diverged from the European lineage as a result of postglacial isolation of freshwater populations by rising sea levels. These findings emphasize the need to rigorously test biogeographical hypothesis and contribute further evidence that postglacial processes may have shaped genetic diversity in temperate fauna.

  12. 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.

  13. Geodetic infrastructure at the Barcelona harbour for sea level monitoring

    Science.gov (United States)

    Martinez-Benjamin, Juan Jose; Gili, Josep; Lopez, Rogelio; Tapia, Ana; Pros, Francesc; Palau, Vicenc; Perez, Begona

    2015-04-01

    The presentation is directed to the description of the actual geodetic infrastructure of Barcelona harbour with three tide gauges of different technologies for sea level determination and contribution to regional sea level rise and understanding past and present sea level rise in the Barcelona harbour. It is intended that the overall system will constitute a CGPS Station of the ESEAS (European Sea Level) and TIGA (GPS Tide Gauge Benchmark Monitoring) networks. At Barcelona harbour there is a MIROS radar tide gauge belonging to Puertos del Estado (Spanish Harbours).The radar sensor is over the water surface, on a L-shaped structure which elevates it a few meters above the quay shelf. 1-min data are transmitted to the ENAGAS Control Center by cable and then sent each 1 min to Puertos del Estado by e-mail. The information includes wave forescast (mean period, significant wave height, sea level, etc.This sensor also measures agitation and sends wave parameters each 20 min. There is a GPS station Leica Geosystems GRX1200 GG Pro and antenna AX 1202 GG. The Control Tower of the Port of Barcelona is situated in the North dike of the so-called Energy Pier in the Barcelona harbor (Spain). This tower has different kind of antennas for navigation monitoring and a GNSS permanent station. As the tower is founded in reclaimed land, and because its metallic structure, the 50 m building is subjected to diverse movements, including periodic fluctuations due to temperature changes. In this contribution the 2009, 2011, 2012, 2013 and 2014 the necessary monitoring campaigns are described. In the framework of a Spanish Space Project, the instrumentation of sea level measurements has been improved by providing the Barcelona site with a radar tide gauge Datamar 2000C from Geonica S.L. in June 2014 near an acoustic tide gauge from the Barcelona Harbour installed in 2013. Precision levelling has been made several times in the last two years because the tower is founded in reclaimed land and

  14. Hiding in Plain Sight: A Case for Cryptic Metapopulations in Brook Trout (Salvelinus fontinalis.

    Directory of Open Access Journals (Sweden)

    David C Kazyak

    Full Text Available A fundamental issue in the management and conservation of biodiversity is how to define a population. Spatially contiguous fish occupying a stream network have often been considered to represent a single, homogenous population. However, they may also represent multiple discrete populations, a single population with genetic isolation-by-distance, or a metapopulation. We used microsatellite DNA and a large-scale mark-recapture study to assess population structure in a spatially contiguous sample of Brook Trout (Salvelinus fontinalis, a species of conservation concern. We found evidence for limited genetic exchange across small spatial scales and in the absence of barriers to physical movement. Mark-recapture and stationary passive integrated transponder antenna records demonstrated that fish from two tributaries very seldom moved into the opposite tributary, but movements between the tributaries and mainstem were more common. Using Bayesian genetic clustering, we identified two genetic groups that exhibited significantly different growth rates over three years of study, yet survival rates were very similar. Our study highlights the importance of considering the possibility of multiple genetically distinct populations occurring within spatially contiguous habitats, and suggests the existence of a cryptic metapopulation: a spatially continuous distribution of organisms exhibiting metapopulation-like behaviors.

  15. Cryptic sexual size dimorphism in Malagasy plovers Charadrius spp ...

    African Journals Online (AJOL)

    Taken together, our work reports SSD in small African plovers that exhibit monomorphic plumage, and we propose that SSD may be more common than currently acknowledged; we term this 'cryptic sexual size dimorphism'. Our results also suggest sexual selection and/or natural selection exert different pressures on body ...

  16. Complete sequence of a cryptic virus from hemp (Cannabis sativa)

    Czech Academy of Sciences Publication Activity Database

    Ziegler, A.; Matoušek, Jaroslav; Steger, G.; Schubert, J.

    2012-01-01

    Roč. 157, č. 2 (2012), s. 383-385 ISSN 0304-8608 R&D Projects: GA ČR GCP501/10/J018 Institutional research plan: CEZ:AV0Z50510513 Keywords : Cannabis sativa * Partitivirus * cryptic virus Subject RIV: EE - Microbiology, Virology Impact factor: 2.030, year: 2012

  17. Distribution and population structure of North Atlantic harbour seals (Phoca vitulina

    Directory of Open Access Journals (Sweden)

    Liselotte Andersen

    2010-09-01

    Full Text Available A review of the known geographical distribution and current knowledge on the genetic population structure of harbour seals (Phoca vitulina in the North Atlantic is presented. Based on a synthesis of the results fromfive different studies of neutral geneticmarkers (mtDNAand nuclear microsatellites, mainly twelve genetically distinct populations were identified in the North Atlantic: USA/Canada, Iceland, west coast of Norway, Ireland-Scotland, English east coast, Channel area, Wadden Sea, Limfjord, Skagerrak, Kattegat, West Baltic, and East Baltic. Most of the studies addressed the population structure at the regional level, while only a few addressed the structuring at a local level, i.e. within countries. Due to the limited number of studies conducted, the identified population units were considered preliminary andmore detailed, local studieswould probably reveal structuring on a finer scale. The choice of genetic markers, their properties, resolution in time and applicability in population structure studies is shortly discussed and compared to ecological methods used to delineate populations.

  18. Organochlorine residues in harbour porpoises from Southwest Greenland

    Energy Technology Data Exchange (ETDEWEB)

    Borrell, Asuncion; Aguilar, Alex; Cantos, Gemma; Lockyer, Christina; Heide-Joergensen, Mads Peter; Jensen, Jette

    2004-02-01

    During the 1995 hunting season, 75 harbour porpoises (Phocoena phocoena) were sampled in three locations in West Greenland: Maniitsoq, Nuuk, and Paamiut. Sex, age, morphometrics, reproductive condition, and organochlorine compound (OC) levels in blubber were determined for each individual. OC levels were extremely low and, therefore considered unlikely to affect the population adversely: mean blubber concentrations, expressed on lipid weight basis were 1.98 (S.D.=1.1) mg/kg for PCBs, 2.76 (S.D.=1.66) mg/kg for tDDT and 0.21 (S.D.=0.11) mg/kg for HCB. No statistical differences were observed among individuals caught in the various locations. OC concentrations showed statistically significant positive associations with age in males but negative in females; consequently, mature females presented lower pollutant loads than their male counterparts. Juveniles did not show differences between sexes. A higher proportion of less chlorinated and more metabolizable polychlorinated biphenyls (PCBs) compared to tPCBs was found in calves (age<=1) than in mature females, indicating that the feeding habits of these two groups differ and that a greater transfer of less chlorinated compounds is passed from females to their pups through lactation and parturition. Harbour porpoises significantly contribute to the dietary intake of OCs by local Inuit populations. This contribution could be reduced if mature males were selectively avoided; however, current hunting procedures make this selection impracticable. - While organochlorine levels in W. Greenland harbour porpoises are low, their contribution to Inuit dietary intake should not be disregarded.

  19. Organochlorine residues in harbour porpoises from Southwest Greenland

    International Nuclear Information System (INIS)

    Borrell, Asuncion; Aguilar, Alex; Cantos, Gemma; Lockyer, Christina; Heide-Joergensen, Mads Peter; Jensen, Jette

    2004-01-01

    During the 1995 hunting season, 75 harbour porpoises (Phocoena phocoena) were sampled in three locations in West Greenland: Maniitsoq, Nuuk, and Paamiut. Sex, age, morphometrics, reproductive condition, and organochlorine compound (OC) levels in blubber were determined for each individual. OC levels were extremely low and, therefore considered unlikely to affect the population adversely: mean blubber concentrations, expressed on lipid weight basis were 1.98 (S.D.=1.1) mg/kg for PCBs, 2.76 (S.D.=1.66) mg/kg for tDDT and 0.21 (S.D.=0.11) mg/kg for HCB. No statistical differences were observed among individuals caught in the various locations. OC concentrations showed statistically significant positive associations with age in males but negative in females; consequently, mature females presented lower pollutant loads than their male counterparts. Juveniles did not show differences between sexes. A higher proportion of less chlorinated and more metabolizable polychlorinated biphenyls (PCBs) compared to tPCBs was found in calves (age<=1) than in mature females, indicating that the feeding habits of these two groups differ and that a greater transfer of less chlorinated compounds is passed from females to their pups through lactation and parturition. Harbour porpoises significantly contribute to the dietary intake of OCs by local Inuit populations. This contribution could be reduced if mature males were selectively avoided; however, current hunting procedures make this selection impracticable. - While organochlorine levels in W. Greenland harbour porpoises are low, their contribution to Inuit dietary intake should not be disregarded

  20. Poinsettia latent virus is not a cryptic virus, but a natural polerovirus-sobemovirus hybrid

    International Nuclear Information System (INIS)

    Siepen, Marc aus dem; Pohl, Jens O.; Koo, Bong-Jin; Wege, Christina; Jeske, Holger

    2005-01-01

    The biochemical and genetic features of Poinsettia latent virus (PnLV, formerly named Poinsettia cryptic virus), which is spread worldwide in commercial cultivars of Euphorbia pulcherrima without inducing symptoms, have been determined using virus-purification, immunological techniques, electron microscopy, cloning, and sequencing. PnLV was found to be a chimeric virus with one 4652 bases, plus strand RNA showing a close relationship to poleroviruses within the first three quarters of its genome but to sobemoviruses in the last quarter. Thus, we propose to classify this virus as 'polemovirus'. Similarities of protein and nucleic acid sequences at the 5' and extreme 3' end of its RNA suggest a replication mode like that of poleroviruses, whereas the coat protein sequence is closely related to that of sobemoviruses. Consistent with these results, PnLV forms stable icosahedra of 34 nm in diameter. The consequences for the taxonomy of PnLV and for gardeners' practice are discussed

  1. Phylogenetic relationships of Acheilognathidae (Cypriniformes: Cyprinoidea) as revealed from evidence of both nuclear and mitochondrial gene sequence variation: Evidence for necessary taxonomic revision in the family and the identification of cryptic species

    Czech Academy of Sciences Publication Activity Database

    Chang, H.-C.; Li, F.; Shao, K.-T.; Lin, Y.-S.; Morosawa, T.; Kim, S.; Koo, H.; Kim, W.; Lee, J.-S.; He, S.; Smith, Carl; Reichard, Martin; Miya, M.; Sado, T.; Uehara, K.; Lavoué, S.; Chen, W.-J.; Mayden, R. L.

    2014-01-01

    Roč. 81, December (2014), s. 182-194 ISSN 1055-7903 Institutional support: RVO:68081766 Keywords : Acheilognathinae * Cyprinidae * Cryptic species * Nuclear loci * Cytochrome b * European bitterling Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.916, year: 2014

  2. Molecular evidence of cryptic speciation in the "cosmopolitan" excavating sponge Cliona celata (Porifera, Clionaidae).

    Science.gov (United States)

    Xavier, J R; Rachello-Dolmen, P G; Parra-Velandia, F; Schönberg, C H L; Breeuwer, J A J; van Soest, R W M

    2010-07-01

    Over the past several decades molecular tools have shown an enormous potential to aid in the clarification of species boundaries in the marine realm, particularly in morphologically simple groups. In this paper we report a case of cryptic speciation in an allegedly cosmopolitan and ecologically important species-the excavating sponge Cliona celata (Clionaidae, Hadromerida). In the Northeast Atlantic and Mediterranean C. celata displays a discontinuous distribution of its putative growth stages (boring, encrusting, and massive) leading us to investigate its specific status. Phylogenetic reconstructions of mitochondrial (COI, Atp8) and nuclear (28S) gene fragments revealed levels of genetic diversity and divergence compatible with interspecific relationships. We therefore demonstrate C. celata as constituting a species complex comprised of at least four morphologically indistinct species, each showing a far more restricted distribution: two species on the Atlantic European coasts and two on the Mediterranean and adjacent Atlantic coasts (Macaronesian islands). Our results provide further confirmation that the different morphotypes do indeed constitute either growth stages or ecologically adapted phenotypes as boring and massive forms were found in two of the four uncovered species. We additionally provide an overview of the cases of cryptic speciation which have been reported to date within the Porifera, and highlight how taxonomic crypsis may confound scientific interpretation and hamper biotechnological advancement. Our work together with previous studies suggests that overconservative systematic traditions but also morphological stasis have led to genetic complexity going undetected and that a DNA-assisted taxonomy may play a key role in uncovering the hidden diversity in this taxonomic group. Copyright 2010 Elsevier Inc. All rights reserved.

  3. Pollution effects on ecobiology of benthic polychaetes in Visakhapatnam Harbour (Bay of Bengal)

    Energy Technology Data Exchange (ETDEWEB)

    Raman, A.V.; Ganapati, P.N.

    1983-02-01

    Rapid urbanization and industrialization of Visakhapatnam and construction of an outer harbour, restricting water flow, have markedly increased the organic load in the inner harbour. Studies of the physico-chemical and biological characteristics of six selected stations along a decreasing gradient of organic pollution have been carried out over a period of two years. The predominantly polychaete benthic fauna occurs in three distinct assemblages: Capitella capitata-Nereis glandicincta in the inner harbour; Cossura coasta-Tharyx marioni in the outer harbour; and a Chloeia-Axiothella-Chaetozone-Nephtys assemblage in the open sea.

  4. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  5. Chemical tracers of shipping emissions in a Mediterranean harbour

    Science.gov (United States)

    Viana, M.; Amato, F.; Alastuey, A.; Querol, X.; Román, A.; García, M.

    2009-04-01

    Particle emissions from transport-related activities are known as one of the most important sources contributing to the PM mass concentrations in urban environments. However, only limited information is currently available in the literature on the contribution to PM levels by specific transport related sources such as shipping emissions, even though according to the latest IPCC report (Ribeiro et al., 2007), shipping emissions are receiving increased scrutiny by international and regional regulatory agencies because of their potential impact on air quality and human health in communities downwind from major shipping lanes and ports (Dominguez et al., 2008). One of the main reasons for this lack of information is the complexity in the detection of shipping emissions, given that no specific emission tracers have so far been identified as a consequence of the vast variability of combustion fuels burnt by vessels. The city of Melilla was selected for the study of shipping emissions due to its location on the South-Western sector of the Mediterranean basin, on the Northern coast of Morocco and less than 200 km from the Gibraltar Strait (35°17´40" N, 2°56´30" W). The city covers an extension of 13.4 km2, with a population of 70000 inhabitants. The monitoring station selected for the present study is representative of urban background levels, and it is located at approximately 150 m from the Melilla harbour. The harbour is mainly characterised by commercial traffic (passanger and container), although minerals and other loose materials are also stocked on the docks located farthest away from the monitoring site. PM10, PM2.5 and PM1 levels were determined on an hourly basis between 12/01/2008 and 19/12/2008 using a GRIMM laser spectrometer, which produced more than 8000 data points for each size fraction (24000 data points in total). In addition, PM10 and PM2.5 levels were sampled on quartz fibre filter substrates (Munktell) by means of high-volume samplers (PM1025 MCV

  6. The National Trust and the Heritage of Sydney Harbour

    Directory of Open Access Journals (Sweden)

    Cameron Logan

    2015-11-01

    Full Text Available Campaigns to preserve the legacy of the past in Australian cities have been particularly focused on the protection of natural landscapes and public open space. From campaigns to protect Perth’s Kings Park and the Green Bans of the Builders Labourers Federation in New South Wales to contemporary controversies such as the Perth waterfront redevelopment, Melbourne’s East West Link, and new development at Middle Harbour in Sydney’s Mosman, heritage activists have viewed the protection and restoration of ‘natural’ vistas, open spaces and ‘scenic landscapes’ as a vital part of the effort to preserve the historic identity of urban places. The protection of such landscapes has been a vital aspect of establishing a positive conception of the environment as a source of both urban and national identity. Drawing predominantly on the records of the National Trust of Australia (NSW, this paper examines the formation and early history of the Australian National Trust, in particular its efforts to preserve and restore the landscapes of Sydney Harbour. It then uses that history as a basis for examining the debate surrounding the landscape reconstruction project that forms part of Sydney’s highly contested Barangaroo development.

  7. Effects of the Horns Reef wind farm on harbour porpoises

    International Nuclear Information System (INIS)

    Tougaard, J.; Teilmann, J.; Rye Hansen, J.

    2004-09-01

    Horns Reef offshore wind farm was established in 2002. It consists of 80 2 MW wind turbines, mounted on steel monopile foundations. A harbour porpoise monitoring program was set up in connection with the environmental impact assessment (EIA) of the wind farm project. This monitoring program started in 1999 with collection of baseline data and has continued though construction and operational period. The program continues through 2005. Baseline studies showed that harbour porpoises are abundant in the area, including the area where the wind farm is now located. Significant effects on behaviour and distribution of the porpoises were observed during the construction of the wind farm. Changes could be linked to pile driving operations, where monopile foundations were rammed into the seabed. This procedure produced high levels of underwater noise and mitigation procedures in the form of a ramp up procedure and deployment of acoustic alarms were employed. During the construction period very few animals were observed inside the wind farm area. Acoustic monitoring data showed a significant increase in waiting time between porpoise encounters in connection with pile driving operations, followed by a rapid return to levels normal for the construction period as a whole. However, when the entire construction period was considered as a whole, T-POD activity increased relative to baseline. Observations during operation of the wind farm in 2003 showed a return to baseline levels on most of the indicators derived from the acoustic monitoring and animals were again seen inside the wind farm area. (au)

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

    Directory of Open Access Journals (Sweden)

    Jörger Katharina M

    2012-12-01

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

  9. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

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

    Science.gov (United States)

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

    2006-10-01

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

  11. Evolution in karst massifs: Cryptic diversity among bent-toed geckos along the Truong Son Range with descriptions of three new species and one new country record from Laos.

    Science.gov (United States)

    Luu, Vinh Quang; Bonkowski, Michael; Nguyen, Truong Quang; Le, Minh Duc; Schneider, Nicole; Ngo, Hanh Thi; Ziegler, Thomas

    2016-05-02

    Species designated as 'cryptic' share a similar morphotype, and are often only clearly separable by molecular data. Cyrtodactylus, the most diverse gecko genus of the family Gekkonidae, is a prime example, because many morphologically similar taxa have only recently been identified as new species as a result of available genetic evidence. However, while cryptic diversity of Cyrtodactylus is already well documented on the Vietnamese side of the Truong Son range, only scarce data is available from central Laos. In this study, we address this issue by means of an integrative approach, which employs morphological, molecular, and ecological data to distinguish cryptic species of the Cyrtodacylus phongnhakebangensis species group primarily distributed along the northern Truong Son Range. Our analyses based on 12 selected morphological characters, a partial mitochondrial gene (COI), and five ecological parameters revealed three undescribed cryptic Cyrtodactylus species from Hin Nam No National Protected Area, which are described as Cyrtodactylus calamei sp. nov., Cyrtodactylus hinnamnoensis sp. nov., and Cyrtodactylus sommerladi sp. nov. A fourth discovered Cyrtodactylus population in Hin Nam No proved to be the first country record of C. cryptus for Laos. Our results highlight the importance of applying an integrative approach to resolving the taxonomy of complex and cryptic species groups, and the role of the Truong Son Range in maintaining the high level of biodiversity over time.

  12. Cryptic invasion of Northern Leopard Frogs (Rana pipiens) across phylogeographic boundaries and a dilemma for conservation of a declining amphibian

    Science.gov (United States)

    O'Donnell, Ryan P.; Drost, Charles A.; Mock, Karen E.

    2017-01-01

    Anthropogenic introduction of species is a major contributor to loss of biodiversity. Translocations within the range of a species are less frequently recognized, but have the potential for negative effects as well. Genetic mixing may lead to loss of local adaptations or further decline through outbreeding depression. These cryptic invasions may be quite difficult to recognize, but genetic tools can be used to recognize and monitor such intraspecific introductions. Conversely, translocations within species can be an important conservation tool to reduce inbreeding depression and replace lost genetic diversity. Thus, cryptic invasions can be either an aid or a hindrance to conservation efforts. We tested for the presence of non-native genotypes and assessed the extent and nature of introgression in populations of Northern Leopard Frog (Rana pipiens) in the southwestern US, where populations have declined to a few remnant populations. The most abundant and diverse complex of populations in the region contained a mitochondrial haplotype that was not native to the western US, probably resulting from the introduction of released pets, laboratory animals, or release during fish stocking. These non-native haplotypes were well integrated into a large complex of ponds and lakes, contributing to high genetic diversity in this area. Logistically, the geographic extent of non-native genetic influence within this population precludes eliminating or controlling the non-native component of this population. We recommend assessing the progress and fate of the introgression over time—along with population fitness parameters—to determine whether this introduction is beneficial or detrimental to population persistence. Meanwhile, translocations from nearby locations with similar environmental conditions have the best prospects for avoiding problems with outbreeding depression in other declining populations and will also most effectively preserve regional genetic diversity.

  13. Sydney harbourings, rehabilitations and the politics of procurement

    Directory of Open Access Journals (Sweden)

    Catherine de Lorenzo

    2002-09-01

    Full Text Available In the last three years Sydney has been transformed to an unprecedented extent by public art projects, most of which have been developed by government instrumentalities, agencies or partnerships. The central city council has initiated a Sculpture Walk through the streets and around the rocky foreshores of the inner city; the Sydney Olympic site at Homebush Bay is home to a number of public art works; the government’s water utility company has sponsored an annual, temporary art installation walk along a spectacularly rugged ocean escarpment linking several medium-density suburbs; another instrumentality recently established to oversee the reuse of abandoned heavy industrial sites in the harbour, has established the ‘Promenart’ program along fifteen kilometres of harbour foreshores; and a government-appointed statutory authority responsible for the redevelopment of an extensive and highly polluted former industrial site between the CDB and the airport, has worked closely with designers and artists to develop comprehensive briefs addressing environmental rehabilitation and social interaction. This impressive list is by no means exhaustive. The surge in bureaucratic and artistic creative energy demands critical evaluation. In this paper I will contrast two sets of projects. This first concerns actual projects, in or near the spectacular Sydney Harbour setting, which are premised on placemaking principles and on the whole elicit actual or imagined histories for the delight and reverie of the promenader. Despite the popular and aesthetic success of these projects, one of them, the ambitious Sculpture Walk, is currently being re-evaluated. The second set, in more mundane suburban environments and centred on toxic waterways, concerns projects that at this stage are either being implemented or nearing commencement by interdisciplinary groups of artists, designers, engineers, environmentalists, community representatives, and other specialists. Their

  14. Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera).

    Science.gov (United States)

    Gómez, Africa; Serra, Manuel; Carvalho, Gary R; Lunt, David H

    2002-07-01

    Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

  15. Diagnosis of Familial Wolf-Hirschhorn Syndrome due to a Paternal Cryptic Chromosomal Rearrangement by Conventional and Molecular Cytogenetic Techniques

    Directory of Open Access Journals (Sweden)

    Carlos A. Venegas-Vega

    2013-01-01

    Full Text Available The use of conventional cytogenetic techniques in combination with fluorescent in situ hybridization (FISH and single-nucleotide polymorphism (SNP microarrays is necessary for the identification of cryptic rearrangements in the diagnosis of chromosomal syndromes. We report two siblings, a boy of 9 years and 9 months of age and his 7-years- and 5-month-old sister, with the classic Wolf-Hirschhorn syndrome (WHS phenotype. Using high-resolution GTG- and NOR-banding karyotypes, as well as FISH analysis, we characterized a pure 4p deletion in both sibs and a balanced rearrangement in their father, consisting in an insertion of 4p material within a nucleolar organizing region of chromosome 15. Copy number variant (CNV analysis using SNP arrays showed that both siblings have a similar size of 4p deletion (~6.5 Mb. Our results strongly support the need for conventional cytogenetic and FISH analysis, as well as high-density microarray mapping for the optimal characterization of the genetic imbalance in patients with WHS; parents must always be studied for recognizing cryptic balanced chromosomal rearrangements for an adequate genetic counseling.

  16. Diagnosis of Familial Wolf-Hirschhorn Syndrome due to a Paternal Cryptic Chromosomal Rearrangement by Conventional and Molecular Cytogenetic Techniques

    Science.gov (United States)

    Venegas-Vega, Carlos A.; Zepeda, Luis M.; Garduño-Zarazúa, Luz M.; Berumen, Jaime; Kofman, Susana; Cervantes, Alicia

    2013-01-01

    The use of conventional cytogenetic techniques in combination with fluorescent in situ hybridization (FISH) and single-nucleotide polymorphism (SNP) microarrays is necessary for the identification of cryptic rearrangements in the diagnosis of chromosomal syndromes. We report two siblings, a boy of 9 years and 9 months of age and his 7-years- and 5-month-old sister, with the classic Wolf-Hirschhorn syndrome (WHS) phenotype. Using high-resolution GTG- and NOR-banding karyotypes, as well as FISH analysis, we characterized a pure 4p deletion in both sibs and a balanced rearrangement in their father, consisting in an insertion of 4p material within a nucleolar organizing region of chromosome 15. Copy number variant (CNV) analysis using SNP arrays showed that both siblings have a similar size of 4p deletion (~6.5 Mb). Our results strongly support the need for conventional cytogenetic and FISH analysis, as well as high-density microarray mapping for the optimal characterization of the genetic imbalance in patients with WHS; parents must always be studied for recognizing cryptic balanced chromosomal rearrangements for an adequate genetic counseling. PMID:23484094

  17. A Holocene pollen and sediment record of Whangape Harbour, far northern New Zealand

    International Nuclear Information System (INIS)

    Horrocks, M.; Nichol, S.L.; Gregory, M.R.; Creese, R.; Augustinus, P.C.

    2001-01-01

    The sediment record of Whangape Harbour shows that there were significant fluctuations in depositional energy in the harbour during the period from c. >8000 cal. yr BP to some time within the last millenium, and that fluvial influences increased as the harbour infilled. The pollen record (highly discontinuous) from Whangape Harbour indicates that conifer-hardwood forest covered the hills surrounding the harbour during this period. The main canopy conifers were Dacrydium and Prumnopitys taxifolia, with some Libocedrus, Dacrycarpus, and Phyllocladus. Agathis was also present. Common canopy hardwoods were Metrosideros and, in the latter part of the period, Elaeocarpus. Ascarina and Cyathea were abundant in the sub-canopy. Leptospermum grew on disturbed areas fringing the estuary. Marsh or swamp environments probably never developed on a large scale in the harbour. Avicennia, extremely under-represented in the pollen flora, has been present on tidal flats in the harbour since at least c. 2500 cal. yr BP. Large-scale anthropogenic deforestation by burning commenced in the Whangape catchment some time during or since 700-430 cal. yr BP. The associated increase in erosion rates in the catchment resulted in a change towards a sandier sediment regime in the harbour which has continued to the present day. Weinmannia and Ackama, previously rare in the catchment, expanded in remaining forest. (author). 39 refs., 3 figs., 1 tab

  18. Telemetry studies in harbour porpoises - An overview of the technical and practical state of the art

    NARCIS (Netherlands)

    Lucke, K.

    2013-01-01

    Information on the life functions and ecology of harbour porpoises is still scarce. Only a limited number of animals are available for research in controlled situations. Satellite tracking allows to gather information on individual movements of harbour porpoises, hence providing direct insight into

  19. Biochemical indicators of pollution exposure in shorthorn sculpin (Myoxocephalus scorpius), caught in four harbours on the southwest coast of Iceland.

    Science.gov (United States)

    Stephensen; Svavarsson; Sturve; Ericson; Adolfsson-Erici; Förlin

    2000-04-01

    Shorthorn sculpins (Myoxocephalus scorpius) were caught in four Icelandic harbours, differing in size, use and traffic. Biochemical responses in liver were measured and chemicals analysed in bile. Eyrarbakki harbour, which has not been in use for many years was chosen as a control site. Njar partial differentialvík harbour is a small fishing harbour and a marina, Sandger partial differentiali harbour is a large fishing harbour, and Reykjavík harbour is a large fishing harbour and an international transport harbour. Higher levels of DNA-adducts and cytochrome P4501A (CYP1A) in the fish from the harbours in Sandger partial differentiali, Njar partial differentialvík and Reykjavík, compared to Eyrarbakki harbour, indicate PAH exposure. This was confirmed by PAH analysis in bile. The higher activities of the antioxidant enzymes catalase (CAT), glutathione peroxidase (GPx) and glutathione reductase (GR) in fish caught in Sandger partial differentiali, than in fish caught in the other harbours, indicate exposure of sculpin to prooxidative compounds in Sandger partial differentiali harbour. Shorthorn sculpin seems to be a convenient species for monitoring pollution in northern coastal areas.

  20. Cryptic Species Due to Hybridization: A Combined Approach to Describe a New Species (Carex: Cyperaceae).

    Science.gov (United States)

    Maguilla, Enrique; Escudero, Marcial

    2016-01-01

    Disappearance of diagnostic morphological characters due to hybridization is considered to be one of the causes of the complex taxonomy of the species-rich (ca. 2000 described species) genus Carex (Cyperaceae). Carex furva s.l. belongs to section Glareosae. It is an endemic species from the high mountains of the Iberian Peninsula (Spain and Portugal). Previous studies suggested the existence of two different, cryptic taxa within C. furva s.l. Intermediate morphologies found in the southern Iberian Peninsula precluded the description of a new taxa. We aimed to determine whether C. furva s.l. should be split into two different species based on the combination of morphological and molecular data. We sampled ten populations across its full range and performed a morphological study based on measurements on herbarium specimens and silica-dried inflorescences. Both morphological and phylogenetic data support the existence of two different species within C. furva s.l. Nevertheless, intermediate morphologies and sterile specimens were found in one of the southern populations (Sierra Nevada) of C. furva s.l., suggesting the presence of hybrid populations in areas where both supposed species coexist. Hybridization between these two putative species has blurred morphological and genetic limits among them in this hybrid zone. We have proved the utility of combining molecular and morphological data to discover a new cryptic species in a scenario of hybridization. We now recognize a new species, C. lucennoiberica, endemic to the Iberian Peninsula (Sierra Nevada, Central system and Cantabrian Mountains). On the other hand, C. furva s.s. is distributed only in Sierra Nevada, where it may be threatened by hybridization with C. lucennoiberica. The restricted distribution of both species and their specific habitat requirements are the main limiting factors for their conservation.

  1. Sources of contamination and modelled pollutant trajectories in a Mediterranean harbour (Tarragona, Spain).

    Science.gov (United States)

    Mestres, M; Sierra, J P; Mösso, C; Sánchez-Arcilla, A

    2010-06-01

    The proximity of commercial harbours to residential areas and the growing environmental awareness of society have led most port authorities to include environmental management within their administration plan. Regarding water quality, it is necessary to have the capacity and tools to deal with contamination episodes that may damage marine ecosystems and human health, but also affect the normal functioning of harbours. This paper presents a description of the main pollutant sources in Tarragona Harbour (Spain), and a numerical analysis of several pollution episodes based on the Port Authority's actual environmental concerns. The results show that pollution generated inside the harbour tends to remain confined within the port, whereas it is very likely that oil spills from a nearby monobuoy may affect the neighbouring beaches. The present combination of numerical models proves itself a useful tool to assess the environmental risk associated to harbour activities and potential pollution spills.

  2. Role of commercial harbours and recreational marinas in the spread of non-indigenous fouling species.

    Science.gov (United States)

    Ferrario, Jasmine; Caronni, Sarah; Occhipinti-Ambrogi, Anna; Marchini, Agnese

    2017-09-01

    The role of commercial harbours as sink and source habitats for non-indigenous species (NIS) and the role of recreational boating for their secondary spread were investigated by analysing the fouling community of five Italian harbours and five marinas in the western Mediterranean Sea. It was first hypothesised that NIS assemblages in the recreational marinas were subsets of those occurring in commercial harbours. However, the data did not consistently support this hypothesis: the NIS pools of some marinas significantly diverged from harbours even belonging to the same coastal stretches, including NIS occurring only in marinas. This study confirms harbours as hotspots for marine NIS, but also reveals that numbers of NIS in some marinas is higher than expected, suggesting that recreational vessels effectively facilitate NIS spread. It is recommended that this vector of NIS introduction is taken into account in the future planning of sustainable development of maritime tourism in Europe.

  3. Distribution of uranium at Mumbai Harbour Bay (MHB)

    International Nuclear Information System (INIS)

    Sugandhi, S.; Prabhu, S.P.; Mishra, D.G.; Ravi, P.M.; Hegde, A.G.

    2010-01-01

    Mumbai Harbour Bay (MHB) is a recipient of low level treated effluents from BARC, Trombay. In addition, the Bay is also a recipient of domestic and industrial wastes from the city of Mumbai and adjoining areas. Uranium though considered as a rare element, occurs in seawater. The present study is dealt with the distribution of uranium in seawater of Mumbai Harbour Bay (MHB). Uranium is mainly present as Tricarbanato uranyl anion ((UO 2 (CO 3 ) 3 ) 4- ) in seawater and its concentration varies with the locality and depth. The average value of uranium concentration reported for Indian Bay water at Tarapur and Mumbai is ∼ 3.0 ppb which is comparable with the reported value for Arabian sea. As such the global average is reported to be ∼ 3.3 ppb by Oceanologists. A total of 18 seawater samples covering the upstream, downstream and middle stream of MHB were collected and filtered through 0.22 μm filter paper. 10 L of filtered sample was subjected to chemical separation using ion-exchange technique which involved the following steps: the filtered samples were acidified with conc. HNO 3 and digested. Ca 3 (PO 4 ) 2 was precipitated at pH 8-9 by addition of liquid ammonia which coprecipitates uranium. The precipitate was allowed to settle overnight, supernatant discarded; precipitate was washed thoroughly with distilled water twice, dissolved in electronic grade conc. HNO 3 and evaporated to dryness. Residue formed was heated with electronic grade conc. HCI and taken up in 8M HCI and loaded on to Dowex 1x8 (Cl -1 for, 1.5 g, 100-200 mesh, anion exchanger), preconditioned with 8M HCI. Uranium adsorbed on the resin was eluted with 1 M HNO 3 . The eluant was evaporated to dryness and electrodeposited on a stainless steel planchette and the uranium content was estimated by alpha spectrometry (PIPS, Type IPC). The uranium activity in MHB by alpha spectrometry was found to be between 1.0-4.4 ppb with an average concentration of 2.5 ppb which is comparable with the earlier

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

    Science.gov (United States)

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

    2017-01-01

    Abstract 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. PMID:28973577

  5. 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.

  6. Catch history and status of the harbour seal (Phoca vitulina in Greenland

    Directory of Open Access Journals (Sweden)

    Aqqalu Rosving-Asvid

    2010-09-01

    Full Text Available The number of harbour seals (Phoca vitulina in West Greenland declined rapidly after the 1950s and the seals have now abandoned their traditional haulout locations along the Greenland west coast. However, in recent years, a previously undetected group of about 60-100 harbour seals has been observed approximately 80 km upstream in a large river, and some traditional hauloutlocations are still in use near the south-eastern tip of Greenland. A small number of harbour seals is caught annually far from any of these locations, indicating that other groups might live unnoticed. Catch statistics provide the best evidence of the presence and locations of these remnant harbour seals. Therefore efforts were made to validate the recent catch statistics and to describe the catch history for the past 60 years. The catch statistics were also used to estimate plausibleranges of past and present numbers of harbour seals based on the assumption that hunting has caused the observed decline. The total number of harbour seals in Greenland according to these estimates was about 3,000 in 1950 and fewer than 1,000 in 2007. The number of harbour seals caught in the southernmost part of Greenland has, unlike in the rest of Greenland, increased significantly in some of the recent years. This change seems to be related to changes in the amount of drift ice. Drift ice reduces the frequency of contact between hunters and harbour seals in South Greenland and above normal quantities of drift ice from the mid 1960s to the mid 1980s probably allowed these seals to increase in numbers. Record low inflow of drift ice in some of the recent years, however, has resulted in record high catches, which likely have reduced the seals again. The remaining harbour seals in Greenland are few and without protection these sealsare potentially in danger of extinction.

  7. Biofilm architecture of Phanerozoic cryptic carbonate marine veneers

    Science.gov (United States)

    Riding, Robert

    2002-01-01

    Thin (mushrooms, and plumes. All can be interpreted as characteristics of attached bacterial communities, i.e., aggregates as microcolonies, originally embedded in a matrix of extracellular polymeric substances; channels as water conduits and/or uncolonized nutrient-poor spaces; external protuberances as localized growths; and plumes as surface streamers. Cryptic habitat favored pristine biofilm preservation by precluding disturbance and overgrowth, and suggests aphotic and anoxic conditions. These examples provide diagnostic morphologic criteria for wider recognition of biofilm in Phanerozoic and older carbonates.

  8. DNA barcoding as a screening tool for cryptic diversity

    DEFF Research Database (Denmark)

    Huemer, Peter; Karsholt, Ole; Mutanen, Marko

    2014-01-01

    We explore the potential value of DNA barcode divergence for species delimitation in the genus Caryocolum Gregor & Povolný, 1954 (Lepidoptera, Gelechiidae), based on data from 44 European species (including 4 subspecies). Low intraspecific divergence of the DNA barcodes of the mtCOI (cytochrome c...... oxidase 1) gene and/or distinct barcode gaps to the nearest neighbor support species status for all examined nominal taxa. However, in 8 taxa we observed deep splits with a maximum intraspecific barcode divergence beyond a threshold of 3%, thus indicating possible cryptic diversity. The taxonomy...

  9. Cryptic chemical identification as a crime intelligence aid.

    Science.gov (United States)

    Sturaro, A; Rella, R; Parvoli, G; Doretti, L

    1999-01-01

    A dead body was found near the sea and a commercial port in north-east Italy. The man had been shot and then burnt, by using a large volume of fire accelerant. The chemical composition of the flammable mixture had to be determined in order to aid police investigations. GC-MS analysis of residual cloth and soil identified a common gasoline, together with some unrelated compounds deriving from the container used to carry the inflammable liquid. A reconstruction of the event, an examination of the surroundings where the crime took place and the cryptic chemicals found, enabled the investigators to restrict and intensify their enquiries within a specific area.

  10. n-Alkanes in surficial sediments of Visakhapatnam harbour, east coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Punyu, V.R.; Harji, R.R.; Bhosle, N.B.; Sawant, S.S.; Venkat, K.

    -alkanes mainly at C15, C17 and C19 Keywords. Sediments; lipids; n-alkanes; Visakhapatnam harbour. J. Earth Syst. Sci. 122, No. 2, April 2013, pp. 467–477 c© Indian Academy of Sciences 467 468 V R Punyu et al while terrestrial plants exhibit predominance of long... steel plant, a fertilizer plant and a lead and zinc smelter in the vicinity are discharged into this harbour. The harbour handles items such as man- ganese and iron ore, coal and oil products. Added to this, it receives most of the urban run...

  11. Seasonal, diel, tidal, and geographical variation in male harbour seal (Phoca vitulina) vocalizations in southern Scandinavia

    DEFF Research Database (Denmark)

    Faxe Sabinsky, Puk; Tougaard, Jakob; Wahlberg, Magnus

    Male harbour seals make underwater calls in the mating season but remarkable little is known about the circumstances under which the calls are made and the role of the calls in mating. This study reports on the first recordings of harbour seal calls from Danish waters and investigates...... calling behavior of harbour seals. This gives prospects of a tool, which can aid in identifying essential underwater areas used in mating behavior by the seals, and can allow assessment of the need for adequate protection of these areas as required by the Habitats Directive....

  12. OPINIONS REGARDING THE TOURISTIC POTENTIAL OF THE DANUBIAN HARBOURS

    Directory of Open Access Journals (Sweden)

    Elena MATEI

    2013-12-01

    Full Text Available In the context of European integration, the creation of transnational tourism products represents the brand of an inter-state collaboration, which, based on a common strategy, implies objectives that aim at achieving the global development of a destination, making thus possible an efficient and effective allocation of resources, in order to achieve a sustainable development, both from a touristic point of view and from an economic, social, cultural, technological, etc. one. The route of the Danube could represent one of the most important European destinations, appertaining to more than one country; therefore, in order to develop and sustain its touristic potential, a common strategy is necessary, with an integrated marketing image, associated to a consistent tourism product, inspiring common values, regardless of the territory of the country it is located in. In this direction, a quantitative marketing research, conducted on 992 respondents, aged 18-24, in order to determine the opinions concerning the touristic potential of the Danubian harbours – as a fundamental element, precursory to the market analysis.

  13. Insect symbiotic bacteria harbour viral pathogens for transovarial transmission.

    Science.gov (United States)

    Jia, Dongsheng; Mao, Qianzhuo; Chen, Yong; Liu, Yuyan; Chen, Qian; Wu, Wei; Zhang, Xiaofeng; Chen, Hongyan; Li, Yi; Wei, Taiyun

    2017-03-06

    Many insects, including mosquitoes, planthoppers, aphids and leafhoppers, are the hosts of bacterial symbionts and the vectors for transmitting viral pathogens 1-3 . In general, symbiotic bacteria can indirectly affect viral transmission by enhancing immunity and resistance to viruses in insects 3-5 . Whether symbiotic bacteria can directly interact with the virus and mediate its transmission has been unknown. Here, we show that an insect symbiotic bacterium directly harbours a viral pathogen and mediates its transovarial transmission to offspring. We observe rice dwarf virus (a plant reovirus) binding to the envelopes of the bacterium Sulcia, a common obligate symbiont of leafhoppers 6-8 , allowing the virus to exploit the ancient oocyte entry path of Sulcia in rice leafhopper vectors. Such virus-bacterium binding is mediated by the specific interaction of the viral capsid protein and the Sulcia outer membrane protein. Treatment with antibiotics or antibodies against Sulcia outer membrane protein interferes with this interaction and strongly prevents viral transmission to insect offspring. This newly discovered virus-bacterium interaction represents the first evidence that a viral pathogen can directly exploit a symbiotic bacterium for its transmission. We believe that such a model of virus-bacterium communication is a common phenomenon in nature.

  14. Aspergillus niger contains the cryptic phylogenetic species A. awamori.

    Science.gov (United States)

    Perrone, Giancarlo; Stea, Gaetano; Epifani, Filomena; Varga, János; Frisvad, Jens C; Samson, Robert A

    2011-11-01

    Aspergillus section Nigri is an important group of species for food and medical mycology, and biotechnology. The Aspergillus niger 'aggregate' represents its most complicated taxonomic subgroup containing eight morphologically indistinguishable taxa: A. niger, Aspergillus tubingensis, Aspergillus acidus, Aspergillus brasiliensis, Aspergillus costaricaensis, Aspergillus lacticoffeatus, Aspergillus piperis, and Aspergillus vadensis. Aspergillus awamori, first described by Nakazawa, has been compared taxonomically with other black aspergilli and recently it has been treated as a synonym of A. niger. Phylogenetic analyses of sequences generated from portions of three genes coding for the proteins β-tubulin (benA), calmodulin (CaM), and the translation elongation factor-1 alpha (TEF-1α) of a population of A. niger strains isolated from grapes in Europe revealed the presence of a cryptic phylogenetic species within this population, A. awamori. Morphological, physiological, ecological and chemical data overlap occurred between A. niger and the cryptic A. awamori, however the splitting of these two species was also supported by AFLP analysis of the full genome. Isolates in both phylospecies can produce the mycotoxins ochratoxin A and fumonisin B₂, and they also share the production of pyranonigrin A, tensidol B, funalenone, malformins, and naphtho-γ-pyrones. In addition, sequence analysis of four putative A. awamori strains from Japan, used in the koji industrial fermentation, revealed that none of these strains belong to the A. awamori phylospecies. Copyright © 2011 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  15. 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.

  16. 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

  17. Minimized state complexity of quantum-encoded cryptic processes

    Science.gov (United States)

    Riechers, Paul M.; Mahoney, John R.; Aghamohammadi, Cina; Crutchfield, James P.

    2016-05-01

    The predictive information required for proper trajectory sampling of a stochastic process can be more efficiently transmitted via a quantum channel than a classical one. This recent discovery allows quantum information processing to drastically reduce the memory necessary to simulate complex classical stochastic processes. It also points to a new perspective on the intrinsic complexity that nature must employ in generating the processes we observe. The quantum advantage increases with codeword length: the length of process sequences used in constructing the quantum communication scheme. In analogy with the classical complexity measure, statistical complexity, we use this reduced communication cost as an entropic measure of state complexity in the quantum representation. Previously difficult to compute, the quantum advantage is expressed here in closed form using spectral decomposition. This allows for efficient numerical computation of the quantum-reduced state complexity at all encoding lengths, including infinite. Additionally, it makes clear how finite-codeword reduction in state complexity is controlled by the classical process's cryptic order, and it allows asymptotic analysis of infinite-cryptic-order processes.

  18. Monitoring cryptic amphibians and reptiles in a Florida state park.

    Science.gov (United States)

    Engeman, Richard M; Meshaka, Walter E; Severson, Robert; Severson, Mary Ann; Kaufman, Greg; Groninger, N Paige; Smith, Henry T

    2016-04-01

    We monitored cryptic herpetofauna at Savannas Preserve State Park, Florida, by combining artificial cover counts with a quantitative paradigm for constructing and calculating population indices. Weekly indices were calculated from two consecutive days of data collection each week for 7 months from mid-winter to mid-summer in three habitats. Seventeen species were observed at least once, and time trends using index values were followed for six species. Among these, abundance and seasonal pattern information were obtained for an exotic species (greenhouse frog) and a species identified by the Florida Committee on Rare and Endangered Plants and Animals as threatened (Florida scrub lizard). We identified winter as the optimal time in this area to monitor populations for conducting annual assessments. This combined observation and indexing approach could provide managers or researchers with an economical means to quantitatively index population trends for multiple cryptic herpetofauna species simultaneously. Using artificial cover to sample within a population indexing design can be generalized beyond monitoring herpetofauna. Other forms of artificial cover that can be used as observation stations include aquatic artificial substrates, artificial tree cavities, artificial reefs, and other artificial aquatic structures and artificial sea grass units, among many others, and a wide range of taxa are suitable for population monitoring using artificial cover as observation stations in the approach we present, including insects, soil invertebrates, micro and macro aquatic invertebrates, fish, crustaceans, and small mammals.

  19. Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada.

    Science.gov (United States)

    Starrett, James; Hayashi, Cheryl Y; Derkarabetian, Shahan; Hedin, Marshal

    2018-01-01

    The relative roles of ecological niche conservatism versus niche divergence in promoting montane speciation remains an important topic in biogeography. Here, our aim was to test whether lineage diversification in a species complex of trapdoor spiders corresponds with riverine barriers or with an ecological gradient associated with elevational tiering. Aliatypus janus was sampled from throughout its range, with emphasis on populations in the southern Sierra Nevada Mountains of California. We collected multi-locus genetic data to generate a species tree for A. janus and its close relatives. Coalescent based hypothesis tests were conducted to determine if genetic breaks within A. janus conform to riverine barriers. Ecological niche models (ENM) under current and Last Glacial Maximum (LGM) conditions were generated and hypothesis tests of niche conservatism and divergence were performed. Coalescent analyses reveal deeply divergent genetic lineages within A. janus, likely corresponding to cryptic species. Two primary lineages meet along an elevational gradient on the western slopes of the southern Sierra Nevada Mountains. ENMs under both current and LGM conditions indicate that these groups occupy largely non-overlapping niches. ENM hypothesis testing rejected niche identity between the two groups, and supported a sharp ecological gradient occurring where the groups meet. However, the niche similarity test indicated that the two groups may not inhabit different background niches. The Sierra Nevada Mountains provide a natural laboratory for simultaneously testing ecological niche divergence and conservatism and their role in speciation across a diverse range of taxa. Aliatypus janus represents a species complex with cryptic lineages that may have diverged due to parapatric speciation along an ecological gradient, or been maintained by the evolution of ecological niche differences following allopatric speciation. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Determination of petroleum hydrocarbons in sediment samples from Bombay harbour, Dharamtar creek and Amba river estuary

    Digital Repository Service at National Institute of Oceanography (India)

    Ingole, S.A.; Dhaktode, S.S.; Kadam, A.N.

    The surface sediment samples were collected by van Veen grab sampler during premonsoon, monsoon and postmonsoon seasons from Bombay harbour, Dharamtar creek and Amba river estuary Moisture content of the samples ranges from 36 to 67.5...

  1. Extractable organics in surface sediments from Thana creek and Bombay harbour

    Digital Repository Service at National Institute of Oceanography (India)

    Rokade, M.A.; Bhosle, N.B.; Kadam, A.N.

    Considerable variations in hydrocarbon and fatty acid levels in surface sediments from Thana creek and Bombay harbour were observed Sediments from the westernside nearshore locations yielded higher values The residues were characterised by infrared...

  2. TECHNOLOGY EVALUATION REPORT: TORONTO HARBOUR COMMISSIONERS (THC) SOIL RECYCLE TREATMENT TRAIN. Project Summary

    Science.gov (United States)

    A demonstration of the Toronto Harbour Commissioners' (THC) Soil Recycle Treatment Train was performed under the Superfund Innovative Technology Evaluation (SITE) Program at a pilot plant facility in Toronto, Ontario, Canada. The Soil Recycle Treatment Train, which consists of s...

  3. Investigations on oil patches around 'M.T.Lajpatrai' Bombay harbour

    Digital Repository Service at National Institute of Oceanography (India)

    Kadam, A.N.; Zingde, M.D.

    Samples from three oil patches observed around the burning tanker 'M. T. Lajpatrai' at Bombay Harbour were characterised using proton magnetic resonance spectroscopy (PMR). Two of them were found to be from used lubricating oils. As indicated by gas...

  4. Phytoplankton characteristics in a polluted Bombay Harbour-Thana-Bassein creek estuarine complex

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, Neelam; Ramaiah, N.; Nair, V.R.

    Annual variations in phytoplankton characteristics were studied from Bombay Harbour-Thana creek-Bassein creek (BHTCBC) estuarine confluence to assess the levels of pigment concentration, productivity and, qualitative and qunatitative nature...

  5. Mixing in Visakhapatnam harbour and nutrient inputs to nearshore waters, east coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    RamaRaju, V.S.; Sarma, V.V.; Raju, G.R.K.; Rao, V.S.

    The flushing time (t) and replacement time CD are computed for different seasons to understand mixing in Visakhapatnam harbour. Replacement times are higher than the flushing times indicating that the transverse mixing in the tidal flow...

  6. Species composition, abundance and distribution of hydromedusae from Dharamtar estuarine system, adjoining Bombay Harbour

    Digital Repository Service at National Institute of Oceanography (India)

    Santhakumari, V.; Tiwari, L.R.; Nair, V.R.

    Species composition, abundance and distribution of hydromedusae from Dharamtar estuarine system, adjoining Bombay Harbour, Maharashtra, India were investigated during 1984-1985. Twenty six species belonging to 19 genera were obtained from this area...

  7. A new species of Acartia (Copepoda, Calanoida) from Cochin Harbour, India, and adjacent areas

    Digital Repository Service at National Institute of Oceanography (India)

    Abraham, S.

    During the course of a study of the family Acartiidae of Cochin harbour and its neighbourhood, a species of Acartia different from all other known species of Acartia, was found. Its characteristics, habitat and seasonal distribution form the theme...

  8. Radioactivity concentrations and their radiological significance in sediments of the Tema Harbour (Greater Accra, Ghana)

    OpenAIRE

    Benjamin O. Botwe; Antonio Schirone; Ivana Delbono; Mattia Barsanti; Roberta Delfanti; Peter Kelderman; Elvis Nyarko; Piet N.L. Lens

    2017-01-01

    Studies on environmental radioactivity in tropical Africa are scarce. Therefore, a baseline study of natural (238U, 210Pb, 226Ra, 232Th, 228Ra, 228Th, 40K) and anthropogenic (137Cs) radionuclides was carried out on Tema Harbour (Greater Accra, Ghana) surface sediments and on their radiological significance. Grab surface sediment samples were collected from 21 stations within the Tema Harbour and their radioactivity concentrations measured by gamma spectrometry. The mean sediment radioactivity...

  9. A Novel Three-Colour Fluorescence in Situ Hybridization Approach for the Detection of t(7;12)(q36;p13) in Acute Myeloid Leukaemia Reveals New Cryptic Three Way Translocation t(7;12;16)

    Energy Technology Data Exchange (ETDEWEB)

    Naiel, Abdulbasit [Leukaemia and Chromosome Research Laboratory, Division of Biosciences, Brunel University, London, Middlesex UB8 3PH (United Kingdom); Vetter, Michael [MetaSystems, Altlussheim 68804 (Germany); Plekhanova, Olga [Regional Children’s Hospital N 1, Ekaterinburg 620149 (Russian Federation); Fleischman, Elena; Sokova, Olga [N.N. Blokhin Russian Cancer Research Center Russian Academy of Medical Science, Moscow 115478 (Russian Federation); Tsaur, Grigory [Regional Children’s Hospital N 1, Ekaterinburg 620149 (Russian Federation); Research Institute of Medical Cell Technologies, Ekaterinburg 620149 (Russian Federation); Harbott, Jochen [Oncogenetic Laboratory, Department of Paediatric Haematology and Oncology, Justus Liebig University, Giessen 35392 (Germany); Tosi, Sabrina, E-mail: sabrina.tosi@brunel.ac.uk [Leukaemia and Chromosome Research Laboratory, Division of Biosciences, Brunel University, London, Middlesex UB8 3PH (United Kingdom)

    2013-03-11

    The t(7;12)(q36;p13) translocation is a recurrent chromosome abnormality that involves the ETV6 gene on chromosome 12 and has been identified in 20–30% of infant patients with acute myeloid leukaemia (AML). The detection of t(7;12) rearrangements relies on the use of fluorescence in situ hybridization (FISH) because this translocation is hardly visible by chromosome banding methods. Furthermore, a fusion transcript HLXB9-ETV6 is found in approximately 50% of t(7;12) cases, making the reverse transcription PCR approach not an ideal screening method. Considering the report of few cases of variant translocations harbouring a cryptic t(7;12) rearrangement, we believe that the actual incidence of this abnormality is higher than reported to date. The clinical outcome of t(7;12) patients is believed to be poor, therefore an early and accurate diagnosis is important in the clinical management and treatment. In this study, we have designed and tested a novel three-colour FISH approach that enabled us not only to confirm the presence of the t(7;12) in a number of patients studied previously, but also to identify a cryptic t(7;12) as part of a complex rearrangement. This new approach has proven to be an efficient and reliable method to be used in the diagnostic setting.

  10. The spatial and temporal distribution of heavy metals in sediments of Victoria Harbour, Hong Kong

    International Nuclear Information System (INIS)

    Tang, Chloe Wing-yee; Ip, Carman Ching-man; Zhang Gan; Shin, Paul K.S.; Qian Peiyuan; Li Xiangdong

    2008-01-01

    Victoria Harbour has received substantial loadings of pollutants from industrial and municipal wastewater discharged since the 1950s. Inputs of contaminants have declined dramatically during the last two decades as a result of better controls at the source and improved wastewater treatment facilities. To assess the spatial and temporal changes of metal contaminants in sediments in Victoria Harbour, core and grab sediments were collected. The central harbour areas were generally contaminated with heavy metals. The spatial distribution of trace metals can probably be attributed to the proximity of major urban and industrial discharge points, and to the effect of tidal flushing in the harbour. In the sediment cores, the highest concentrations of trace metals were observed to have accumulated during the 1950s-1980s, corresponding with the period of rapid urban and industrial development in Hong Kong. From the late 1980s, there has been a major decline in the concentrations of trace metals, due to a reduction in industrial activities and to the enactment of wastewater pollution controls in the territory. The Pb isotopic compositions of the sediments revealed the anthropogenic inputs of Pb to the harbour. The 206 Pb/ 207 Pb ratios varied from 1.154 to 1.190, which were lower than those of background geological materials in Hong Kong ( 206 Pb/ 207 Pb: 1.201-1.279). The data also indicated that the Pb in the harbour sediments most likely originated from mixed sources, including the leaded gasoline used in the past and other anthropogenic sources

  11. Molecular data raise the possibility of cryptic species in the Brazilian endemic prawn Macrobrachiumpotiuna (Decapoda, Palaemonidae

    Directory of Open Access Journals (Sweden)

    Fabrício L de Carvalho

    2013-09-01

    Full Text Available A recent taxonomic revision indicated that Macrobrachiumpotiuna, an endemic prawn in Brazilian freshwater drainages, exhibits wide morphological variability along its limited geographical distribution. However, in some cases, taxonomic doubts at the species level have no clear morphological resolution. Considering that no molecular data of M. potiuna along its distribution were available to provide a complete and integrated overview, we analyzed 21 partial sequences (531 bp from the mitochondrial 16S rRNA gene of M. potiuna and 9 sequences from outgroup species, by maximum likelihood and parsimony, in order to investigate the possibility of the existence of cryptic species, within the morphologically based M. potiuna. The topologies obtained revealed that M. potiuna represents a monophyletic clade. Nevertheless, two clades supported by both analyses were formed within the M. potiuna taxon. The mean genetic divergence between these two groups was 0.044 ± 0.007, and within each group (i.e., M. potiuna "sensu stricto" andM. potiuna "Affinis-Clade" the divergences were 0.010 ± 0.003 and 0.028 ± 0.005, respectively. As far as we know, this is the first report to show a genetic separation between populations of prawns with abbreviated larval development in South American drainages. Pending additional analysis, to propose a conclusive inference, the existence of these distinct genetic groups must be considered in future studies with the morphologically based M. potiuna. In addition, we extended the known northern distribution with a record from the state of Bahia.

  12. Spawning segregation and philopatry are major prezygotic barriers in sympatric cryptic Mugil cephalus species.

    Science.gov (United States)

    Shen, Kang-Ning; Chang, Chih-Wei; Durand, Jean-Dominique

    2015-12-01

    The flathead mullet, Mugil cephalus, is a commercially vital fish in fisheries and aquaculture worldwide. Genetic analyses have recently revealed three cryptic species of M. cephalus in the Northwest Pacific. These species are sympatric in Taiwanese waters and specific reproductive behaviors have been suggested to be a major prezygotic barrier. Species composition was evaluated in samples of M. cephalus at different growth stages collected from various habitats (offshore spawning ground, estuarine nursery and feeding areas) over several months or years. The gonadosomatic index of adults and the body length of juveniles were recorded to determine the reproductive season and recruitment periods in estuaries. The results revealed partially temporal spawning isolation between species pairs, spatial segregation on specific spawning grounds and strong philopatry preclude hybridization. Thus, the results imply that traditional fisheries of mature fish in the Taiwan Strait target only one species, whereas aquaculture in Taiwan contain juveniles of all three species collected in estuaries. The ecological niche and demography of these species must be investigated further to estimate the impact of juvenile sources on aquaculture. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  13. Cunea n. g. (Amoebozoa, Dactylopodida) with two cryptic species isolated from different areas of the ocean

    KAUST Repository

    Kudryavtsev, Alexander

    2015-06-01

    © 2015 Elsevier GmbH. This paper describes a new genus, Cunea n. g., of marine naked amoebae with two cryptic species, Cunea profundata and Cunea thuwala, isolated from distant localities in the ocean and different depths (Brazilian abyssal plain, Western Atlantic Ocean, depth >5. km and the Red Sea off the Saudi Arabian coast, depth ca. 58.7. m). Both species are very similar to each other in the set of light microscopic and ultrastructural characters and might be described as a single species, yet their genetic divergence based on 3 molecular markers (small-subunit ribosomal RNA, actin and cytochrome c oxidase subunit 1) corresponds to the level of variation typically observed between different morphospecies of Amoebozoa. In addition, the studied strains differ strongly in their temperature tolerance ranges, C. profundata isolated from the cold Atlantic deep-sea habitat being able to reproduce under lower temperatures than C. thuwala isolated from the warm Red Sea benthos. Molecular phylogenetic analysis based on SSU rRNA gene shows that the new genus robustly branches within the Dactylopodida, but forms an independent clade within this order that does not group with any of its known genera.

  14. Regulation of gene expression: Cryptic β-glucoside (bgl operon of Escherichia coli as a paradigm

    Directory of Open Access Journals (Sweden)

    Dharmesh Harwani

    2014-12-01

    Full Text Available Bacteria have evolved various mechanisms to extract utilizable substrates from available resources and consequently acquire fitness advantage over competitors. One of the strategies is the exploitation of cryptic cellular functions encoded by genetic systems that are silent under laboratory conditions, such as the bgl (β-glucoside operon of E. coli. The bgl operon of Escherichia coli, involved in the uptake and utilization of aromatic β-glucosides salicin and arbutin, is maintained in a silent state in the wild type organism by the presence of structural elements in the regulatory region. This operon can be activated by mutations that disrupt these negative elements. The fact that the silent bgl operon is retained without accumulating deleterious mutations seems paradoxical from an evolutionary view point. Although this operon appears to be silent, specific physiological conditions might be able to regulate its expression and/or the operon might be carrying out function(s apart from the utilization of aromatic β-glucosides. This is consistent with the observations that the activated operon confers a Growth Advantage in Stationary Phase (GASP phenotype to Bgl+ cells and exerts its regulation on at least twelve downstream target genes.

  15. Regulation of gene expression: cryptic β-glucoside (bgl) operon of Escherichia coli as a paradigm.

    Science.gov (United States)

    Harwani, Dharmesh

    2014-01-01

    Bacteria have evolved various mechanisms to extract utilizable substrates from available resources and consequently acquire fitness advantage over competitors. One of the strategies is the exploitation of cryptic cellular functions encoded by genetic systems that are silent under laboratory conditions, such as the bgl (β-glucoside) operon of E. coli. The bgl operon of Escherichia coli, involved in the uptake and utilization of aromatic β-glucosides salicin and arbutin, is maintained in a silent state in the wild type organism by the presence of structural elements in the regulatory region. This operon can be activated by mutations that disrupt these negative elements. The fact that the silent bgl operon is retained without accumulating deleterious mutations seems paradoxical from an evolutionary view point. Although this operon appears to be silent, specific physiological conditions might be able to regulate its expression and/or the operon might be carrying out function(s) apart from the utilization of aromatic β-glucosides. This is consistent with the observations that the activated operon confers a Growth Advantage in Stationary Phase (GASP) phenotype to Bgl(+) cells and exerts its regulation on at least twelve downstream target genes.

  16. Cunea n. g. (Amoebozoa, Dactylopodida) with two cryptic species isolated from different areas of the ocean

    KAUST Repository

    Kudryavtsev, Alexander; Pawlowski, Jan

    2015-01-01

    © 2015 Elsevier GmbH. This paper describes a new genus, Cunea n. g., of marine naked amoebae with two cryptic species, Cunea profundata and Cunea thuwala, isolated from distant localities in the ocean and different depths (Brazilian abyssal plain, Western Atlantic Ocean, depth >5. km and the Red Sea off the Saudi Arabian coast, depth ca. 58.7. m). Both species are very similar to each other in the set of light microscopic and ultrastructural characters and might be described as a single species, yet their genetic divergence based on 3 molecular markers (small-subunit ribosomal RNA, actin and cytochrome c oxidase subunit 1) corresponds to the level of variation typically observed between different morphospecies of Amoebozoa. In addition, the studied strains differ strongly in their temperature tolerance ranges, C. profundata isolated from the cold Atlantic deep-sea habitat being able to reproduce under lower temperatures than C. thuwala isolated from the warm Red Sea benthos. Molecular phylogenetic analysis based on SSU rRNA gene shows that the new genus robustly branches within the Dactylopodida, but forms an independent clade within this order that does not group with any of its known genera.

  17. 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.

  18. Cryptic differentiation in the endemic micromoth Galagete darwini (Lepidoptera, Autostichidae) on Galápagos volcanoes.

    Science.gov (United States)

    Schmitz, Patrick; Cibois, Alice; Landry, Bernard

    2008-10-27

    To gain insight into the early stages of speciation, we reconstructed a DNA-based phylogeny, using combined mitochondrial (cytochrome c oxidase subunits I and II: 1008 bp) and nuclear (elongation factor 1-alpha and wingless: 1062 bp) markers of populations of the moth Galagete darwini endemic to the Galápagos, which belongs to an insular radiation similar in size to that of Darwin's finches. Adults of G. darwini were collected in the arid lowlands of 11 of the Galápagos Islands (Baltra, Española, Fernandina, Floreana, Isabela, Pinta, Pinzón, San Cristobal, Santa Cruz, Santiago and Seymour) and the humid highlands of a subset of 5 of them (Fernandina, Floreana, Isabela, Santa Cruz and Santiago). The combined phylogeographic analysis surprisingly revealed that G. darwini populations at higher elevation on the western islands (Fernandina, Isabela and Santiago) represent a distinct lineage from the one in the low arid zones of these same islands. This is the first reported case in the archipelago of genetic cryptic differentiation correlated with elevation on the western Galápagos volcanoes.

  19. Early events in speciation: Cryptic species of Drosophila aldrichi.

    Science.gov (United States)

    Castro Vargas, Cynthia; Richmond, Maxi Polihronakis; Ramirez Loustalot Laclette, Mariana; Markow, Therese Ann

    2017-06-01

    Understanding the earliest events in speciation remains a major challenge in evolutionary biology. Thus identifying species whose populations are beginning to diverge can provide useful systems to study the process of speciation. Drosophila aldrichi , a cactophilic fruit fly species with a broad distribution in North America, has long been assumed to be a single species owing to its morphological uniformity. While previous reports either of genetic divergence or reproductive isolation among different D. aldrichi strains have hinted at the existence of cryptic species, the evolutionary relationships of this species across its range have not been thoroughly investigated. Here we show that D. aldrichi actually is paraphyletic with respect to its closest relative, Drosophila wheeleri , and that divergent D. aldrichi lineages show complete hybrid male sterility when crossed. Our data support the interpretation that there are at least two species of D. aldrichi, making these flies particularly attractive for studies of speciation in an ecological and geographical context.

  20. CRYPTIC AND PSEUDO-CRYPTIC DIVERSITY IN DIATOMS-WITH DESCRIPTIONS OF PSEUDO-NITZSCHIA HASLEANA SP. NOV. AND P. FRYXELLIANA SP. NOV.(1).

    Science.gov (United States)

    Lundholm, Nina; Bates, Stephen S; Baugh, Keri A; Bill, Brian D; Connell, Laurie B; Léger, Claude; Trainer, Vera L

    2012-04-01

    A high degree of pseudo-cryptic diversity was reported in the well-studied diatom genus Pseudo-nitzschia. Studies off the coast of Washington State revealed the presence of hitherto undescribed diversity of Pseudo-nitzschia. Forty-one clonal strains, representing six different taxa of the P. pseudodelicatissima complex, were studied morphologically using LM and EM, and genetically using genes from three different cellular compartments: the nucleus (D1-D3 of the LSU of rDNA and internal transcribed spacers [ITSs] of rDNA), the mitochondria (cytochrome c oxidase 1), and the plastids (LSU of RUBISCO). Strains in culture at the same time were used in mating studies to study reproductive isolation of species, and selected strains were examined for the production of the neurotoxin domoic acid (DA). Two new species, P. hasleana sp. nov. and P. fryxelliana sp. nov., are described based on morphological and molecular data. In all phylogenetic analyses, P. hasleana appeared as sister taxa to a clade comprising P. calliantha and P. mannii, whereas the position of P. fryxelliana was more uncertain. In the phylogenies of ITS, P. fryxelliana appeared to be most closely related to P. cf. turgidula. Morphologically, P. hasleana differed from most other species of the complex because of a lower density of fibulae, whereas P. fryxelliana had fewer sectors in the poroids and a higher poroid density than most of the other species. P. hasleana did not produce detectable levels of DA; P. fryxelliana was unfortunately not tested. In P. cuspidata, production of DA in offspring cultures varied from higher than the parent cultures to undetectable. © 2012 Phycological Society of America.

  1. Cryptic Plutella species show deep divergence despite the capacity to hybridize.

    Science.gov (United States)

    Perry, Kym D; Baker, Gregory J; Powis, Kevin J; Kent, Joanne K; Ward, Christopher M; Baxter, Simon W

    2018-05-29

    Understanding genomic and phenotypic diversity among cryptic pest taxa has important implications for the management of pests and diseases. The diamondback moth, Plutella xylostella L., has been intensively studied due to its ability to evolve insecticide resistance and status as the world's most destructive pest of brassicaceous crops. The surprise discovery of a cryptic species endemic to Australia, Plutella australiana Landry & Hebert, raised questions regarding the distribution, ecological traits and pest status of the two species, the capacity for gene flow and whether specific management was required. Here, we collected Plutella from wild and cultivated brassicaceous plants from 75 locations throughout Australia and screened 1447 individuals to identify mtDNA lineages and Wolbachia infections. We genotyped genome-wide SNP markers using RADseq in coexisting populations of each species. In addition, we assessed reproductive compatibility in crossing experiments and insecticide susceptibility phenotypes using bioassays. The two Plutella species coexisted on wild brassicas and canola crops, but only 10% of Plutella individuals were P. australiana. This species was not found on commercial Brassica vegetable crops, which are routinely sprayed with insecticides. Bioassays found that P. australiana was 19-306 fold more susceptible to four commonly-used insecticides than P. xylostella. Laboratory crosses revealed that reproductive isolation was incomplete but directionally asymmetric between the species. However, genome-wide nuclear SNPs revealed striking differences in genetic diversity and strong population structure between coexisting wild populations of each species. Nuclear diversity was 1.5-fold higher in P. australiana, yet both species showed limited variation in mtDNA. Infection with a single Wolbachia subgroup B strain was fixed in P. australiana, suggesting that a selective sweep contributed to low mtDNA diversity, while a subgroup A strain infected just 1

  2. Life history and ecology of harbour porpoises (Phocoena phocoena from West Greenland

    Directory of Open Access Journals (Sweden)

    C Lockyer

    2003-07-01

    Full Text Available During 1988, 1989 and 1995, 187 harbour porpoises (Phocoena phocoena were sampled from the catches off West Greenland. The samples were taken in 3 areas between 62° N and 70° N: northerly (n=134, Maniitsoq and locations Kangaamiut, Qeqertarsuaq and Qasigiannguit further north, southerly (n=30, Nuuk and southernmost (n=23, Paamiut. A suite of biological measurements and data were collected from these samples. Comparison of age and length distributions between years and areas indicated that while there were no statistical differences between the Maniitsoq and northerly samples in different years, the southerly Nuuk and Paamiut samples were biased to younger age classes. Application of the Gompertz growth model to length and weight at age data indicated an asymptotic length of 154 cm in females and 143 cm in males with weights of 64 kg and 52 kg respectively. A number of correlations were observed between length, midgirth(G3, body and blubber weights and blubber thickness. Indicators of body condition showed that overall pregnant females were fattest but that blubber thickness was greatest in juveniles. The blubber lipid content was generally 92-95% wet weight of tissue. Stomach content analysis for 92 animals indicated regional differences, although capelin (Mallotus villosus was predominant in all samples. The presence of fish, squid and crustaceans indicated opportunistic feeding. Females ovulated from age 3-4 years at a length of about 140 cm; combined testis weights >200 g indicated maturation in males from age 2 years upwards at a length >125 cm. Several small embryos were found, consistent with a mating season in late summer. Testis hypertrophy in August also supported a late summer breeding. Analysis of ovarian corpora indicated annual ovulation. Certain biological parameters, including body condition indicators, indicate differences between WestGreenland and eastern North Atlantic populations that agree with published genetic findings.

  3. Bite injuries of grey seals (Halichoerus grypus) on harbour porpoises (Phocoena phocoena).

    Science.gov (United States)

    Jauniaux, Thierry; Garigliany, Mutien-Marie; Loos, Pauline; Bourgain, Jean-Luc; Bouveroux, Thibaut; Coignoul, Freddy; Haelters, Jan; Karpouzopoulos, Jacky; Pezeril, Sylvain; Desmecht, Daniel

    2014-01-01

    Bite-like skin lesions on harbour porpoises (Phocoena phocoena) have been suspected to be caused by grey seals (Halichoerus grypus), and a few field observations have been reported. Bite-like skin lesions observed on stranded animals were characterized by two main components: large flaps of loose or missing skin and blubber with frayed edges and puncture lesions. Definitive demonstration of predation by a grey seal was not reported so far in those stranded animals. In this study, five stranded porpoises with bite-like skin lesions were swabbed for genetic investigations. In addition, the head of a recently dead grey seal was used to mimic bite-like skin injuries on a porpoise carcass. Subsequently, the artificial skin injuries were swabbed, along with the gum of the seal used for inflicting them (positive controls). Total DNA was extracted from the swabs and was used to retrieve a fragment of mitochondrial DNA by PCR. Primers were designed to amplify a specific stretch of mitochondrial DNA known to differ between grey seals and porpoises. The amplicon targeted was successfully amplified from the positive control and from two of the stranded porpoises, and grey seal-specific mitochondrial DNA was retrieved from all those samples. We conclude that (1) it is possible to detect grey seal DNA from dead porpoises even after several days in seawater and (2) bite-like skin lesions found on dead porpoises definitively result from grey seals attacks. The attacks are most likely linked with predation although, in a number of cases, scavenging and aggressive behaviour cannot be excluded.

  4. Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona (Soestella caerulea, (order: Haplosclerida to Palmyra Atoll, Central Pacific

    Directory of Open Access Journals (Sweden)

    Ingrid S. Knapp

    2015-08-01

    Full Text Available Cryptic species are widespread across the phylum Porifera making the identification of non-indigenous species difficult, an issue not easily resolved by the use of morphological characteristics. The widespread order Haplosclerida is a prime example due to limited and plastic morphological features. Here, we study the reported introduction of Haliclona (Soestella caerulea from the Caribbean to Palmyra Atoll via Hawaiʻi using morphological characteristics and genetic analyses based on one nuclear (18s rDNA and three mitochondrial (COI, the barcoding COI extension (COI ext. and rnl rDNA markers. Despite no clear division in lengths of the oxea spicules between the samples, both mtDNA and nDNA phylogenetic trees supported similar topologies resolving two distinct clades. Across the two clades, the concatenated mtDNA tree resolved twelve subclades, with the COI ext. yielding most of the variability between the samples. Low sequence divergence values (0.68% between two of the subclades indicate that the same species is likely to occur at Palmyra, Hawaiʻi and the Caribbean, supporting the hypothesis that H. caerulea was introduced to Palmyra from the Caribbean, although whether species came directly from the Caribbean to Palmyra or from Hawaiʻi remains unresolved. Conversely, the pattern of highly divergent cryptic species supports the notion that traditionally used spicule measurements are taxonomically unreliable in this group. This study illustrates how understanding the scale of within- as opposed to between-species level genetic variation is critical for interpreting biogeographic patterns and inferring the origins of introduced organisms.

  5. Differential responses of cryptic bat species to the urban landscape.

    Science.gov (United States)

    Lintott, Paul R; Barlow, Kate; Bunnefeld, Nils; Briggs, Philip; Gajas Roig, Clara; Park, Kirsty J

    2016-04-01

    Urbanization is a key global driver in the modification of land use and has been linked to population declines even in widespread and relatively common species. Cities comprise a complex assortment of habitat types yet we know relatively little about the effects of their composition and spatial configuration on species distribution. Although many bat species exploit human resources, the majority of species are negatively impacted by urbanization. Here, we use data from the National Bat Monitoring Programme, a long-running citizen science scheme, to assess how two cryptic European bat species respond to the urban landscape. A total of 124 × 1 km(2) sites throughout Britain were surveyed. The landscape surrounding each site was mapped and classified into discrete biotope types (e.g., woodland). Generalized linear models were used to assess differences in the response to the urban environment between the two species, and which landscape factors were associated with the distributions of P. pipistrellus and P. pygmaeus. The relative prevalence of P. pygmaeus compared to P. pipistrellus was greater in urban landscapes with a higher density of rivers and lakes, whereas P. pipistrellus was frequently detected in landscapes comprising a high proportion of green space (e.g., parklands). Although P. pipistrellus is thought to be well adapted to the urban landscape, we found a strong negative response to urbanization at a relatively local scale (1 km), whilst P. pygmaeus was detected more regularly in wooded urban landscapes containing freshwater. These results show differential habitat use at a landscape scale of two morphologically similar species, indicating that cryptic species may respond differently to anthropogenic disturbance. Even species considered relatively common and well adapted to the urban landscape may respond negatively to the built environment highlighting the future challenges involved in maintaining biodiversity within an increasingly urbanized

  6. Cryptic trace-element alteration of Anorthosite, Stillwater complex, Montana

    Science.gov (United States)

    Czamanske, G.K.; Loferski, P.J.

    1996-01-01

    Evidence of cryptic alteration and correlations among K, Ba, and LREE concentrations indicate that a post-cumulus, low-density aqueous fluid phase significantly modified the trace-element contents of samples from Anorthosite zones I and II of the Stillwater Complex, Montana. Concentrations of Ba, Ca, Co, Cr, Cu, Fe, Hf, K, Li, Mg, Mn, Na, Ni, Sc, Sr, Th, Zn, and the rare-earth elements (REE) were measured in whole rocks and plagioclase separates from five traverses across the two main plagioclase cumulate (anorthosite) zones and the contiguous cumulates of the Stillwater Complex in an attempt to better understand the origin and solidification of the anorthosites. However, nearly the entire observed compositional range for many trace elements can be duplicated at a single locality by discriminating between samples rich in oikocrystic pyroxene and those which are composed almost entirely of plagioclase and show anhedral-granular texture. Plagioclase separates with high trace-element contents were obtained from the pyroxene-poor samples, for which maps of K concentration show plagioclase grains to contain numerous fractures hosting a fine-grained, K-rich phase, presumed to be sericite. Secondary processes in layered intrusions have the potential to cause cryptic disturbance, and the utmost care must be taken to ensure that samples provide information about primary processes. Although plagioclase from Anorthosite zones I and II shows significant compositional variation, there are no systematic changes in the major- or trace-element compositions of plagioclase over as much as 630 m of anorthosite thickness or 18 km of strike length. Plagioclase in the two major anorthosite zones shows little distinction in trace-element concentrations from plagioclase in the cumulates immediately below, between, and above these zones.

  7. Organo chlorine pesticides (OCPs) contaminants in sediments from Karachi harbour, Pakistan

    International Nuclear Information System (INIS)

    Khan, N.; Khan, S.H.; Amjad, S.; Muller, J.; Nizamani, S.; Bhanger, M.I.

    2010-01-01

    Mangrove swamps, inter tidal mud flats and creeks of backwaters represent main feature of Karachi harbour area. Karachi harbour sediment is under continuous influence of untreated industrial effluents and domestic waste discharged into the Harbour area via Lyari River. Sediment samples from sixteen locations were collected to evaluate the levels of contamination of organo chlorine pesticides (OCPs) in Karachi harbour and adjoining areas. It has been observed that residual concentrations of various organo chlorine pesticides were considerably higher in the semi-enclosed area of the upper Harbour in the vicinity of the discharge point of Lyari River. The residue of DDT mainly its metabolites (DDE and DDD) were widely distributed and have been detected in most of the sediment samples in relatively higher concentrations as compared to other OCPs. The higher levels of the DDTs would attribute to low tidal flushing of the area. The high proportion of pp'-DDE in the most sediment sampled (41-95%) suggested old inputs of DDTs in the environment. Ratio of sigma DDT and DDT was in the range of 0.04 - 0.24 at all locations which also reflects that the discharges of DDT were negligible in the Harbour area. This may be due to the restrictions being implemented on the use of DDTs and Pakistan has also switched over to natural pest control or using safer formulas. The data obtained during the study showed that concentration levels of other pesticides such as HCHs, HCB and Cyclodienes in the sediment were generally lower than the threshold levels known to harm wildlife by OCPs. The results clearly indicate that elevated concentration of organo chlorine pesticides (OCPs) in the marine sediment of Karachi harbour and adjoining area was localized and much lower than the concentrations reported from neighbouring and regional countries which suggests/confirms that the present use of pesticide in Pakistan is environmentally safe. (author)

  8. Listeria monocytogenes isolates from food and food environment harbouring tetM and ermB resistance genes.

    Science.gov (United States)

    Haubert, L; Mendonça, M; Lopes, G V; de Itapema Cardoso, M R; da Silva, W P

    2016-01-01

    Listeria monocytogenes is a foodborne pathogen that has become an important cause of human and animal diseases worldwide. The purpose of this study was to evaluate the serotypes, virulence potential, antimicrobial resistance profile, and genetic relationships of 50 L. monocytogenes isolates from food and food environment in southern Brazil. In this study, the majority of L. monocytogenes isolates belonged to the serotypes 1/2b (42%) and 4b (26%), which are the main serotypes associated with human listeriosis. In addition, all isolates harboured internalin genes (inlA, inlC, inlJ), indicating a virulence potential. The isolates were sensitive to most of the antimicrobial compounds analysed, and five isolates (10%) were multi-resistant. Two isolates harboured antimicrobial resistance genes (tetM and ermB) and in one of them, the gene was present in the plasmid. Moreover, according to the pulsed field gel electrophoresis assay, two multi-resistant isolates were a single clone isolated from food and the processing plant. The isolates were susceptible to the most frequently used antibiotics for listeriosis treatment. However, the presence of multidrug-resistant isolates and antimicrobial resistance genes including in the plasmid could even be transferred between bacterial species, suggesting a potential health risk to consumers and a potential risk of spreading multi-resistance genes to other bacteria. Listeria monocytogenes is an important agent of foodborne diseases. The results of this study suggest a potential capacity of L. monocytogenes isolates from food and food environment to cause human infections. Antimicrobial multi-resistance profiles were detected in 10%, and two isolates harboured tetM and ermB resistance genes. Moreover, the present research can help to build up a better knowledge about antimicrobial resistance of L. monocytogenes. Additionally, we found one isolate carrying tetM resistance gene in a plasmid, that suggests a possible transmission

  9. Causative Agents of Aspergillosis Including Cryptic Aspergillus Species and A. fumigatus.

    Science.gov (United States)

    Toyotome, Takahito

    2016-01-01

    Aspergillosis is an important deep mycosis. The causative agents are Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, and Aspergillus terreus, of which A. fumigatus is the most prevalent. Cryptic Aspergillus spp., which morphologically resemble representative species of each Aspergillus section, also cause aspergillosis. Most of the cryptic species reveal different susceptibility patterns and/or different secondary metabolite profiles, also called exometabolome in this manuscript, from those representative species. On the other hand, azole-resistant A. fumigatus strains in clinical specimens and in the environment have been reported. Therefore, it is imperative to precisely identify the species, including cryptic Aspergillus spp., and evaluate the susceptibility of isolates.In this manuscript, some of the causative cryptic Aspergillus spp. are briefly reviewed. In addition, the exometabolome of Aspergillus section Fumigati is described. Finally, azole resistance of A. fumigatus is also discussed, in reference to several studies from Japan.

  10. Seven new species of Oculatella (Pseudanabaenales, Cyanobacteria): taxonomically recognizing cryptic diversification

    Czech Academy of Sciences Publication Activity Database

    Osorio-Santos, K.; Pietrasiak, N.; Bohunická, Markéta; Miscoe, L. H.; Kováčik, L.; Martin, M.P.; Johansen, J. R.

    2014-01-01

    Roč. 49, č. 4 (2014), s. 450-470 ISSN 0967-0262 Institutional support: RVO:67985939 Keywords : cryptic species * cyanobacteria * Pseudanabaenaceae Subject RIV: EF - Botanics Impact factor: 1.912, year: 2014

  11. Deciphering natural to anthropogenic control on sedimentation: the Late Holocene Magdala (Kinneret Lake, Israel) harbour hystory

    Science.gov (United States)

    Sarti, G.; Rossi, V.; Amorosi, A.; Bertoni, D.; Ribolini, A.; Sammartino, I.; Zanchetta, G.

    2012-04-01

    Using a multidisciplinary approach involving geologists, geomorphologists and archeologists, the late Holocene sedimentary succession buried beneath the ancient Magdala harbour area (Kinneret Lake, Israel) was studied, in order to highlight the strict relationships among harbour evolutive phases (e.g. foundation, siltation, abandonment), natural events (e.g. sea-level variations, climatic changes and earthquakes among the most important) and, obviously, archaeological history. Recent excavations performed within the "Magdala Project" have discovered a harbour structure with late Hellenistic-Roman mooring stones at altitudes of 208.100 m and 208.320 m bsl respectively, suggestive of a higher lake-level (about 212 m bsl) than previously hypothesized. Along the most representative sections of trenches, integrated sedimentological, micropalaeontological (benthic meiofauna and pollen) and geochemical analyses were carried out on sedimentary deposits underlying and overlying the harbour structures, to define the main depositional facies and evolution phases that took place during the last millennia. Spatial variability of coeval palaeoenvironments across the archaeological site allowed to reconstruct a comprehensive picture of the harbour complex, evidencing the occurrence of three main evolution phases, similar to those reported from several Mediterranean Sea harbour systems: 1) a pre-harbor foundation phase; 2) a sin-harbor activity phase and 3) an harbor-abandonment phase. The first phase corresponds to the development of a natural lacustrine sandy beach barren in archaeological remains and containing an ostracod fauna very similar to the one observed within the present-day lake basin at ca. 5 m water depth. The second phase was characterized by the formation of an early Hellenistic sheltered lacustrine basin, recording the first anthropogenic control exerted on coastal sedimentation by the construction of harbour structures ("anthropogenically forced sheltered basin

  12. Environmental assessment of metal exposure to corals living in Castle Harbour, Bermuda

    Science.gov (United States)

    Prouty, N.G.; Goodkin, N.F.; Jones, R.; Lamborg, C.H.; Storlazzi, C.D.; Hughen, K.A.

    2013-01-01

    Environmental contamination in Castle Harbour, Bermuda, has been linked to the dissolution and leaching of contaminants from the adjacent marine landfill. This study expands the evidence for environmental impact of leachate from the landfill by quantitatively demonstrating elevated metal uptake over the last 30 years in corals growing in Castle Harbour. Coral Pb/Ca, Zn/Ca and Mn/Ca ratios and total Hg concentrations are elevated relative to an adjacent control site in John Smith's Bay. The temporal variability in the Castle Harbour coral records suggests that while the landfill has increased in size over the last 35 years, the dominant input of metals is through periodic leaching of contaminants from the municipal landfill and surrounding sediment. Elevated contaminants in the surrounding sediment suggest that resuspension is an important transport medium for transferring heavy metals to corals. Increased winds, particularly during the 1990s, were accompanied by higher coral metal composition at Castle Harbour. Coupled with wind-induced resuspension, interannual changes in sea level within the Harbour can lead to increased bioavailability of sediment-bound metals and subsequent coral metal assimilation. At John Smith's Bay, large scale convective mixing may be driving interannual metal variability in the coral record rather than impacts from land-based activities. Results from this study provide important insights into the coupling of natural variability and anthropogenic input of contaminants to the nearshore environment.

  13. The Coffs Harbour 'Our Living City Settlement Strategy' Health Impact Assessment

    International Nuclear Information System (INIS)

    Tugwell, Andrew; Johnson, Pamela

    2011-01-01

    Aim: The short report reviews an experience of conducting a Health Impact Assessment (HIA) in the local government context. The aim of this review was to identify if carrying out an HIA would result in recommendations that could influence council planning and help establish ongoing working relationships between North Coast Area Health Service (NCAHS) staff and the Coffs Harbour City Council. Methods: A process and impact evaluation was conducted on the Coffs Harbour 'Our Living City Settlement Strategy' HIA, which focused on the Coffs Harbour City Council's strategic planning document. Information gained through the evaluation was themed and the findings were reviewed against published information on HIA experience. Main findings: HIA has reported benefits for both the Coffs Harbour City Council and NCAHS as it provides a tool to address many of the issues facing these organisations. Local council has increasing responsibilities including the environment, housing and urban planning, which all have health implications. HIA has been demonstrated as an effective tool for NCAHS staff and the Coffs Harbour City Council to engage and build relationships, increase the understanding of all planning aspects related to health, and most importantly utilise evidence to inform decision making. Conclusion: HIA should be adopted as a key tool to facilitate effective working partnerships between organisations. Improved engagement, partnerships and use of evidence to produce shared outcomes can result from utilising this tool.

  14. Volatile compounds in cryptic species of the Aneura pinguis complex and Aneura maxima (Marchantiophyta, Metzgeriidae).

    Science.gov (United States)

    Wawrzyniak, Rafał; Wasiak, Wiesław; Bączkiewicz, Alina; Buczkowska, Katarzyna

    2014-09-01

    Aneura pinguis is one of the liverwort species complexes that consist of several cryptic species. Ten samples collected from different regions in Poland are in the focus of our research. Eight of the A. pinguis complex belonging to four cryptic species (A, B, C, E) and two samples of closely related species Aneura maxima were tested for the composition of volatile compounds. The HS-SPME technique coupled to GC/FID and GC/MS analysis has been applied. The fiber coated with DVB/CAR/PDMS has been used. The results of the present study, revealed the qualitative and quantitative differences in the composition of the volatile compounds between the studied species. Mainly they are from the group of sesquiterpenoids, oxygenated sesquiterpenoids and aliphatic hydrocarbons. The statistical methods (CA and PCA) showed that detected volatile compounds allow to distinguish cryptic species of A. pinguis. All examined cryptic species of the A. pinguis complex differ from A. maxima. Species A and E of A. pinguis, in CA and PCA, form separate clusters remote from two remaining cryptic species of A. pinguis (B and C) and A. maxima. Relationship between the cryptic species appeared from the chemical studies are in accordance with that revealed on the basis of DNA sequences. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Economic study for the establishment of A food irradiation facility at port said harbour

    International Nuclear Information System (INIS)

    EL-Gameel, E.A.

    2004-01-01

    The present study discusses the economic aspects of establishing food irradiation facility at Port Said harbour and the effect of various parameters on the unit processing costs. The study is concerned with carrying out an economic evaluation for the application of food exports from Port Said harbour and the marketing and technical aspects where the suitable commodity mix has been determined for the agricultural crops which were proposed for irradiation. The investment criteria utilized for commercial evaluation were internal rate of return (IRR) and pay back period (PEP). The irradiation cost and the additional income are also discussed. The results of this analysis showed that the establishment of food irradiation unit in Port Said harbour in Egypt would be economically feasible

  16. Chemometric Analysis for Pollution Source Assessment of Harbour Sediments in Arctic Locations

    DEFF Research Database (Denmark)

    Pedersen, Kristine B.; Lejon, Tore; Jensen, Pernille Erland

    2015-01-01

    Pollution levels, pollutant distribution and potential source assessments based on multivariate analysis (chemometrics) were made for harbour sediments from two Arctic locations; Hammerfest in Norway and Sisimiut in Greenland. High levels of heavy metals were detected in addition to organic...... pollutants. Preliminary assessments based on principal component analysis (PCA) revealed different sources and pollutant distribution in the sediments of the two harbours. Tributyltin (TBT) was, however, found to originate from point source(s), and the highest concentrations of TBT in both harbours were...... indicated relation primarily to German, Russian and American mixtures in Hammerfest; and American, Russian and Japanese mixtures in Sisimiut. PCA was shown to be an important tool for identifying pollutant sources and differences in pollutant composition in relation to sediment characteristics....

  17. Lungworm seroprevalence in free-ranging harbour seals and molecular characterisation of marine mammal MSP

    Directory of Open Access Journals (Sweden)

    Sophia Arlena Ulrich

    2016-04-01

    Full Text Available Harbour seals (Phoca vitulina are frequently infected with the lungworms Otostrongylus circumlitus and Parafilaroides gymnurus. The infection is often accompanied by secondary bacterial infections and can cause severe bronchopneumonia and even death in affected animals. Hitherto, the detection of lungworm infections was based on post mortem investigations from animals collected within stranding networks and a valid detection method for live free-ranging harbour seals was not available. Recently, an ELISA was developed for detecting lungworm antibodies in harbour seal serum, using major sperm protein (MSP of the bovine lungworm, Dictyocaulus viviparus as recombinant diagnostic antigen. To determine lungworm seroprevalence in free-ranging harbour seals, serum was taken from four different seal age groups (n = 313 resulting in an overall prevalence of 17.9% (18.9% of males, 16.7% of females. 0.7% of harbour seals up to six weeks of age were seropositive, as were 89% of seals between six weeks and six months, 53.6% between six and 18 months and 24.2% of seals over 18 months of age. In the 18 months and over age group, seropositive animals showed statistically significant reductions in body weight (P = 0.003 and length (P < 0.001. Sera from lungworm infected harbour seals in rehabilitation (n = 6 revealed that duration of antibody persistence may be similar to that of lungworm infected cattle, but further studies are needed to confirm this. Phylogenetic analyses of MSP sequences of different marine and terrestrial mammal parasitic nematodes revealed that lungworm MSP of the genus Dictyocaulus (superfamily Trichostrongyloidea is more closely related to metastrongylid marine mammal lungworms than to trichostrongylid nematodes of terrestrial hosts.

  18. Phocine distemper virus (PDV) seroprevalence as predictor for future outbreaks in harbour seals.

    Science.gov (United States)

    Ludes-Wehrmeister, Eva; Dupke, Claudia; Harder, Timm C; Baumgärtner, Wolfgang; Haas, Ludwig; Teilmann, Jonas; Dietz, Rune; Jensen, Lasse F; Siebert, Ursula

    2016-02-01

    Phocine distemper virus (PDV) infections caused the two most pronounced mass mortalities in marine mammals documented in the past century. During the two outbreaks, 23,000 and 30,000 harbour seals (Phoca vitulina), died in 1988/1989 and 2002 across populations in the Wadden Sea and adjacent waters, respectively. To follow the mechanism and development of disease spreading, the dynamics of Morbillivirus-specific antibodies in harbour seal populations in German and Danish waters were examined. 522 serum samples of free-ranging harbour seals of different ages were sampled between 1990 and 2014. By standard neutralisation assays, Morbillivirus-specific antibodies were detected, using either the PDV isolate 2558/Han 88 or the related canine distemper virus (CDV) strain Onderstepoort. A total of 159 (30.5%) of the harbour seals were seropositive. Annual seroprevalence rates showed an undulating course: Peaks were seen in the post-epidemic years 1990/1991 and 2002/2003. Following each PDV outbreak, seroprevalence decreased and six to eight years after the epidemics samples were tested seronegative, indicating that the populations are now again susceptible to new PDV outbreak. After the last outbreak in 2002, the populations grew steadily to an estimated maximum (since 1975) of about 39,100 individuals in the Wadden Sea in 2014 and about 23,540 harbour seals in the Kattegat area in 2013. A re-appearence of PDV would presumably result in another epizootic with high mortality rates as encountered in the previous outbreaks. The current high population density renders harbour seals vulnerable to rapid spread of infectious agents including PDV and the recently detected influenza A virus. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. The spatial and temporal distribution of heavy metals in sediments of Victoria Harbour, Hong Kong

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Chloe Wing-yee; Ip, Carman Ching-man [Department of Civil and Structural Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon (Hong Kong); Zhang Gan [State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640 (China); Shin, Paul K.S. [Department of Biology and Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon (Hong Kong); Qian Peiyuan [Department of Biology and Coastal Marine Laboratory, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon (Hong Kong); Li Xiangdong [Department of Civil and Structural Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon (Hong Kong)], E-mail: cexdli@polyu.edu.hk

    2008-07-01

    Victoria Harbour has received substantial loadings of pollutants from industrial and municipal wastewater discharged since the 1950s. Inputs of contaminants have declined dramatically during the last two decades as a result of better controls at the source and improved wastewater treatment facilities. To assess the spatial and temporal changes of metal contaminants in sediments in Victoria Harbour, core and grab sediments were collected. The central harbour areas were generally contaminated with heavy metals. The spatial distribution of trace metals can probably be attributed to the proximity of major urban and industrial discharge points, and to the effect of tidal flushing in the harbour. In the sediment cores, the highest concentrations of trace metals were observed to have accumulated during the 1950s-1980s, corresponding with the period of rapid urban and industrial development in Hong Kong. From the late 1980s, there has been a major decline in the concentrations of trace metals, due to a reduction in industrial activities and to the enactment of wastewater pollution controls in the territory. The Pb isotopic compositions of the sediments revealed the anthropogenic inputs of Pb to the harbour. The {sup 206}Pb/{sup 207}Pb ratios varied from 1.154 to 1.190, which were lower than those of background geological materials in Hong Kong ({sup 206}Pb/{sup 207}Pb: 1.201-1.279). The data also indicated that the Pb in the harbour sediments most likely originated from mixed sources, including the leaded gasoline used in the past and other anthropogenic sources.

  20. Year-round spatiotemporal distribution of harbour porpoises within and around the Maryland wind energy area.

    Science.gov (United States)

    Wingfield, Jessica E; O'Brien, Michael; Lyubchich, Vyacheslav; Roberts, Jason J; Halpin, Patrick N; Rice, Aaron N; Bailey, Helen

    2017-01-01

    Offshore windfarms provide renewable energy, but activities during the construction phase can affect marine mammals. To understand how the construction of an offshore windfarm in the Maryland Wind Energy Area (WEA) off Maryland, USA, might impact harbour porpoises (Phocoena phocoena), it is essential to determine their poorly understood year-round distribution. Although habitat-based models can help predict the occurrence of species in areas with limited or no sampling, they require validation to determine the accuracy of the predictions. Incorporating more than 18 months of harbour porpoise detection data from passive acoustic monitoring, generalized auto-regressive moving average and generalized additive models were used to investigate harbour porpoise occurrence within and around the Maryland WEA in relation to temporal and environmental variables. Acoustic detection metrics were compared to habitat-based density estimates derived from aerial and boat-based sightings to validate the model predictions. Harbour porpoises occurred significantly more frequently during January to May, and foraged significantly more often in the evenings to early mornings at sites within and outside the Maryland WEA. Harbour porpoise occurrence peaked at sea surface temperatures of 5°C and chlorophyll a concentrations of 4.5 to 7.4 mg m-3. The acoustic detections were significantly correlated with the predicted densities, except at the most inshore site. This study provides insight into previously unknown fine-scale spatial and temporal patterns in distribution of harbour porpoises offshore of Maryland. The results can be used to help inform future monitoring and mitigate the impacts of windfarm construction and other human activities.

  1. Effects of wind farms on harbour porpoise behaviour and population dynamics

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Jacob; Tougaard, Jakob; Teilmann, Jonas

    We developed an individual-based simulation model in order to study the cumulative impacts of wind farms and ship traffic on the long-term survival and population dynamics of the harbour porpoise (Phocoena phocoena) in Kattegat and the Belt Seas. The model is based on knowl- edge of the porpoises...... at distances >1 km. Our simulations suggest that operating wind farms and wind farms under construction do not affect the size or dynamics of the harbour porpoise population in Kattegat. Ship traffic may, in contrast, cause the population size to decrease....

  2. Identification of a novel gammaherpesvirus associated with (muco)cutaneous lesions in harbour porpoises (Phocoena phocoena).

    Science.gov (United States)

    van Beurden, Steven J; IJsseldijk, Lonneke L; Ordonez, Soledad R; Förster, Christine; de Vrieze, Geert; Gröne, Andrea; Verheije, M Hélène; Kik, Marja

    2015-12-01

    Herpesviruses infect a wide range of vertebrates, including toothed whales of the order Cetacea. One of the smallest toothed whales is the harbour porpoise (Phocoena phocoena), which is widespread in the coastal waters of the northern hemisphere, including the North Sea. Here, we describe the detection and phylogenetic analysis of a novel gammaherpesvirus associated with mucocutaneous and skin lesions in stranded harbour porpoises along the Dutch coast, tentatively designated phocoenid herpesvirus 1 (PhoHV1). Phylogenetically, PhoHV1 forms a monophyletic clade with all other gammaherpesviruses described in toothed whales (Odontoceti) to date, suggesting a common evolutionary origin.

  3. Empirical data and optimal monitoring policies: the case of four Russian sea harbours

    Energy Technology Data Exchange (ETDEWEB)

    Deissenberg, C. [CEFI-CNRS, Les Milles (France); Gurman, V.; Shevchuk, E. [RAS, Program Systems Inst., Pereslavl-Zalessky (Russian Federation); Ryumina, E. [Russian Academy of Sciences, Moscow (Russian Federation). Inst. of Economic Market Problems; Shevlyagin, K. [State Committee of the Environment Protection of the Russian Federation, Moscow (Russian Federation). Marine Environment Dept.

    2001-07-01

    In this paper, we describe the present state of empirical information about oil spills and oil monitoring activities in Russian harbours. We explain how we gathered, organized, and estimated the data needed to run the monitoring efforts optimization model of Deissenberg et al. (2001). We present, analyse, and discuss the results of the optimizations carried out with this model on the basis of the empirical data. These results show, in particular, that the economic efficiency of the monitoring activities decreases rapidly as the corresponding budget increases. This suggests that, rather urgently, measures other than monitoring should be initiated to control sea harbour pollution. (Author)

  4. Codes of Practice related to Harbour and Coastal Engineering in Denmark

    DEFF Research Database (Denmark)

    Burcharth, H. F.

    2000-01-01

    Codes of practice for building and civil engineering works have been produced since 1893 by the "Danish Society of Engineers". Among the early codes are: Reinforces concrete structures (1908, 1943), calculation of reinforced concrete structures in harbour works (1926), Harbour Works (1927), Steel...... structures (1941). The codes were based on the principle of allowable stresses. However, already in 1948 a Danish consulting engineer used a partial safety factor concept for a power station design in order to secure satisfactory safety. The concept was in fact old as it was used by Gerber in his design...

  5. Species-wide phylogeography of North American mule deer (Odocoileus hemionus): cryptic glacial refugia and postglacial recolonization.

    Science.gov (United States)

    Latch, Emily K; Heffelfinger, James R; Fike, Jennifer A; Rhodes, Olin E

    2009-04-01

    Quaternary climatic oscillations greatly influenced the present-day population genetic structure of animals and plants. For species with high dispersal and reproductive potential, phylogeographic patterns resulting from historical processes can be cryptic, overshadowed by contemporary processes. Here we report a study of the phylogeography of Odocoileus hemionus, a large, vagile ungulate common throughout western North America. We examined sequence variation of mitochondrial DNA (control region and cytochrome b) within and among 70 natural populations across the entire range of the species. Among the 1766 individual animals surveyed, we recovered 496 haplotypes. Although fine-scale phylogenetic structure was weakly resolved using phylogenetic methods, network analysis clearly revealed the presence of 12 distinct haplogroups. The spatial distribution of haplogroups showed a strong genetic discontinuity between the two morphological types of O. hemionus, mule deer and black-tailed deer, east and west of the Cascade Mountains in the Pacific Northwest. Within the mule deer lineage, we identified several haplogroups that expanded before or during the Last Glacial Maximum, suggesting that mule deer persisted in multiple refugia south of the ice sheets. Patterns of genetic diversity within the black-tailed deer lineage suggest a single refugium along the Pacific Northwest coast, and refute the hypothesis that black-tailed deer persisted in one or more northern refugia. Our data suggest that black-tailed deer recolonized areas in accordance with the pattern of glacial retreat, with initial recolonization northward along a coastal route and secondary recolonization inland.

  6. Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae), a major vector of stolbur phytoplasma: Evidence of cryptic speciation.

    Science.gov (United States)

    Kosovac, Andrea; Johannesen, Jes; Krstić, Oliver; Mitrović, Milana; Cvrković, Tatjana; Toševski, Ivo; Jović, Jelena

    2018-01-01

    The stolbur phytoplasma vector Hyalesthes obsoletus is generally considered as a polyphagous species associated with numerous wild and cultivated plants. However, recent research in southeastern Europe, the distribution centre of H. obsoletus and the area of most stolbur-inflicted crop diseases, points toward specific host-plant associations of the vector, indicating specific vector-based transmission routes. Here, we study the specificity of populations associated with four host-plants using mitochondrial and nuclear genetic markers, and we evaluate the evolution of host-shifts in H. obsoletus. Host-plant use was confirmed for Convolvulus arvensis, Urtica dioica, Vitex agnus-castus and Crepis foetida. Mitochondrial genetic analysis showed sympatric occurrence of three phylogenetic lineages that were ecologically delineated by host-plant preference, but were morphologically inseparable. Nuclear data supported the existence of three genetic groups (Evanno's ΔK(3) = 803.72) with average genetic membership probabilities > 90%. While populations associated with C. arvensis and U. dioica form a homogenous group, populations affiliated with V. agnus-castus and C. foetida constitute two independent plant-associated lineages. The geographical signal permeating the surveyed populations indicated complex diversification processes associated with host-plant selection and likely derived from post-glacial refugia in the eastern Mediterranean. This study provides evidence for cryptic species diversification within H. obsoletus sensu lato: i) consistent mitochondrial differentiation (1.1-1.5%) among host-associated populations in syntopy and in geographically distant areas, ii) nuclear genetic variance supporting mitochondrial data, and iii) average mitochondrial genetic distances among host-associated meta-populations are comparable to the most closely related, morphologically distinguishable species, i.e., Hyalesthes thracicus (2.1-3.3%).

  7. Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae, a major vector of stolbur phytoplasma: Evidence of cryptic speciation.

    Directory of Open Access Journals (Sweden)

    Andrea Kosovac

    Full Text Available The stolbur phytoplasma vector Hyalesthes obsoletus is generally considered as a polyphagous species associated with numerous wild and cultivated plants. However, recent research in southeastern Europe, the distribution centre of H. obsoletus and the area of most stolbur-inflicted crop diseases, points toward specific host-plant associations of the vector, indicating specific vector-based transmission routes. Here, we study the specificity of populations associated with four host-plants using mitochondrial and nuclear genetic markers, and we evaluate the evolution of host-shifts in H. obsoletus. Host-plant use was confirmed for Convolvulus arvensis, Urtica dioica, Vitex agnus-castus and Crepis foetida. Mitochondrial genetic analysis showed sympatric occurrence of three phylogenetic lineages that were ecologically delineated by host-plant preference, but were morphologically inseparable. Nuclear data supported the existence of three genetic groups (Evanno's ΔK(3 = 803.72 with average genetic membership probabilities > 90%. While populations associated with C. arvensis and U. dioica form a homogenous group, populations affiliated with V. agnus-castus and C. foetida constitute two independent plant-associated lineages. The geographical signal permeating the surveyed populations indicated complex diversification processes associated with host-plant selection and likely derived from post-glacial refugia in the eastern Mediterranean. This study provides evidence for cryptic species diversification within H. obsoletus sensu lato: i consistent mitochondrial differentiation (1.1-1.5% among host-associated populations in syntopy and in geographically distant areas, ii nuclear genetic variance supporting mitochondrial data, and iii average mitochondrial genetic distances among host-associated meta-populations are comparable to the most closely related, morphologically distinguishable species, i.e., Hyalesthes thracicus (2.1-3.3%.

  8. Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae), a major vector of stolbur phytoplasma: Evidence of cryptic speciation

    Science.gov (United States)

    Kosovac, Andrea; Johannesen, Jes; Krstić, Oliver; Cvrković, Tatjana; Toševski, Ivo

    2018-01-01

    The stolbur phytoplasma vector Hyalesthes obsoletus is generally considered as a polyphagous species associated with numerous wild and cultivated plants. However, recent research in southeastern Europe, the distribution centre of H. obsoletus and the area of most stolbur-inflicted crop diseases, points toward specific host-plant associations of the vector, indicating specific vector-based transmission routes. Here, we study the specificity of populations associated with four host-plants using mitochondrial and nuclear genetic markers, and we evaluate the evolution of host-shifts in H. obsoletus. Host-plant use was confirmed for Convolvulus arvensis, Urtica dioica, Vitex agnus-castus and Crepis foetida. Mitochondrial genetic analysis showed sympatric occurrence of three phylogenetic lineages that were ecologically delineated by host-plant preference, but were morphologically inseparable. Nuclear data supported the existence of three genetic groups (Evanno’s ΔK(3) = 803.72) with average genetic membership probabilities > 90%. While populations associated with C. arvensis and U. dioica form a homogenous group, populations affiliated with V. agnus-castus and C. foetida constitute two independent plant-associated lineages. The geographical signal permeating the surveyed populations indicated complex diversification processes associated with host-plant selection and likely derived from post-glacial refugia in the eastern Mediterranean. This study provides evidence for cryptic species diversification within H. obsoletus sensu lato: i) consistent mitochondrial differentiation (1.1–1.5%) among host-associated populations in syntopy and in geographically distant areas, ii) nuclear genetic variance supporting mitochondrial data, and iii) average mitochondrial genetic distances among host-associated meta-populations are comparable to the most closely related, morphologically distinguishable species, i.e., Hyalesthes thracicus (2.1–3.3%). PMID:29738577

  9. Troublesome Trimes: Potential cryptic speciation of the Trimeresurus (Popeia) popeiorum complex (Serpentes: Crotalidae) around the Isthmus of Kra (Myanmar and Thailand).

    Science.gov (United States)

    Mulcahy, Daniel G; Lee, Justin L; Miller, Aryeh H; Zug, George R

    2017-11-13

    The taxonomic identity of the Trimeresurus (Popeia) popeiorum complex from the Isthmus of Kra and to the north was investigated. Several studies over the last decade have produced several specimens and associated mtDNA sequence data for a variety of individuals of the T. popeiorum and "T. sabahi" complexes. Here, we combine four mitochondrial genes (12S, 16S, ND4, and CytB) from all available specimens in GenBank with the addition of five new specimens collected from the mainland, Tanintharyi Region of Myanmar. Maximum Likelihood and Bayesian analyses identified that T. popeiorum sensu lato is paraphyletic with two geographically distinct clades: a northern clade representing populations from northern Myanmar, Laos and northern Thailand and a southern clade representing samples from the Tanintharyi Region and adjacent west Thailand. While the two clades have considerable genetic distance, they appear to be morphologically identical, leading to the hypothesis that the southern clade represents a cryptic, undescribed species. Because they appear to be cryptic species and the limitation of only five specimens from the southern lineage, this does not permit us to formally describe the new species. In accordance to past molecular studies, we uncovered paraphyly and lack of genetic support for the validity of taxa within the T. sabahi complex. However, we suggest recognizing these populations as subspecies within T. sabahi.

  10. Nodule worm infection in humans and wild primates in Uganda: cryptic species in a newly identified region of human transmission.

    Directory of Open Access Journals (Sweden)

    Ria R Ghai

    Full Text Available Soil-transmitted helminths (STHs are a major health concern in tropical and sub-tropical countries. Oesophagostomum infection is considered endemic to West Africa but has also been identified in Uganda, East Africa, among primates (including humans. However, the taxonomy and ecology of Oesophagostomum in Uganda have not been studied, except for in chimpanzees (Pan troglodytes, which are infected by both O. bifurcum and O. stephanostomum.We studied Oesophagostomum in Uganda in a community of non-human primates that live in close proximity to humans. Prevalence estimates based on microscopy were lower than those based on polymerase chain reaction (PCR, indicating greater sensitivity of PCR. Prevalence varied among host species, with humans and red colobus (Procolobus rufomitratus infected at lowest prevalence (25% and 41% by PCR, respectively, and chimpanzees, olive baboons (Papio anubis, and l'hoest monkeys (Cercopithecus lhoesti infected at highest prevalence (100% by PCR in all three species. Phylogenetic regression showed that primates travelling further and in smaller groups are at greatest risk of infection. Molecular phylogenetic analyses revealed three cryptic clades of Oesophagostomum that were not distinguishable based on morphological characteristics of their eggs. Of these, the clade with the greatest host range had not previously been described genetically. This novel clade infects humans, as well as five other species of primates.Multiple cryptic forms of Oesophagostomum circulate in the people and primates of western Uganda, and parasite clades differ in host range and cross-species transmission potential. Our results expand knowledge about human Oesophagostomum infection beyond the West African countries of Togo and Ghana, where the parasite is a known public health concern. Oesophagostomum infection in humans may be common throughout Sub-Saharan Africa, and the transmission of this neglected STH among primates, including zoonotic

  11. Hypertensive cerebellar hemorrhage and cerebellar hemorrhage caused by cryptic angioma

    International Nuclear Information System (INIS)

    Yoshida, Shinichi; Sano, Keiji; Kwak, Suyong; Saito, Isamu.

    1981-01-01

    A series of 44 patients with hypertensive cerebellar hemorrhage and nine patients with cerebellar hemorrhage caused by small angiomas is described. Hypertensive hemorrhage occurred most frequently in the patients in their seventies, whereas the onset of angioma-caused hemorrhage was often seen below the age of 40. Clinical syndromes of cerebellar hemorrhages can be categorized into three basic types: the vertigo syndrome, cerebellar dysfunction syndrome and brain stem compression syndrome. Patients with small (>= 2 cm in diameter in CT scans) and medium-sized (2 cm = 3 cm) hematomas deteriorated into unresponsive conditions and developed signs of brain stem compression. Surgical mortality was 32% in the hypertensive group, while it was 0% in the angioma group. Mortality as well as morbidity in both groups was strongly influenced by the preoperative status of consciousness. Our results suggest that substantial improvement could be obtained in the overall outcome of this disease by emergency craniectomy and removal of hematomas in all patients with large hematomas regardless of the levels of consciousness and regardless of the causes of bleeding. Furthermore, when clinical information and CT findings are suggestive of a ''cryptic'' angioma as the causative lesion, posterior fossa surgery may be indicated to extirpate the lesion, even if the hematoma is small. (author)

  12. Fishing for food : feeding ecology of harbour porpoises Phocoena phocoena and white-beaked dolphins Lagenorhynchus albirostris in Dutch waters

    NARCIS (Netherlands)

    Jansen, O.E.

    2013-01-01

    Harbour porpoises and white-beaked dolphins are the most common small cetaceans in the North Sea and Dutch coastal waters. The distribution and relative abundance of harbour porpoises and white-beaked dolphins from the Dutch coastal waters has changed significantly over the past decades. This

  13. Environmental change, phenotypic plasticity, and genetic compensation.

    Science.gov (United States)

    Grether, Gregory F

    2005-10-01

    When a species encounters novel environmental conditions, some phenotypic characters may develop differently than in the ancestral environment. Most environmental perturbations of development are likely to reduce fitness, and thus selection would usually be expected to favor genetic changes that restore the ancestral phenotype. I propose the term "genetic compensation" to refer to this form of adaptive evolution. Genetic compensation is a subset of genetic accommodation and the reverse of genetic assimilation. When genetic compensation has occurred along a spatial environmental gradient, the mean trait values of populations in different environments may be more similar in the field than when representatives of the same populations are raised in a common environment (i.e., countergradient variation). If compensation is complete, genetic divergence between populations may be cryptic, that is, not detectable in the field. Here I apply the concept of genetic compensation to three examples involving carotenoid-based sexual coloration and then use these and other examples to discuss the concept in a broader context. I show that genetic compensation may lead to a cryptic form of reproductive isolation between populations evolving in different environments, may explain some puzzling cases in which heritable traits exposed to strong directional selection fail to show the expected evolutionary response, and may complicate efforts to monitor populations for signs of environmental deterioration.

  14. Phylogeography of a Morphologically Cryptic Golden Mole Assemblage from South-Eastern Africa.

    Directory of Open Access Journals (Sweden)

    Samantha Mynhardt

    Full Text Available The Greater Maputaland-Pondoland-Albany (GMPA region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage (Amblysomus endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus, with emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic reconstructions show that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs, some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5-3 million years ago (Ma, habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity.

  15. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles.

    Science.gov (United States)

    Labate, Joanne A; Robertson, Larry D

    2012-08-07

    Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Each marker was mapped with high confidence (etomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help

  16. Distribution of polycyclic aromatic hydrocarbons (PAHs) and tributyltin (TBT) in Barcelona harbour sediments and their impact on benthic communities

    Energy Technology Data Exchange (ETDEWEB)

    Martinez-Llado, Xavier [Environmental Technology Area, CTM-UPC, Avda. Bases de Manresa 1, 08240 Manresa (Spain); Gibert, Oriol [Environmental Technology Area, CTM-UPC, Avda. Bases de Manresa 1, 08240 Manresa (Spain); Marti, Vicens [Environmental Technology Area, CTM-UPC, Avda. Bases de Manresa 1, 08240 Manresa (Spain)]. E-mail: vicens.marti@upc.edu; Diez, Sergi [Environmental Chemistry Department, IIQAB-CSIC, c/Jordi Girona 18-26, 08034 Barcelona (Spain); Environmental Geology Department, ICTJA-CSIC, Lluis Sole i Sabaris, s/n, 08028 Barcelona (Spain); Romo, Javier [Environmental Service of Barcelona Harbour Authority, Carretera de la Circumval.lacio, s/n, Tram VI, Sector 6, Barcelona (Spain); Bayona, Josep Maria [Environmental Chemistry Department, IIQAB-CSIC, c/Jordi Girona 18-26, 08034 Barcelona (Spain); Pablo, Joan de [Environmental Technology Area, CTM-UPC, Avda. Bases de Manresa 1, 08240 Manresa (Spain)

    2007-09-15

    Sediments have long been recognised as a sink for many contaminants like polycyclic aromatic hydrocarbons (PAHs) and tributyltin (TBT), which by virtue of their nature can strongly adsorb onto sediments affecting the benthic community inhabiting them. Using geographical information systems, this study reports and combines the results of several already existing studies along Barcelona harbour in order to assess the potential ecological impacts of these contaminants on the benthos of the harbour ecosystem. Chemical analysis indicated low to moderate contents of PAHs and high contents of TBT in sediments in Barcelona harbour. Comparison against existing sediment quality guidelines (SQGs) indicated that acutely toxic effects would not be expected for PAHs but for TBT, which represents a serious environmental threat for the benthic community. Benthos surveys revealed a deterioration of the benthic community throughout the harbour, especially in the inner port. - A possible correlation exists between TBT concentration in sediments and ecological effects on benthos in Barcelona harbour.

  17. Distribution of polycyclic aromatic hydrocarbons (PAHs) and tributyltin (TBT) in Barcelona harbour sediments and their impact on benthic communities

    International Nuclear Information System (INIS)

    Martinez-Llado, Xavier; Gibert, Oriol; Marti, Vicens; Diez, Sergi; Romo, Javier; Bayona, Josep Maria; Pablo, Joan de

    2007-01-01

    Sediments have long been recognised as a sink for many contaminants like polycyclic aromatic hydrocarbons (PAHs) and tributyltin (TBT), which by virtue of their nature can strongly adsorb onto sediments affecting the benthic community inhabiting them. Using geographical information systems, this study reports and combines the results of several already existing studies along Barcelona harbour in order to assess the potential ecological impacts of these contaminants on the benthos of the harbour ecosystem. Chemical analysis indicated low to moderate contents of PAHs and high contents of TBT in sediments in Barcelona harbour. Comparison against existing sediment quality guidelines (SQGs) indicated that acutely toxic effects would not be expected for PAHs but for TBT, which represents a serious environmental threat for the benthic community. Benthos surveys revealed a deterioration of the benthic community throughout the harbour, especially in the inner port. - A possible correlation exists between TBT concentration in sediments and ecological effects on benthos in Barcelona harbour

  18. Establishment of gravity stations and inference of crustal thickness around Mormugao Harbour and NIO

    Digital Repository Service at National Institute of Oceanography (India)

    Subbaraju, L.V.; Krishna, K.S.

    Complete descriptions and basic facts of nine gravity stations of Marmugao Harbour, Goa, India are presented. They exhibit a maximum Bouguer difference of 2.12 mGal in an overall distance of about 2 km. Keeping in view the limited amount of data...

  19. Analysis of Wave Reflection from Wave Energy Converters Installed as Breakwaters in Harbour

    DEFF Research Database (Denmark)

    Zanuttigh, B.; Margheritini, Lucia; Gambles, L.

    2009-01-01

    loads on the structure, i.e. better survivability. Nevertheless these devices must comply with the requirements of harbour protection structures and thus cope with problems due to reflection of incoming waves, i.e. dangerous sea states close to harbors entrances and intensified sediment scour, which can...

  20. The Westward Movement of Chinese Export Harbour Views : Significant Paintings with a Social Function

    NARCIS (Netherlands)

    Poel, van der R.H.M.

    2012-01-01

    Article (Chapter) in proceedings of the First Rombouts Graduate Conference Globalization and Glocalization in China, at Leiden University, held in Leiden on 6 and 7 September 2011. This article offers a closer examination of Chinese export harbour views and, in doing so, reveals that waterfronts and

  1. Petroleum hydrocarbons and trace metals in Visakhapatnam harbour and Kakinada Bay, east coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Sarma, V.V.; VaraPrasad, S.J.D.; Gupta, G.V.M.; Sudhakar, U.

    High concentrations of PHC were observed in the inner channels (viz. South lighter canal, Northern arm, North Western arm and Western arm) of Visakhapatnam Harbour, Andhra Pradesh, India. The estimation of trace metals (Cu, Zn, Pb, Cd, Co, Ni and Cr...

  2. Tide dependent seasonal changes in water quality and assimilative capacity of anthropogenically influenced Mormugao harbour water

    Digital Repository Service at National Institute of Oceanography (India)

    Shirodkar, P.V.; Deepthi, M.; Vethamony, P.; Mesquita, A.M.; Pradhan, U.K.; Babu, M.T.; Verlecar, X.N.; Haldankar, S.R.

    Water quality data from Mormugao harbour area at the mouth of Zuari estuary in Goa have been obtained over two tidal cycles monthly for the year 2003 to 2004. R-mode factor analyses of the data indicated strong positive loadings of coliforms...

  3. Settling fluxes and ecotoxicological risk assessment of fine sedimentary metals in Tema Harbour (Ghana).

    Science.gov (United States)

    Botwe, Benjamin O; Nyarko, Elvis; Lens, Piet N L

    2018-01-01

    Sediment traps were deployed in the Tema Harbour to estimate the settling fluxes of silt-clay particles and associated metals (Fe, Mn, Pb, Cr, Cu, Zn, Ni, Hg, Sn and As) and characterise their potential ecotoxicological risks. The mean daily settling fluxes of the silt-clay particles and associated metals ranged from 42.7 to 85.0gm -2 d -1 and 1.3×10 -2 to 49.4mgm -2 d -1 , respectively, and were characterised by large fluctuations at each station. The silt-clay and metal fluxes strongly correlated, indicating the important role of the silt-clay particles in metal transport and distribution in the harbour. Geochemical indices indicated anthropogenic influences on the harbour as the Pb, Cr, Zn, Hg, Sn and As content in the settling silt-clay particles exceeded their average crustal concentrations. Sediment quality guidelines indicated these metals pose appreciable ecotoxicological risks, particularly As. Increasing temporal trends in As necessitates increased pollution control efforts at the harbour. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Metal contamination in harbours impacts life-history traits and metallothionein levels in snails.

    Directory of Open Access Journals (Sweden)

    Maria Alexandra Bighiu

    Full Text Available Harbours with limited water exchange are hotspots of contaminant accumulation. Antifouling paints (AF contribute to this accumulation by leaching biocides that may affect non-target species. In several leisure boat harbours and reference areas in the Baltic Sea, chronic exposure effects were evaluated using caging experiments with the snail Theodoxus fluviatilis. We analysed variations in ecologically relevant endpoints (mortality, growth and reproduction in concert with variation in metallothionein-like proteins (MTLP levels. The latter is a biomarker of exposure to metals, such as copper (Cu and zinc (Zn, which are used in AF paints as active ingredient and stabilizer, respectively. In addition, environmental samples (water, sediment were analysed for metal (Cu and Zn and nutrient (total phosphorous and nitrogen concentrations. All life-history endpoints were negatively affected by the exposure, with higher mortality, reduced growth and lower fecundity in the harbours compared to the reference sites. Metal concentrations were the key explanatory variables for all observed adverse effects, suggesting that metal-driven toxicity, which is likely to stem from AF paints, is a source of anthropogenic stress for biota in the harbours.

  5. Radioactivity concentrations and their radiological significance in sediments of the Tema Harbour (Greater Accra, Ghana

    Directory of Open Access Journals (Sweden)

    Benjamin O. Botwe

    2017-01-01

    Full Text Available Studies on environmental radioactivity in tropical Africa are scarce. Therefore, a baseline study of natural (238U, 210Pb, 226Ra, 232Th, 228Ra, 228Th, 40K and anthropogenic (137Cs radionuclides was carried out on Tema Harbour (Greater Accra, Ghana surface sediments and on their radiological significance. Grab surface sediment samples were collected from 21 stations within the Tema Harbour and their radioactivity concentrations measured by gamma spectrometry. The mean sediment radioactivity concentrations (Bq kg−1 dw were 34 for 238U, 210 for 210Pb, 14 for 226Ra, 30 for 232Th, 29 for 228Ra, 31 for 228Th, 320 for 40K, and 1.5 for 137Cs. Large 238U/226Ra disequilibria were observed in the harbour sediments and a complex dynamics of several mixed sources of sediments within the Tema Harbour can be inferred from the spatial variations in the radioactivity concentrations. The estimated total absorbed dose rate in air (D, radium equivalent activity (Raeq, external hazard index (Hex, annual gonadal dose equivalent (AGDE and annual effective dose equivalent (AEDE indicated no significant radiological risks from the sediment radioactivity concentrations. Application of the Environmental Risk from Ionising Contaminants Assessment and Management tool (ERICA confirmed that the potential dose rates to biota from the sediment radioactivity concentrations are unlikely to pose appreciable ecological risks. The radioactivity levels are compared with levels reported in sediments from other coastal areas of the world.

  6. Variation of physico-chemical characteristics with tide in Visakhapatnam harbour waters, east coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    RamaRaju, V.S.; Rao, T.V.N.; Rathod, V.

    Variations in physico-chemical parameters (DO, BOD, NO2, SiO4, PO4 suspended solids, salinity and currents) observed in the waters of main channel of Visakhapatnam Harbour over a tidal cycle in different seasons from February 1982 to January 1983...

  7. Detection and direction discrimination of single vortex rings by harbour seals (Phoca vitulina).

    Science.gov (United States)

    Krüger, Yvonne; Hanke, Wolf; Miersch, Lars; Dehnhardt, Guido

    2018-04-25

    Harbour seals possess highly sensitive vibrissae that enable them to track hydrodynamic trails left behind by a swimming fish. Most of these trails contain vortex rings as a main hydrodynamic component. They may reveal information about their generator as the trails differ depending on the fish species, the fish's body shape, size and swimming style. In addition, fish generate single vortex rings in diverse natural situations. In this study, the ability of blindfolded stationary harbour seals to detect and analyse single vortex rings regarding directional information has been investigated. In three different behavioural experiments, the animals were trained to respond to single artificially generated vortex rings. The results show that harbour seals are able to respond to a variety of different vortex rings upon vibrissal stimulation. The investigation of the minimum hydrodynamically perceivable angle revealed that it is at least as small as 5.7 deg, which was the smallest adjustable angle. Moreover, harbour seals are capable of analysing the travel direction of a vortex ring perceived by the mystacial vibrissae irrespective of whether the vibrissae were stimulated ipsilaterally or contralaterally. In situations in which no complex hydrodynamic trail is available, it is advantageous for a hunting seal to be able to extract information from a single vortex ring. © 2018. Published by The Company of Biologists Ltd.

  8. TORONTO HARBOUR COMMISSIONERS (THC) SOIL RECYCLE TREATMENT TRAIN - APPLICATIONS ANALYSIS REPORT

    Science.gov (United States)

    The Toronto Harbour Commissioners (THC) have developed a soil treatment train designed to treat inorganic and organic contaminants in soils. THC has conducted a large-scale demonstration of these technologies in an attempt to establish that contaminated soils at the Toronto Port ...

  9. Correlation between the seasonal distribution of harbour porpoises and their prey in the Sound, Baltic Sea

    DEFF Research Database (Denmark)

    Sveegaard, Signe; Andreasen, Heidi; Mouritsen, Kim N.

    2012-01-01

    herring and Atlantic cod were equally important during the low-density season. Prey availability and predictability are suggested as the main drivers for harbour porpoise distribution, and this could be caused by the formation of frontal zones in spring in the northern part of the Sound, leading to prey...

  10. Identification and typing of Brucella spp. in stranded harbour porpoises (Phocoena phocoena) on the Dutch coast

    NARCIS (Netherlands)

    Maio, Elisa; Begeman, Lineke; Bisselink, Yvette; van Tulden, Peter; Wiersma, Lidewij; Hiemstra, Sjoukje; Ruuls, Robin; Gröne, Andrea; Roest, Hendrik-Ido-Jan; Willemsen, Peter; van der Giessen, Joke

    2014-01-01

    The presence of Brucella (B.) spp. in harbour porpoises stranded between 2008 and 2011 along the Dutch coast was studied. A selection of 265 tissue samples from 112 animals was analysed using conventional and molecular methods. In total, 4.5% (5/112) of the animals corresponding with 2.3% (6/265)

  11. Identification and typing of Brucella spp. in stranded harbour porpoises (Phocoena phocoena) on the Dutch coast.

    NARCIS (Netherlands)

    Maio, E.; Begeman, L.; Bisselink, Y.J.W.M.; Tulden, van P.W.; Wiersma, L.; Hiemstra, S.; Ruuls, R.; Gröne, A.; Roest, H.I.J.; Willemsen, P.T.J.; Giessen, van der J.

    2014-01-01

    The presence of Brucella (B.) spp. in harbour porpoises stranded between 2008 and 2011 along the Dutch coast was studied. A selection of 265 tissue samples from 112 animals was analysed using conventional and molecular methods. In total, 4.5% (5/112) of the animals corresponding with 2.3% (6/265)

  12. No serological evidence that harbour porpoises are additional hosts of influenza B viruses.

    Directory of Open Access Journals (Sweden)

    Rogier Bodewes

    Full Text Available Influenza A and B viruses circulate among humans causing epidemics almost annually. While various hosts for influenza A viruses exist, influenza B viruses have been detected only in humans and seals. However, recurrent infections of seals in Dutch coastal waters with influenza B viruses that are antigenetically distinct from influenza B viruses circulating among humans suggest that influenza B viruses have been introduced into this seal population by another, non-human, host. Harbour porpoises (Phocoena phocoena are sympatric with seals in these waters and are also occasionally in close contact with humans after stranding and subsequent rehabilitation. In addition, virus attachment studies demonstrated that influenza B viruses can bind to cells of the respiratory tract of these animals. Therefore, we hypothesized that harbour porpoises might be a reservoir of influenza B viruses. In the present study, an unique set of serum samples from 79 harbour porpoises, stranded alive on the Dutch coast between 2003 and 2013, was tested for the presence of antibodies against influenza B viruses by use of the hemagglutination inhibition test and for antibodies against influenza A viruses by use of a competitive influenza A nucleoprotein ELISA. No antibodies were detected against either virus, suggesting that influenza A and B virus infections of harbour porpoises in Dutch coastal waters are not common, which was supported by statistical analysis of the dataset.

  13. The use of desorbing agents in electrodialytic remediation of harbour sediment

    DEFF Research Database (Denmark)

    Nystrøm, Gunvor Marie; Pedersen, Anne Juul; Ottosen, Lisbeth M.

    2006-01-01

    Electrodialytic removal of Cu, Zn, Pb and Cd from contaminated harbour sediment was made with the emphasis of testing the effectiveness of different desorbing agents: HCl, NaCl, citric acid, lactic acid, ammonium citrate and distilled water. Extraction experiments with the desorbing agents were...

  14. Grey seal attacks on harbour porpoises in the Eastern Scheldt: cases of survival and mortality

    NARCIS (Netherlands)

    Podt, Annemieke; IJsseldijk, L.L.

    2017-01-01

    In the southern North Sea, hundreds of mutilated harbour porpoise carcasses (Phocoena phocoena) are found each year on beaches. Recent studies have confirmed that these concern the remains of predation by grey seals (Halichoerus grypus). A retrospective study of post mortem photos helped to further

  15. Exposing the grey seal as a major predator of harbour porpoises

    NARCIS (Netherlands)

    Leopold, M.F.; Begeman, L.; van Bleijswijk, J.D.L.; IJsseldijk, L.L.; Witte, H.; Gröne, A.

    2015-01-01

    Harbour porpoises (Phocoena phocoena) stranding in large numbers around the southern North Sea with fatal, sharp-edged mutilations have spurred controversy among scientists, the fishing industry and conservationists, whose views about the likely cause differ. The recent detection of grey seal

  16. Distribution of 137Cs in sediments in Xiangshan, Xiamen and Yangpu harbours, China

    International Nuclear Information System (INIS)

    Pan, S.; Xu, Q.

    1999-01-01

    Xiangshan Harbour (Zhejing Province), Xiamen Harbour (Fujian Province) and Yangpu Harbour (Hainan Province) are tide-channel type bays, located on the southeast coast of China. Six sediment cores were collected in the Harbours in several projects respectively. Sediment samples were collected with a Lehigh gravity corer which utilized a 10.3 cm diameter, PVC core barrel. Styrofoam sediment core retainers were fitted into the top of the core barrel following core recovery to facilitate core sampling without loss of sediment from the barrel. The core barrels were split lengthwise using a circular saw. Following visual inspection for geological parameters (colour, texture, etc.) and photography of the cores, they were subsampled at 1-2 cm or 5 cm intervals for the entire length of the core. The sediment samples were stored in air-tight, plastic containers and returned to Nanjing University for 137 Cs and other types of analysis. The sediment samples were oven dried at approximately 100 deg. C. at the Nanjing University isotope laboratory and the % loss of water used to determine the wet and dry densities. The contents of 137 Cs were counted using an n-type HPGe γ-ray spectrometry system. The coaxial detector has an efficiency of 25%, with a lead shield 12 cm thick. Each sample was measured for 12h

  17. Coastal Changes due to the Construction of Artificial Harbour Entrances and Practical Solutions, including Beach Replenishment

    NARCIS (Netherlands)

    Bijker, E.W.; Van der Leijé, J.P.; Pilon, J.J.; Svasek, J.N.; In 't Veld, J.K.; Verhagen, H.J.

    1981-01-01

    When longshore sediment transport is interrupted by a construction along a coast, e.g harbour moles or a dredged approach channel, the equilibrium of the coastline may be disturbed. When the disruption is caused by breakwaters, the longshore transport that is held back will cause accretion updrift

  18. Comparative sensitivity of harbour and grey seals to several environmental contaminants using in vitro exposure

    International Nuclear Information System (INIS)

    Dufresne, M.M.; Frouin, H.; Pillet, S.; Lesage, V.; De Guise, S.; Fournier, M.

    2010-01-01

    In this study, we investigated the effects of cadmium chloride (CdCl 2 ), mercury chloride (HgCl 2 ), methylmercury chloride (CH 3 HgCl), and PCBs on lymphocyte proliferation in phocids. PBMCs isolated from harbour and grey seals were exposed in vitro to varying concentrations of contaminants. A reduction of viability occurred when cells were exposed to 10 -4 M HgCl 2 or CH 3 HgCl or to 50 ppm of Aroclor 1254. In both grey and harbour seals, T-lymphocyte proliferation was suppressed when their cells were incubated with 5 x 10 -5 M CdCl 2 or 10 -4 M HgCl 2 . An inhibition of proliferation occurred with CH 3 HgCl from 10 -6 M in grey seals and from 10 -5 M in harbour seals. In grey seals, Aroclor 1254 reduced lymphocyte proliferation at 15 ppm. In both harbour and grey seals, CH 3 HgCl was ten times more immunotoxic that HgCl 2 . From IC 50 , chemicals were ranked in terms of toxicity as followed: CH 3 HgCl > CdCl 2 > HgCl 2 > Aroclor 1254.

  19. Monitoring effects of offshore windfarms on harbour porpoises using PODs (porpoise detectors)

    International Nuclear Information System (INIS)

    Teilmann, J.; Damsgaard Henriksen, O.; Carstensen, Jacob; Skov, H.

    2002-02-01

    The areas designated for offshore windfarms in Denmark, are all known habitats for harbour porpoises. It is possible that some of the activities involved in erection and operation of offshore windfarms will have a negative impact on the harbour porpoises in and around the windfarms. The most significant sources of these effects are thought to be the physical presence and the noise from ships and construction work as well as temporary and even permanent loss of suitable habitats near the windfarms. The noise from existing offshore windturbines has been measured and a detection distance of 20 m was calculated in the EIA study regarding the Roedsand windfarm. In order to study possible effects from the erection and operation of windfarms on harbour porpoises a number of studies were suggested as part of the EIA background study on harbour porpoises. Among these suggestions was the use of acoustic dataloggers (PODs). The POD is recording click sounds of short duration. It is programmable and can be set to specifically record the echolocation signals that harbour porpoises uses for orientation and foraging. This method will potentially give data on harbour porpoise activity in a specific area on a diurnal and year-round basis. The construction work will take place over several months and since there is no available information on the seasonal sensitivity of porpoises to disturbance, the data necessary to detect and evaluate the effect of the windfarm would need to cover all seasons. No other method is feasible to provide data on the presence of harbour porpoises year round in a particular area. However, this method has its limitations in that only porpoises echolocating are recorded. No data exists on the seasonal, diurnal and area specific use of echolocation but since echolocation is believed to be the primary sense for porpoises we expect that porpoises used their echolocation most of the time and that it is correlated to the density of porpoises. However, the actual

  20. Monitoring effects of offshore windfarms on harbour porpoises using PODs (porpoise detectors)

    Energy Technology Data Exchange (ETDEWEB)

    Teilmann, J.; Damsgaard Henriksen, O. [National Environmental Res. Inst., Dept. of Arctic Enviroment, Roskilde (Denmark); Carstensen, Jacob [National Environmental Res. Lab., Dept. of Marine Ecology, Roskilde (Denmark); Skov, H. [Ornis Consult A/S, Copenhagen (Denmark)

    2002-02-15

    The areas designated for offshore windfarms in Denmark, are all known habitats for harbour porpoises. It is possible that some of the activities involved in erection and operation of offshore windfarms will have a negative impact on the harbour porpoises in and around the windfarms. The most significant sources of these effects are thought to be the physical presence and the noise from ships and construction work as well as temporary and even permanent loss of suitable habitats near the windfarms. The noise from existing offshore windturbines has been measured and a detection distance of 20 m was calculated in the EIA study regarding the Roedsand windfarm. In order to study possible effects from the erection and operation of windfarms on harbour porpoises a number of studies were suggested as part of the EIA background study on harbour porpoises. Among these suggestions was the use of acoustic dataloggers (PODs). The POD is recording click sounds of short duration. It is programmable and can be set to specifically record the echolocation signals that harbour porpoises uses for orientation and foraging. This method will potentially give data on harbour porpoise activity in a specific area on a diurnal and year-round basis. The construction work will take place over several months and since there is no available information on the seasonal sensitivity of porpoises to disturbance, the data necessary to detect and evaluate the effect of the windfarm would need to cover all seasons. No other method is feasible to provide data on the presence of harbour porpoises year round in a particular area. However, this method has its limitations in that only porpoises echolocating are recorded. No data exists on the seasonal, diurnal and area specific use of echolocation but since echolocation is believed to be the primary sense for porpoises we expect that porpoises used their echolocation most of the time and that it is correlated to the density of porpoises. However, the actual

  1. Partial mitochondrial DNA sequences suggest the existence of a cryptic species within the Leucosphyrus group of the genus Anopheles (Diptera: Culicidae), forest malaria vectors, in northern Vietnam.

    Science.gov (United States)

    Takano, Kohei Takenaka; Nguyen, Ngoc Thi Hong; Nguyen, Binh Thi Huong; Sunahara, Toshihiko; Yasunami, Michio; Nguyen, Manh Duc; Takagi, Masahiro

    2010-04-30

    During the last decade, Southeast Asian countries have been very successful in reducing the burden of malaria. However, malaria remains endemic in these countries, especially in remote and forested areas. The Leucosphyrus group of the genus Anopheles harbors the most important malaria vectors in forested areas of Southeast Asia. In Vietnam, previous molecular studies have resulted in the identification of only Anopheles dirus sensu stricto (previously known as An. dirus species A) among the Leucosphyrus group members. However, Vietnamese entomologists have recognized that mosquitoes belonging to the Leucosphyrus group in northern Vietnam exhibit morphological characteristics similar to those of Anopheles takasagoensis, which has been reported only from Taiwan. Here, we aimed to confirm the genetic and morphological identities of the members of the Leucosphyrus group in Vietnam. In the molecular phylogenetic trees reconstructed using partial COI and ND6 mitochondrial gene sequences, samples collected from southern and central Vietnam clustered together with GenBank sequences of An. dirus that were obtained from Thailand. However, samples from northern Vietnam formed a distinct clade separated from both An. dirus and An. takasagoensis by other valid species. The results suggest the existence of a cryptic species in northern Vietnam that is morphologically similar to, but phylogenetically distant from both An. dirus and An. takasagoensis. We have tentatively designated this possible cryptic species as Anopheles aff. takasagoensis for convenience, until a valid name is assigned. However, it is difficult to distinguish the species solely on the basis of morphological characteristics. Further studies on such as karyotypes and polytene chromosome banding patterns are necessary to confirm whether An. aff. takasagoensis is a valid species. Moreover, studies on (1) the geographic distribution, which is potentially spreading along the Vietnam, China, Laos, and Myanmar borders

  2. Evaluation of trophic state and plankton abundance from the environmental parameters of Visakhapatnam Harbour and near-shore waters, east coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Tripathy, S.C.; KusumaKumari, B.A.V.L.; Sarma, V.V.; Murty, T.V.R.

    The present work describes the nutrient indices of the Visakhapatnam harbour and near-shore waters. The inner channels of Visakhapatnam harbour are considered to be eutrophic while near-shore waters (coastal and inshore waters) associated...

  3. Development in Harbour Construction, Infrastructure and Topography on the Eve of the Early Modern Age in the Baltic (1450-1600)

    DEFF Research Database (Denmark)

    Springmann, Maik Jens O R

    2016-01-01

    Ships are no Flying Dutchmen! They need a harbour. Therefore, the development of ship construction is pretty much connected with that of harbour construction, and beyond this, they influence the topography and infrastructure of a harbour. The transition between the Medieval period and the Early M...... construction, topography and infrastructure follow the development of ship construction. The paper focuses on the deep impact that larger multi-mast sailing ships had on the development of Baltic harbours...

  4. Comparative phylogeography of reef fishes from the Gulf of Aden to the Arabian Sea reveals two cryptic lineages

    KAUST Repository

    DiBattista, Joseph; Gaither, Michelle R.; Hobbs, Jean-Paul A.; Saenz Agudelo, Pablo; Piatek, Marek J.; Bowen, Brian W.; Rocha, Luiz A.; Howard Choat, J.; McIlwain, Jennifer H.; Priest, Mark; Sinclair-Taylor, Tane; Berumen, Michael L.

    2017-01-01

    The Arabian Sea is a heterogeneous region with high coral cover and warm stable conditions at the western end (Djibouti), in contrast to sparse coral cover, cooler temperatures, and upwelling at the eastern end (southern Oman). We tested for barriers to dispersal across this region (including the Gulf of Aden and Gulf of Oman), using mitochondrial DNA surveys of 11 reef fishes. Study species included seven taxa from six families with broad distributions across the Indo-Pacific and four species restricted to the Arabian Sea (and adjacent areas). Nine species showed no significant genetic partitions, indicating connectivity among contrasting environments spread across 2000 km. One butterflyfish (Chaetodon melannotus) and a snapper (Lutjanus kasmira) showed phylogenetic divergences of d = 0.008 and 0.048, respectively, possibly indicating cryptic species within these broadly distributed taxa. These genetic partitions at the western periphery of the Indo-Pacific reflect similar partitions recently discovered at the eastern periphery of the Indo-Pacific (the Hawaiian and the Marquesan Archipelagos), indicating that these disjunctive habitats at the ends of the range may serve as evolutionary incubators for coral reef organisms.

  5. Comparative phylogeography of reef fishes from the Gulf of Aden to the Arabian Sea reveals two cryptic lineages

    KAUST Repository

    DiBattista, Joseph

    2017-02-01

    The Arabian Sea is a heterogeneous region with high coral cover and warm stable conditions at the western end (Djibouti), in contrast to sparse coral cover, cooler temperatures, and upwelling at the eastern end (southern Oman). We tested for barriers to dispersal across this region (including the Gulf of Aden and Gulf of Oman), using mitochondrial DNA surveys of 11 reef fishes. Study species included seven taxa from six families with broad distributions across the Indo-Pacific and four species restricted to the Arabian Sea (and adjacent areas). Nine species showed no significant genetic partitions, indicating connectivity among contrasting environments spread across 2000 km. One butterflyfish (Chaetodon melannotus) and a snapper (Lutjanus kasmira) showed phylogenetic divergences of d = 0.008 and 0.048, respectively, possibly indicating cryptic species within these broadly distributed taxa. These genetic partitions at the western periphery of the Indo-Pacific reflect similar partitions recently discovered at the eastern periphery of the Indo-Pacific (the Hawaiian and the Marquesan Archipelagos), indicating that these disjunctive habitats at the ends of the range may serve as evolutionary incubators for coral reef organisms.

  6. Features of cryptic promoters and their varied reliance on bromodomain-containing factors.

    Directory of Open Access Journals (Sweden)

    Samantha G Pattenden

    Full Text Available The Set2-Rpd3S pathway is important for the control of transcription memory. Mutation of components of this pathway results in cryptic transcription initiation within the coding region of approximately 30% of yeast genes. Specifically, deletion of the Set2 histone methyltransferase or Rco1, a component of the Rpd3S histone deacetylase complex leads to hyperacetylation of certain open reading frames (ORFs. We used this mutant as a system to study the role of histone modifications and co-activator recruitment in preinitiation complex (PIC formation. Specifically, we looked at the dependence of promoters on the bromodomain-containing RSC complex and the Bdf1 protein. We found that the dependence of cryptic promoters for these proteins varied. Overall, our data indicate that cryptic promoters are independently regulated, and their activation is dependent on factors that govern gene activation at canonical promoters.

  7. Diversity and environmental relations of cryptic, systemic Botrytis infections in symptomless hosts.

    Directory of Open Access Journals (Sweden)

    Michael W. Shaw

    2016-05-01

    Full Text Available Botrytis species are generally considered to be aggressive, necrotrophic plant pathogens. By contrast to this general perception, however, Botrytis species could frequently be isolated from the interior of multiple tissues in apparently healthy hosts of many species. Infection frequencies reached 50% of samples or more, but were commonly less, and cryptic infections were rare or absent in some plant species. Prevalence varied substantially from year to year and from tissue to tissue, but some host species routinely had high prevalence. The same genotype was found to occur throughout a host, representing mycelial spread. B. cinerea and B. pseudocinerea are the species that most commonly occur as cryptic infections, but phylogenetically distant isolates of Botrytis were also detected, one of which does not correspond to previously described species. Sporulation and visible damage occurred only when infected tissues were stressed, or became mature or senescent. There was no evidence of cryptic infection having a deleterious effect on growth of the host, and prevalence was probably greater in plants grown in high light conditions. Isolates from cryptic infections were often capable of causing disease (to varying extents when spore suspensions were inoculated onto their own host as well as on distinct host species, arguing against co-adaptation between cryptic isolates and their hosts. These data collectively suggest that several Botrytis species, including the most notorious pathogenic species, exist frequently in cryptic form to an extent that has thus far largely been neglected, and do not need to cause disease on healthy hosts in order to complete their life-cycles.

  8. Risk of Gonadoblastoma Development in Patients with Turner Syndrome with Cryptic Y Chromosome Material.

    Science.gov (United States)

    Kwon, Ahreum; Hyun, Sei Eun; Jung, Mo Kyung; Chae, Hyun Wook; Lee, Woo Jung; Kim, Tae Hyuk; Kim, Duk Hee; Kim, Ho-Seong

    2017-06-01

    Current guidelines recommend that testing for Y chromosome material should be performed only in patients with Turner syndrome harboring a marker chromosome and exhibiting virilization in order to detect individuals who are at high risk of gonadoblastoma. However, cryptic Y chromosome material is suggested to be a risk factor for gonadoblastoma in patients with Turner syndrome. Here, we aimed to estimate the frequency of cryptic Y chromosome material in patients with Turner syndrome and determine whether Y chromosome material increased the risk for development of gonadoblastoma. A total of 124 patients who were diagnosed with Turner syndrome by conventional cytogenetic techniques underwent additional molecular analysis to detect cryptic Y chromosome material. In addition, patients with Turner syndrome harboring Y chromosome cell lines had their ovaries removed prophylactically. Finally, we assessed the occurrence of gonadoblastoma in patients with Turner syndrome. Molecular analysis demonstrated that 10 patients had Y chromosome material among 118 patients without overt Y chromosome (8.5%). Six patients with overt Y chromosome and four patients with cryptic Y chromosome material underwent oophorectomy. Histopathological analysis revealed that the occurrence of gonadoblastoma in the total group was 2.4%, and gonadoblastoma occurred in one of six patients with an overt Y chromosome (16.7%) and 2 of 10 patients with cryptic Y chromosome material (20.0%). The risk of developing gonadoblastoma in patients with cryptic Y chromosome material was similar to that in patients with overt Y chromosome. Therefore, molecular screening for Y chromosome material should be recommended for all patients with Turner syndrome to detect individuals at a high risk of gonadoblastoma and to facilitate proper management of the disease.

  9. Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida

    Directory of Open Access Journals (Sweden)

    Maria J. Uriz

    2017-03-01

    Full Text Available Background Sponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale. Methods Hemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from the Red Sea and Pacific. From two to three specimens per species and locality were extracted, amplified for Cytochrome C Oxidase I (COI (M1–M6 partition, 18S rRNA, and 28S (D3–D5 partition and sequenced. Sequences were aligned using Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ, Bayesian inference (BI, and maximum likelihood (ML criteria as implemented in Geneious software 9.01. Moreover, spicules of the target species were observed through a Scanning Electron microscope. Results The several phylogenetic reconstructions retrieved both Crella and Hemimycale polyphyletic. Strong differences in COI sequences indicated that C. cyathophora from the Red Sea might belong in a different genus, closer to Hemimycale arabica than to the Atlanto-Mediterranean Crella spp. Molecular and external morphological differences between Hemimycale arabica and the

  10. Detection and effects of harmful algal toxins in Scottish harbour seals and potential links to population decline.

    Science.gov (United States)

    Jensen, Silje-Kristin; Lacaze, Jean-Pierre; Hermann, Guillaume; Kershaw, Joanna; Brownlow, Andrew; Turner, Andrew; Hall, Ailsa

    2015-04-01

    Over the past 15 years or so, several Scottish harbour seal (Phoca vitulina) populations have declined in abundance and several factors have been considered as possible causes, including toxins from harmful algae. Here we explore whether a link could be established between two groups of toxins, domoic acid (DA) and saxitoxins (STXs), and the decline in the harbour seal populations in Scotland. We document the first evidence that harbour seals are exposed to both DA and STXs from consuming contaminated fish. Both groups of toxins were found in urine and faeces sampled from live captured (n = 162) and stranded animals (n = 23) and in faecal samples collected from seal haul-out sites (n = 214) between 2008 and 2013. The proportion of positive samples and the toxins levels measured in the excreta were significantly higher in areas where harbour seal abundance is in decline. There is also evidence that DA has immunomodulatory effects in harbour seals, including lymphocytopenia and monocytosis. Scottish harbour seals are exposed to DA and STXs through contaminated prey at potentially lethal levels and with this evidence we suggest that exposure to these toxins are likely to be important factors driving the harbour seal decline in some regions of Scotland. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Macro- and meiofaunal community features in the critical environmental system of a tourist harbour (Rapallo, Ligurian Sea, NW Mediterranean).

    Science.gov (United States)

    Harriague, Anabella Covazzi; Albertelli, Giancarlo; Misic, Cristina

    2012-03-01

    Two samplings were carried out in a tourist harbour, during low and high touristic activity periods, to study the macro- and meiofaunal communities in relation to the environmental features. A multivariate analysis showed close relationships: the maritime traffic disturbance and the food quality and availability drive the spatial differences of the assemblages, dividing the area into three sub-areas: the area near the Boate torrent that empties into the harbour, the harbour proper, and the external area (just outside the harbour). Macro- and meiofauna showed notably different temporal trends, indicating competition for the resources and the higher sensitivity of the macrofauna to environmental pressures. The macrofauna strongly decreased as a response to heavier harbour activities, with increasing turbidity also affecting the external station outside the harbour. Finally, comparing the macrofaunal communities to those sampled in the same area 10 years before, we found that their abundance, richness and biomass had notably decreased, highlighting the worsening of the harbour environment due to the increased organic load and turbidity. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species

    DEFF Research Database (Denmark)

    Razgour, Orly; Clare, Elizabeth L.; Zeale, Matt R. K.

    2011-01-01

    Sympatric cryptic species, characterized by low morphological differentiation, pose a challenge to understanding the role of interspecific competition in structuring ecological communities. We used traditional (morphological) and novel molecular methods of diet analysis to study the diet of two...... of the cryptic bats, 60% of which were assigned to a likely species or genus. The findings from the molecular study supported the results of microscopic analyses in showing that the diets of both species were dominated by lepidopterans. However, HTS provided a sufficiently high resolution of prey identification...

  13. A novel widespread cryptic species and phylogeographic patterns within several giant clam species (Cardiidae: Tridacna) from the Indo-Pacific Ocean.

    Science.gov (United States)

    Huelsken, Thomas; Keyse, Jude; Liggins, Libby; Penny, Shane; Treml, Eric A; Riginos, Cynthia

    2013-01-01

    Giant clams (genus Tridacna) are iconic coral reef animals of the Indian and Pacific Oceans, easily recognizable by their massive shells and vibrantly colored mantle tissue. Most Tridacna species are listed by CITES and the IUCN Redlist, as their populations have been extensively harvested and depleted in many regions. Here, we survey Tridacna crocea and Tridacna maxima from the eastern Indian and western Pacific Oceans for mitochondrial (COI and 16S) and nuclear (ITS) sequence variation and consolidate these data with previous published results using phylogenetic analyses. We find deep intraspecific differentiation within both T. crocea and T. maxima. In T. crocea we describe a previously undocumented phylogeographic division to the east of Cenderawasih Bay (northwest New Guinea), whereas for T. maxima the previously described, distinctive lineage of Cenderawasih Bay can be seen to also typify western Pacific populations. Furthermore, we find an undescribed, monophyletic group that is evolutionarily distinct from named Tridacna species at both mitochondrial and nuclear loci. This cryptic taxon is geographically widespread with a range extent that minimally includes much of the central Indo-Pacific region. Our results reinforce the emerging paradigm that cryptic species are common among marine invertebrates, even for conspicuous and culturally significant taxa. Additionally, our results add to identified locations of genetic differentiation across the central Indo-Pacific and highlight how phylogeographic patterns may differ even between closely related and co-distributed species.

  14. A novel widespread cryptic species and phylogeographic patterns within several giant clam species (Cardiidae: Tridacna from the Indo-Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Thomas Huelsken

    Full Text Available Giant clams (genus Tridacna are iconic coral reef animals of the Indian and Pacific Oceans, easily recognizable by their massive shells and vibrantly colored mantle tissue. Most Tridacna species are listed by CITES and the IUCN Redlist, as their populations have been extensively harvested and depleted in many regions. Here, we survey Tridacna crocea and Tridacna maxima from the eastern Indian and western Pacific Oceans for mitochondrial (COI and 16S and nuclear (ITS sequence variation and consolidate these data with previous published results using phylogenetic analyses. We find deep intraspecific differentiation within both T. crocea and T. maxima. In T. crocea we describe a previously undocumented phylogeographic division to the east of Cenderawasih Bay (northwest New Guinea, whereas for T. maxima the previously described, distinctive lineage of Cenderawasih Bay can be seen to also typify western Pacific populations. Furthermore, we find an undescribed, monophyletic group that is evolutionarily distinct from named Tridacna species at both mitochondrial and nuclear loci. This cryptic taxon is geographically widespread with a range extent that minimally includes much of the central Indo-Pacific region. Our results reinforce the emerging paradigm that cryptic species are common among marine invertebrates, even for conspicuous and culturally significant taxa. Additionally, our results add to identified locations of genetic differentiation across the central Indo-Pacific and highlight how phylogeographic patterns may differ even between closely related and co-distributed species.

  15. The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex.

    Science.gov (United States)

    Gribble, Kristin E; Mark Welch, David B

    2012-08-01

    Chemically mediated prezygotic barriers to reproduction likely play an important role in speciation. In facultatively sexual monogonont rotifers from the Brachionus plicatilis cryptic species complex, mate recognition of females by males is mediated by the Mate Recognition Protein (MRP), a globular glycoprotein on the surface of females, encoded by the mmr-b gene family. In this study, we sequenced mmr-b copies from 27 isolates representing 11 phylotypes of the B. plicatilis species complex, examined the mode of evolution and selection of mmr-b, and determined the relationship between mmr-b genetic distance and mate recognition among isolates. Isolates of the B. plicatilis species complex have 1-4 copies of mmr-b, each composed of 2-9 nearly identical tandem repeats. The repeats within a gene copy are generally more similar than are gene copies among phylotypes, suggesting concerted evolution. Compared to housekeeping genes from the same isolates, mmr-b has accumulated only half as many synonymous differences but twice as many non-synonymous differences. Most of the amino acid differences between repeats appear to occur on the outer face of the protein, and these often result in changes in predicted patterns of phosphorylation. However, we found no evidence of positive selection driving these differences. Isolates with the most divergent copies were unable to mate with other isolates and rarely self-crossed. Overall the degree of mate recognition was significantly correlated with the genetic distance of mmr-b. Discrimination of compatible mates in the B. plicatilis species complex is determined by proteins encoded by closely related copies of a single gene, mmr-b. While concerted evolution of the tandem repeats in mmr-b may function to maintain identity, it can also lead to the rapid spread of a mutation through all copies in the genome and thus to reproductive isolation. The mmr-b gene is evolving rapidly, and novel alleles may be maintained and increase in

  16. The mate recognition protein gene mediates reproductive isolation and speciation in the Brachionus plicatilis cryptic species complex

    Directory of Open Access Journals (Sweden)

    Gribble Kristin E

    2012-08-01

    Full Text Available Abstract Background Chemically mediated prezygotic barriers to reproduction likely play an important role in speciation. In facultatively sexual monogonont rotifers from the Brachionus plicatilis cryptic species complex, mate recognition of females by males is mediated by the Mate Recognition Protein (MRP, a globular glycoprotein on the surface of females, encoded by the mmr-b gene family. In this study, we sequenced mmr-b copies from 27 isolates representing 11 phylotypes of the B. plicatilis species complex, examined the mode of evolution and selection of mmr-b, and determined the relationship between mmr-b genetic distance and mate recognition among isolates. Results Isolates of the B. plicatilis species complex have 1–4 copies of mmr-b, each composed of 2–9 nearly identical tandem repeats. The repeats within a gene copy are generally more similar than are gene copies among phylotypes, suggesting concerted evolution. Compared to housekeeping genes from the same isolates, mmr-b has accumulated only half as many synonymous differences but twice as many non-synonymous differences. Most of the amino acid differences between repeats appear to occur on the outer face of the protein, and these often result in changes in predicted patterns of phosphorylation. However, we found no evidence of positive selection driving these differences. Isolates with the most divergent copies were unable to mate with other isolates and rarely self-crossed. Overall the degree of mate recognition was significantly correlated with the genetic distance of mmr-b. Conclusions Discrimination of compatible mates in the B. plicatilis species complex is determined by proteins encoded by closely related copies of a single gene, mmr-b. While concerted evolution of the tandem repeats in mmr-b may function to maintain identity, it can also lead to the rapid spread of a mutation through all copies in the genome and thus to reproductive isolation. The mmr-b gene is evolving

  17. Management of fisheries in harbour porpoise (Phocoena phocoena) marine protected areas

    DEFF Research Database (Denmark)

    Kindt-Larsen, Lotte

    , Member States are obliged to nominate candidate protected areas in their waters to the EU Commission and within six years establish legislation to implement them as special areas of conservation and prepare management plans. Up to this point in time, however, no such management plans exist. This Ph...... thus be used as a tool to identify areas of porpoise bycatch risk and thereby support the management of both fisheries and harbour porpoises in accordance with the Habitats Directive. Thirdly, the behaviour of porpoises in relation to two different pinger types with different acoustic properties.......D. thesis focuses on research methods and management tools, which can contribute to a better scientific understanding in the preparation of fisheries management plans for Natura2000 sites designated for harbour porpoises. Firstly, it investigates the potential use of CCTV cameras to document bycatch...

  18. From echolocation clicks to animal density – acoustic sampling of harbour porpoises with static dataloggers

    DEFF Research Database (Denmark)

    Kyhn, Line Anker; Tougaard, Jakob; Thomas, L.

    2012-01-01

    Monitoring abundance and population trends of small odontocetes is notoriously difficult and labour intensive. There is a need to develop alternative methods to the traditional visual line transect surveys, especially for low density areas. Here, the prospect of obtaining robust density estimates....... This provides a method suitable for monitoring in areas with densities too low for visual surveys to be practically feasible, e.g. the endangered harbour porpoise population in the Baltic....... for porpoises by passive acoustic monitoring (PAM) is demonstrated by combining rigorous application of methods adapted from distance sampling to PAM. Acoustic dataloggers (T-PODs) were deployed in an area where harbour porpoises concurrently were tracked visually. Probability of detection was estimated...

  19. Screening of variable importance for optimizing electrodialytic remediation of heavy metals from polluted harbour sediments

    DEFF Research Database (Denmark)

    Pedersen, Kristine B.; Lejon, Tore; Ottosen, Lisbeth M.

    2015-01-01

    Using multivariate design and modelling, the optimal conditions for electrodialytic remediation (EDR) of heavy metals were determined for polluted harbour sediments from Hammerfest harbour located in the geographic Arctic region of Norway. The comparative importance of the variables, current......) was computed and variable importance in the projection was used to assess the influence of the experimental variables. Current density and remediation time proved to have the highest influence on the remediation of the heavy metals Cr, Cu, Ni, Pb and Zn in the studied experimental domain. In addition......, it was shown that excluding the acidification time improved the PLS model, indicating the importance of applying a limited experimental domain that covers the removal phases of each heavy metal in the specific sediment. Based on PLS modelling, the optimal conditions for remediating the Hammerfest sediment were...

  20. An empirically tractable model of optimal oil spills prevention in Russian sea harbours

    Energy Technology Data Exchange (ETDEWEB)

    Deissenberg, C. [CEFI-CNRS, Les Milles (France); Gurman, V.; Tsirlin, A. [RAS, Program Systems Inst., Pereslavl-Zalessky (Russian Federation); Ryumina, E. [Russian Academy of Sciences, Moscow (Russian Federation). Inst. of Economic Market Problems

    2001-07-01

    Based on previous theoretical work by Gottinger (1997, 1998), we propose a simple model of optimal monitoring of oil-related activities in harbour areas that is suitable for empirical estimation within the Russian-Ukrainian context, in spite of the poor availability of data in these countries. Specifically, the model indicates how to best allocate at the steady state a given monitoring budget between different monitoring activities. An approximate analytical solution to the optimization problem is derived, and a simple procedure for estimating the model on the basis of the actually available data is suggested. An application using data obtained for several harbours of the Black and Baltic Seas is given. It suggests that the current Russian monitoring practice could be much improved by better allocating the available monitoring resources. (Author)

  1. Environmental Risk Assessment of dredging processes – application to Marin harbour (NW Spain)

    OpenAIRE

    A. G. Gómez; J. García Alba; A. Puente; J. A. Juanes

    2014-01-01

    ABSTRACT. A methodological procedure to estimate the environmental risk of dredging operations in aquatic systems has been developed. Environmental risk estimations are based on numerical models results, which provide an appropriated spatio-temporal framework analysis to guarantee an effective decision-making process. The methodological procedure has been applied on a real dredging operation in the port of Marin (NW Spain). Results from Marin harbour confirmed the suitabi...

  2. Environmental Risk Assessment of dredging processes - application to Marin harbour (NW Spain)

    Science.gov (United States)

    Gómez, A. G.; García Alba, J.; Puente, A.; Juanes, J. A.

    2014-04-01

    A methodological procedure to estimate the environmental risk of dredging operations in aquatic systems has been developed. Environmental risk estimations are based on numerical models results, which provide an appropriated spatio-temporal framework analysis to guarantee an effective decision-making process. The methodological procedure has been applied on a real dredging operation in the port of Marin (NW Spain). Results from Marin harbour confirmed the suitability of the developed methodology and the conceptual approaches as a comprehensive and practical management tool.

  3. Effects of granulometric gradient on macrofaunal assemblages in Los Cristianos harbour (Tenerife, Canary Islands)

    OpenAIRE

    Riera, Rodrigo; Monterroso, Óscar; Núñez, Jorge

    2012-01-01

    Along the rapid increase of coastal tourism worldwide, evidence is accumulating on the numerous environmental coastal impacts that it causes on marine environments. One of the most important anthropogenic pressures is the construction of marinas or recreational harbours. Typically, most of the studies provide snapshots of the spatial distribution of macrobenthic communities inside and outside of the marina area. However, there is no much information about sedimentary dynamics inside the harbo...

  4. Patterns of Occurrence of Sharks in Sydney Harbour, a Large Urbanised Estuary.

    Science.gov (United States)

    Smoothey, Amy F; Gray, Charles A; Kennelly, Steve J; Masens, Oliver J; Peddemors, Victor M; Robinson, Wayne A

    2016-01-01

    Information about spatial and temporal variability in the distribution and abundance of shark-populations are required for their conservation, management and to update measures designed to mitigate human-shark interactions. However, because some species of sharks are mobile, migratory and occur in relatively small numbers, estimating their patterns of distribution and abundance can be very difficult. In this study, we used a hierarchical sampling design to examine differences in the composition of species, size- and sex-structures of sharks sampled with bottom-set longlines in three different areas with increasing distance from the entrance of Sydney Harbour, a large urbanised estuary. During two years of sampling, we obtained data for four species of sharks (Port Jackson, Heterodontus portusjacksoni; wobbegong, Orectolobus maculatus; dusky whaler, Carcharhinus obscurus and bull shark, Carcharhinus leucas). Only a few O. maculatus and C. obscurus were caught, all in the area closest to the entrance of the Harbour. O. maculatus were caught in all seasons, except summer, while C. obscurus was only caught in summer. Heterodontus portusjacksoni were the most abundant species, caught in the entrance location mostly between July to November, when water temperature was below 21.5°C. This pattern was consistent across both years. C. leucas, the second most abundant species, were captured in all areas of Sydney Harbour but only in summer and autumn when water temperatures were above 23°C. This study quantified, for this first time, how different species utilise different areas of Sydney Harbour, at different times of the year. This information has implications for the management of human-shark interactions, by enabling creation of education programs to modify human behaviour in times of increased risk of potentially dangerous sharks.

  5. Review on utilization and research on harbour seal (Phoca vitulina in Iceland

    Directory of Open Access Journals (Sweden)

    Erlingur Hauksson

    2010-09-01

    Full Text Available Harbour seals (Phoca vitulina have been harvested in Iceland since the first settlers arrived in the 9th century. Pups were generally netted, clubbed and harpooned until 1875 when general use of guns for hunting began. Seal-hunting has been traditional amongst the farms legal rights. Seal hunting was an important supplement to other economic resources. Harbour seal skins, salted ordried, were exported and large dataset of catch statistics is available from trading logbooks since the late 19th century. In the early 20th century catch was about 6,000. In the ‘bounty’ period 1982 – 1989, maximum catches were of 4,000 animals with about 350 hunters participated; in 2006 catches were only about 100 animals with 18 hunters. After 1989 the population continued to decline even though catches decreased markedly. Unreported by-catch in fishing gear, hunt for local consumption and shooting of seals swimming in salmon rivers estuaries may have kept the total removal from the stock above sustainable levels. A considerable Icelandic knowledge base had been compiled about the biology of the harbour seal since the late 16th century, with the first written reference in 1588-1589. In the last decades, research on various aspects of its biology and monitoring have been intensified, with focus on abundance, distribution, diet and nematode infestation. The main results show that the Icelandic harbour seal population - has declined annually about 5% in the period 1980-2006, - was most abundant on the NW-coast, - feeds mainly on sand-eels and gadoids, - and was less infected with anisakid nematodes than grey seals. Seal watching, as a low-consumptive indirect utilization, may represent a new economical opportunity if properly regulated.

  6. A system shift in tidal choking due to the construction of Yangshan Harbour, Shanghai, China

    Science.gov (United States)

    Guo, Wenyun; Wang, Xiao Hua; Ding, Pingxing; Ge, Jianzhong; Song, Dehai

    2018-06-01

    Tidal choking is a geometric feature caused by a narrowed channel. Construction of the Yangshan Harbour, Shanghai, China obstructed three key channels and intensively changed the local geometry and topography. In this study nine numerical experiments based on the Finite-Volume Community Ocean Model are conducted to study the project's influence on tidal characteristics. Results show that stronger tidal choking happened at the East Entrance after project, mainly due to the jet induced water-level drop forced by Bernoulli law and the longer and narrower geometry. The stronger tidal choking forces a faster flow and larger tidal energy flux at the choked channel while reducing the tidal amplitude in the Inner Harbour Area (IHA). The scouring on this channel reduces the choking effect but further enlarges tidal energy flux. Moreover, damming the channels decrease the tidal amplitude at the lee side of tidal propagating direction while increasing the amplitude on the stoss side. The dams also decrease the tidal current on both sides, and meanwhile develop two patches with stronger current aside the dam. The project induced changes in tidal characteristics are complex in space, and perturbations in bathymetry increase this complexity. Yangshan Harbour's construction induces little changes in the total tidal energy density in the IHA, but induces obvious changes in the spatial distribution of tidal energy. Although this study is site-specific, the findings may be applicable to tidal dynamics in land reclamation close to open seas, such as the dramatic reclamation of islands in the South China Sea.

  7. Rapid reassessment of the eutrophication status of Kingston Harbour, Jamaica using the zooplankton community

    Directory of Open Access Journals (Sweden)

    Patrice A. Francis

    2014-09-01

    Full Text Available Previous extensive studies of zooplankton distribution in the eutrophic Kingston Harbour established that it was being continuously contaminated. We assessed the community in 2011, 17 years after a previous study and five years after the introduction of a tertiary waste water system. Sampling was conducted for four weeks at eight stations identical to those sampled in a previous study. We used horizontal surface tows with a 200µm net. A total of 73 zooplankton taxa were identified and copepods dominated with 20 species. Mean total abundances were high, ranging from a minimum of 2 383 animals m-3 in the southern region of Hunts Bay to 194 166 animals m-3at the Inner Harbour. Five zooplankton taxa (Acartia tonsa, Paracalanus spp., Temora turbinata, Penilia avirostris and Lucifer faxoni that were previously identified as indicators, were again important in the Harbour. The overall zooplankton abundances were similar and in some cases higher than the previous study. There was no significant improvement in the water quality since the introduction of the treatment system at Soapberry. This may be a result of unknown nutrient inputs or of nutrient remaining in the sediments.

  8. The effect of wind turbines on the bird population at Blyth Harbour

    International Nuclear Information System (INIS)

    Still, D.; Little, B.; Lawrence, S.

    1996-01-01

    Bird monitoring was carried out at Blyth Harbour Wind Farm which consists of a line of nine 300kW wind turbines distributed at 200m intervals along a 1.2km breakwater. The harbour breakwater is designated as part of a Site of Special Scientific Interest as it supports an internationally important winter population of Purple Sandpipers. The Blyth estuary is to be designated as part of a Special Protection Area under the EC Habitats Directive and as part of a proposed RAMSAR site due to its peak periods up to c.5000 bird movements/day occur adjacent to the windfarm. Mortality surveys (at one week intervals) were carried out on adjacent beaches to the wind farm in order to assess the background numbers of bird corpses and locate wind farm casualties. Supplementary mortality searches were carried out near power lines less than 2.5 km upstream from the wind farm. Tests of the efficiency of the mortality surveys have been carried out in order to assess the likely impact on the local bird populations. In spite of the large bird population supported by the harbour and its close proximity to the wind farm there have been relatively few collision victims (31) since the windfarm was commissioned. This is equivalent to less than 1.34 bird strike/wind turbine per annum. (author)

  9. Removal of Historic Low-Level Radioactive Sediment from the Port Hope Harbour - 13314

    Energy Technology Data Exchange (ETDEWEB)

    Kolberg, Mark [Baird and Associates, 1267 Cornwall Rd., Suite 100, Oakville ON, L6J7T5 (Canada); Case, Glenn [Atomic Energy of Canada Limited, Port Hope, ON (Canada); Ferguson Jones, Andrea [MMM Group Limited, Thornhill, ON (Canada)

    2013-07-01

    At the Port Hope Harbour, located on the north shore of Lake Ontario, the presence of low-level radioactive sediment, resulting from a former radium and uranium refinery that operated alongside the Harbour, currently limits redevelopment and revitalization opportunities. These waste materials contain radium-226, uranium, arsenic and other contaminants. Several other on-land locations within the community of Port Hope are also affected by the low-level radioactive waste management practices of the past. The Port Hope Project is a community initiated undertaking that will result in the consolidation of an estimated 1.2 million cubic metres of the low-level radioactive waste from the various sites in Port Hope into a new engineered above ground long-term waste management facility. The remediation of the estimated 120,000 m{sup 3} of contaminated sediments from the Port Hope Harbour is one of the more challenging components of the Port Hope Project. Following a thorough review of various options, the proposed method of contaminated sediment removal is by dredging. The sediment from the dredge will then be pumped as a sediment-water slurry mixture into geo-synthetic containment tubes for dewatering. Due to the hard substrate below the contaminated sediment, the challenge has been to set performance standards in terms of low residual surface concentrations that are attainable in an operationally efficient manner. (authors)

  10. Removal of Historic Low-Level Radioactive Sediment from the Port Hope Harbour - 13314

    International Nuclear Information System (INIS)

    Kolberg, Mark; Case, Glenn; Ferguson Jones, Andrea

    2013-01-01

    At the Port Hope Harbour, located on the north shore of Lake Ontario, the presence of low-level radioactive sediment, resulting from a former radium and uranium refinery that operated alongside the Harbour, currently limits redevelopment and revitalization opportunities. These waste materials contain radium-226, uranium, arsenic and other contaminants. Several other on-land locations within the community of Port Hope are also affected by the low-level radioactive waste management practices of the past. The Port Hope Project is a community initiated undertaking that will result in the consolidation of an estimated 1.2 million cubic metres of the low-level radioactive waste from the various sites in Port Hope into a new engineered above ground long-term waste management facility. The remediation of the estimated 120,000 m 3 of contaminated sediments from the Port Hope Harbour is one of the more challenging components of the Port Hope Project. Following a thorough review of various options, the proposed method of contaminated sediment removal is by dredging. The sediment from the dredge will then be pumped as a sediment-water slurry mixture into geo-synthetic containment tubes for dewatering. Due to the hard substrate below the contaminated sediment, the challenge has been to set performance standards in terms of low residual surface concentrations that are attainable in an operationally efficient manner. (authors)

  11. Conservation genetics and genomics of amphibians and reptiles.

    Science.gov (United States)

    Shaffer, H Bradley; Gidiş, Müge; McCartney-Melstad, Evan; Neal, Kevin M; Oyamaguchi, Hilton M; Tellez, Marisa; Toffelmier, Erin M

    2015-01-01

    Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.

  12. Predation cues rather than resource availability promote cryptic behaviour in a habitat-forming sea urchin.

    Science.gov (United States)

    Spyksma, Arie J P; Taylor, Richard B; Shears, Nick T

    2017-03-01

    It is well known that predators often influence the foraging behaviour of prey through the so-called "fear effect". However, it is also possible that predators could change prey behaviour indirectly by altering the prey's food supply through a trophic cascade. The predator-sea urchin-kelp trophic cascade is widely assumed to be driven by the removal of sea urchins by predators, but changes in sea urchin behaviour in response to predators or increased food availability could also play an important role. We tested whether increased crevice occupancy by herbivorous sea urchins in the presence of abundant predatory fishes and lobsters is a response to the increased risk of predation, or an indirect response to higher kelp abundances. Inside two New Zealand marine reserves with abundant predators and kelp, individuals of the sea urchin Evechinus chloroticus were rarer and remained cryptic (i.e. found in crevices) to larger sizes than on adjacent fished coasts where predators and kelp are rare. In a mesocosm experiment, cryptic behaviour was induced by simulated predation (the addition of crushed conspecifics), but the addition of food in the form of drift kelp did not induce cryptic behaviour. These findings demonstrate that the 'fear' of predators is more important than food availability in promoting sea urchin cryptic behaviour and suggest that both density- and behaviourally mediated interactions are important in the predator-sea urchin-kelp trophic cascade.

  13. ACTIVATION OF A CRYPTIC D-SERINE DEAMINASE (DSD) GENE FROM PSEUDOMONAS CEPACIA 17616

    Science.gov (United States)

    D-serine inhibits growth of P. cepacia 17616; however, resistant mutants able to express an ordinarily cryptic D-serine deaminase (dsd) gene were isolated readily. The resistant strains formed high levels of a D-serine deaminase active on D-threonine as well as D-serine. IS eleme...

  14. CHARACTERIZATION OF SINGLE-STRAND ORIGINS OF CRYPTIC ROLLING-CIRCLE PLASMIDS FROM BACILLUS-SUBTILIS

    NARCIS (Netherlands)

    MEIJER, WJJ; VENEMA, G; BRON, S

    1995-01-01

    In this paper we describe the isolation and characterization of single strand origins (SSOs) of several cryptic Bacillus subtilis plasmids which use the rolling-circle mechanism of replication, The plasmids used in this study involved pTA1015, pTA1020, pTA1030, pTA1040, pTA1050 and pTA1060, The SSO

  15. Reflections on fourteen cryptic issues concerning the nature of statistical inference

    NARCIS (Netherlands)

    Kardaun, O.J.W.F.; Salomé, D.; Schaafsma, W; Steerneman, A.G.M.; Willems, J.C; Cox, D.R.

    The present paper provides the original formulation and a joint response of a group of statistically trained scientists to fourteen cryptic issues for discussion, which were handed out to the public by Professor Dr. D.R. Cox after his Bernoulli Lecture 1997 at Groningen University.

  16. Mitochondrial phylogeny of grey mullets (Acanthopterygii: Mugilidae) suggests high proportion of cryptic species.

    Science.gov (United States)

    Durand, Jean-Dominique; Borsa, Philippe

    2015-04-01

    The low level of morphometric variability and the poor phylogenetic information borne by the morpho-anatomical characters used thus far in the systematics of grey mullets (Mugilidae) emphasize the utility of molecular systematics in this family. A recent mitochondrial phylogeny of grey mullets has uncovered multiple deep lineages within several species, flagging putative cryptic species. Here, we considered that several of the deeply divergent lineages represent separate species based on either the tree topology, independent data from nuclear markers, geographic distributions, or a combination of the foregoing. By analogy with these well-documented cases, we considered other deep lineages in seven genera we focused on to represent putative cryptic species. Up to two cryptic species were thus potentially detected in the genus Chelon, three in Crenimugil (including two within the single Crenimugil seheli), two in Dajaus, one in Ellochelon, 16 in Mugil (including 13 within the single M. cephalus), two in Osteomugil, and 10 in Planiliza. Wherever possible, we kept the current species epithets to designate those lineages that unambiguously correspond to the type material, based on type locality, and we assigned arbitrary letters (sp. A, B, etc.) to the other lineages. We present a molecular diagnosis for 24 of the species analysed in this work, as well as for 25 putative cryptic species. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  17. Cryptic species of sharp-nosed reed frogs in the Hyperolius nasutus ...

    African Journals Online (AJOL)

    The sharp-nosed reed frog is widespread in Africa. Although currently recognized as one species, suggestions have been made that more than one species might exist. We analysed 237 calls of 69 males from 19 localities in the western to southern parts of Africa. Calls fall into three groups, which we recognize as cryptic ...

  18. Molecular evidence of cryptic speciation in the "cosmopolitan" excavating sponge Cliona celata (Porifera, Clionaidae)

    NARCIS (Netherlands)

    Xavier, J.R.; Rachello-Dolmen, P.G.; Parra-Velandia, F.; Schönberg, C.H.L.; Breeuwer, J.A.J.; van Soest, R.W.M.

    2010-01-01

    Over the past several decades molecular tools have shown an enormous potential to aid in the clarification of species boundaries in the marine realm, particularly in morphologically simple groups. In this paper we report a case of cryptic speciation in an allegedly cosmopolitan and ecologically

  19. Cryptic species Anopheles daciae (Diptera: Culicidae) found in the Czech Republic and Slovakia

    Czech Academy of Sciences Publication Activity Database

    Blažejová, Hana; Šebesta, Oldřich; Rettich, F.; Mendel, Jan; Čabanová, V.; Miterpáková, M.; Betášová, Lenka; Peško, Juraj; Hubálek, Zdeněk; Kampen, H.; Rudolf, Ivo

    2018-01-01

    Roč. 117, č. 1 (2018), s. 315-321 ISSN 0932-0113 R&D Projects: GA ČR(CZ) GA16-20054S Institutional support: RVO:68081766 Keywords : Anophelinae * Maculipennis complex * Anopheles daciae * Mosquitoes * Cryptic species * Vector-borne diseases Subject RIV: EG - Zoology Impact factor: 2.329, year: 2016

  20. Molecules and morphology reveal cryptic variation among digeneans infecting sympatric mullets in the Mediterranean

    Czech Academy of Sciences Publication Activity Database

    Blasco-Costa, I.; Balbuena, J. A.; Raga, J. A.; Kostadinova, Aneta; Olson, P. D.

    2010-01-01

    Roč. 137, č. 2 (2010), s. 287-302 ISSN 0031-1820 R&D Projects: GA MŠk LC522 Institutional research plan: CEZ:AV0Z60220518 Keywords : Digenea * Haploporidae * Saccocoelium * Mugilidae * cryptic species * molecules * morphology * rDNA Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 2.522, year: 2010

  1. Field identification of the cryptic vespertilionid bats, Myotis lucifugus and M. yumanensis

    Science.gov (United States)

    Theodore J. Weller; Shonene A. Scott; Thomas J. Rodhouse; Patricia C. Ormsbee; Jan M. Zinck

    2007-01-01

    Recent advances in molecular techniques have provided new tools for confirming species identities, however they can be expensive and results are not immediately available. Myotis lucificugus and M. yumanensis are morphologically cryptic species of bats sympatric in western North America that can be difficult to distinguish in the...

  2. Cyanomargarita gen. nov. (Nostocales, Cyanobacteria): convergent evolution resulting in a cryptic genus

    Czech Academy of Sciences Publication Activity Database

    Shalygin, S.; Shalygina, R.; Johansen, J. R.; Pietrasiak, N.; Gómez, E. B.; Bohunická, M.; Mareš, Jan; Sheil, C.A.

    2017-01-01

    Roč. 53, č. 4 (2017), s. 762-777 ISSN 0022-3646 Institutional support: RVO:60077344 Keywords : 16S rRNA gene phylogeny * 16S-23S ITS * cryptic genus * Cyanobacteria * Cyanomargarita Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 2.608, year: 2016

  3. Cyanomargarita gen. nov. (Nostocales, Cyanobacteria): convergent evolution resulting in a cryptic genus

    Czech Academy of Sciences Publication Activity Database

    Shalygin, S.; Shalygina, R.; Johansen, J. R.; Pietrasiak, N.; Gómez, E. B.; Bohunická, Markéta; Mareš, Jan; Sheil, C.A.

    2017-01-01

    Roč. 53, č. 4 (2017), s. 762-777 ISSN 0022-3646 R&D Projects: GA ČR(CZ) GA15-11912S Institutional support: RVO:67985939 Keywords : 16S rRNA gene * cryptic genus * Cyanomargarita Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 2.608, year: 2016

  4. Movement of foraging Tundra Swans explained by spatial pattern in cryptic food densities

    NARCIS (Netherlands)

    Klaassen, R.H.G.; Nolet, B.A.; Bankert, D.

    2006-01-01

    We tested whether Tundra Swans use information on the spatial distribution of cryptic food items (belowground Sago pondweed tubers) to shape their movement paths. In a continuous environment, swans create their own food patches by digging craters, which they exploit in several feeding bouts. Series

  5. Allopatric origin of cryptic butterfly species that were discovered feeding on distinct host plants in sympatry.

    NARCIS (Netherlands)

    McBride, L.C.; Velzen, van R.; Larsen, T.B.

    2009-01-01

    Surveys of tropical insects are increasingly uncovering cryptic species ¿ morphologically similar yet reproductively isolated taxa once thought to comprise a single interbreeding entity. The vast majority of such species are described from a single location. This leaves us with little information on

  6. Sporadic diffuse segmental interstitial cell of Cajal hyperplasia harbouring two gastric gastrointestinal stromal tumours (GIST mimicking hereditary GIST syndromes

    Directory of Open Access Journals (Sweden)

    Mafalda Costa Neves

    2015-01-01

    Conclusion: We describe a diffuse form of sporadic ICC hyperplasia harbouring multifocal GISTs, mimicking diffuse ICC hyperplasia in hereditary GIST syndromes. Detection of somatic c-KIT exon 11 mutation ruled out a hereditary disorder.

  7. Impact of water quality changes on harbour environment due to port activities along the west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Shirodkar, P.V.; Pradhan, U.K.; Vethamony, P.

    modeling were used to understand the dominant parameters influencing water quality, trace the sources of contaminants, their impact on harbour environments and their fate. Factor analyses showed the dominance of anthropogenic nutrients, petroleum...

  8. A compact self-recording pressure based sea level gauge suitable for deployments at harbour and offshore environments

    Digital Repository Service at National Institute of Oceanography (India)

    Desa, E.; Peshwe, V.B.; Joseph, A.; Mehra, P.; Naik, G.P.; Kumar, V.; Desa, E.S.; Desai, R.G.P.; Nagvekar, S.; Desai, S.P.

    A compact and lightweight self-recording pressure based sea level gauge has been designed to suit deployments from harbour and offshore environments. A novel hydraulic coupling device designed in-house was used to transfer the seawater pressure...

  9. Variation in PAH inputs and microbial community in surface sediments of Hamilton Harbour: Implications to remediation and monitoring

    International Nuclear Information System (INIS)

    Slater, G.F.; Cowie, B.R.; Harper, N.; Droppo, I.G.

    2008-01-01

    Variations in concentrations of polycyclic aromatic hydrocarbons (PAHs) and microbial community indicators were investigated in representative highly contaminated and less contaminated surface sediment sites of Hamilton Harbour. Inputs of PAH to the upper 3 cm of sediments up to four times the average upper sediment concentrations were observed. Associated PAH fingerprint profiles indicated that the source was consistent with the PAH source to the industrial region of the harbour. Increased PAH loadings were associated with decreased bacterial populations as indicated by phospholipid fatty acid (PLFA) concentrations. However, relatively minor impacts on overall community composition were indicated. Porewater methane concentrations and isotopic data indicated a difference in the occurrence of methane oxidation between the two sites. This study confirms temporally limited transport of contaminants from highly impacted regions as a vector for contaminants within the harbour and the impact on microbial carbon cycling and bed stability. - Variations in PAH inputs to harbour sediments have implications to implementation and monitoring of mitigation/remediation efforts

  10. Targeting a Hidden Enemy: Pyriproxyfen Autodissemination Strategy for the Control of the Container Mosquito Aedes albopictus in Cryptic Habitats.

    Directory of Open Access Journals (Sweden)

    Kshitij Chandel

    2016-12-01

    Full Text Available The Asian tiger mosquito, Aedes albopictus, is a vector of dengue, Chikungunya, and Zika viruses. This mosquito inhabits a wide range of artificial water-holding containers in urban and suburban areas making it difficult to control. We tested the hypothesis that female-driven autodissemination of an insect growth regulator could penetrate cryptic oviposition habitats difficult to treat with conventional insecticidal sprays.Oviposition preferences of Ae. albopictus females for open and cryptic cups were tested in semi-field experiments. Two conventional larvicidal sprayers were tested to determine droplet penetration and larvicidal efficacy in open and cryptic habitats using Bacillus thuringiensis var. israelensis (Bti in the field. Finally, the efficacy of pyriproxyfen autodissemination stations was assessed in cryptic and open cups in residential areas during 2013 and 2014.Gravid females strongly preferred cryptic (53.1±12.9 eggs/cup over open (10.3±4.3 eggs/cup cups for oviposition. Cryptic cups showed limited droplet penetration and produced 0.1-0.3% larval mortality with a conventional backpack and low-volume sprays of Bti. The autodissemination stations effectively contaminated these cryptic cups (59.3-84.6% and produced 29.7-40.8% pupal mortality during 2013-2014. Significant pupal mortality was also observed in open cups.The autodissemination station effectively exploits the oviposition behavior of wild gravid females to deliver pyriproxyfen to targeted oviposition habitats. Although the pupal mortality in cryptic cups was relatively lower than expected for the effective vector control. Autodissemination approach may be a suitable supporting tool to manage Ae. albopictus immatures in the cryptic habitats those are less accessible to conventional larvicidal sprays.

  11. Effects of waves and currents on the siltation problem of Damietta harbour, Nile Delta coast, Egypt

    Directory of Open Access Journals (Sweden)

    ABO BAKER.I. ABO ZED

    2007-12-01

    Full Text Available This study evaluates the effect of prevailing dynamic factors on the sedimentation process in Damietta Harbour along the Nile delta coast of Egypt. The monitoring program spanned the period between 1978 and 1999 and included measurements of waves, currents and bathymetric profiles. The evaluation was based on determination of erosion and accretion rates, current regime, sediment transport, wave characteristics and wave refraction. Results revealed that the predominant wave direction from N-NW sector (86 % throughout the year is responsible for generation of a longshore eastward current. Less frequent waves from the N-NE sector generate an opposing longshore westward current. The refraction pattern for the prevailing wave direction indicates that the harbour and its navigation channel are located within a divergence of wave orthogonal and in an accretion sediment sink area. The annual net rate of littoral drift on the western side of the harbour is about 1.43 * 105 m3 (accretion, while the annual net rate of littoral drift on the eastern side is about 2.54 * 105 m3 (erosion. Currents fluctuate tremendously in speed and direction, especially during the winter months. Hence, sediment transport takes place in offshore, eastward, and onshore directions. Progressive vector diagrams show that the largest near bottom offshore, onshore and easterly net drift occurs during summer, spring and winter respectively. The onshore sediment transport generated during spring and summer plays an important role in the redistribution of eroded sediments during the winter. The overall study of dynamic factors indicated that the harbour site is characterized by eastern, western, offshore and onshore sediment movements. Therefore, the north-south orientation of the navigation channel, with its depth greater than the surrounding area, interrupts sediment drift from different directions and reduces the current speed. Consequently, the sediments sink within the navigation

  12. Cryptic species as a window into the paradigm shift of the species concept.

    Science.gov (United States)

    Fišer, Cene; Robinson, Christopher T; Malard, Florian

    2018-02-01

    The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty. © 2018 John Wiley & Sons Ltd.

  13. The effect of Kingston Harbour outflow on the zooplankton populations of Hellshire, south-east coast, Jamaica

    Science.gov (United States)

    Lindo, Mona K.

    1991-06-01

    Zooplankton sampling was conducted at 16 stations located at the mouth of Kingston Harbour and throughout the Hellshire area from November 1985 to March 1987. Parameters examined included total biomass, total numbers and numbers of numerically important zooplankton species. Maximum values were recorded west of the Harbour mouth (station 1) and these gradually decreased with distance from the Harbour especially at the 'offshore' stations, producing a gradient effect in this area. Mean biomass and abundance for the period sampled ranged from 14 g m -3 and 16 313 individuals m -3 at the western side of the Harbour mouth to 0·4 g m -3 and 172 individuals m -3 at Wreck Reef. Stations within the bays of Hellshire occasionally had values similar to those recorded at the mouth of Kingston Harbour and here there was less evidence of a gradual decline. Considerable monthly fluctuation occurred in these parameters but there was no discernible seasonal pattern. Copepods dominated the population at most stations and the sergestid Lucifer faxoni also proved an important member at the western Harbour mouth station.

  14. Aerial ULV control of Aedes aegypti with naled (Dibrom) inside simulated rural village and urban cryptic habitats.

    Science.gov (United States)

    Britch, Seth C; Linthicum, Kenneth J; Aldridge, Robert L; Breidenbaugh, Mark S; Latham, Mark D; Connelly, Peter H; Rush, Mattie J E; Remmers, Jennifer L; Kerce, Jerry D; Silcox, Charles A

    2018-01-01

    We conducted aerial fixed wing ultra low volume (ULV) spray trials with naled to investigate penetration of exposed and simulated cryptic habitat within opened buildings, partially sealed buildings, and outdoor locations targeting sentinel adult Aedes aegypti mosquitoes in north central Florida. Mortality was observed in open and closed buildings and outdoors, even in mosquitoes placed in cryptic habitats. Observations on the impact of building type, mosquito exposure method such as placement in cryptic habitat, and spray nozzle size on mosquito mortality are described and analyzed.

  15. Developing a DNA barcode library for perciform fishes in the South China Sea: Species identification, accuracy and cryptic diversity.

    Science.gov (United States)

    Hou, Gang; Chen, Wei-Tao; Lu, Huo-Sheng; Cheng, Fei; Xie, Song-Guang

    2018-01-01

    DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2-parameter (K2P) distances within species, genera and families were 0.31%, 8.71% and 14.52%, respectively. A neighbour-joining (NJ) tree, Bayesian inference (BI) and maximum-likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single-species-representing clusters, respectively. Barcoding gap analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95.2%), with the minimum interspecific distance to the nearest neighbour larger than the maximum intraspecific distance. A group of three Thunnus species (T. albacares, T. obesus and T. tonggol), a pair of Gerres species (G. oyena and G. japonicus), a pair of Istiblennius species (I. edentulous and I. lineatus) and a pair of Uranoscopus species (U. oligolepis and U. kaianus) were observed with low interspecific distances and overlaps between intra- and interspecific genetic distances. Three species (Apogon ellioti, Naucrates ductor and Psenopsis anomala) showed deep intraspecific divergences and generated two lineages each, suggesting the possibility of cryptic species. Our results demonstrated that DNA barcodes are highly reliable for delineating species of Perciformes in the SCS. The DNA barcode library established in this study will shed light on further research on the diversity of Perciformes in the SCS. © 2017 John Wiley & Sons Ltd.

  16. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

    Science.gov (United States)

    Pyron, R. Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H.; Guayasamin, Juan M.

    2016-01-01

    Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history. PMID:27120100

  17. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

    Science.gov (United States)

    Arteaga, Alejandro; Pyron, R Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H; Guayasamin, Juan M

    2016-01-01

    Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

  18. Environmental quality assessment of Grand Harbour (Valletta, Maltese Islands): a case study of a busy harbour in the Central Mediterranean Sea.

    Science.gov (United States)

    Romeo, Teresa; D'Alessandro, Michela; Esposito, Valentina; Scotti, Gianfranco; Berto, Daniela; Formalewicz, Malgorzata; Noventa, Seta; Giuliani, Silvia; Macchia, Simona; Sartori, Davide; Mazzola, Angelo; Andaloro, Franco; Giacobbe, Salvatore; Deidun, Alan; Renzi, Monia

    2015-12-01

    Contamination levels by plastic debris, trace elements and persistent organic pollutants were assessed and related to macrobenthic diversity within soft bottoms of Grand Harbour (Malta, Central Mediterranean). Sediment toxicity was evaluated by ecotoxicological method, deploying Bacteria (Vibrio fischeri), Echinodermata (Paracentrotus lividus) and Crustacea (Corophium orientale). Univariate analysis (Pearson's test) was used to test relationships between biodiversity indices, pollutants and grain size. A multivariate approach (PERMANOVA) was applied to investigate for any significant differences among sampling stations concerning plastic abundances and to test the relationship between infaunal abundances and pollutant concentrations (the BIOENV test). Significant differences in the plastic abundances were found between sampling stations. The lowest value for Shannon-Wiener biodiversity index was associated to the highest sediment pollution level. Multivariate analyses suggest that MBT and TBT were factors that most influenced macrozoobenthic abundance and biodiversity. The bivalve Corbula gibba and the introduced polychaete Monticellina dorsobranchialis were the most abundant found species.

  19. Discovery of cryptic Armillaria solidipes genotypes within the Colorado Plateau

    Science.gov (United States)

    J. W. Hanna; N. B. Klopfenstein; M. -S. Kim; S. M. Ashiglar; A. L. Ross-Davis; G. I. McDonald

    2012-01-01

    Armillaria solidipes (= A. ostoyae) is a root-disease pathogen that causes severe losses in growth and productivity of forest trees throughout the Northern Hemisphere. This species is genetically diverse with variable disease activities across different regions of the world. In North America, A. solidipes in the Colorado Plateau exists in drier habitats and causes more...

  20. Bosaso Harbour

    DEFF Research Database (Denmark)

    Burcharth, H. F.; Toschi, P.B; Turrio, E.

    1991-01-01

    The paper deals with some design and construction aspects related to the new port at Bosaso, which is the terminal of the newly completed road system which connects northern Somalia with Mogadishu in the south. The port and the road project was financed by The Ministry of Foreign Affairs, Funding...

  1. DNA barcoding, ecology and geography of the cryptic species of Aneura pinguis and their relationships with Aneura maxima and Aneura mirabilis (Metzgeriales, Marchantiophyta).

    Science.gov (United States)

    Bączkiewicz, Alina; Szczecińska, Monika; Sawicki, Jakub; Stebel, Adam; Buczkowska, Katarzyna

    2017-01-01

    Aneura pinguis is a thalloid liverwort species with broad geographical distribution. It is composed of cryptic species, however, the number of cryptic species within A. pinguis is not known. Five cpDNA regions (matK, rbcL, rpoC1, trnH-psbA and trnL-trnF) and the entire nuclear ITS region were studied in 130 samples of A. pinguis from different geographical regions. The relationships between the cryptic species of A. pinguis, A. maxima and A. mirabilis were analyzed. All of the examined samples were clustered into 10 clades corresponding to 10 cryptic species of A. pinguis (marked A to J). Aneura mirabilis and A. maxima were nested among different cryptic species of A. pinguis, which indicates that A. pinguis is a paraphyletic taxon. Subgroups were found in cryptic species A, B, C and E. As single barcodes, all tested DNA regions had 100% discriminant power and fulfilled DNA barcode criteria for species identification; however, the only combination detected in all subgroups was trnL-trnF with trnH-psbA or ITS2. The distances between cryptic species were 11- to 35-fold higher than intraspecific distances. In all analyzed DNA regions, the distances between most pairs of cryptic A. pinguis species were higher than between A. maxima and A. mirabilis. All cryptic species of A. pinguis clearly differed in their habitat preferences, which suggests that habitat adaptation could be the main driving force behind cryptic speciation within this taxon.

  2. Nest Construction by a Ground-nesting Bird Represents a Potential Trade-off Between Egg Crypticity and Thermoregulation

    Science.gov (United States)

    Predation selects against conspicuous colors in bird eggs and nests, while thermoregulatory constraints select for nest building behavior that regulates incubation temperatures. We present results that reveal a trade-off between nest crypticity and thermoregulation of eggs base...

  3. Age- and sex-specific mortality patterns in an emerging wildlife epidemic: the phocine distemper in European harbour seals.

    Directory of Open Access Journals (Sweden)

    Tero Härkönen

    Full Text Available Analyses of the dynamics of diseases in wild populations typically assume all individuals to be identical. However, profound effects on the long-term impact on the host population can be expected if the disease has age and sex dependent dynamics. The Phocine Distemper Virus (PDV caused two mass mortalities in European harbour seals in 1988 and in 2002. We show the mortality patterns were highly age specific on both occasions, where young of the year and adult (>4 yrs animals suffered extremely high mortality, and sub-adult seals (1-3 yrs of both sexes experienced low mortality. Consequently, genetic differences cannot have played a main role explaining why some seals survived and some did not in the study region, since parents had higher mortality levels than their progeny. Furthermore, there was a conspicuous absence of animals older than 14 years among the victims in 2002, which strongly indicates that the survivors from the previous disease outbreak in 1988 had acquired and maintained immunity to PDV. These specific mortality patterns imply that contact rates and susceptibility to the disease are strongly age and sex dependent variables, underlining the need for structured epidemic models for wildlife diseases. Detailed data can thus provide crucial information about a number of vital parameters such as functional herd immunity. One of many future challenges in understanding the epidemiology of the PDV and other wildlife diseases is to reveal how immune system responses differ among animals in different stages during their life cycle. The influence of such underlying mechanisms may also explain the limited evidence for abrupt disease thresholds in wild populations.

  4. HLA-G 14-bp Ins/Ins Genotype in Patients Harbouring Helicobacter pylori Infection: A Potential Risk Factor?

    Science.gov (United States)

    Genre, J; Reginaldo, F P Santos; Andrade, J Marco de Leon; Lima, F P; da Camara, A V Coutinho; Donadi, E A; Crispim, J C

    2016-01-01

    H. pylori is a potent pathogen due to its capacity to successfully evade host defence mechanisms. Despite inducing immune responses in infected individuals, sometimes these responses fail to clear the infection and the bacterium establishes a persistent infection leading to chronic inflammation. In this context, we hypothesized that human leucocyte antigen G (HLA-G), a non-classical major histocompatibility complex molecule that has the ability to regulate immune responses both in physiological and in pathological conditions, may play an important role in promoting tolerance and helping H. pylori to subvert host defence and consequently establish a chronic infection. Therefore, we evaluated the expression of HLA-G 14-bp Ins/Del polymorphism in patients harbouring H. pylori infection, as well as their relationship with histological and demographic variables, to gain a better understanding of the actual role of HLA-G and its genetic polymorphisms in bacterial infection. Sixty-eight patients with clinical symptoms suggestive of H. pylori infection were enrolled to assess HLA-G 14-bp Ins/Del polymorphism allele and genotype frequencies. After adjustment for covariates (age and gender), the odds of having the genotype Ins/Ins, compared to Del/Del, were 3.77 times greater among HP+ cases than among controls. These findings suggest that the 14-bp Ins/Ins genotype, already associated with inflammatory and autoimmune diseases as well as some viral and parasitic infections, could confer a greater risk of developing H. pylori infection. © 2015 The Foundation for the Scandinavian Journal of Immunology.

  5. Phylogenetic analysis reveals a cryptic species Blastomyces gilchristii, sp. nov. within the human pathogenic fungus Blastomyces dermatitidis.

    Directory of Open Access Journals (Sweden)

    Elizabeth M Brown

    Full Text Available Analysis of the population genetic structure of microbial species is of fundamental importance to many scientific disciplines because it can identify cryptic species, reveal reproductive mode, and elucidate processes that contribute to pathogen evolution. Here, we examined the population genetic structure and geographic differentiation of the sexual, dimorphic fungus Blastomyces dermatitidis, the causative agent of blastomycosis.Criteria for Genealogical Concordance Phylogenetic Species Recognition (GCPSR applied to seven nuclear loci (arf6, chs2, drk1, fads, pyrF, tub1, and its-2 from 78 clinical and environmental isolates identified two previously unrecognized phylogenetic species. Four of seven single gene phylogenies examined (chs2, drk1, pyrF, and its-2 supported the separation of Phylogenetic Species 1 (PS1 and Phylogenetic Species 2 (PS2 which were also well differentiated in the concatenated chs2-drk1-fads-pyrF-tub1-arf6-its2 genealogy with all isolates falling into one of two evolutionarily independent lineages. Phylogenetic species were genetically distinct with interspecific divergence 4-fold greater than intraspecific divergence and a high Fst value (0.772, P<0.001 indicative of restricted gene flow between PS1 and PS2. Whereas panmixia expected of a single freely recombining population was not observed, recombination was detected when PS1 and PS2 were assessed separately, suggesting reproductive isolation. Random mating among PS1 isolates, which were distributed across North America, was only detected after partitioning isolates into six geographic regions. The PS2 population, found predominantly in the hyper-endemic regions of northwestern Ontario, Wisconsin, and Minnesota, contained a substantial clonal component with random mating detected only among unique genotypes in the population.These analyses provide evidence for a genetically divergent clade within Blastomyces dermatitidis, which we use to describe a novel species

  6. Characterisation of microcontaminants in Darwin Harbour, a tropical estuary of northern Australia undergoing rapid development.

    Science.gov (United States)

    French, Veronica A; Codi King, Susan; Kumar, Anu; Northcott, Grant; McGuinness, Keith; Parry, David

    2015-12-01

    The detection of microcontaminants in aquatic environments raises concerns about their potential to exert ecotoxicological effects and impact human health. In contrast to freshwater habitats, little information is available on environmental concentrations in urban estuarine and marine environments. This study investigated an extensive range of organic and inorganic microcontaminants in the Darwin Harbour catchment, a tropical estuary in northern Australia undergoing rapid urbanisation and industrial development. We sampled wastewater effluent and surface water from seven sites in Darwin Harbour for pharmaceuticals and personal care products, alkylphenols, hormones, pesticides, herbicides and metals. In vitro bioassays were used to estimate the (anti)estrogenic and (anti)androgenic activities of samples. Seventy-nine of 229 organic microcontaminants analysed were detected at concentrations ranging from 0.01 to 20 μg/L, with acesulfame, paracetamol, cholesterol, caffeine, DEET and iopromide detected at the highest concentrations in wastewater effluent (20 μg/L, 17 μg/L, 11 μg/L, 11 μg/L, 10 μg/L and 7.6 μg/L, respectively). Levels of estrogenic activity ranged from estradiol equivalency quotients (EEQs) of <0.10 to 6.29±0.16 ng/L while levels of androgenic activity ranged from dihydrotestosterone equivalency quotients (DHTEQs) of <3.50 to 138.23±3.71 ng/L. Environmental concentrations of organic microcontaminants were comparable to ranges reported from aquatic environments worldwide with sewage effluent discharges representing the dominant source of entry into Darwin Harbour. The measured concentration range of DEET was higher than ranges reported in previous studies. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. Hydrodynamic sensory threshold in harbour seals (Phoca vitulina) for artificial flatfish breathing currents.

    Science.gov (United States)

    Niesterok, Benedikt; Dehnhardt, Guido; Hanke, Wolf

    2017-07-01

    Harbour seals have the ability to detect benthic fish such as flatfish using the water currents these fish emit through their gills (breathing currents). We investigated the sensory threshold in harbour seals for this specific hydrodynamic stimulus under conditions which are realistic for seals hunting in the wild. We used an experimental platform where an artificial breathing current was emitted through one of eight different nozzles. Two seals were trained to search for the active nozzle. Each experimental session consisted of eight test trials of a particular stimulus intensity and 16 supra-threshold trials of high stimulus intensity. Test trials were conducted with the animals blindfolded. To determine the threshold, a series of breathing currents differing in intensity was used. For each intensity, three sessions were run. The threshold in terms of maximum water velocity within the breathing current was 4.2 cm s -1 for one seal and 3.7 cm s -1 for the other. We measured background flow velocities from 1.8 to 3.4 cm s -1 Typical swimming speeds for both animals were around 0.5 m s -1 Swimming speed differed between successful and unsuccessful trials. It appears that swimming speed is restricted for the successful detection of a breathing current close to the threshold. Our study is the first to assess a sensory threshold of the vibrissal system for a moving harbour seal under near-natural conditions. Furthermore, this threshold was defined for a natural type of stimulus differing from classical dipole stimuli which have been widely used in threshold determination so far. © 2017. Published by The Company of Biologists Ltd.

  8. Patterns of the non-indigenous isopod Cirolana harfordi in Sydney Harbour.

    Directory of Open Access Journals (Sweden)

    Ana B Bugnot

    Full Text Available Biological introductions can alter the ecology of local assemblages and are an important driver of global environmental change. The first step towards understanding the impact of a non-indigenous species is to study its distribution and associations in the invaded area. In Sydney Harbour, the non-indigenous isopod Cirolana harfordi has been reported in densities up to 0.5 individuals per cm(2 in mussel-beds. Abundances of this species have, however, been largely overlooked in other key habitats. The first aim of this study was to evaluate the abundances and distribution of C. harfordi across different habitats representative of Sydney Harbour. Results showed that C. harfordi occurred in oyster and mussel-beds, being particularly abundant in oyster-beds. We also aimed to determine the role of C. harfordi as a predator, scavenger and detritus feeder by investigating the relationships between densities of C. harfordi and (i the structure of the resident assemblages, and (ii deposited organic matter in oyster-beds. Densities of C. harfordi were not related to the structure of the assemblages, nor amounts of deposited organic matter. These findings suggested little or no ecological impacts of C. harfordi in oyster-beds. These relationships may, however, affect other variables such as growth of individuals, or be disguised by high variability of assemblages among different locations. Future studies should, therefore, test the impacts of C. harfordi on the size of organisms in the assemblage and use manipulative experiments to control for spatial variation. This study is the first published work on the ecology of the invasion of C. harfordi and provides the starting-point for the study of the impacts of this species in Sydney Harbour.

  9. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence.

    Directory of Open Access Journals (Sweden)

    Pablo D Lavinia

    Full Text Available Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%, with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana. In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

  10. Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence.

    Science.gov (United States)

    Lavinia, Pablo D; Núñez Bustos, Ezequiel O; Kopuchian, Cecilia; Lijtmaer, Darío A; García, Natalia C; Hebert, Paul D N; Tubaro, Pablo L

    2017-01-01

    Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

  11. Echoes from the past: Regional variations in recovery within a harbour seal population.

    Directory of Open Access Journals (Sweden)

    Sophie M J M Brasseur

    Full Text Available Terrestrial and marine wildlife populations have been severely reduced by hunting, fishing and habitat destruction, especially in the last centuries. Although management regulations have led to the recovery of some populations, the underlying processes are not always well understood. This study uses a 40-year time series of counts of harbour seals (Phoca vitulina in the Wadden Sea to study these processes, and demonstrates the influence of historical regional differences in management regimes on the recovery of this population. While the Wadden Sea is considered one ecologically coupled zone, with a distinct harbour seal population, the area is divided into four geo-political regions i.e. the Netherlands, Lower Saxony including Hamburg, Schleswig-Holstein and Denmark. Gradually, seal hunting was banned between 1962 and 1977 in the different regions. Counts of moulting harbour seals and pup counts, obtained during aerial surveys between 1974 and 2014, show a population growth from approximately 4500 to 39,000 individuals. Population growth models were developed to assess if population growth differed between regions, taking into account two Phocine Distemper Virus (PDV epizootics, in 1988 and 2002 which seriously affected the population. After a slow start prior to the first epizootic, the overall population grew exponentially at rates close to assumed maximum rates of increase in a harbour seal population. Recently, growth slowed down, potentially indicative of approaching carrying capacity. Regional differences in growth rates were demonstrated, with the highest recovery in Netherlands after the first PDV epizootic (i.e. 17.9%, suggesting that growth was fuelled by migration from the other regions, where growth remained at or below the intrinsic growth rate (13%. The seals' distribution changed, and although the proportion of seals counted in the German regions declined, they remained by far the most important pupping region, with approximately

  12. Echoes from the past: Regional variations in recovery within a harbour seal population.

    Science.gov (United States)

    Brasseur, Sophie M J M; Reijnders, Peter J H; Cremer, Jenny; Meesters, Erik; Kirkwood, Roger; Jensen, Lasse Fast; Jeβ, Armin; Galatius, Anders; Teilmann, Jonas; Aarts, Geert

    2018-01-01

    Terrestrial and marine wildlife populations have been severely reduced by hunting, fishing and habitat destruction, especially in the last centuries. Although management regulations have led to the recovery of some populations, the underlying processes are not always well understood. This study uses a 40-year time series of counts of harbour seals (Phoca vitulina) in the Wadden Sea to study these processes, and demonstrates the influence of historical regional differences in management regimes on the recovery of this population. While the Wadden Sea is considered one ecologically coupled zone, with a distinct harbour seal population, the area is divided into four geo-political regions i.e. the Netherlands, Lower Saxony including Hamburg, Schleswig-Holstein and Denmark. Gradually, seal hunting was banned between 1962 and 1977 in the different regions. Counts of moulting harbour seals and pup counts, obtained during aerial surveys between 1974 and 2014, show a population growth from approximately 4500 to 39,000 individuals. Population growth models were developed to assess if population growth differed between regions, taking into account two Phocine Distemper Virus (PDV) epizootics, in 1988 and 2002 which seriously affected the population. After a slow start prior to the first epizootic, the overall population grew exponentially at rates close to assumed maximum rates of increase in a harbour seal population. Recently, growth slowed down, potentially indicative of approaching carrying capacity. Regional differences in growth rates were demonstrated, with the highest recovery in Netherlands after the first PDV epizootic (i.e. 17.9%), suggesting that growth was fuelled by migration from the other regions, where growth remained at or below the intrinsic growth rate (13%). The seals' distribution changed, and although the proportion of seals counted in the German regions declined, they remained by far the most important pupping region, with approximately 70% of all pups

  13. INNOVATIVE SOLUTIONS FOR SMALL SCALE VERTICAL AXIS WIND TURBINES USED IN HARBOURS AND SHORE AREAS

    Directory of Open Access Journals (Sweden)

    IONESCU Raluca Dora

    2014-09-01

    Full Text Available The paper aims to analyse the wind turbine solutions implemented in harbours and on shore areas. Also a thorough study of the blade design solutions for small power Vertical axis wind turbines (VAWTs has been conducted, with their advantages and disadvantages, in order to find the best solution that minimises the loads and helps with the self-starting capabilities of the wind turbine. First are presented all the solutions, next are discussed several research results for each solution and, in the end, a combination of solutions is chosen for our new small power VAWT with a pre-dimensioning analysis.

  14. Possible causes of a harbour porpoise mass stranding in Danish waters in 2005

    DEFF Research Database (Denmark)

    Wright, Andrew J.; Maar, Marie; Mohn, Christian

    2013-01-01

    An unprecedented 85 harbour porpoises stranded freshly dead along approximately 100 km of Danish coastline from 7-15 April, 2005. This total is considerably above the mean weekly stranding rate for the whole of Denmark, both for any time of year, 1.23 animals/week (ranging from 0 to 20 during 2003......-2008, excluding April 2005), and specifically in April, 0.65 animals/week (0 to 4, same period). Bycatch was established as the cause of death for most of the individuals through typical indications of fisheries interactions, including net markings in the skin and around the flippers, and loss of tail flukes...

  15. Oil spills in open seas and harbours - impact on marine environment

    International Nuclear Information System (INIS)

    Siddiqui, S.H.

    1995-01-01

    In this article the environmental impacts of sea water near Karachi (Pakistan) harbour (Arabian Sea) are discussed. The water pollution is caused due to oil leakage from ships. The toxicity of various oils (crude oils and refined oils) to different species of marine varies greatly. The second main source of water is municipal waste water. For the control of sea water pollution, there must be education as lack of awareness of the public to ask for clean beaches and absence of coordination between concerned oil companies, tanker operating agencies, port authorities and government (A.B.)

  16. Toxic effects of tributyltin and its metabolites on harbour seal (Phoca vitulina) immune cells in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Frouin, Heloise [Institut National de la Recherche Scientifique - Institut Armand-Frappier, Laval, Quebec H7V 1B7 (Canada); Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, Quebec G5H 3Z4 (Canada)], E-mail: heloise.frouin@iaf.inrs.ca; Lebeuf, Michel [Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, Quebec G5H 3Z4 (Canada); Saint-Louis, Richard [Institut des Sciences de la Mer de Rimouski (ISMER), Universite du Quebec a Rimouski, Rimouski, Quebec G5L 3A1 (Canada); Hammill, Mike [Fisheries and Oceans Canada, Maurice Lamontagne Institute, Mont-Joli, Quebec G5H 3Z4 (Canada); Pelletier, Emilien [Institut des Sciences de la Mer de Rimouski (ISMER), Universite du Quebec a Rimouski, Rimouski, Quebec G5L 3A1 (Canada); Fournier, Michel [Institut National de la Recherche Scientifique - Institut Armand-Frappier, Laval, Quebec H7V 1B7 (Canada)

    2008-11-21

    The widespread environmental contamination, bioaccumulation and endocrine disruptor effects of butyltins (BTs) to wildlife are well documented. Although suspected, potential effects of BTs exposure on the immune system of marine mammals have been little investigated. In this study, we assessed the effects of tributyltin (TBT) and its dealkylated metabolites dibutyltin (DBT) and monobutyltin (MBT) on the immune responses of harbour seals. Peripheral blood mononuclear cells isolated from pup and adult harbour seals were exposed in vitro to varying concentrations of BTs. DBT resulted in a significant decrease at 100 and 200 nM of phagocytotic activity and reduced significantly phagocytic efficiency at 200 nM in adult seals. There was no effect in phagocytosis with TBT and MBT. In pups, the highest concentration (200 nM) of DBT inhibited phagocytic efficiency. A reduction of tumor-killing capacity of adult natural killer (NK) cells occurred when leukocytes were incubated in vitro with 50 nM DBT and 200 nM TBT for 24 h. In adult seals, T-lymphocyte proliferation was significantly suppressed when the cells were exposed to 200 nM TBT and 100 nM DBT. In pups, the proliferative response increased after an exposure to 100 nM TBT and 50 nM DBT, but decreased with 200 nM TBT and 100 nM DBT. The immune functions were more affected by BTs exposure in adults than in pups, suggesting that other unsuspected mechanisms could trigger immune parameters in pups. The toxic potential of BTs followed the order of DBT > TBT > MBT. BT concentrations of harbour seal pups from the St. Lawrence Estuary (Bic National Park) ranged between 0.1-0.4 ng Sn/g wet weight (ww) and 1.2-13.4 ng Sn/g ww in blood and blubber, respectively. For these animals, DBT concentrations were consistently below the quantification limit of 0.04 ng Sn/g ww in blood and 0.2 ng Sn/g ww in blubber. Results suggest that concentrations measured in pups are considered too low to induce toxic effects to their immune system

  17. Toxic effects of tributyltin and its metabolites on harbour seal (Phoca vitulina) immune cells in vitro

    International Nuclear Information System (INIS)

    Frouin, Heloise; Lebeuf, Michel; Saint-Louis, Richard; Hammill, Mike; Pelletier, Emilien; Fournier, Michel

    2008-01-01

    The widespread environmental contamination, bioaccumulation and endocrine disruptor effects of butyltins (BTs) to wildlife are well documented. Although suspected, potential effects of BTs exposure on the immune system of marine mammals have been little investigated. In this study, we assessed the effects of tributyltin (TBT) and its dealkylated metabolites dibutyltin (DBT) and monobutyltin (MBT) on the immune responses of harbour seals. Peripheral blood mononuclear cells isolated from pup and adult harbour seals were exposed in vitro to varying concentrations of BTs. DBT resulted in a significant decrease at 100 and 200 nM of phagocytotic activity and reduced significantly phagocytic efficiency at 200 nM in adult seals. There was no effect in phagocytosis with TBT and MBT. In pups, the highest concentration (200 nM) of DBT inhibited phagocytic efficiency. A reduction of tumor-killing capacity of adult natural killer (NK) cells occurred when leukocytes were incubated in vitro with 50 nM DBT and 200 nM TBT for 24 h. In adult seals, T-lymphocyte proliferation was significantly suppressed when the cells were exposed to 200 nM TBT and 100 nM DBT. In pups, the proliferative response increased after an exposure to 100 nM TBT and 50 nM DBT, but decreased with 200 nM TBT and 100 nM DBT. The immune functions were more affected by BTs exposure in adults than in pups, suggesting that other unsuspected mechanisms could trigger immune parameters in pups. The toxic potential of BTs followed the order of DBT > TBT > MBT. BT concentrations of harbour seal pups from the St. Lawrence Estuary (Bic National Park) ranged between 0.1-0.4 ng Sn/g wet weight (ww) and 1.2-13.4 ng Sn/g ww in blood and blubber, respectively. For these animals, DBT concentrations were consistently below the quantification limit of 0.04 ng Sn/g ww in blood and 0.2 ng Sn/g ww in blubber. Results suggest that concentrations measured in pups are considered too low to induce toxic effects to their immune system

  18. Toxic effects of tributyltin and its metabolites on harbour seal (Phoca vitulina) immune cells in vitro.

    Science.gov (United States)

    Frouin, Héloïse; Lebeuf, Michel; Saint-Louis, Richard; Hammill, Mike; Pelletier, Emilien; Fournier, Michel

    2008-11-21

    The widespread environmental contamination, bioaccumulation and endocrine disruptor effects of butyltins (BTs) to wildlife are well documented. Although suspected, potential effects of BTs exposure on the immune system of marine mammals have been little investigated. In this study, we assessed the effects of tributyltin (TBT) and its dealkylated metabolites dibutyltin (DBT) and monobutyltin (MBT) on the immune responses of harbour seals. Peripheral blood mononuclear cells isolated from pup and adult harbour seals were exposed in vitro to varying concentrations of BTs. DBT resulted in a significant decrease at 100 and 200 nM of phagocytotic activity and reduced significantly phagocytic efficiency at 200 nM in adult seals. There was no effect in phagocytosis with TBT and MBT. In pups, the highest concentration (200 nM) of DBT inhibited phagocytic efficiency. A reduction of tumor-killing capacity of adult natural killer (NK) cells occurred when leukocytes were incubated in vitro with 50 nM DBT and 200 nM TBT for 24h. In adult seals, T-lymphocyte proliferation was significantly suppressed when the cells were exposed to 200 nM TBT and 100 nM DBT. In pups, the proliferative response increased after an exposure to 100 nM TBT and 50 nM DBT, but decreased with 200 nM TBT and 100 nM DBT. The immune functions were more affected by BTs exposure in adults than in pups, suggesting that other unsuspected mechanisms could trigger immune parameters in pups. The toxic potential of BTs followed the order of DBT>TBT>MBT. BT concentrations of harbour seal pups from the St. Lawrence Estuary (Bic National Park) ranged between 0.1-0.4 ng Sn/g wet weight (ww) and 1.2-13.4 ng Sn/g ww in blood and blubber, respectively. For these animals, DBT concentrations were consistently below the quantification limit of 0.04 ng Sn/g ww in blood and 0.2 ng Sn/g ww in blubber. Results suggest that concentrations measured in pups are considered too low to induce toxic effects to their immune system during

  19. Uncovering governance mechanisms surrounding harbour porpoise conservation in the Danish Skagerrak Sea

    DEFF Research Database (Denmark)

    Sørensen, Thomas Kirk; Kindt-Larsen, Lotte

    2016-01-01

    mainly by the economy and the varying perceptions of the bycatch issue, with great differences between government, NGO's and fishers. Interviews with fishers and fishing effort data reveal intra-sectoral conflicts pertaining to the incompatibility of active trawling and passive gillnetting in the areas......The harbour porpoise (Phocoena phocoena) is the focus of a range of conservation efforts and policies, including the Habitats Directive, aimed at reducing the bycatch of non-target species in gillnet fisheries. This paper describes the governance process and analyses the governance mechanisms...

  20. Measurements of boat motion in waves at Durban harbour for qualitative validation of motion model

    CSIR Research Space (South Africa)

    Mosikare, OR

    2010-09-01

    Full Text Available in Waves at Durban Harbour for Qualitative Validation of Motion Model O.R. Mosikare1,2, N.J. Theron1, W. Van der Molen 1 University of Pretoria, South Africa, 0001 2Council for Scientific and Industrial Research, Meiring Naude Rd, Brummeria, 0001... stream_source_info Mosikare_2010.pdf.txt stream_content_type text/plain stream_size 3033 Content-Encoding UTF-8 stream_name Mosikare_2010.pdf.txt Content-Type text/plain; charset=UTF-8 Measurements of Boat Motion...

  1. Geodetic Infrastructure in the Ibiza and Barcelona Harbours for Sea Level Monitoring

    Science.gov (United States)

    Martinez-Benjamin, J. J.; Gili, J.; Lopez, R.; Tapia, A.; Perez, B.; Pros, F.

    2013-12-01

    The presentation is directed to the description of the actual situation and relevant information of the geodetic infrastructure of Ibiza and Barcelona sites for sea level determination and contribution to regional sea level rise. Time series are being analysed for mean sea level variations www.puertos.es. .In the framework of a Spanish Space Project, the instrumentation of sea level measurements has been improved by providing the Barcelona site with a radar tide gauge Datamar 2000C from Geonica s.l. near an acoustic tide gauge. Puertos del Estado installed in 2007 a MIROS radar tide gauge and the Barcelona Harbour Authority a GPS referente station in the roof of the new Control Tower situated in the Energy Pier. The radar sensor is over the water surface, on a L-shaped structure which elevates it a few meters above the quay shelf. 1-min data are transmitted to the ENAGAS Control Center by cable and then sent each 1 min to Puertos del Estado by e-mail. There is a GPS station Leica Geosystems GRX1200 GG Pro and antenna 1202. Precision levelling has been made several times in the last two years because the tower is founded in reclaimed land. The measured settlement rate is about 1cm/year that may be could mask the values registered by the tide gauge. A description of the actual infrastructure at Ibiza harbour at Marina de Botafoch, is presented and its applications to sea level monitoring and altimeter calibration in support of the main CGPS at Ibiza harbour. It is described the geometrical precision levelling made in June 2013 between the radar tide gauge and the GPS station. In particular, the CGPS located at Ibiza harbour is essential for its application to the marine campaign Baleares 2013, near Ibiza island. The main objective is to determine the altimeter bias for Jason-2, about 9:09 UTC September 15, 2013, and Saral/AltiKa, about 05:30 UTC September 16, UTC. These activities has been received funding of the Ministerio de Ciencia e Innovacion under Spanish

  2. Splicing modulation therapy in the treatment of genetic diseases

    Directory of Open Access Journals (Sweden)

    Arechavala-Gomeza V

    2014-12-01

    Full Text Available Virginia Arechavala-Gomeza,1 Bernard Khoo,2 Annemieke Aartsma-Rus3 1Neuromuscular Disorders Group, BioCruces Health Research Institute, Barakaldo, Bizkaia, Spain; 2Endocrinology, Division of Medicine, University College London, London, UK; 3Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands All authors contributed equally to this manuscript Abstract: Antisense-mediated splicing modulation is a tool that can be exploited in several ways to provide a potential therapy for rare genetic diseases. This approach is currently being tested in clinical trials for Duchenne muscular dystrophy and spinal muscular atrophy. The present review outlines the versatility of the approach to correct cryptic splicing, modulate alternative splicing, restore the open reading frame, and induce protein knockdown, providing examples of each. Finally, we outline a possible path forward toward the clinical application of this approach for a wide variety of inherited rare diseases. Keywords: splicing, therapy, antisense oligonucleotides, cryptic splicing, alternative splicing

  3. Cryptic variation in morphological evolution: HSP90 as a capacitor for loss of eyes in cavefish.

    Science.gov (United States)

    Rohner, Nicolas; Jarosz, Dan F; Kowalko, Johanna E; Yoshizawa, Masato; Jeffery, William R; Borowsky, Richard L; Lindquist, Susan; Tabin, Clifford J

    2013-12-13

    In the process of morphological evolution, the extent to which cryptic, preexisting variation provides a substrate for natural selection has been controversial. We provide evidence that heat shock protein 90 (HSP90) phenotypically masks standing eye-size variation in surface populations of the cavefish Astyanax mexicanus. This variation is exposed by HSP90 inhibition and can be selected for, ultimately yielding a reduced-eye phenotype even in the presence of full HSP90 activity. Raising surface fish under conditions found in caves taxes the HSP90 system, unmasking the same phenotypic variation as does direct inhibition of HSP90. These results suggest that cryptic variation played a role in the evolution of eye loss in cavefish and provide the first evidence for HSP90 as a capacitor for morphological evolution in a natural setting.

  4. Assessment of DDT, HCH and PAH contamination and associated ecotoxicological risks in surface sediments of coastal Tema Harbour (Ghana).

    Science.gov (United States)

    Botwe, Benjamin O; Kelderman, Peter; Nyarko, Elvis; Lens, Piet N L

    2017-02-15

    This study assessed DDTs, HCHs and PAHs contamination in sediments from the Tema Harbour (Ghana) and the associated ecotoxicological risks. The results showed widespread DDTs, HCHs and PAHs contamination in the harbour sediments with mean concentrations ranging from 6.0-12.8, 2.8-12.7 and 2750-5130μg·kg -1 d·w, respectively. The silt-clay and total organic carbon contents of the sediments poorly correlated with the pollutant concentrations. DDTs and HCHs contamination relate to past use of DDT and lindane, which under the anoxic harbour conditions resulted in disproportionately higher concentrations of p,p'-DDD and γ-HCH in the sediments. No conclusion could be drawn on the sources of PAHs as either petrogenic or pyrogenic. The pollutant concentrations in the harbour sediments, particularly γ-HCH, may pose high ecotoxicological risks. In comparison to a previous study, this study indicates there has been a considerable reduction in PAH contamination in the Tema Harbour since the last major oil spill in 2007. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Recolonization of macrofauna in unpolluted sands placed in a polluted yachting harbour: A field approach using experimental trays

    Science.gov (United States)

    Guerra-García, J. M.; García-Gómez, J. C.

    2009-01-01

    A field experiment using trays was conducted at Ceuta's yachting harbour, North Africa, to study the effect in recolonization of placing trays with unpolluted defaunate sediments (fine and gross sands with low contents of organic matter) inside an enclosed yachting harbour characterized by high percentages of silt and clay and high concentrations of organic matter. Sediment recolonization in the trays was mainly undertaken by the species living naturally at the yachting harbour, which recolonized both uncontaminated gross and fine sand trays (such as the crustaceans Corophium runcicorne, Corophium sextonae and Nebalia bipes, the mollusc Parvicardium exiguum and the polychaete Pseudomalacoceros tridentata). However, other species like the polychaetes Cirriformia tentaculata and Platynereis dumerilii, although also abundant in the yachting harbour, were unable to colonize the trays through transport of larvae and/or adults in the water column. The recolonization was very quick, and after the first month, the values of abundance, species richness, diversity and evenness were similar in the experimental trays and in the reference area (yachting harbour). Although the multivariate analysis showed that the species composition differed between the trays and the reference area, there were no significant differences in recolonization of gross and fine sands, indicating that other factors different from the granulometry are modulating the recolonization patterns.

  6. How to deal with cryptic species in Enchytraeidae, with recommendations on taxonomical descriptions

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    Schmelz, R. M.

    2017-11-01

    Full Text Available During the 12th International Symposium on Enchytraeidae, held in Tihany, Hungary (27–29 June 2016, the participants discussed cryptic species, i.e., species that are morphologically so similar that they are classified as the same species (Bickford et al. 2007, and how to deal with them taxonomically. Here we summarise the discussion together with a few additional comments, and we give recommendations for species descriptions in Enchytraeidae.

  7. Temperature effects on gametophyte life-history traits and geographic distribution of two cryptic kelp species.

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    L Valeria Oppliger

    Full Text Available A major determinant of the geographic distribution of a species is expected to be its physiological response to changing abiotic variables over its range. The range of a species often corresponds to the geographic extent of temperature regimes the organism can physiologically tolerate. Many species have very distinct life history stages that may exhibit different responses to environmental factors. In this study we emphasized the critical role of the haploid microscopic stage (gametophyte of the life cycle to explain the difference of edge distribution of two related kelp species. Lessonia nigrescens was recently identified as two cryptic species occurring in parapatry along the Chilean coast: one located north and the other south of a biogeographic boundary at latitude 29-30°S. Six life history traits from microscopic stages were identified and estimated under five treatments of temperature in eight locations distributed along the Chilean coast in order to (1 estimate the role of temperature in the present distribution of the two cryptic L. nigrescens species, (2 compare marginal populations to central populations of the two cryptic species. In addition, we created a periodic matrix model to estimate the population growth rate (λ at the five temperature treatments. Differential tolerance to temperature was demonstrated between the two species, with the gametophytes of the Northern species being more tolerant to higher temperatures than gametophytes from the south. Second, the two species exhibited different life history strategies with a shorter haploid phase in the Northern species contrasted with considerable vegetative growth in the Southern species haploid stage. These results provide strong ecological evidence for the differentiation process of the two cryptic species and show local adaptation of the life cycle at the range limits of the distribution. Ecological and evolutionary implications of these findings are discussed.

  8. Harbour porpoises on Horns Reef - Effects of the Horns Reef wind farm. Annual status report 2003

    International Nuclear Information System (INIS)

    Tougaard, J.; Carstensen, J.; Henriksen, Oluf. D.; Teilmann, J.; Rye Hansen, J.

    2004-06-01

    Occurrence and distribution of harbour porpoises (Phocoena phocoena) in and around the off-shore wind farm on Horns Reef, Denmark, was investigated. This report describes data collected in 2003 as part of an ongoing monitoring program, covering a period before construction of the wind farm (baseline), the construction period in 2002 and one year following construction of the wind farm. Data from acoustic dataloggers (T-PODs) and visual surveys conducted from ships confirmed the presence of harbour porpoises inside the wind farm area during all periods investigated. Comparison with baseline data from 1999-2001 and with control areas outside the wind farm did not show a statistical significant change in sighting rates inside the wind farm area in the first year following construction relative to baseline. T-POD data showed a pronounced effect of the construction of the wind farm on the indicators 'encounter duration' (measure of how long porpoises remain close to the POD) and 'waiting time' (measure of time interval between porpoise encounters). Both parameters seem to indicate higher levels of porpoise activity during construction (encounter duration went up, waiting time went down) compared to baseline. A partial return to baseline levels was seen for these two indicators in 2003. (au)

  9. Harbour porpoises on Horns Reef - Effects of the Horns Reef wind farm. Annual status report 2003

    Energy Technology Data Exchange (ETDEWEB)

    Tougaard, J.; Carstensen, J.; Henriksen, Oluf. D.; Teilmann, J. [National Environmental Research Inst., Roskilde (Denmark); Rye Hansen, J. [DDH Consulting A/S, Roskilde (Denmark)

    2004-06-15

    Occurrence and distribution of harbour porpoises (Phocoena phocoena) in and around the off-shore wind farm on Horns Reef, Denmark, was investigated. This report describes data collected in 2003 as part of an ongoing monitoring program, covering a period before construction of the wind farm (baseline), the construction period in 2002 and one year following construction of the wind farm. Data from acoustic dataloggers (T-PODs) and visual surveys conducted from ships confirmed the presence of harbour porpoises inside the wind farm area during all periods investigated. Comparison with baseline data from 1999-2001 and with control areas outside the wind farm did not show a statistical significant change in sighting rates inside the wind farm area in the first year following construction relative to baseline. T-POD data showed a pronounced effect of the construction of the wind farm on the indicators 'encounter duration' (measure of how long porpoises remain close to the POD) and 'waiting time' (measure of time interval between porpoise encounters). Both parameters seem to indicate higher levels of porpoise activity during construction (encounter duration went up, waiting time went down) compared to baseline. A partial return to baseline levels was seen for these two indicators in 2003. (au)

  10. Developing a Social, Cultural and Economic Report Card for a Regional Industrial Harbour.

    Directory of Open Access Journals (Sweden)

    Sean Pascoe

    Full Text Available Report cards are increasingly used to provide ongoing snap-shots of progress towards specific ecosystem health goals, particularly in coastal regions where planners need to balance competing demands for coastal resources from a range of industries. While most previous report cards focus on the biophysical components of the system, there is a growing interest in including the social and economic implications of ecosystem management to provide a greater social-ecological system understanding. Such a report card was requested on the Gladstone Harbour area in central Queensland, Australia. Gladstone Harbour adjoins the southern Great Barrier Reef, and is also a major industrial and shipping port. Balancing social, economic and environmental interests is therefore of great concern to the regional managers. While environmental benchmarking procedures are well established within Australia (and elsewhere, a method for assessing social and economic performance of coastal management is generally lacking. The key aim of this study was to develop and pilot a system for the development of a report card relating to appropriate cultural, social and economic objectives. The approach developed uses a range of multicriteria decision analysis methods to assess and combine different qualitative and quantitative measures, including the use of Bayesian Belief Networks to combine the different measures and provide an overall quantitative score for each of the key management objectives. The approach developed is readily transferable for purposes of similar assessments in other regions.

  11. Endoparasitic helminths of the harbour seal, Phoca vitulina, in the Netherlands

    Science.gov (United States)

    Borgsteede, F. H. M.; Bus, H. G. J.; Verplanke, J. A. W.; van Burg, W. P. J.

    The endoparasitic helminth fauna of harbour seals which had died during the epidemic of the phocine distemper virus in 1988 was studied. Lungs, heart and gastrointestinal tracts of 94 animals collected along the Dutch coast were available for investigation. The following parasites and infection percentages were found: Nematoda: Dipetalonema spirocauda (24.5%), Otostrongylus circumlitus (6.4%), Parafilaroides gymnurus (24.5%), Ascaridoidea spec. (58.5%); Trematoda: Phagicola septentrionalis (66.0%), Cryptocotyle lingua (74.5%); Cestoda: Diphyllobothrium spec. (8.5%); Acanthocephala: Corynosoma strumosum (70.2%). The presence of worm species was not evenly distributed over the age classes. Seals younger than one year harboured fewer parasites. The highest percentages were found in 1 to 2 year old seals. The number of worms per seal varied greatly. The highest burden for ascarids was 253, for P. septentrionalis 123 000, for C. lingua 112 000 and for C. strumosum 251. A comparison of the present results with those described in the literature shows that in Dutch seals the same species were present and that numbers of worms were not higher than before the 1988 mass mortality. It is therefore concluded that helminth parasites did not cause the mass mortality.

  12. Source apportionment of PAH in Hamilton Harbour suspended sediments: comparison of two factor analysis methods.

    Science.gov (United States)

    Sofowote, Uwayemi M; McCarry, Brian E; Marvin, Christopher H

    2008-08-15

    A total of 26 suspended sediment samples collected over a 5-year period in Hamilton Harbour, Ontario, Canada and surrounding creeks were analyzed for a suite of polycyclic aromatic hydrocarbons and sulfur heterocycles. Hamilton Harbour sediments contain relatively high levels of polycyclic aromatic compounds and heavy metals due to emissions from industrial and mobile sources. Two receptor modeling methods using factor analyses were compared to determine the profiles and relative contributions of pollution sources to the harbor; these methods are principal component analyses (PCA) with multiple linear regression analysis (MLR) and positive matrix factorization (PMF). Both methods identified four factors and gave excellent correlation coefficients between predicted and measured levels of 25 aromatic compounds; both methods predicted similar contributions from coal tar/coal combustion sources to the harbor (19 and 26%, respectively). One PCA factor was identified as contributions from vehicular emissions (61%); PMF was able to differentiate vehicular emissions into two factors, one attributed to gasoline emissions sources (28%) and the other to diesel emissions sources (24%). Overall, PMF afforded better source identification than PCA with MLR. This work constitutes one of the few examples of the application of PMF to the source apportionment of sediments; the addition of sulfur heterocycles to the analyte list greatly aided in the source identification process.

  13. Respiratory transmission of an avian H3N8 influenza virus isolated from a harbour seal

    Science.gov (United States)

    Karlsson, Erik A.; Ip, Hon S.; Hall, Jeffrey S.; Yoon, Sun W.; Johnson, Jordan; Beck, Melinda A.; Webby, Richard J.; Schultz-Cherry, Stacey

    2014-01-01

    The ongoing human H7N9 influenza infections highlight the threat of emerging avian influenza viruses. In 2011, an avian H3N8 influenza virus isolated from moribund New England harbour seals was shown to have naturally acquired mutations known to increase the transmissibility of highly pathogenic H5N1 influenza viruses. To elucidate the potential human health threat, here we evaluate a panel of avian H3N8 viruses and find that the harbour seal virus displays increased affinity for mammalian receptors, transmits via respiratory droplets in ferrets and replicates in human lung cells. Analysis of a panel of human sera for H3N8 neutralizing antibodies suggests that there is no population-wide immunity to these viruses. The prevalence of H3N8 viruses in birds and multiple mammalian species including recent isolations from pigs and evidence that it was a past human pandemic virus make the need for surveillance and risk analysis of these viruses of public health importance.

  14. Identification and typing of Brucella spp. in stranded harbour porpoises (Phocoena phocoena) on the Dutch coast.

    Science.gov (United States)

    Maio, Elisa; Begeman, Lineke; Bisselink, Yvette; van Tulden, Peter; Wiersma, Lidewij; Hiemstra, Sjoukje; Ruuls, Robin; Gröne, Andrea; Roest, Hendrik-Ido-Jan; Willemsen, Peter; van der Giessen, Joke

    2014-09-17

    The presence of Brucella (B.) spp. in harbour porpoises stranded between 2008 and 2011 along the Dutch coast was studied. A selection of 265 tissue samples from 112 animals was analysed using conventional and molecular methods. In total, 4.5% (5/112) of the animals corresponding with 2.3% (6/265) Brucella positive tissue samples were Brucella positive by culture and these were all confirmed by real-time polymerase chain reaction (real-time PCR) based on the insertion element 711 (IS711). In addition, two more Brucella-positive tissue samples from two animals collected in 2011 were identified using real-time PCR resulting in an overall Brucella prevalence of 6.3% (7/112 animals). Brucella spp. were obtained from lungs (n=3), pulmonary lymph node (n=3) and lungworms (n=2). Multi Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) typing based on the MLVA-16 showed that the Brucella isolates were B. ceti. Additional in silico Multi Locus Sequence typing (MLST) after whole genome sequencing of the 6 Brucella isolates confirmed B. ceti ST 23. According to the Brucella 2010 MLVA database, the isolated Brucella strains encountered were of five genotypes, in two distinct subclusters divided in two different time periods of harbour porpoises collection. This study is the first population based analyses for Brucella spp. infections in cetaceans stranded along the Dutch coast. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  15. An X-Band Radar System for Bathymetry and Wave Field Analysis in a Harbour Area

    Directory of Open Access Journals (Sweden)

    Giovanni Ludeno

    2015-01-01

    Full Text Available Marine X-band radar based systems are well tested to provide information about sea state and bathymetry. It is also well known that complex geometries and non-uniform bathymetries provide a much bigger challenge than offshore scenarios. In order to tackle this issue a retrieval method is proposed, based on spatial partitioning of the data and the application of the Normalized Scalar Product (NSP, which is an innovative procedure for the joint estimation of bathymetry and surface currents. The strategy is then applied to radar data acquired around a harbour entrance, and results show that the reconstructed bathymetry compares well with ground truth data obtained by an echo-sounder campaign, thus proving the reliability of the whole procedure. The spectrum thus retrieved is then analysed to show the evidence of reflected waves from the harbour jetties, as confirmed by chain of hydrodynamic models of the sea wave field. The possibility of using a land based radar to reveal sea wave reflection is entirely new and may open up new operational applications of the system.

  16. Recent changes in estuarine benthic and suprabenthic communities resulting from the development of harbour infrastructure.

    Science.gov (United States)

    Dauvin, J C; Desroy, N; Janson, A L; Vallet, C; Duhamel, S

    2006-01-01

    Using a Before/During/After sampling protocol, the effects of the Le Havre harbour extension, which was started at the end of 2001, on the macrobenthic and suprabenthic communities in the eastern Bay of Seine (English Channel) were examined. As the construction phase has not yet been completed, the results presented here reflect only the data collected before and during the operations (September 2000 and 2002 for benthos sampling and March 2001, September 2001, October 2002 and March 2003 for suprabenthos sampling). Although bio-sedimentary changes did occur at the mouth of the Seine river, an analysis of benthic assemblages reveals that the dredging and construction operations do not seem to have influenced assemblage structure or the spatial distribution of organisms. Comparisons of the suprabenthic assemblages at each sampling date indicate that seasonal dynamics was mainly responsible for determining species distribution. We conclude that, 1 year into the harbour management plan, the observed changes in benthic and suprabenthic assemblage abundance do not exceed the range of spatial variability that exists naturally in the Seine estuary. Despite this compensatory actions designed to protect the aquatic habitats and to preserve a sustainable and healthy ecosystem have been added to the infrastructure development plan.

  17. Hydrodynamic determination of the moving direction of an artificial fin by a harbour seal (Phoca vitulina).

    Science.gov (United States)

    Wieskotten, S; Dehnhardt, G; Mauck, B; Miersch, L; Hanke, W

    2010-07-01

    Harbour seals can use their vibrissal system to detect and follow hydrodynamic trails left by moving objects. In this study we determined the maximum time after which a harbour seal could indicate the moving direction of an artificial fish tail and analysed the hydrodynamic parameters allowing the discrimination. Hydrodynamic trails were generated using a fin-like paddle moving from left to right or from right to left in the calm water of an experimental box. The blindfolded seal was able to recognise the direction of the paddle movement when the hydrodynamic trail was up to 35 s old. Particle Image Velocimetry (PIV) revealed that the seal might have perceived and used two different hydrodynamic parameters to determine the moving direction of the fin-like paddle. The structure and spatial arrangement of the vortices in the hydrodynamic trail and high water velocities between two counter-rotating vortices are characteristic of the movement direction and are within the sensory range of the seal.

  18. The impact of glide phases on the trackability of hydrodynamic trails in harbour seals (Phoca vitulina).

    Science.gov (United States)

    Wieskotten, S; Dehnhardt, G; Mauck, B; Miersch, L; Hanke, W

    2010-11-01

    The mystacial vibrissae of harbour seals (Phoca vitulina) constitute a highly sensitive hydrodynamic receptor system enabling the seals to detect and follow hydrodynamic trails. In the wild, hydrodynamic trails, as generated by swimming fish, consist of cyclic burst-and-glide phases, associated with various differences in the physical parameters of the trail. Here, we investigated the impact of glide phases on the trackability of differently aged hydrodynamic trails in a harbour seal. As fish are not easily trained to swim certain paths with predetermined burst-and-glide phases, the respective hydrodynamic trails were generated using a remote-controlled miniature submarine. Gliding phases in hydrodynamic trails had a negative impact on the trackability when trails were 15 s old. The seal lost the generated trails more often within the transition zones, when the submarine switched from a burst to a glide moving pattern. Hydrodynamic parameter analysis (particle image velocimetry) revealed that the smaller dimensions and faster decay of hydrodynamic trails generated by the gliding submarine are responsible for the impaired success of the seal tracking the gliding phase. Furthermore, the change of gross water flow generated by the submarine from a rearwards-directed stream in the burst phase to a water flow passively dragged behind the submarine during gliding might influence the ability of the seal to follow the trail as this might cause a weaker deflection of the vibrissae. The possible ecological implications of intermittent swimming behaviour in fish for piscivorous predators are discussed.

  19. Acoustic divergence in the communication of cryptic species of nocturnal primates (Microcebus ssp.

    Directory of Open Access Journals (Sweden)

    Zimmermann Elke

    2008-05-01

    Full Text Available Abstract Background A central question in evolutionary biology is how cryptic species maintain species cohesiveness in an area of sympatry. The coexistence of sympatrically living cryptic species requires the evolution of species-specific signalling and recognition systems. In nocturnal, dispersed living species, specific vocalisations have been suggested to act as an ideal premating isolation mechanism. We studied the structure and perception of male advertisement calls of three nocturnal, dispersed living mouse lemur species, the grey mouse lemur (Microcebus murinus, the golden brown mouse lemur (M. ravelobensis and the Goodman's mouse lemur (M. lehilahytsara. The first two species occur sympatrically, the latter lives allopatrically to them. Results A multi-parameter sound analysis revealed prominent differences in the frequency contour and in the duration of advertisement calls. To test whether mouse lemurs respond specifically to calls of the different species, we conducted a playback experiment with M. murinus from the field using advertisement calls and alarm whistle calls of all three species. Individuals responded significantly stronger to conspecific than to heterospecific advertisement calls but there were no differences in response behaviour towards statistically similar whistle calls of the three species. Furthermore, sympatric calls evoked weaker interest than allopatric advertisement calls. Conclusion Our results provide the first evidence for a specific relevance of social calls for speciation in cryptic primates. They furthermore support that specific differences in signalling and recognition systems represent an efficient premating isolation mechanism contributing to species cohesiveness in sympatrically living species.

  20. Taxonomic richness and abundance of cryptic peracarid crustaceans in the Puerto Morelos Reef National Park, Mexico

    Directory of Open Access Journals (Sweden)

    Luz Veronica Monroy-Velázquez

    2017-06-01

    Full Text Available Background and Aims Cryptic peracarids are an important component of the coral reef fauna in terms of diversity and abundance, yet they have been poorly studied. The aim of this study was to evaluate the taxonomic richness and abundance of cryptic peracarids in coral rubble in the Puerto Morelos Reef National Park, Mexico (PMRNP, and their relationship with depth. Methods Three reef sites were selected: (1 Bonanza, (2 Bocana, and (3 Jardines. At each site six kilograms of coral rubble were collected over four sampling periods at three depths: 3 m (back-reef, 6–8 m (fore-reef, and 10–12 m (fore-reef. Results A total of 8,887 peracarid crustaceans belonging to 200 taxa distributed over five orders and 63 families was obtained; 70% of the taxa were identified to species and 25% to genus level. Fifty species of those collected represent new records for the Mexican Caribbean Sea. Isopoda was the most speciose order while Tanaidacea was the most abundant. Discussion Cryptic peracarid taxonomic richness and abundance were related to depth with higher values of both parameters being found in the shallow (3 m back-reef, possibly due to a higher reef development and a greater accumulation of coral rubble produced during hurricanes. Peracarid data obtained in the present study can be used as a baseline for future monitoring programs in the PMRNP.

  1. Partial mitochondrial DNA sequences suggest the existence of a cryptic species within the Leucosphyrus group of the genus Anopheles (Diptera: Culicidae, forest malaria vectors, in northern Vietnam

    Directory of Open Access Journals (Sweden)

    Yasunami Michio

    2010-04-01

    Full Text Available Abstract Background During the last decade, Southeast Asian countries have been very successful in reducing the burden of malaria. However, malaria remains endemic in these countries, especially in remote and forested areas. The Leucosphyrus group of the genus Anopheles harbors the most important malaria vectors in forested areas of Southeast Asia. In Vietnam, previous molecular studies have resulted in the identification of only Anopheles dirus sensu stricto (previously known as An. dirus species A among the Leucosphyrus group members. However, Vietnamese entomologists have recognized that mosquitoes belonging to the Leucosphyrus group in northern Vietnam exhibit morphological characteristics similar to those of Anopheles takasagoensis, which has been reported only from Taiwan. Here, we aimed to confirm the genetic and morphological identities of the members of the Leucosphyrus group in Vietnam. Results In the molecular phylogenetic trees reconstructed using partial COI and ND6 mitochondrial gene sequences, samples collected from southern and central Vietnam clustered together with GenBank sequences of An. dirus that were obtained from Thailand. However, samples from northern Vietnam formed a distinct clade separated from both An. dirus and An. takasagoensis by other valid species. Conclusions The results suggest the existence of a cryptic species in northern Vietnam that is morphologically similar to, but phylogenetically distant from both An. dirus and An. takasagoensis. We have tentatively designated this possible cryptic species as Anopheles aff. takasagoensis for convenience, until a valid name is assigned. However, it is difficult to distinguish the species solely on the basis of morphological characteristics. Further studies on such as karyotypes and polytene chromosome banding patterns are necessary to confirm whether An. aff. takasagoensis is a valid species. Moreover, studies on (1 the geographic distribution, which is potentially

  2. Contribution of harbour activities to atmospheric aerosol in the Brindisi area

    Science.gov (United States)

    Donateo, Antonio; Cesari, Daniela; Nocioni, Alessandra; Grasso, Fabio M.; Merico, Eva; Giua, Roberto; Contini, Daniele

    2013-04-01

    The port areas are economic centres and transport hubs, that bring together different transport modes (sea, road, railway transport) and also industrial activities. Ship emissions when docked and during port manoeuvring can have a substantial negative effect on local air quality. The Fagerli and Tarrason (2001) simulation results indicated that ship traffic emissions contribute to 5% and 10% of PM10 concentrations in large parts of Great Britain, Portugal and Italy; similarly to what was obtained by Dalsoren et al. (2009). At the beginning of 2012 it was started the research project CESAPO (Contribution of Emission Sources on the Air quality of the POrt-cities in Greece and Italy), funded within the framework of Interreg Italy-Greece (2007/2013), having as objective the quantification of the contribution to atmospheric particles of emission sources in two important Mediterranean port-cities, namely Patra (Greece) and Brindisi (Italy). In this work the first results of the CESAPO project will be presented giving more emphasis on the analysis of the maritime transport and the activities within the harbour of Brindisi that is characterized by several emission sources operating concurrently. In 2010 and 2011, in the port of Brindisi freight traffic and total goods movement accounted for more than 9.5 million tons, with over 520,000 passengers. To recognize the contribution of harbour activities to PM2.5 and to the total number concentration of particles with respect to other emission sources (urban traffic and industrial pollution) it has been performed an intensive observation period (IOP) of 5 months (June 1 to October 31, 2012). During the IOP the data of 10 fixed monitoring stations (of the regional network managed by ARPA Puglia) and those from two additional stations specifically installed during the project inside the harbour area. A station was used to characterize the chemical composition of PM2.5 and PAHs (in the gaseous and aerosol phases) and the other was

  3. Description of the first cryptic avian malaria parasite, Plasmodium homocircumflexum n. sp., with experimental data on its virulence and development in avian hosts and mosquitoes.

    Science.gov (United States)

    Palinauskas, Vaidas; Žiegytė, Rita; Ilgūnas, Mikas; Iezhova, Tatjana A; Bernotienė, Rasa; Bolshakov, Casimir; Valkiūnas, Gediminas

    2015-01-01

    For over 100 years studies on avian haemosporidian parasite species have relied on similarities in their morphology to establish a species concept. Some exceptional cases have also included information about the life cycle and sporogonic development. More than 50 avian Plasmodium spp. have now been described. However, PCR-based studies show a much broader diversity of haemosporidian parasites, indicating the possible existence of a diverse group of cryptic species. In the present study, using both similarity and phylogenetic species definition concepts, we believe that we report the first characterised cryptic speciation case of an avian Plasmodium parasite. We used sequence information on the mitochondrial cytochrome b gene and constructed phylogenies of identified Plasmodium spp. to define their position in the phylogenetic tree. After analysis of blood stages, the morphology of the parasite was shown to be identical to Plasmodium circumflexum. However, the geographic distribution of the new parasite, the phylogenetic information, as well as patterns of development of infection, indicate that this parasite differs from P. circumflexum. Plasmodium homocircumflexum n. sp. was described based on information about genetic differences from described lineages, phylogenetic position and biological characters. This parasite develops parasitemia in experimentally infected birds - the domestic canary Serinus canaria domestica, siskin Carduelis spinus and crossbill Loxia curvirostra. Anaemia caused by high parasitemia, as well as cerebral paralysis caused by exoerythrocytic stages in the brain, are the main reasons for mortality. Exoerythrocytic stages also form in other organs (heart, kidneys, liver, lungs, spleen, intestines and pectoral muscles). DNA amplification was unsuccessful from faecal samples of heavily infected birds. The sporogonic development initiates, but is abortive, at the oocyst stage in two common European mosquito species, Culex pipiens pipiens (forms

  4. CD4+ T cells targeting dominant and cryptic epitopes from Bacillus anthracis Lethal Factor

    Directory of Open Access Journals (Sweden)

    Stephanie eAscough

    2016-01-01

    Full Text Available Anthrax is an endemic infection in many countries, particularly in the developing world. The causative agent, Bacillus anthracis, mediates disease through the secretion of binary exotoxins. Until recently, research into adaptive immunity targeting this bacterial pathogen has largely focused on the humoral response to these toxins. There is, however, growing recognition that cellular immune responses involving IFNγ producing CD4+ T cells also contribute significantly to a protective memory response. An established concept in adaptive immunity to infection is that during infection of host cells, new microbial epitopes may be revealed, leading to immune recognition of so called ‘cryptic’ or ‘subdominant’ epitopes. We analysed the response to both cryptic and immunodominant T cell epitopes derived from the toxin component lethal factor and presented by a range of HLA-DR alleles. Using IFNγ-ELISPOT assays we characterised epitopes that elicited a response following immunisation with synthetic peptide and the whole protein and tested their capacities to bind purified HLA-DR molecules in vitro. We found that DR1 transgenics demonstrated T cell responses to a greater number of domain III cryptic epitopes than other HLA-DR transgenics, and that this pattern was repeated with the immunodominant epitopes, a greater proportion of these epitopes induced a T cell response when presented within the context of the whole protein. Immunodominant epitopes LF457-476 and LF467-487 were found to induce a T cell response to the peptide, as well as to the whole native LF protein in DR1 and DR15, but not in DR4 trangenics. The analysis of Domain I revealed the presence of several unique cryptic epitopes all of which showed a strong to moderate relative binding affinity to HLA-DR4 molecules. However, none of the cryptic epitopes from either domain III or I displayed notably high binding affinities across all HLA-DR alleles assayed. These responses were

  5. Stress level in wild harbour porpoises (Phocoena phocoena) during satellite tagging measured by respiration, heart rate and cortisol

    DEFF Research Database (Denmark)

    Eskesen, Ida Grønborg; Teilmann, J.; Geertsen, B. M.

    2009-01-01

    During satellite tagging of harbour porpoises (Phocoena phocoena), heart rate, respiration rate and cortisol value were measured to evaluate stress effects during handling and tagging. Respiration rates were obtained using video recordings, heart rates were recorded and serum cortisol levels were...... between cortisol and month of year, sex and body length. As high individual variations occurred in response to tagging of harbour porpoises, it is not possible to give general advice based oil the factors investigated, on how to reduce stress during handling. However, pouring water over the animal...

  6. Comparison of the iPCoD and DEPONS models for modelling population consequences of noise on harbour porpoises

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Jacob; Harwood, John

    Two different frameworks have been developed to assess the potential effects of noise associated with offshore renewable energy developments on harbour porpoise populations: The Interim Population Consequences of Disturbance (iPCoD) and Disturbance Effects of Noise on the Harbour Porpoise...... Population in the North Sea (DEPONS). Although both models simulate population dynamics based on the birth and survival rates of individual animals, they model survival in a different way. iPCoD uses average survival rates derived from data from North Sea animals. In the DEPONS model, survival emerges from...

  7. Dinoflagellate cyst assemblages in recent sediments of Visakhapatnam harbour, east coast of India: Influence of environmental characteristics

    Digital Repository Service at National Institute of Oceanography (India)

    DeSilva, M.S.; Anil, A.C.; Sawant, S.S.

    . There are 18 and 6 berths in the inner and outer harbour area with two moorings respectively. The climate in Visakhapatnam is governed by its location in the tropics and mainly affected by seasonal monsoons (south–west and north–east). There is inadequate... was classified based on geographic location and environmental characteristics into two zones; the inner (Stations 1–14) and outer (Stations 15–24) harbour stations (Fig. 1). 2.3. Sediment sampling, processing and analysis for dinocysts Sediment samples were...

  8. Treerunners, cryptic lizards of the Plica plica group (Squamata, Sauria, Tropiduridae) of northern South America

    Science.gov (United States)

    Murphy, John C.; Jowers, Michael J.

    2013-01-01

    Abstract The arboreal, Neotropical lizard Plica plica (Linnaeus, 1758) has been long considered a widespread species with a distribution east of the Andes. A preliminary examination of 101 specimens from about 28 locations mostly north of the Amazon suggests that Plica plica is a cryptic species complex with taxa that can be distinguished on the basis of the number of scale rows at mid-body; the arrangement, shape and ornamentation of scales on the snout; the number of lamellae on the fourth toe; the number of subocular plates; as well as other commonly used external morphological traits. The allopatric species discussed here are concordant with northern South American geography. Plica plica (Linnaeus, 1758) is associated with the Guiana Shield (Suriname, Guyana and Venezuela). A second species, P. caribeana sp. n. is associated with the Caribbean Coastal Range of Venezuela including Trinidad and Tobago. A third, distinctive species, P. rayi sp. n. is associated with the middle Orinoco at the eastern edge of the Guiana Shield. Two other species, P. kathleenae sp. n. and P. medemi sp. n., each based upon a single specimen, one from the Sierra Acarai Mountains of Guyana, and the other from southern Meta, Colombia are described. In addition to morphological analyses, we sequenced 12S and 16S rDNA gene fragments from one Plica plica from Trinidad to assess its relationship and taxonomy to other mainland Plica cf. plica. The results suggest Plica caribeana sp. n. likely diverged prior to the separation of Trinidad from northern Venezuela. Isolation in the Caribbean Coastal Range during its rapid uplift in the late Miocene, combined with a marine incursion into northern Venezuela may have contributed to their genetic divergence from other populations. PMID:24363569

  9. The Identification of Land Subsidance by Levelling Measurement and GPR Data at Tanjung Emas Harbour, Semarang

    Directory of Open Access Journals (Sweden)

    Purnomo Raharjo

    2017-10-01

    Full Text Available Recently, the main problem in Semarang City is flood. This area has low relief that consists of coastal alluvial deposits, swamp and marine sediments. The coastline is characterized by muddy, sandy, and rocky coasts, and mangrove coast. Ground Penetrating Radar (GPR records, show that subsurface geological condition of northern part of Semarang is coastal alluvial deposit and in the south is volcanic rocks. The aims of this this research is to determine land subsidence by levelling measurement in 2005 in Tanjung Emas Harbour area built on 1995. During ten years, there are various land subsidance in this area: in Coaster Street (21 – 41 cm, container wharf (62 – 94 cm, north breakwater (64 – 79 cm, west breakwater (74 – 140 cm, east groin (76 – 89 cm, and stacking area ( 77 – 109 cm. According to this research, it is concluded that one reason causes of flooding in this area is land subsidence.

  10. Abundance and recruitment data for Undaria pinnatifida in Brest harbour, France: Model versus field results

    Directory of Open Access Journals (Sweden)

    James T. Murphy

    2016-06-01

    Full Text Available The data presented in this article are related to the research article entitled “A modelling approach to explore the critical environmental parameters influencing the growth and establishment of the invasive seaweed Undaria pinnatifida in Europe” [1]. This article describes raw simulation data output from a novel individual-based model of the invasive kelp species Undaria pinnatifida. It also includes field data of monthly abundance and recruitment values for a population of invasive U. pinnatifida (in Brest harbour, France that were used to validate the model. The raw model output and field data are made publicly available in order to enable critical analysis of the model predictions and to inform future modelling efforts of the study species.

  11. Kidnapping small icy asteroids in Earth near encounter to harbour life and to deflect trajectory

    Science.gov (United States)

    Fargion, Daniele

    2016-07-01

    The inter-planetary flight for human being is under danger because of unscreened and lethal solar flare radioactive showers. The screening of the astronauts by huge superconducting magnetic fields is unrealistic by many reasons. On the contrary the ability to reach nearby icy asteroids, to harbour there a complete undergound room where ecological life systems are first set, this goal may offer a later natural and safe currier for future human stations and enterprise. The need to deflect such a small size (a few thousands tons objects) maybe achieved by micro nuclear engines able to dig the asteroid icy skin, to heat and propel the soil by a synchronous jet engine array, bending and driving it to any desired trajectories. The need for such a wide collection of icy asteroid stations, often in a robotic ibernated state, it will offer the safe help station, raft in the wide space sea, where to collect material or energy in long human planetary travels.

  12. A comparative study of macrobenthic community from harbours along the central west coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Ingole, B.S.; Sivadas, S.; Nanajkar, M.; Sautya, S.; Nag, A.

    and exploitation for sustainable development and conservation on fish stocks, V.S. Somvanshi, (Ed.)), Fishery Survey of India, (pp 54-58). 17. Hines, A.H., Hadden, A.E. & Weichest, L.A. 1990. Guild structure and foraging impact of blue crabs and epibenthic fish...) between the harbours A 0 0.5 1 1.5 2 2.5 s p eci es r i ch n ess ± S E B 0 0.5 1 1.5 2 2.5 Rat1 Rat2 Goa 1 Goa 2 Kar 1 Kar 2 Stations D i ve r s it y ± S E 0 0.2 0.4 0.6 0.8 1 E ven n ess ± S E H J 23 Fig. 6: ABC curve...

  13. Incidence of Child cancers in the Finistere and around the Brest harbour between 1991 and 2005

    International Nuclear Information System (INIS)

    2008-01-01

    The objective of the study was to describe the temporal variations of child cancers incidence in the Finistere department and around the Brest harbour between 1991 and 2005 looking for any excess. In case of identification of an aggregate of cases, the secondary objective was to describe the aggregate by seeking common risk factors for cases in particular in relation to the activities of 'Ile Longue'. A leukemia excess was highlighted in Brest on the period 200-2005 and more particularly in 200-2001. This peak of incidence seems isolated in time, that is not in favour of a persistent environmental cause but should be the object of a follow-up in the future. Besides, no argument in favour of an occupational exposure of the parents of suffering children was highlighted. (N.C.)

  14. Environmental drivers of harbour porpoise fine‑scale movements

    DEFF Research Database (Denmark)

    van Beest, Floris; Teilmann, Jonas; Dietz, Rune

    2018-01-01

    Quantifying intraspecific variation in movement behaviour of marine predators and the underlying environmental drivers is important to inform conservation management of protected species. Here, we provide the first empirical data on fine-scale movements of free-ranging harbour porpoises (Phocoena...... of various static and dynamic environmental conditions on the movement characteristics: speed, turning angle, dive duration, dive depth, dive wiggliness (a proxy for prey chasing behaviour), and post-dive duration. Despite substantial individual differences in horizontal and vertical movement patterns, we...... found that all the tracked porpoises responded similar to variation in environmental conditions and displayed movements that indicate a higher likelihood of foraging behaviour in shallower and more saline waters. Our study contributes to the identification of important feeding areas for porpoises...

  15. Differential leaching of 137Cs from sediment core depth fractions of Bombay harbour bay

    International Nuclear Information System (INIS)

    Hemalatha, P.; Desai, M.V.M.

    1998-01-01

    Bombay harbour bay receives 137 Cs from the effluents of research reactors, fuel reprocessing plant and isotope laboratories. 137 Cs is strongly taken up by suspended particulates and sediments and is trapped in the layer lattices of the clay minerals. As the siltation rate is high in the bay, 137 Cs gets distributed vertically along the depth of sediment. NaCl solution has been proved to desorb 137 Cs from clay minerals effectively. NaCl solution of ionic strength 1.6 was used to desorb 137 Cs from depth fractions of a sediment core to obtain a possible gradient of leaching with the depth. A definite rate of leaching was observed for the 137 Cs in the core sediment depth fractions. About 13% to 56% of 137 Cs was leached. As the depth increases removal rate of cesium decreases. This is expected to bring out a relation between age of 137 Cs and rate of its leaching. (author)

  16. Canine distemper virus ISCOMS induce protection in harbour seals (Phoca vitulina) against phocid distemper but still allow subsequent infection with phocid distemper virus-1.

    NARCIS (Netherlands)

    I.K.G. Visser (Ilona); E.J. Vedder (Lies); C. Örvell; T. Barrett (Thomas); A.D.M.E. Osterhaus (Albert); M.W.G. van de Bildt (Marco)

    1992-01-01

    textabstractA candidate canine distemper virus (CDV) ISCOM vaccine has been shown to be effective in protecting harbour seals (Phoca vitulina) from phocid distemper in 1988. However, of the 35 harbour seals receiving this vaccine upon admission to a seal rehabilitation and research centre

  17. Movements and site fidelity of harbour seals (Phoca vitulina) in Kattegat, Denmark, with implications for the epidemiology of the phocine distemper virus

    DEFF Research Database (Denmark)

    Dietz, R.; Teilmann, J.; Andersen, S.M.

    2013-01-01

    Twenty-seven harbour seals were caught and tagged at the island of Anholt in central Kattegat, Denmark, the epicentre of the phocine distemper virus (PDV) outbreaks in 1988 and 2002 that killed 50–60% of the populations. The satellite tagging shows that harbour seals from Anholt moved widely across...

  18. Spatial avoidance to experimental increase of intermittent and continuous sound in two captive harbour porpoises.

    Science.gov (United States)

    Kok, Annebelle C M; Engelberts, J Pamela; Kastelein, Ronald A; Helder-Hoek, Lean; Van de Voorde, Shirley; Visser, Fleur; Slabbekoorn, Hans

    2018-02-01

    The continuing rise in underwater sound levels in the oceans leads to disturbance of marine life. It is thought that one of the main impacts of sound exposure is the alteration of foraging behaviour of marine species, for example by deterring animals from a prey location, or by distracting them while they are trying to catch prey. So far, only limited knowledge is available on both mechanisms in the same species. The harbour porpoise (Phocoena phocoena) is a relatively small marine mammal that could quickly suffer fitness consequences from a reduction of foraging success. To investigate effects of anthropogenic sound on their foraging efficiency, we tested whether experimentally elevated sound levels would deter two captive harbour porpoises from a noisy pool into a quiet pool (Experiment 1) and reduce their prey-search performance, measured as prey-search time in the noisy pool (Experiment 2). Furthermore, we tested the influence of the temporal structure and amplitude of the sound on the avoidance response of both animals. Both individuals avoided the pool with elevated sound levels, but they did not show a change in search time for prey when trying to find a fish hidden in one of three cages. The combination of temporal structure and SPL caused variable patterns. When the sound was intermittent, increased SPL caused increased avoidance times. When the sound was continuous, avoidance was equal for all SPLs above a threshold of 100 dB re 1 μPa. Hence, we found no evidence for an effect of sound exposure on search efficiency, but sounds of different temporal patterns did cause spatial avoidance with distinct dose-response patterns. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. The harbours in Bremen as a 'neutral zone' for nuclear fuels?

    International Nuclear Information System (INIS)

    Ruttloff, Marc

    2013-01-01

    The federal legislator has delivered his energy policy commitment as part of the energy turnaround with the decision on the forced backing out from nuclear energy to be completed until the end of 2022 at the latest. This was obviously not enough for the parliamentary groups of the SPD and Die Gruenen (Green party) of the Bremen City Parliament. With an Act dated 25 January 2012, the Bremen Parliament decided to amend the Harbour Operation Act insofar as '..the turnover of nuclear fuels in the sense of paragraph 2 Para. 1 of the Nuclear Act is excluded..'. This means that the turnover of nuclear fuels in the Bremer harbours is principally forbidden, unless the senate grants an explicit exception. However: Can a federal legislator enforce its energy policies like that? In order to receive an answer to this question, the representatives of the CDU parliamentary group of the Bremen Parliament lodged a complaint of unconstitutionality at the Bremen State Court of Justice. The decision was delivered on 12 April 2013 (AZ: St 1/12). And what answer did the CDU parliamentary group receive to their question? None. The Bremen State Court of Justice did not make a decision on this politically controversial issue. As its position, the State Court stated that the rules of the Basic Law on the limitations for the legislative jurisdiction between the Federation and the federal states do not constitute a component of the Bremen federal state constitution. And the legal criterion of the State Court of Justice is solely the Bremen constitution, not however, the Basic Law. In short: The State Court of Justice declares itself de facto not competent. (orig.)

  20. High-yielding Wheat Varieties Harbour Superior Plant Growth Promoting-Bacterial Endophytes

    Directory of Open Access Journals (Sweden)

    Mehwish Yousaf

    2017-06-01

    Full Text Available Background and Objective: The purpose of this study was to compare the endophytic microbial flora of different wheat varieties to check whether a better yielding variety also harbours superior plant growth promoting bacteria. Such bacteria are helpful in food biotechnology as their application can enhance the yield of the crop.Material and Methods: Three wheat varieties (Seher, Faisalabad and Lasani were selected, Seher being the most superior variety. endophytic bacteria were isolated from the histosphere of the leaves and roots at different growth phases of the plants. The isolates were analyzed for plant growth promoting activities. Isolates giving best results were identified through 16S rRNA gene sequencing. Statistical analysis was done using Microsoft Excel 2013. All the experiments were conducted in triplicates.Results and Conclusion: The endophytes of Seher variety showed maximum plant growth promoting abilities. Among the shoot endophytes, the highest auxin production was shown by Seher isolate SHHP1-3 up to 51.9μg ml-1, whereas in the case of root endophytes, the highest auxin was produced by SHHR1-5 up to 36 μg ml-1. The bacteria showing significant plant growth promoting abilities were identified by 16S rRNA sequencing. Bacillus, Proteobacteria and Actinobacteria species were the dominant bacteria showing all the traits of plant growth promotion. It can be concluded that Seher variety harbours superior plant growth promoting endophytes that must be one of the reasons for its better growth and yield as compared to the other two varieties. The investigated results support possible utilization of the selected isolates in wheat growth promotion with respect to increase in agro-productivity. The application of such bacteria could be useful to enhance wheat yield and can help in food biotechnology.Conflict of interest: The authors declare no conflict of interest.

  1. Testing the effects of an acoustic harassment device on the behaviour of harbour porpoises (Phocoena Phocoena)

    Energy Technology Data Exchange (ETDEWEB)

    Diederichs, Ansgar; Brandt, Miriam J.; Hoeschle, Caroline; Betke, Klaus; Nehls, Georg

    2011-07-01

    Full text: The use of monopile foundations for offshore wind farm construction goes along with considerable underwater noise emissions during pile driving, which can potentially harm marine mammals in the vicinity of the sound source. In order to avoid hearing damage in porpoises and seals the use of deterring devices is mandatory during pile driving in German waters. However, so far there is too little information to judge if the deterring effect is sufficient to prevent physical damage in these marine mammals. Using a combination of visual observations and passive acoustic monitoring (C-PODs) we investigated the spatial effects of a Lofitech seal scarer on harbour porpoises. The seal scarer emits pulses at 14 kHz at a source level of about 189dB re 1 muPa, and sound measurements at various distances where carried out. Sighting rates of porpoises significantly declined within the whole 1 km observation radius. Recordings of porpoise echolocation signals by C-PODs were significantly reduced out to a distance of 7 km, with the strongest effect at the nearest PODs and a weak effect at further distances. Minimum observed approach distance during 28 hours of seal scarer activity was 700 m. A response study revealed clear avoidance reactions by porpoises out to the maximum studied distance of 2.6 km. However, in some cases no reaction was found, and occasionally porpoises were also recorded by PODs at close distances. This shows that there may be substantial variation between individuals, different motivational states or different environmental conditions. These results show that the application of seal scarers is useful for reducing the number of harbour porpoises that may suffer hearing damage caused by pile driving. However, since complete exclusion of all animals cannot be achieved, alternative mitigation measures should be considered. (Author)

  2. Differences in the response of a striped dolphin (Stenella coeruleoalba) and a harbour porpoise (Phocoena phocoena) to an acoustic alarm

    NARCIS (Netherlands)

    Kastelein, R.A.; Jennings, N.; Verboom, W.C.; Haan, D.de; Schooneman, N.M.

    2006-01-01

    Small cetacean bycatch in gillnet fisheries may be reduced by deterring odontocetes from nets acoustically. However, different odontocete species may respond differently to acoustic signals from alarms. Therefore, in this study a striped dolphin and a harbour porpoise were subjected simultaneously

  3. Differences in the response of a striped dolphin (Stenella coeruleoalba) and a harbour popoise (Phocoena phocoena) to an acoustic alarm

    NARCIS (Netherlands)

    Kastelein, R.A.; Jennings, N.; Verboom, W.C.; Haan, de D.; Schooneman, N.M.

    2006-01-01

    Small cetacean bycatch in gillnet fisheries may be reduced by deterring odontocetes from nets acoustically. However, different odontocete species may respond differently to acoustic signals from alarms. Therefore, in this study a striped dolphin and a harbour porpoise were subjected simultaneously

  4. In search of virus carriers of the 1988 and 2002 phocine distemper virus outbreaks in European harbour seals

    NARCIS (Netherlands)

    Kreutzer, M.; Kreutzer, R.; Siebert, U.; Muller, G.; Reijnders, P.J.H.; Brasseur, S.M.J.M.; Harkonen, T.; Dietz, R.; Sonne, C.; Born, E.W.; Baumgartner, W.

    2008-01-01

    European harbour seal (Phoca vitulina) populations decreased substantially during the phocine distemper virus (PDV) outbreaks of 1988 and 2002. Different hypotheses have stated that various seals and terrestrial carnivore species might be the source of infection. To further analyse these hypotheses,

  5. Vaccination of harbour seals (Phoca vitulina) against phocid distemper with two different inactivated canine distemper virus (CDV) vaccines.

    NARCIS (Netherlands)

    I.K.G. Visser (Ilona); M.W.G. van de Bildt (Marco); H.N. Brugge; P.J.H. Reijnders; E.J. Vedder (Lies); J. Kuiper; P. de Vries (Petra); J. Groen (Jan); H.C. Walvoort; F.G.C.M. Uytdehaag (Fons); A.D.M.E. Osterhaus (Albert)

    1989-01-01

    textabstractTwo inactivated canine distemper virus (CDV) vaccines--an adjuvanted whole inactivated virus and a subunit ISCOM preparation--were tested for their ability to induce protective immunity in harbour seals (Phoca vitulina) against phocid distemper, a disease that recently killed greater

  6. Applicability of market-based instruments for safeguarding water quality in coastal waterways: Case study for Darwin Harbour, Australia

    Science.gov (United States)

    Greiner, Romy

    2014-02-01

    Water pollution of coastal waterways is a complex problem due to the cocktail of pollutants and multiplicity of polluters involved and pollution characteristics. Pollution control therefore requires a combination of policy instruments. This paper examines the applicability of market-based instruments to achieve effective and efficient water quality management in Darwin Harbour, Northern Territory, Australia. Potential applicability of instruments is examined in the context of biophysical and economic pollution characteristics, and experience with instruments elsewhere. The paper concludes that there is potential for inclusion of market-based instruments as part of an instrument mix to safeguard water quality in Darwin Harbour. It recommends, in particular, expanding the existing licencing system to include quantitative pollution limits for all significant point polluters; comprehensive and independent pollution monitoring across Darwin Harbour; public disclosure of water quality and emissions data; positive incentives for landholders in the Darwin Harbour catchment to improve land management practices; a stormwater offset program for greenfield urban developments; adoption of performance bonds for developments and operations which pose a substantial risk to water quality, including port expansion and dredging; and detailed consideration of a bubble licensing scheme for nutrient pollution. The paper offers an analytical framework for policy makers and resource managers tasked with water quality management in coastal waterways elsewhere in Australia and globally, and helps to scan for MBIs suitable in any given environmental management situation.

  7. Passive acoustic monitoring of bottlenose dolphin and harbour porpoise, in Cardigan Bay, Wales, with implications for habitat use and partitioning

    DEFF Research Database (Denmark)

    Simon, Malene Juul; Nuuttila, Hanna; Reyes-Zamudio, Mercedes M

    2010-01-01

    Knowledge about harbour porpoise and bottlenose dolphin occurrence in Cardigan Bay Special Area of Conservation (SAC), Wales, is limited to daylight hours during summer, when conditions are suitable for traditional visual surveys. T-PODs are autonomous instruments programmed to log time-cues of s...

  8. Modelling the distribution of hard seabed using calibrated multibeam acoustic backscatter data in a tropical, macrotidal embayment: Darwin Harbour, Australia

    Science.gov (United States)

    Siwabessy, P. Justy W.; Tran, Maggie; Picard, Kim; Brooke, Brendan P.; Huang, Zhi; Smit, Neil; Williams, David K.; Nicholas, William A.; Nichol, Scott L.; Atkinson, Ian

    2018-06-01

    Spatial information on the distribution of seabed substrate types in high use coastal areas is essential to support their effective management and environmental monitoring. For Darwin Harbour, a rapidly developing port in northern Australia, the distribution of hard substrate is poorly documented but known to influence the location and composition of important benthic biological communities (corals, sponges). In this study, we use angular backscatter response curves to model the distribution of hard seabed in the subtidal areas of Darwin Harbour. The angular backscatter response curve data were extracted from multibeam sonar data and analysed against backscatter intensity for sites observed from seabed video to be representative of "hard" seabed. Data from these sites were consolidated into an "average curve", which became a reference curve that was in turn compared to all other angular backscatter response curves using the Kolmogorov-Smirnov goodness-of-fit. The output was used to generate interpolated spatial predictions of the probability of hard seabed ( p-hard) and derived hard seabed parameters for the mapped area of Darwin Harbour. The results agree well with the ground truth data with an overall classification accuracy of 75% and an area under curve measure of 0.79, and with modelled bed shear stress for the Harbour. Limitations of this technique are discussed with attention to discrepancies between the video and acoustic results, such as in areas where sediment forms a veneer over hard substrate.

  9. Variations of the entrepreneurial city: Goals, roles visions in Rotterdam’s Kop van Zuid and the Glasgow Harbour megaprojects

    NARCIS (Netherlands)

    Doucet, B.M.

    2013-01-01

    Both Rotterdam’s Kop van Zuid and the Glasgow Harbour waterfront developments are examples of different forms of European urban entrepreneurial megaprojects. They are both situated on formerly vacant land in older industrial cities. In Rotterdam, the municipality has taken the initiative in

  10. Comparison of 2-compartment, 3-compartment and stack designs for electrodialytic removal of heavy metals from harbour sediments

    DEFF Research Database (Denmark)

    Pedersen, Kristine B.; Ottosen, Lisbeth M.; Jensen, Pernille Erland

    2015-01-01

    Comparisons of cell and stack designs for the electrodialytic removal of heavy metals from two harbour sediments, were made. Multivariate modelling showed that sediment properties and experimental set-ups had the highest influence on the heavy metal removal indicating that they should be modelled...

  11. Fine-scale hydrodynamics influence the spatio-temporal distribution of harbour porpoises at a coastal hotspot

    NARCIS (Netherlands)

    Jones, A.R.; Hosegood, P.; Wynn, R.B.; Boer, de M.N.; Butler-Cowdry, S.; Embling, C.B.

    2014-01-01

    The coastal Runnelstone Reef, off southwest Cornwall (UK), is characterised by complex topography and strong tidal flows and is a known high-density site for harbour porpoise (Phocoena phocoena); a European protected species. Using a multidisciplinary dataset including: porpoise sightings from a

  12. Application of a Spectral Wave Model to Assess Breakwater Configurations at a Small Craft Harbour on Lake Ontario

    Directory of Open Access Journals (Sweden)

    Amelia H. Cooper

    2016-08-01

    Full Text Available A surface wave model using three nested grids is applied to the eastern end of Lake Ontario to investigate wave propagation from an open lake environment to a small craft harbour protected by a breakwater. The Simulating WAves Nearshore (SWAN spectral wave model, coupled with the Delft3D hydrodynamic model, is applied to simulate a series of storms in November, 2013. The model results are compared to observations from two pressure sensors, and used to quantify wave properties around existing and future breakwaters to evaluate the bulk changes to the harbour configuration. Overall, the results indicate that the rubblemound breakwater reduces wave heights in the existing harbour by 63% compared to no breakwater, and that the addition of a surface breakwater extension could reduce wave heights by an additional 54%. Wave height attenuation was found to be highly dependent on the incident wave direction relative to breakwater orientation. The spectral wave model is useful for simulating wave transformation for broad directional spectra in wind-sea conditions over large scales to semi-protected areas such as small craft harbours.

  13. What a jerk: prey engulfment revealed by high-rate, super-cranial accelerometry on a harbour seal (Phoca vitulina)

    DEFF Research Database (Denmark)

    Ydesen, Kristina S; Wisniewska, Danuta Maria; Hansen, Janni D

    2014-01-01

    in particular shaped dives or when the animal remains in an area for an extended interval. However, fast movements of the head and jaws may provide reliable feeding cues that can be detected by small low-power accelerometers mounted on the head. To test this notion, a harbour seal (Phoca vitulina) was trained...

  14. Biogeography of tropical Indo-West Pacific parasites: a cryptic species of Transversotrema and evidence for rarity of Transversotrematidae (Trematoda) in French Polynesia.

    Science.gov (United States)

    Cribb, Thomas H; Adlard, Robert D; Bray, Rodney A; Sasal, Pierre; Cutmore, Scott C

    2014-04-01

    We sought transversotrematid trematodes from French Polynesian fishes by examining 304 individual scaled fishes of 53 species from seven families known to harbour the family elsewhere. A single species was found at two locations in the Tuamotus Archipelago on two species of Chaetodontidae (Chaetodon auriga and Chaetodon ephippium) and one species of Lutjanidae (Lutjanus gibbus). The species closely resembles Transversotrema borboleta Hunter & Cribb, 2012 from chaetodontids and lutjanids of the northern Great Barrier Reef (GBR) but differs from it consistently in 8 base positions of ITS2 rDNA. This level of variation exceeds that between some clearly morphologically distinct pairs of species of Transversotrema and the form from French Polynesia is thus interpreted as a distinct, though cryptic, species and named Transversotrema polynesiae n. sp. The new species forms part of a complex of species, here characterised as the T. borboleta complex, associated with chaetodontids and lutjanids in the tropical Indo-West Pacific. Most of the putative species within this complex are yet to be described. Comparison of identical numbers of matched samples of fishes from French Polynesia, Heron Island (southern GBR) and Lizard Island (northern GBR) revealed 1, 4 and 10 species of Transversotrema respectively suggesting that the French Polynesian fauna is depauperate for this family. In addition to those species apparently missing from suitable hosts in French Polynesia, several species from further west infect fishes (especially Nemipteridae) that are themselves absent from French Polynesia. This dramatic east-west decline in richness contrasts strongly with what is known for monogeneans, which appear to maintain their richness over the same scale, and is more precipitate than is known for other groups of trematodes. The decline might be explained in part by the absence of the as yet unknown first intermediate hosts in French Polynesia. However, we predict that it is explained

  15. Dredging up the past -- removal of historic low-level radioactive sediment from the Port Hope harbour

    Energy Technology Data Exchange (ETDEWEB)

    Case, G. [Atomic Energy of Canada Limited, Port Hope, ON (Canada); Kolberg, M. [Baird, Oakville, ON (Canada)

    2011-07-01

    Port Hope is located on the northern shore of Lake Ontario at the confluence of the Ganaraska River and has existed as a Port of Entry since at least 1819. Once operated as a major Lake Ontario port, through periods of vibrant industrial growth, it is now a recreational anchorage for the local yacht club. The history of the Port Hope harbour from the early 1800s to today is typical of other small-town ports along Lake Ontario that have experienced growth and decline in direct relation to Great Lake shipping volumes and the shift in industry and commerce to larger urban areas. However, in the case of the Port Hope harbour, the presence of low-level radioactive sediment, resulting from a former radium and uranium refinery that operated alongside the harbour, currently limits redevelopment and revitalization opportunities. The presence of low-level radioactive waste is not limited to only harbour sediments. Several other on-land locations within the community are also affected by the low-level radioactive waste management practices of the past. To address these situations, the Port Hope Area Initiative project is currently underway to implement a local, safe, long-term waste management solution. The Port Hope Area Initiative is a community initiated undertaking that will result in the consolidation of an estimated 1.2 million cubic metres of the low-level radioactive waste from the various sites in Port Hope into a new engineered above ground long-term waste management facility. The remedial cleanup of the estimated 120,000 cubic metres of contaminated sediments from the Port Hope harbour is one of the more challenging components of the Initiative. This paper demonstrates how the historical development of the harbour over the past 200 years, the nature and extent of the contaminated sediments, and Municipality of Port Hope’s desires for future redevelopment of the waterfront area have all played a role in the design of the remedial cleanup plan for the Port Hope

  16. Dredging up the past -- removal of historic low-level radioactive sediment from the Port Hope harbour

    International Nuclear Information System (INIS)

    Case, G.; Kolberg, M.

    2011-01-01

    Port Hope is located on the northern shore of Lake Ontario at the confluence of the Ganaraska River and has existed as a Port of Entry since at least 1819. Once operated as a major Lake Ontario port, through periods of vibrant industrial growth, it is now a recreational anchorage for the local yacht club. The history of the Port Hope harbour from the early 1800s to today is typical of other small-town ports along Lake Ontario that have experienced growth and decline in direct relation to Great Lake shipping volumes and the shift in industry and commerce to larger urban areas. However, in the case of the Port Hope harbour, the presence of low-level radioactive sediment, resulting from a former radium and uranium refinery that operated alongside the harbour, currently limits redevelopment and revitalization opportunities. The presence of low-level radioactive waste is not limited to only harbour sediments. Several other on-land locations within the community are also affected by the low-level radioactive waste management practices of the past. To address these situations, the Port Hope Area Initiative project is currently underway to implement a local, safe, long-term waste management solution. The Port Hope Area Initiative is a community initiated undertaking that will result in the consolidation of an estimated 1.2 million cubic metres of the low-level radioactive waste from the various sites in Port Hope into a new engineered above ground long-term waste management facility. The remedial cleanup of the estimated 120,000 cubic metres of contaminated sediments from the Port Hope harbour is one of the more challenging components of the Initiative. This paper demonstrates how the historical development of the harbour over the past 200 years, the nature and extent of the contaminated sediments, and Municipality of Port Hope’s desires for future redevelopment of the waterfront area have all played a role in the design of the remedial cleanup plan for the Port Hope

  17. Phylogenetic relationships and cryptic species diversity in the Brazilian egg-brooding tree frog, genus Fritziana Mello-Leitão 1937 (Anura: Hemiphractidae).

    Science.gov (United States)

    Walker, Marina; Lyra, Mariana L; Haddad, Célio F B

    2018-06-01

    The genus Fritziana (Anura: Hemiphractidae) comprises six described species (F. goeldii, F. ohausi, F. fissilis, F. ulei, F. tonimi, and F. izecksohni) that are endemic to the Brazilian Atlantic Forest. Although the genus has been the subject of studies dealing with its taxonomy, phylogeny, and systematics, there is considerable evidence for cryptic diversity hidden among the species. The present study aims to understand the genetic diversity and phylogenetic relationships among the species of Fritziana, as well as the relationships among populations within species. We analyzed 107 individuals throughout the distribution of the genus using three mitochondrial gene fragments (12S, 16S, and COI) and two nuclear genes (RAG1 and SLC8A3). Our data indicated that the species diversity in the genus Fritziana is underestimated by the existence of at least three candidate species hidden amongst the group of species with a closed dorsal pouch (i.e. F. fissilis and F. ulei). We also found four species presenting geographical population structures and high genetic diversity, and thus require further investigations. In addition, we found that two candidate species show a new arrangement for the tRNA-Phe gene, unique in Anura so far. Based on our results, we suggest that the conservation status of the species, as well as the species diversity in the genus Fritziana, needs to be reviewed. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. Members of Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species and the Status of Two Invasive Alien Species in the Yunnan Province (China)

    Science.gov (United States)

    Hu, Jian; Jiang, Zhi-Lin; Nardi, Francesco; Liu, Yuan-Yuan; Luo, Xiao-Rong; Li, Hong-Xiang; Zhang, Zhong-Kai

    2014-01-01

    Abstract Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a cryptic species complex that includes some of the most significant pests of agriculture and horticulture worldwide. To understand the diversity and distribution of B. tabaci cryptic species in Yunnan, a famous biodiversity hotspot in China, a large-scale sampling was conducted from year 2010 to 2013 in 10 prefectures. Mitochondrial cytochrome oxidase I gene sequences were used to identify different cryptic species. Phylogenetic analyses were performed using Bayesian methods to assess the position of a new B. tabaci cryptic species in the context of the B. tabaci diversity in Asia. The survey indicates at least eight B. tabaci cryptic species are present in Yunnan, two invasive (MEAM1 and MED) and six indigenous (China 2, China3, China 4, Asia I, Asia II 1, and Asia II 6), MEAM1, MED, and Asia I being the three predominant cryptic species in Yunnan. Compared with MEAM1, MED has a wider distribution. Based on molecular data, a new cryptic species, here named China 4, was identified that appears to be related to China 1, China 2, and China 3. Future efforts should focus on the interactions between predominant B. tabaci cryptic species and begomoviruses and on the development of effective control strategies. PMID:25502045

  19. The taxonomy of the Caloplaca citrina group (Teloschistaceae) in the Black Sea region; with contributions to the cryptic species concept in lichenology

    DEFF Research Database (Denmark)

    Vondrák, Jan; RÍHA, Pavel; ARUP, Ulf

    2009-01-01

    . The variability and taxonomic importance of particular features are discussed. No significant differences in secondary chemistry were observed among the species. Many examples of convergence and some semi-cryptic species were revealed by molecular data. The term ‘semi-cryptic species' is introduced here...

  20. Biological variables and health status affecting inorganic element concentrations in harbour porpoises (Phocoena phocoena) from Portugal (western Iberian Peninsula)

    International Nuclear Information System (INIS)

    Ferreira, Marisa; Monteiro, Silvia S.; Torres, Jordi; Oliveira, Isabel; Sequeira, Marina; López, Alfredo

    2016-01-01

    The coastal preferences of harbour porpoise (Phocoena phocoena) intensify their exposure to human activities. The harbour porpoise Iberian population is presently very small and information about the threats it endures is vital for the conservation efforts that are being implemented to avoid local extinction. The present study explored the possible relation between the accumulation of trace elements by porpoises and their sex, body length, nutritional state, presence of parasites and gross pathologies. The concentrations of arsenic (As), cadmium (Cd), copper (Cu), mercury (Hg), manganese (Mn), nickel (Ni), lead (Pb), zinc (Zn) and selenium (Se) were evaluated in 42 porpoises stranded in Portugal between 2005 and 2013. Considering European waters, porpoises stranded in Portugal present the highest Hg concentrations and the lowest Cd concentrations, which may reflect dietary preferences and the geographic availability of these pollutants. While no effect of sex on trace element concentrations was detected, there was a positive relationship between porpoise body length and the concentration of Cd, Hg and Pb. Animals in worse nutritional condition showed higher levels of Zn. Harbour porpoises with high parasite burdens showed lower levels of Zn and As in all analysed tissues and also lower levels of renal Ni, while those showing gross pathologies presented higher Zn and Hg levels. This is the first data on the relationship between trace elements and health-related variables in porpoises from southern European Atlantic waters, providing valuable baseline information about the contamination status of this vulnerable population. - Highlights: • High levels of mercury in harbour porpoises from Portugal. • Evidence of bioaccumulation of non-essential trace elements. • Presence of parasites influenced some essential trace elements. • Evidence of nutritional state effect on Zn levels. • Presence of gross pathologies influenced Zn and Hg levels. - The small harbour

  1. DNA barcoding reveals a cryptic nemertean invasion in Atlantic and Mediterranean waters

    Science.gov (United States)

    Fernández-Álvarez, Fernando Ángel; Machordom, Annie

    2013-09-01

    For several groups, like nemerteans, morphology-based identification is a hard discipline, but DNA barcoding may help non-experts in the identification process. In this study, DNA barcoding is used to reveal the cryptic invasion of Pacific Cephalothrix cf. simula into Atlantic and Mediterranean coasts. Although DNA barcoding is a promising method for the identification of Nemertea, only 6 % of the known number of nemertean species is currently associated with a correct DNA barcode. Therefore, additional morphological and molecular studies are necessary to advance the utility of DNA barcoding in the characterisation of possible nemertean alien invasions.

  2. DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes.

    Directory of Open Access Journals (Sweden)

    Tun Nurul Aimi Mat Jaafar

    Full Text Available BACKGROUND: DNA barcodes, typically focusing on the cytochrome oxidase I gene (COI in many animals, have been used widely as a species-identification tool. The ability of DNA barcoding to distinguish species from a range of taxa and to reveal cryptic species has been well documented. Despite the wealth of DNA barcode data for fish from many temperate regions, there are relatively few available from the Southeast Asian region. Here, we target the marine fish Family Carangidae, one of the most commercially-important families from the Indo-Malay Archipelago (IMA, to produce an initial reference DNA barcode library. METHODOLOGY/PRINCIPAL FINDINGS: Here, a 652 bp region of COI was sequenced for 723 individuals from 36 putative species of Family Carangidae distributed within IMA waters. Within the newly-generated dataset, three described species exhibited conspecific divergences up to ten times greater (4.32-4.82% than mean estimates (0.24-0.39%, indicating a discrepancy with assigned morphological taxonomic identification, and the existence of cryptic species. Variability of the mitochondrial DNA COI region was compared within and among species to evaluate the COI region's suitability for species identification. The trend in range of mean K2P distances observed was generally in accordance with expectations based on taxonomic hierarchy: 0% to 4.82% between individuals within species, 0% to 16.4% between species within genera, and 8.64% to 25.39% between genera within families. The average Kimura 2-parameter (K2P distance between individuals, between species within genera, and between genera within family were 0.37%, 10.53% and 16.56%, respectively. All described species formed monophyletic clusters in the Neighbour-joining phylogenetic tree, although three species representing complexes of six potential cryptic species were detected in Indo-Malay Carangidae; Atule mate, Selar crumenophthalmus and Seriolina nigrofasciata. CONCLUSION/SIGNIFICANCE: This

  3. A Cryptic Sulfur Cycle in Oxygen-Minimum-Zone Waters off the Chilean Coast

    Science.gov (United States)

    Canfield, Don E.; Stewart, Frank J.; Thamdrup, Bo; De Brabandere, Loreto; Dalsgaard, Tage; Delong, Edward F.; Revsbech, Niels Peter; Ulloa, Osvaldo

    2010-12-01

    Nitrogen cycling is normally thought to dominate the biogeochemistry and microbial ecology of oxygen-minimum zones in marine environments. Through a combination of molecular techniques and process rate measurements, we showed that both sulfate reduction and sulfide oxidation contribute to energy flux and elemental cycling in oxygen-free waters off the coast of northern Chile. These processes may have been overlooked because in nature, the sulfide produced by sulfate reduction immediately oxidizes back to sulfate. This cryptic sulfur cycle is linked to anammox and other nitrogen cycling processes, suggesting that it may influence biogeochemical cycling in the global ocean.

  4. [Interpretation of laboratory data during cryptic leishmaniasis in dog].

    Science.gov (United States)

    Gravino, A E

    2004-06-01

    Leishmaniasis is a zoonosis caused by an intracellular parasite belonging to the genus Leishmania. In Europe, Africa, South America and China, visceral leishmaniasis is caused by L. infantum. The vectors of leishmaniasis are phlebotomine sandflies belonging to the genera Phlebotomus. According to the World Health Organization there are 2 million new cases each year and 1/10 of the world's population is at risk of infection. Leishmaniasis is considered a zoonosis and human are generally accidental hosts. The animal reservoir includes rodents, dog and other mammals. Several studies have indicate that half of the dogs with antileishmanial antibodies have no signs of disease although, animal with subclinical infections are potentially infectious to sand flies. The factors determining susceptibility or resistence to visceral leishmaniasis remain unclear, but the genetics of the host may play a major role. Clinical signs are: intermittent fever, hepatosplenomegaly, skin lesions and ulcers, alopecia, onychogryphosis, anemia, thrombocytopenia and hypergammaglobulinemia. In mice, the outcome of infection depends on the polarized activation of one of two subsets of CD4+ T cells, Th1 or Th2, the subdivision into Th1 and Th2 cells is based on the pattern of cytokines that they produce. Th1 cells produce gamma interferon (IFN-gamma) and interleukin -2 (IL-2), whereas Th2 cells produce IL-4, IL-5, and IL-10. An important difference between susceptible and resistant mice is that the resistant mice are able to switch to a Th1 profile and control the disease. An important factor in the "decision" to form a Th1 or Th2 phenotype is the early cytokine environment, and IL-12 is one of the cytokines that contributes significantly to the establishment of the Th1 phenotype. Canine leishmaniosis is endemic in the Mediterranean basin and, in most cases is caused by the parasite Leishmania infantum. The main clinical findings are skin lesions, local or generalized lymphoadenopathy, loss of

  5. Insights into Penicillium roqueforti Morphological and Genetic Diversity

    Science.gov (United States)

    Gillot, Guillaume; Jany, Jean-Luc; Coton, Monika; Le Floch, Gaétan; Debaets, Stella; Ropars, Jeanne; López-Villavicencio, Manuela; Dupont, Joëlle; Branca, Antoine; Giraud, Tatiana; Coton, Emmanuel

    2015-01-01

    Fungi exhibit substantial morphological and genetic diversity, often associated with cryptic species differing in ecological niches. Penicillium roqueforti is used as a starter culture for blue-veined cheeses, being responsible for their flavor and color, but is also a common spoilage organism in various foods. Different types of blue-veined cheeses are manufactured and consumed worldwide, displaying specific organoleptic properties. These features may be due to the different manufacturing methods and/or to the specific P. roqueforti strains used. Substantial morphological diversity exists within P. roqueforti and, although not taxonomically valid, several technological names have been used for strains on different cheeses (e.g., P. gorgonzolae, P. stilton). A worldwide P. roqueforti collection from 120 individual blue-veined cheeses and 21 other substrates was analyzed here to determine (i) whether P. roqueforti is a complex of cryptic species, by applying the Genealogical Concordance Phylogenetic Species Recognition criterion (GC-PSR), (ii) whether the population structure assessed using microsatellite markers correspond to blue cheese types, and (iii) whether the genetic clusters display different morphologies. GC-PSR multi-locus sequence analyses showed no evidence of cryptic species. The population structure analysis using microsatellites revealed the existence of highly differentiated populations, corresponding to blue cheese types and with contrasted morphologies. This suggests that the population structure has been shaped by different cheese-making processes or that different populations were recruited for different cheese types. Cheese-making fungi thus constitute good models for studying fungal diversification under recent selection. PMID:26091176

  6. Biological and chemical characterization of harbour sediments from the Stockholm area

    Energy Technology Data Exchange (ETDEWEB)

    Eklund, Britta; Elfstroem, Maria; Bengtsson, Bengt-Erik; Breitholtz, Magnus [Dept. of Applied Environmental Science (ITM), Stockholm Univ. (Sweden); Gallego, Irene [Granada Univ. (Spain)

    2010-01-15

    Purpose: The main objective of the current study was to assess the impact of pleasure boat activities on harbour sediment quality in the Stockholm area. Sediment contamination is a growing ecological issue, and there is consequently a need to use sediment bioassays in combination with chemical analysis to determine the impact on the ecosystem. To generate sediment toxicity data relevant for the Baltic Sea, a secondary objective was to further develop and evaluate two well-established bioassays for saltwater, with the macroalga Ceramium tenuicorne and the crustacean Nitocra spinipes, to be useful also for toxicity testing of whole sediment. A major concern has been to minimize any manipulation of the sediments. A third objective was to assess whether a simple leaching procedure could be used to simulate sediment toxicity by comparing results from whole sediment and leachate tests. Materials and methods: Surface sediments (0-2 cm) from five different types of pleasure boat harbours were collected. Chemical measurements of boat related compounds, i.e. tin organic substances (tributyltin (TBT), dibutyl tin, and monobutyl tin), polyaromatic hydrocarbons (PAHs), copper, zinc, lead, tin and irgarol were conducted. The sediments were tested for toxic effects using the established Microtox {sup registered} test as well as the developed sediment tests with C. tenuicorne and N. spinipes. The endpoints are growth inhibition for the algal test and for the crustacean test mortality of larvae and rate of development expressed as the ratio between nauplia and copepodites. Two different procedures have been compared with both organisms, i.e. exposure to whole sediment and to leachate. The duration of both tests is around 1 week. Results and discussion: All harbour locations were more or less heavily contaminated with remnants from use of antifouling paints. The sediment in a smaller marina (ca. 250 boats) contained the highest levels of TBT (max 1,400 {mu}g/kg dry weight (dw

  7. Growth of plants on TBT-contaminated harbour sludge and effect on TBT removal.

    Science.gov (United States)

    Novak, Jana; Trapp, Stefan

    2005-11-01

    Worldwide, large amounts of sediments have to be dredged annually from waterways and harbours. These sediments are sometimes polluted with a variety of toxic compounds. In some countries, including Belgium, the load with the biocide tributyltin (TBT) from ship coatings prohibits the dumping of harbour sludge into the sea. Land-based dumping is a commonly used alternative. This research investigated the feasibility to use land-deposited harbour sludge for plant production. In a field trial, the growth of 38 more or less salt-tolerant plant species on low and high TBT-contaminated sediments was studied. The elimination of TBT from sludge with and without vegetation was compared. The uptake of TBT and its degradation products di- and monobutyltin (DBT and MBT) into harvest products under field conditions was determined. EXPERIMENTAL SET-UP: Sediments dredged in May 2003 from the brackish waters of the port of Antwerp were analysed in the laboratory for soil texture, pH, electroconductivity, sodium, magnesium, potassium, calcium, ammonium, nitrate, total nitrogen, chloride, sulphur and the organotins TBT, DBT and MBT. The sediments were lagooned for one year to dewater, desalinate and improve their structure. Salt-tolerant domestic and wild plants were selected and sown in May 2004. In August 2004, plants were harvested and the produced biomass was determined. Samples were taken from vegetated and non-vegetated top and bottom sediments and from plants growing above soil and analysed for TBT, DBT and MBT. The fresh sediments showed a good supply with nutrients and a neutral pH, but were rather saline (EC 14 mS cm(-1) of the saturated paste extract). The salinity decreased to 3.7 mS cm(-1) during lagoonation. The high and the low contaminated sediment had initially 43 and 1.6 mg TBT kg(-1) dry weight, respectively. Besides TBT, several other contaminants were present in the sediments at critical levels. The biomass production of the plant species from the field trial

  8. Relating desorption of polycyclic aromatic hydrocarbons from harbour sludges to type of organic material

    Science.gov (United States)

    Heister, K.; Pols, S.; Loch, J. P. G.; Bosma, T.

    2009-04-01

    For decades, polycyclic aromatic hydrocarbons (PAH) cause great concern as environmental pollutants. Especially river and marine harbour sediments are frequently polluted with PAH derived from surface runoff, fuel and oil spills due to shipping and industrial activities, industrial waste and atmospheric deposition. Harbour sediments contain large amounts of organic carbon and clay minerals and are therefore not easy to remediate and have to be stored in sludge depositories after dredging to maintain sufficient water depth for shipping. The organic contaminants will be adsorbed to particles, leached in association with dissolved organic material or microbially degraded. However, compounds of high molecular weight are very persistent, particularly under anaerobic conditions, thus giving rise to the potential to become desorbed again. PAH adsorb mainly to organic material. It has been shown that components of the organic material with a low polarity and a high hydrophobicity like aliphatic and aromatic components exhibit a high sorption capacity for hydrophobic organic contaminants like PAH. Accordingly, not only the amount but also the type of organic material needs to be determined in order to be able to predict contaminant behaviour. In this study, desorption behaviour of the 16 EPA-PAH in two different harbour sludges from the port of Rotterdam, the Netherlands, has been investigated. The Beerkanaal (BK) site is located relatively close to the North Sea and represents a brackish environment; the Beneden Merwede River (BMR) site originates from a fresh water environment and is close to industrial sites. The samples were placed in dialysis membranes and brought into contact with water for a period of 130 days. At several time intervals, water samples were retrieved for analysis of pH, dissolved organic carbon (DOC) content, electrical conductivity and PAH concentrations. The experiment was conducted at 4 and at 20°C. Although the samples were initially treated with

  9. Identification and dynamics of a cryptic suture zone in tropical rainforest

    Science.gov (United States)

    Moritz, C.; Hoskin, C.J.; MacKenzie, J.B.; Phillips, B.L.; Tonione, M.; Silva, N.; VanDerWal, J.; Williams, S.E.; Graham, C.H.

    2009-01-01

    Suture zones, shared regions of secondary contact between long-isolated lineages, are natural laboratories for studying divergence and speciation. For tropical rainforest, the existence of suture zones and their significance for speciation has been controversial. Using comparative phylogeographic evidence, we locate a morphologically cryptic suture zone in the Australian Wet Tropics rainforest. Fourteen out of 18 contacts involve morphologically cryptic phylogeographic lineages, with mtDNA sequence divergences ranging from 2 to 15 per cent. Contact zones are significantly clustered in a suture zone located between two major Quaternary refugia. Within this area, there is a trend for secondary contacts to occur in regions with low environmental suitability relative to both adjacent refugia and, by inference, the parental lineages. The extent and form of reproductive isolation among interacting lineages varies across species, ranging from random admixture to speciation, in one case via reinforcement. Comparative phylogeographic studies, combined with environmental analysis at a fine-scale and across varying climates, can generate new insights into suture zone formation and to diversification processes in species-rich tropical rainforests. As arenas for evolutionary experimentation, suture zones merit special attention for conservation. PMID:19203915

  10. A human PrM antibody that recognizes a novel cryptic epitope on dengue E glycoprotein.

    Directory of Open Access Journals (Sweden)

    Annie Hoi Yi Chan

    Full Text Available Dengue virus (DENV is a major mosquito-borne pathogen infecting up to 100 million people each year; so far no effective treatment or vaccines are available. Recently, highly cross-reactive and infection-enhancing pre-membrane (prM-specific antibodies were found to dominate the anti-DENV immune response in humans, raising concern over vaccine candidates that contain native dengue prM sequences. In this study, we have isolated a broadly cross-reactive prM-specific antibody, D29, during a screen with a non-immunized human Fab-phage library against the four serotypes of DENV. The antibody is capable of restoring the infectivity of virtually non-infectious immature DENV (imDENV in FcγR-bearing K562 cells. Remarkably, D29 also cross-reacted with a cryptic epitope on the envelope (E protein located to the DI/DII junction as evidenced by site-directed mutagenesis. This cryptic epitope, while inaccessible to antibody binding in a native virus particle, may become exposed if E is not properly folded. These findings suggest that generation of anti-prM antibodies that enhance DENV infection may not be completely avoided even with immunization strategies employing E protein alone or subunits of E proteins.

  11. Medical data sheet in safe havens - A tri-layer cryptic solution.

    Science.gov (United States)

    Praveenkumar, Padmapriya; Amirtharajan, Rengarajan; Thenmozhi, K; Balaguru Rayappan, John Bosco

    2015-07-01

    Secured sharing of the diagnostic reports and scan images of patients among doctors with complementary expertise for collaborative treatment will help to provide maximum care through faster and decisive decisions. In this context, a tri-layer cryptic solution has been proposed and implemented on Digital Imaging and Communications in Medicine (DICOM) images to establish a secured communication for effective referrals among peers without compromising the privacy of patients. In this approach, a blend of three cryptic schemes, namely Latin square image cipher (LSIC), discrete Gould transform (DGT) and Rubik׳s encryption, has been adopted. Among them, LSIC provides better substitution, confusion and shuffling of the image blocks; DGT incorporates tamper proofing with authentication; and Rubik renders a permutation of DICOM image pixels. The developed algorithm has been successfully implemented and tested in both the software (MATLAB 7) and hardware Universal Software Radio Peripheral (USRP) environments. Specifically, the encrypted data were tested by transmitting them through an additive white Gaussian noise (AWGN) channel model. Furthermore, the sternness of the implemented algorithm was validated by employing standard metrics such as the unified average changing intensity (UACI), number of pixels change rate (NPCR), correlation values and histograms. The estimated metrics have also been compared with the existing methods and dominate in terms of large key space to defy brute force attack, cropping attack, strong key sensitivity and uniform pixel value distribution on encryption. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Cryptic extended brood care in the facultatively eusocial sweat bee Megalopta genalis.

    Science.gov (United States)

    Quiñones, A E; Wcislo, W T

    As a result of different brood cell provisioning strategies, nest-making insects may differ in the extent to which adults regularly provide extended parental care to their brood beyond nest defense. Mass-provisioning species cache the entire food supply needed for larval development prior to the oviposition and typically seal the brood cell. It is usually assumed that there is no regular contact between the adult(s) and brood. Here, we show that the bee, Megalopta genalis , expresses a form of cryptic brood care, which would not be observed during normal development. Following experimental injections of different provisioning materials into brood cells, foundresses reopened manipulated cells and the brood were aborted in some cases, implying that the foundresses assessed conditions within the cells. In aborted cells, foundresses sometimes laid a second egg after first removing dead larvae, previously stored pollen and contaminants. Our results show that hygienic brood care can be cryptic and hence may be more widespread than previously believed, lending support to the hypothesis that extended parental care is a preadaptation toward eusociality.

  13. Shoot, shovel and shut up: cryptic poaching slows restoration of a large carnivore in Europe.

    Science.gov (United States)

    Liberg, Olof; Chapron, Guillaume; Wabakken, Petter; Pedersen, Hans Christian; Hobbs, N Thompson; Sand, Håkan

    2012-03-07

    Poaching is a widespread and well-appreciated problem for the conservation of many threatened species. Because poaching is illegal, there is strong incentive for poachers to conceal their activities, and consequently, little data on the effects of poaching on population dynamics are available. Quantifying poaching mortality should be a required knowledge when developing conservation plans for endangered species but is hampered by methodological challenges. We show that rigorous estimates of the effects of poaching relative to other sources of mortality can be obtained with a hierarchical state-space model combined with multiple sources of data. Using the Scandinavian wolf (Canis lupus) population as an illustrative example, we show that poaching accounted for approximately half of total mortality and more than two-thirds of total poaching remained undetected by conventional methods, a source of mortality we term as 'cryptic poaching'. Our simulations suggest that without poaching during the past decade, the population would have been almost four times as large in 2009. Such a severe impact of poaching on population recovery may be widespread among large carnivores. We believe that conservation strategies for large carnivores considering only observed data may not be adequate and should be revised by including and quantifying cryptic poaching.

  14. Cryptic Transcription and Early Termination in the Control of Gene Expression

    Directory of Open Access Journals (Sweden)

    Jessie Colin

    2011-01-01

    Full Text Available Recent studies on yeast transcriptome have revealed the presence of a large set of RNA polymerase II transcripts mapping to intergenic and antisense regions or overlapping canonical genes. Most of these ncRNAs (ncRNAs are subject to termination by the Nrd1-dependent pathway and rapid degradation by the nuclear exosome and have been dubbed cryptic unstable transcripts (CUTs. CUTs are often considered as by-products of transcriptional noise, but in an increasing number of cases they play a central role in the control of gene expression. Regulatory mechanisms involving expression of a CUT are diverse and include attenuation, transcriptional interference, and alternative transcription start site choice. This review focuses on the impact of cryptic transcription on gene expression, describes the role of the Nrd1-complex as the main actor in preventing nonfunctional and potentially harmful transcription, and details a few systems where expression of a CUT has an essential regulatory function. We also summarize the most recent studies concerning other types of ncRNAs and their possible role in regulation.

  15. Small mammals as indicators of cryptic plant species diversity in the central Chilean plant endemicity hotspot

    Directory of Open Access Journals (Sweden)

    Meredith Root-Bernstein

    2014-12-01

    Full Text Available Indicator species could help to compensate for a shortfall of knowledge about the diversity and distributions of undersampled and cryptic species. This paper provides background knowledge about the ecological interactions that affect and are affected by herbaceous diversity in central Chile, as part of the indicator species selection process. We focus on the ecosystem engineering role of small mammals, primarily the degu Octodon degus. We also consider the interacting effects of shrubs, trees, avian activity, livestock, slope, and soil quality on herbaceous communities in central Chile. We sampled herbaceous diversity on a private landholding characterized by a mosaic of savanna, grassland and matorral, across a range of degu disturbance intensities. We find that the strongest factors affecting endemic herbaceous diversity are density of degu runways, shrub cover and avian activity. Our results show that the degu, a charismatic and easily identifiable and countable species, could be used as an indicator species to aid potential conservation actions such as private protected area uptake. We map areas in central Chile where degus may indicate endemic plant diversity. This area is larger than expected, and suggests that significant areas of endemic plant communities may still exist, and should be identified and protected. Keywords: Cryptic species, Diversity, Endemic, Indicator species, Octodon degus, Plant

  16. Divergence in cryptic leaf colour provides local camouflage in an alpine plant.

    Science.gov (United States)

    Niu, Yang; Chen, Zhe; Stevens, Martin; Sun, Hang

    2017-10-11

    The efficacy of camouflage through background matching is highly environment-dependent, often resulting in intraspecific colour divergence in animals to optimize crypsis in different visual environments. This phenomenon is largely unexplored in plants, although several lines of evidence suggest they do use crypsis to avoid damage by herbivores. Using Corydalis hemidicentra, an alpine plant with cryptic leaf colour, we quantified background matching between leaves and surrounding rocks in five populations based on an approximate model of their butterfly enemy's colour perception. We also investigated the pigment basis of leaf colour variation and the association between feeding risk and camouflage efficacy. We show that plants exhibit remarkable colour divergence between populations, consistent with differences in rock appearances. Leaf colour varies because of a different quantitative combination of two basic pigments-chlorophyll and anthocyanin-plus different air spaces. As expected, leaf colours are better matched against their native backgrounds than against foreign ones in the eyes of the butterfly. Furthermore, improved crypsis tends to be associated with a higher level of feeding risk. These results suggest that divergent cryptic leaf colour may have evolved to optimize local camouflage in various visual environments, extending our understanding of colour evolution and intraspecific phenotype diversity in plants. © 2017 The Author(s).

  17. Reproductive Failure in UK Harbour Porpoises Phocoena phocoena: Legacy of Pollutant Exposure?

    Directory of Open Access Journals (Sweden)

    Sinéad Murphy

    Full Text Available Reproductive failure in mammals due to exposure to polychlorinated biphenyls (PCBs can occur either through endocrine disrupting effects or via immunosuppression and increased disease risk. To investigate further, full necropsies and determination of summed 25 polychlorinated biphenyls congeners (∑PCBs lipid weight in blubber were undertaken on 329 UK-stranded female harbour porpoises (1990-2012. In sexually mature females, 25/127 (19.7% showed direct evidence of reproductive failure (foetal death, aborting, dystocia or stillbirth. A further 21/127 (16.5% had infections of the reproductive tract or tumours of reproductive tract tissues that could contribute to reproductive failure. Resting mature females (non-lactating or non-pregnant had significantly higher mean ∑PCBs (18.5 mg/kg than both lactating (7.5 mg/kg and pregnant females (6 mg/kg, though not significantly different to sexually immature females (14.0 mg/kg. Using multinomial logistic regression models ΣPCBs was found to be a significant predictor of mature female reproductive status, adjusting for the effects of confounding variables. Resting females were more likely to have a higher PCB burden. Health status (proxied by "trauma" or "infectious disease" causes of death was also a significant predictor, with lactating females (i.e. who successfully reproduced more likely to be in good health status compared to other individuals. Based on contaminant profiles (>11 mg/kg lipid, at least 29/60 (48% of resting females had not offloaded their pollutant burden via gestation and primarily lactation. Where data were available, these non-offloading females were previously gravid, which suggests foetal or newborn mortality. Furthermore, a lower pregnancy rate of 50% was estimated for "healthy" females that died of traumatic causes of death, compared to other populations. Whether or not PCBs are part of an underlying mechanism, we used individual PCB burdens to show further evidence of

  18. Population development and status of harbour seals (Phoca vitulina in the Wadden Sea

    Directory of Open Access Journals (Sweden)

    Peter JH Reijnders

    2010-09-01

    Full Text Available An index for the condition of a population should include a measure of the recuperative power or resilience of the population in question. This measure needs to cover both the demographic and physiological condition of the population. Applied to the harbour seal population in the Wadden Sea we therefore address respectively the population development and distribution, and its health condition, and relate these to environmental conditions. The harbour seal population has been severely depleted by hunting in the first half of the 20th century. After hunting was stopped in the mid-1970s the population recovered gradually. This recovery was twice interrupted by Phocine Distemper Virus (PDV outbreaks in 1988 and 2002. These PDV-epizootics reduced the population by 57% and 50% respectively. They also lead to changes in age and sex structure of the population, which gradually returned to a stable age-structure. Despite the reduction in population size by respectively 57% and 50%, the population showed a strong recovery with a growth rate close to the considered maximum possible for this species. The observed changes in the distribution of the population over the 4 sub-regions indicate that distribution is not a static phenomenon. Long term field and pathological investigations point out that the general health status of the population has improved, particularly that of newborn seals (0-6months old. The increasing prevalence of parasites in lungs and intestine warrants continued monitoring of the health status of seals. This is especially relevant in view of the exponential increase of the population, which may finally approach the carrying capacity of the area. Concluding, we canstate that the condition of the population in terms of demographic and health parameters is satisfactory. The best guarantee for maintaining such a favourable conservation status is to abstain from human interferences (e.g. rescue, rehabilitation and release with natural

  19. Why do different oceanic archipelagos harbour contrasting levels of species diversity? The macaronesian endemic genus Pericallis (Asteraceae) provides insight into explaining the 'Azores diversity Enigma'.

    Science.gov (United States)

    Jones, K E; Pérez-Espona, S; Reyes-Betancort, J A; Pattinson, D; Caujapé-Castells, J; Hiscock, S J; Carine, M A

    2016-10-08

    Oceanic archipelagos typically harbour extensive radiations of flowering plants and a high proportion of endemics, many of which are restricted to a single island (Single Island Endemics; SIEs). The Azores represents an anomaly as overall levels of endemism are low; there are few SIEs and few documented cases of intra-archipelago radiations. The distinctiveness of the flora was first recognized by Darwin and has been referred to as the 'Azores Diversity Enigma' (ADE). Diversity patterns in the Macaronesian endemic genus Pericallis (Asteraceae) exemplify the ADE. In this study we used morphometric, Amplified Length Polymorphisms, and bioclimatic data for herbaceous Pericallis lineages endemic to the Azores and the Canaries, to test two key hypotheses proposed to explain the ADE: i) that it is a taxonomic artefact or Linnean shortfall, ie. the under description of taxa in the Azores or the over-splitting of taxa in the Canaries and (ii) that it reflects the greater ecological homogeneity of the Azores, which results in limited opportunity for ecological diversification compared to the Canaries. In both the Azores and the Canaries, morphological patterns were generally consistent with current taxonomic classifications. However, the AFLP data showed no genetic differentiation between the two currently recognized Azorean subspecies that are ecologically differentiated. Instead, genetic diversity in the Azores was structured geographically across the archipelago. In contrast, in the Canaries genetic differentiation was mostly consistent with morphology and current taxonomic treatments. Both Azorean and Canarian lineages exhibited ecological differentiation between currently recognized taxa. Neither a Linnean shortfall nor the perceived ecological homogeneity of the Azores fully explained the ADE-like pattern observed in Pericallis. Whilst variation in genetic data and morphological data in the Canaries were largely congruent, this was not the case in the Azores, where

  20. Underwater recordings of the whistles of bottlenose dolphins in Fremantle Inner Harbour, Western Australia

    Science.gov (United States)

    Marley, Sarah A.; Erbe, Christine; Kent, Chandra P. Salgado

    2017-09-01

    Dolphins use frequency-modulated whistles for a variety of social functions. Whistles vary in their characteristics according to context, such as activity state, group size, group composition, geographic location, and ambient noise levels. Therefore, comparison of whistle characteristics can be used to address numerous research questions regarding dolphin populations and behaviour. However, logistical and economic constraints on dolphin research have resulted in data collection biases, inconsistent analytical approaches, and knowledge gaps. This Data Descriptor presents an acoustic dataset of bottlenose dolphin (Tursiops aduncus) whistles recorded in the Fremantle Inner Harbour, Western Australia. Data were collected using an autonomous recorder and analysed using a range of acoustic measurements. Acoustic data review identified 336 whistles, which were subsequently measured for six key characteristics using Raven Pro software. Of these, 164 'high-quality' whistles were manually measured to provide an additional five acoustic characteristics. Digital files of individual whistles and corresponding measurements make this dataset available to researchers to address future questions regarding variations within and between dolphin communities.

  1. Harbour porpoises on Horns Reef - Effects of the Horns Reef wind farm. Annual status report 2004

    Energy Technology Data Exchange (ETDEWEB)

    Tougaard, J.; Carstensen, J.; Wisz, M.S.; Teilmann, J.; Bech, N.I. [National Environmental Res. Inst., Roskilde (Denmark); Skov, H. [DHI - Water and Environment, Hoersholm (Denmark); Henriksen, Oluf, D. [DDH-Consulting A/S, Roskilde (Denmark)

    2005-07-15

    This report describes the monitoring of harbour porpoises at Horns Reef Offshore Wind Farm, Denmark, with emphasis on data collected in 2004. Three 2-day surveys with line transect observations of porpoises were conducted in 2004 and data from acoustic data loggers (TPODs) were collected from January through July. Although new data from 2004 was included in the analysis there were no significant additions to conclusions from previous years' reports. On the contrary, the general conclusions regarding effects of construction and operation of the wind farm on porpoise abundance inside and outside the wind farm area have been weakened somewhat compared to previous reports. The specific conclusions regarding short-time effects of construction activities (especially pile drivings) has not been changed, however. Modelling of the spatial distribution of porpoises in the area demonstrated very weak correlations with static environmental variables (water depth, change in water depth and distance to 6 m depth contour). This highlights the importance of dynamic environmental variables, in particular tide and salinity, in determining the fine-scale distribution of porpoises and their prey in the area. a strong correlation between tide and porpoise abundance observed in the T-POD data on some parts of the reef (high abundance at high tide, low at low tide) supports the importance of this variable. Tide and salinity will be included in a forthcoming analysis of the entire dataset from the monitoring program. (au)

  2. Plants of the fynbos biome harbour host species-specific bacterial communities.

    Science.gov (United States)

    Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

    2016-08-01

    The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Harbour porpoises on Horns Reef - Effects of the Horns Reef wind farm. Annual status report 2004

    Energy Technology Data Exchange (ETDEWEB)

    Tougaard, J; Carstensen, J; Wisz, M S; Teilmann, J; Bech, N I [National Environmental Res. Inst., Roskilde (Denmark); Skov, H [DHI - Water and Environment, Hoersholm (Denmark); Henriksen, Oluf, D. [DDH-Consulting A/S, Roskilde (Denmark)

    2005-07-15

    This report describes the monitoring of harbour porpoises at Horns Reef Offshore Wind Farm, Denmark, with emphasis on data collected in 2004. Three 2-day surveys with line transect observations of porpoises were conducted in 2004 and data from acoustic data loggers (TPODs) were collected from January through July. Although new data from 2004 was included in the analysis there were no significant additions to conclusions from previous years' reports. On the contrary, the general conclusions regarding effects of construction and operation of the wind farm on porpoise abundance inside and outside the wind farm area have been weakened somewhat compared to previous reports. The specific conclusions regarding short-time effects of construction activities (especially pile drivings) has not been changed, however. Modelling of the spatial distribution of porpoises in the area demonstrated very weak correlations with static environmental variables (water depth, change in water depth and distance to 6 m depth contour). This highlights the importance of dynamic environmental variables, in particular tide and salinity, in determining the fine-scale distribution of porpoises and their prey in the area. a strong correlation between tide and porpoise abundance observed in the T-POD data on some parts of the reef (high abundance at high tide, low at low tide) supports the importance of this variable. Tide and salinity will be included in a forthcoming analysis of the entire dataset from the monitoring program. (au)

  4. Harbour porpoises on Horns Reef - Effects of the Horns Reef wind farm. Annual status report 2004

    International Nuclear Information System (INIS)

    Tougaard, J.; Carstensen, J.; Wisz, M.S.; Teilmann, J.; Bech, N.I.; Skov, H.; Henriksen, Oluf D.

    2005-01-01

    This report describes the monitoring of harbour porpoises at Horns Reef Offshore Wind Farm, Denmark, with emphasis on data collected in 2004. Three 2-day surveys with line transect observations of porpoises were conducted in 2004 and data from acoustic data loggers (TPODs) were collected from January through July. Although new data from 2004 was included in the analysis there were no significant additions to conclusions from previous years' reports. On the contrary, the general conclusions regarding effects of construction and operation of the wind farm on porpoise abundance inside and outside the wind farm area have been weakened somewhat compared to previous reports. The specific conclusions regarding short-time effects of construction activities (especially pile drivings) has not been changed, however. Modelling of the spatial distribution of porpoises in the area demonstrated very weak correlations with static environmental variables (water depth, change in water depth and distance to 6 m depth contour). This highlights the importance of dynamic environmental variables, in particular tide and salinity, in determining the fine-scale distribution of porpoises and their prey in the area. a strong correlation between tide and porpoise abundance observed in the T-POD data on some parts of the reef (high abundance at high tide, low at low tide) supports the importance of this variable. Tide and salinity will be included in a forthcoming analysis of the entire dataset from the monitoring program. (au)

  5. Vertical distribution of tritium in core sediment of Mumbai Harbour Bay

    International Nuclear Information System (INIS)

    Rupali, C.K.; Joshi, Vikram; Jha, S.K.; Tripathi, R.M.; Sonali, B.; Priyanka, R.

    2014-01-01

    In the past few years there has been an increasing interest in the study of behavior of tritium in the environment, worldwide many countries have initiated monitoring of organically bound tritium in the environmental samples as part of their radiological assessments. Tritium ( 3 H) is ubiquitous in the aquatic environment and has a various sources of origin. It is transported to the earth's surface via hydrological cycle. 3 H is produced in variety of processes in nuclear power plants. Discharges to aquatic environment from these establishment results in locally enhanced water concentrations. Levels of 3 H have been further elevated due to atmospheric weapons testing between 1952 and 1962. Recent studies have demonstrated significant accumulation of tritium in both organic-rich sediments and food chain. The present study describes the vertical profile of tritium distribution in core sediment collected from Mumbai Harbour Bay (MHB). This will help in better understanding of the biogeochemical behavior and ecological impacts of tritium in the sediment

  6. Radiotracer investigations on dispersion of low level effluents discharged into Mumbai Harbour Bay

    International Nuclear Information System (INIS)

    Jacob, Noble; Mendhekar, G.N.; Singh, Sanjay

    2015-01-01

    Two radiotracer investigations (using radioactive 82 Br) were carried out near the CIRUS jetty in the Mumbai Harbour Bay (MHB) to evaluate the dilution and dispersion of low level liquid effluents discharged from the BARC Effluent Treatment Plant (ETP). The first experiment was conducted during an ebb tide while the second was conducted during a flood tide. In both the experiments, about 1.55Ci (57 GBq) of 82 Br was injected into one of the aeration tanks of the ETP. The labelled effluent was discharged into the bay and the movement of the plume in the coastal water was monitored using underwater γ-scintillation detectors. Contour map depicting the spread of the radioactive plume was prepared and dilution factors were estimated. The extent of spread of the tracer was comparatively higher during the ebb tide than in flood tide. A 2-D advection dispersion (analytical) model was used to obtain the system parameters D x and D y (for the ebb tide D x is ∼ 5 m 2 s -1 and D y : 0.7 m 2 s -1 ; for flood tide D x is 5 m 2 s -1 and D y : 0.15 m 2 s -1 ). (author)

  7. Effects of meteorological factors on the temporal distribution of red tides in Tolo Harbour, Hong Kong.

    Science.gov (United States)

    Huang, Jiansheng; Liu, Hao; Yin, Kedong

    2018-01-01

    Red tides represent a major environmental issue in coastal waters globally. However, few studies have examined the relationship between red tides and meteorological factors. Thus, we used a 32-year time-series of frequent red tide events in Tolo Harbour and Channel, to study their relationship with meteorological factors. Most red tides are dominated by dinoflagellates in March, while most diatom red tides in May. Dinoflagellate and diatom red tides respond differently to different meteorological factors. Warming air temperatures in spring favor the generation of dinoflagellate red tides, while precipitation hinders them. The optimum temperature range is approximately 17-23°C and 26-29°C for dinoflagellate and diatom red tides, respectively. Moderate northeasterly winds promote the formation of dinoflagellate red tides. Dinoflagellate red tides are not hindered by cloudy weather and occur in sunlight of varying brightness, whereas diatoms red tides require a certain amount of bright sunlight. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Malignant melanoma arising from a perianal fistula and harbouring a BRAF gene mutation: a case report

    International Nuclear Information System (INIS)

    Martinez-Cadenas, Conrado; Lozoya, Rafael; Boldó, Enrique; Bosch, Nuria; Peñas, Lucas; Flores-Couce, Esther; Ochoa, Enrique; Munárriz, Javier; Aracil, Juan P; Tajahuerce, Marcos; Royo, Ramón

    2011-01-01

    Melanoma of the anal region is a very uncommon disease, accounting for only 0.2-0.3% of all melanoma cases. Mutations of the BRAF gene are usually absent in melanomas occurring in this region as well as in other sun-protected regions. The development of a tumour in a longstanding perianal fistula is also extremely rare. More frequent is the case of a tumour presenting as a fistula, that is, the fistula being a consequence of the cancerous process, although we have found only two cases of fistula-generating melanomas reported in the literature. Here we report the case of a 38-year-old male who presented with a perianal fistula of four years of evolution. Histopathological examination of the fistulous tract confirmed the presence of malignant melanoma. Due to the small size and the central location of the melanoma inside the fistulous tract, we believe the melanoma reported here developed in the epithelium of the fistula once the latter was already formed. Resected sentinel lymph nodes were negative and the patient, after going through a wide local excision, remains disease-free nine years after diagnosis. DNA obtained from melanoma tissue was analysed by automated direct sequencing and the V600E (T1799A) mutation was detected in exon 15 of the BRAF gene. Since fistulae experience persistent inflammation, the fact that this melanoma harbours a BRAF mutation strengthens the view that oxidative stress caused by inflammatory processes plays an important role in the genesis of BRAF gene mutations

  9. Pathogenicity of pan-drug-resistant Serratia marcescens harbouring blaNDM-1.

    Science.gov (United States)

    Gruber, Teresa M; Göttig, Stephan; Mark, Laura; Christ, Sara; Kempf, Volkhard A J; Wichelhaus, Thomas A; Hamprecht, Axel

    2015-04-01

    To characterize a pan-drug-resistant Serratia marcescens clinical isolate carrying the New Delhi metallo-β-lactamase (NDM)-1. The presence of β-lactamase genes was examined by PCR and sequencing. Antibiotic susceptibility was determined by antibiotic gradient test. Transformation assays, transconjugation assays, PFGE and PCR-based replicon typing were used for plasmid analysis. Horizontal gene transfer was evaluated by liquid mating using Escherichia coli J53 as a recipient. Pathogenicity of NDM-1 expressing S. marcescens was analysed using the Galleria mellonella infection model. S. marcescens isolate SM1890 was non-susceptible to all tested antibiotics, with minocycline retaining intermediate activity. blaNDM-1 was located on a 140 kb IncA/C-type plasmid which was transferable to E. coli and Klebsiella pneumoniae by conjugation. The LD50 of the NDM-positive, SM1890 isolate was higher than that of other, NDM-1 negative, S. marcescens strains. The presence of a blaNDM-1-harbouring IncA/C plasmid resulted in marked resistance to β-lactam antibiotics, but had no significant effect on virulence of isogenic strains. Because of the intrinsic resistance of S. marcescens to colistin and reduced susceptibility to tigecycline, treatment options for infections by NDM-1-positive isolates are extremely limited in this species. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Biological effects of rice harbouring Bph14 and Bph15 on brown planthopper, Nilaparvata lugens.

    Science.gov (United States)

    Li, Jie; Chen, Qiuhong; Wang, Liangquan; Liu, Jia; Shang, Keke; Hua, Hongxia

    2011-05-01

    Brown planthopper (Nilaparvata lugens Stål; BPH) resistance genes Bph14 and Bph15 have been introgressed singly or pyramided into rice variety Minghui 63 (MH63). The antibiosis and antixenosis effects of these rice lines on BPH and the expression of five P450 genes of BPH regulated by these rice lines were investigated in this study. The resistance level of rice lines harbouring resistance genes was improved compared with MH63. MH63::14 (carrying Bph14) had negative effects on the development of males, honeydew excretion of females, the female ratio and the copulation rate compared with MH63. MH63::14 also exhibited antixenosis action against BPH nymphs, female adults and oviposition. Besides these negative effects, MH63::15 (carrying Bph15) could also retard the development of females, lower the fecundity and shorten the lifespan of females. The antixenosis action of MH63::15 was stronger than that of MH63::14. When Bph14 and Bph15 were pyramided, antibiosis and antixenosis effects were significantly enhanced relative to single-introgression lines. Among the five P450 genes of BPH, expression of three genes was upregulated, one gene was downregulated and one gene was unchanged by resistant hosts. Both Bph14 and Bph15 could improve resistance levels of MH63. MH63::15 and MH63::14&15 had greater potential to control BPH infestations than MH63::14. Copyright © 2011 Society of Chemical Industry.

  11. Exposure of harbour seals Phoca vitulina to Brucella in declining populations across Scotland.

    Science.gov (United States)

    Kershaw, Joanna L; Stubberfield, Emma J; Foster, Geoffrey; Brownlow, Andrew; Hall, Ailsa J; Perrett, Lorraine L

    2017-09-20

    Since 2000 there has been a major decline in the abundance of Scottish harbour seals Phoca vitulina. The causes of the decline remain uncertain. The aim of this study was to establish the extent to which the seals in the regions of greatest decline have been exposed to Brucella, a bacterial pathogen that causes reproductive failure in terrestrial mammalian hosts. Tissues from dead seals collected between 1992 and 2013 were cultured for Brucella (n = 150). Serum samples collected from live capture-released seals (n = 343) between 1997 and 2012 were tested for Brucella antibodies using the Rose Bengal plate agglutination test (RBT) and a competitive enzyme-linked immunosorbent assay (cELISA). In total, 16% of seals cultured had Brucella isolated from one or more tissues, but there were no pathological signs of infection. The cELISA results were more sensitive than the RBT results, showing that overall 25.4% of seals were seropositive, with the highest seroprevalence in juveniles. As there was no evidence of either a higher seroprevalence or higher circulating antibody levels in seropositive animals in the areas with the greatest declines, it was concluded that Brucella infection is likely not a major contributing factor to recent declines. However, the consistently high proportion of seals exposed to Brucella indicates possible endemicity in these populations, likely due to B. pinnipedialis, which has demonstrated a preference for pinniped hosts. Importantly, given the close proximity between seals, humans and livestock in many areas, there is the potential for cross-species infections.

  12. Generation of mice harbouring a conditional loss-of-function allele of Gata6

    Directory of Open Access Journals (Sweden)

    Duncan Stephen A

    2006-04-01

    Full Text Available Abstract The zinc finger transcription factor GATA6 is believed to have important roles in the development of several organs including the liver, gastrointestinal tract and heart. However, analyses of the contribution of GATA6 toward organogenesis have been hampered because Gata6-/- mice fail to develop beyond gastrulation due to defects in extraembryonic endoderm function. We have therefore generated a mouse line harbouring a conditional loss-of-function allele of Gata6 using Cre/loxP technology. LoxP elements were introduced into introns flanking exon 2 of the Gata6 gene by homologous recombination in ES cells. Mice containing this altered allele were bred to homozygosity and were found to be viable and fertile. To assess the functional integrity of the loxP sites and to confirm that we had generated a Gata6 loss-of-function allele, we bred Gata6 'floxed' mice to EIIa-Cre mice in which Cre is ubiquitously expressed, and to Villin-Cre mice that express Cre in the epithelial cells of the intestine. We conclude that we have generated a line of mice in which GATA6 activity can be ablated in a cell type specific manner by expression of Cre recombinase. This line of mice can be used to establish the role of GATA6 in regulating embryonic development and various aspects of mammalian physiology.

  13. Lichens as indicators of fluoride emission from a phosphorus plant, Long Harbour, Newfoundland, Canada

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, B.A.; Thompson, L.K.

    1980-01-01

    Fluoride concentrations in the terrestrial lichens Cladina rangiferina (L.) Harm. and Cladina stellaris (Opiz.) Brodo. were correlated inversely with distance from an industrial plant producing elemental phosphorus at Long Harbour, Nfld., in the direction (NE) of the prevailing wind. The fluoride concentrations ranged from 2830 ppm dry weight in a severely damaged area close to the emission source to 15.5 ppm (dry weight) 12 km NE of the industrial plant. Control samples from unpolluted areas had an average fluoride content of 6.4 ppm dry weight. The minimum observed damage symptoms occurred when these lichens had a fluoride content of 25 ppm dry weight. Damage symptoms included discolouration and structure loss. Discolouration effects were not as pronounced as observed on Abies balsamea (L.) Mill. or on Polytrichum commune (Hedw.) but combined with structure loss allowed the degree of damage to be readily identified in the field. Fluoride concentrations in these terrestrial lichens are compared with levels in soil humus, A. balsamea and some terrestrial bryophytes in four damage zones. The lichen tissue had, on average, twice as much fluoride as occurred in soil humus from the same site and about one half the amount of fluoride found in the terrestrial bryophyte P. commune. The effects of fluoride emissions on the epiphytic lichens Hypogymnia physodes (L.) W. Wats. and Alectoria sarmentosa (Ach.) Ach. in this area are also discussed.

  14. Glas Journal: Deep Mappings of a Harbour or the Charting of Fragments, Traces and Possibilities

    Directory of Open Access Journals (Sweden)

    Silvia Loeffler

    2015-09-01

    Full Text Available With reference to a hybrid ethnographic project entitled Glas Journal (2014–2016, this article invites readers to reflect on the cultural mapping of spaces we intimately inhabit. Developed with the participation of local inhabitants of Dún Laoghaire Harbour, Ireland, Glas Journal seeks to explore the maritime environment as a liminal space, whereby the character of buildings and an area’s economic implications determine our relationship to space as much as our daily spatial rhythms and feelings of safety. Deep mapping provides the methodological blueprint for Glas Journal. In order to create a heteroglossic narrative of place and belonging, I will contextualise the project with references to seminal works in the visual arts, literature, film and geography that emotionally map spaces. Chronotopes of the threshold will be used to elaborate on spatial and cultural phenomena that occur when crossings from public to private and interior to exterior take place. Touching upon questions such as “What is a space of protection?”, “Who am I in it?”, and “Who is the Other?”, this article traces forms of liquid mapping that do not strive to conquer but rather to gain insight into the inner landscapes that are reflected in outer space.

  15. Autonomously hyperfunctioning cystic nodule harbouring thyroid carcinoma - Case report and literature review.

    Science.gov (United States)

    Lima, Maria João; Soares, Virgínia; Koch, Pedro; Silva, Artur; Taveira-Gomes, António

    2018-01-01

    Hyperthyroidism is rarely associated with malignancy, but it cannot rule out thyroid cancer. Although there is published data describing this coexistence, thyroid carcinomas inside autonomously functioning nodules are uncommon. A 49-year-old woman presented with a cervical mass, unexplained weight loss and anxiousness, sweating and insomnia. On physical examination, she had a palpable left thyroid nodule. Thyroid function tests showed suppressed TSH (nodule. 99mTC thyroid scintigraphy showed a hyperfunctioning nodule with suppression of the remainder parenchyma. Fine-needle aspiration cytology was nondiagnostic (cystic fluid). The patient was started on thiamazole 5 mg daily with subsequent normalization of thyroid function, but she developed cervical foreign body sensation and a left hemithyroidectomy was performed. Histology showed a 4 cm cystic nodule with a follicular variant papillary carcinoma and the patient underwent completion thyroidectomy, followed by radio-iodine ablation. Published literature showed an increased prevalence of autonomously functioning nodules, harbouring thyroid carcinomas in adults. Papillary carcinoma is the most frequently described but the follicular variant is rare. Although rare, thyroid cancer is not definitively excluded in hyperthyroid patients and it should always be considered as differential diagnosis. Copyright © 2018. Published by Elsevier Ltd.

  16. Gas exchange and heart rate in the harbour porpoise, Phocoena phocoena

    DEFF Research Database (Denmark)

    Reed, J.Z.; Chambers, C.; Hunter, C.J.

    2000-01-01

    a comparatively high minute rate of gas exchange. Oxygen consumption under these experimental conditions (247 +/- 13.8 ml O-2. min(-1)) was 1.9- fold higher than predicted by standard scaling relations. These data together with an estimate of the total oxygen stores predicted an aerobic dive limit of 5.4 min......The respiratory physiology, heart rates and metabolic rates of two captive juvenile male harbour porpoises (both 28 kg) were measured using a rapid-response respiratory gas analysis system in the laboratory. Breath-hold durations in the laboratory (12 +/- 0.3 s, mean +/- SEM) were shorter than...... field observations. although a few breath-holds of over 40 s were recorded. The mean percentage time spent submerged was 89 +/- 0.4%. Relative to similarly-sized terrestrial mammals, the respiratory frequency was low (4.9 +/- 0.19 breaths min(-1)) but with high tidal volumes (1.1 +/- 0.01 l), enabling...

  17. MOCCA-SURVEY Database I: Is NGC 6535 a dark star cluster harbouring an IMBH?

    Science.gov (United States)

    Askar, Abbas; Bianchini, Paolo; de Vita, Ruggero; Giersz, Mirek; Hypki, Arkadiusz; Kamann, Sebastian

    2017-01-01

    We describe the dynamical evolution of a unique type of dark star cluster model in which the majority of the cluster mass at Hubble time is dominated by an intermediate-mass black hole (IMBH). We analysed results from about 2000 star cluster models (Survey Database I) simulated using the Monte Carlo code MOnte Carlo Cluster simulAtor and identified these dark star cluster models. Taking one of these models, we apply the method of simulating realistic `mock observations' by utilizing the Cluster simulatiOn Comparison with ObservAtions (COCOA) and Simulating Stellar Cluster Observation (SISCO) codes to obtain the photometric and kinematic observational properties of the dark star cluster model at 12 Gyr. We find that the perplexing Galactic globular cluster NGC 6535 closely matches the observational photometric and kinematic properties of the dark star cluster model presented in this paper. Based on our analysis and currently observed properties of NGC 6535, we suggest that this globular cluster could potentially harbour an IMBH. If it exists, the presence of this IMBH can be detected robustly with proposed kinematic observations of NGC 6535.

  18. Homogenous stands of a wetland grass harbour diverse consortia of arbuscular mycorrhizal fungi.

    Science.gov (United States)

    Wirsel, Stefan G R

    2004-05-01

    A molecular approach was applied to investigate the colonisation of arbuscular mycorrhizal fungi (AMF) on the wetland grass Phragmites australis. A PCR assay targeting the traditional families of the Glomeromycota yielded products that were used to construct libraries of 18S rDNA. Five hundred and forty six clones were typed by restriction analysis and 76 representatives were sequenced. The majority corresponded to a wide range of taxa within Glomus group A, a few belonged to the "Diversisporaceae" and none to the genera Scutellospora or Acaulospora. Among these sequences, some were very similar to those reported earlier, e.g. Glomus mosseae and G. fasciculatum, other pointed to various new taxa. Although this wetland habitat harboured just one single plant species, phylogenetic analysis exhibited 21 AMF phylotypes, which is in the same range as reported for other natural ecosystems composed of more diverse host communities. Diversity indices supported the perception that the AMF mycoflora associated with this natural grass "monoculture" is not depauperate as it had been described for grasses of crop monocultures. Soil conditions determined the mycorrhizal state of the host, since AMF were not detected at the lakeward front of the reed belt, which is permanently waterlogged.

  19. MOCCA-SURVEY Database I: Galactic Globular Clusters Harbouring a Black Hole Subsystem

    Science.gov (United States)

    Askar, Abbas; Sedda, Manuel Arca; Giersz, Mirek

    2018-05-01

    There have been increasing theoretical speculations and observational indications that certain globular clusters (GCs) could contain a sizeable population of stellar mass black holes (BHs). In this paper, we shortlist at least 29 Galactic GCs that could be hosting a subsystem of BHs (BHS). In a companion paper, we analysed results from a wide array of GC models (simulated with the MOCCA code for cluster simulations) that retained few tens to several hundreds of BHs at 12 Gyr and showed that the properties of the BHS in those GCs correlate with the GC's observable properties. Building on those results, we use available observational properties of 140 Galactic GCs to identify 29 GCs that could potentially be harbouring up to a few hundreds of BHs. Utilizing observational properties and theoretical scaling relations, we estimate the density, size and mass of the BHS in these GCs. We also calculate the total number of BHs and the fraction of BHs contained in a binary system for our shortlisted Galactic GCs. Additionally, we mention other Galactic GCs that could also contain significant number of single BHs or BHs in binary systems.

  20. Contamination delays the release of Laricobius osakensis for biological control of hemlock woolly adelgid: cryptic diversity in Japanese Laricobius spp

    Science.gov (United States)

    Melissa J. Fischer; Nathan P. Havill; Carrie S. Jubb; Sean W. Prosser; Brent D. Opell; Scott M. Salom; Loke T. Kok

    2014-01-01

    Laricobius osakensis (Coleoptera: Derodontidae) was imported from Japan to the United States in 2006 for study in quarantine facilities as a potential biological control of Hemlock Woolly Adelgid. Laricobius osakensis was released from quarantine in 2010, but it was soon discovered that the colony also contained a cryptic species...

  1. Resolution of three cryptic agricultural pests (Ceratitis fasciventris, C. anonae, C. rosa, Diptera: Tephritidae) using cuticular hydrocarbon profiling

    Czech Academy of Sciences Publication Activity Database

    Vaníčková, Lucie; Virgilio, M.; Tomčala, Aleš; Břízová, Radka; Ekesi, S.; Hoskovec, Michal; Kalinová, Blanka; do Nascimento, R. R.; De Meyer, M.

    2014-01-01

    Roč. 104, č. 5 (2014), s. 631-638 ISSN 0007-4853 Institutional support: RVO:61388963 Keywords : cryptic species complex * genus Ceratitis * cuticular hydrocarbons * polymorphic microsatellite loci * chemotaxonomy Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 1.910, year: 2014

  2. Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority

    KAUST Repository

    Pearman, John K.; Leray, M.; Villalobos, R.; Machida, R. J.; Berumen, Michael L.; Knowlton, N.; Carvalho, Susana

    2018-01-01

    (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA genes, to investigate changes in the cryptic reef biodiversity. ARMS, deployed at 11 sites across a near- to off-shore gradient in the Red Sea were

  3. Identification of high-risk areas for harbour porpoise Phocoena phocoena bycatch using remote electronic monitoring and satellite telemetry data

    DEFF Research Database (Denmark)

    Kindt-Larsen, Lotte; Berg, Casper Willestofte; Tougaard, J.

    2016-01-01

    grounds, quantify fishing effort and document harbour porpoise bycatch. Movement data from 66 harbour porpoises equipped with satellite transmitters from 1997 to 2012 were used to model population density. A simple model was constructed to investigate the relationship between the response (number...... telemetry or REM data allow for identification of areas of potential high and low bycatch risk, and better predictions are obtained when combining the 2 sources of data. The final model can thus be used as a tool to identify areas of bycatch risk...... and lower risk of porpoise bycatch. From May 2010 to April 2011, 4 commercial gillnet vessels were equipped with remote electronic monitoring (REM) systems. The REM system recorded time, GPS position and closed-circuit television (CCTV) footage of all gillnet hauls. REM data were used to identify fishing...

  4. Hydrodynamic discrimination of wakes caused by objects of different size or shape in a harbour seal (Phoca vitulina)

    DEFF Research Database (Denmark)

    Wieskotten, S.; Mauck, B.; Miersch, L.

    2011-01-01

    Harbour seals can use their mystacial vibrissae to detect and track hydrodynamic wakes. We investigated the ability of a harbour seal to discriminate objects of different size or shape by their hydrodynamic signature and used particle image velocimetry to identify the hydrodynamic parameters...... that a seal may be using to do so. Hydrodynamic trails were generated by different sized or shaped paddles that were moved in the calm water of an experimental box to produce a characteristic signal. In a two-alternative forced-choice procedure the blindfolded subject was able to discriminate size differences...... of down to 3.6. cm (Weber fraction 0.6) when paddles were moved at the same speed. Furthermore the subject distinguished hydrodynamic signals generated by flat, cylindrical, triangular or undulated paddles of the same width. Particle image velocimetry measurements demonstrated that the seal could have...

  5. Monitoring water quality in Sydney Harbour using blue mussels during remediation of the Sydney Tar Ponds, Nova Scotia, Canada.

    Science.gov (United States)

    Walker, Tony R; MacAskill, Devin

    2014-03-01

    Using mussels as monitoring tools we measured water quality in Sydney Harbour during a large scale, multi-year remediation project of the Sydney Tar Ponds (STPs); one of Canada's most contaminated sites. Chemical contaminants were measured in blue mussels (Mytilus edulis) in Sydney Harbour, which were used as monitoring tools to assess the spatio-temporal distribution of polycyclic aromatic hydrocarbons (PAHs); polychlorinated biphenyls (PCBs); metals (As, Cd, Cu, Hg, Pb, Zn) and lipid content during baseline and 3 years of remediation. The overall spatio-temporal distribution of chemicals in mussels was also compared to contaminants in other marine indicators (e.g., sediment, water and crab tissue). Measured metal concentrations in mussels showed some minor temporal variability (4 years), but these did not appear to be directly related to remediation activities, with the highest concentrations of As, Hg and Zn measured at reference stations. Most measured contaminants showed stable or potentially decreasing concentrations during the study, except Pb and Zn. Individual PAH compounds were mostly undetected during baseline and remediation, except for fluoranthene and pyrene. Concentrations of fluoranthene in mussels and deep water samples were moderately related. Generally, PCBs were undetected (remediation at some near-field stations. Contaminants measured during this study were at much lower concentrations than previously reported in other studies of mussels in Sydney Harbour and eastern Canada. This is likely due to the ongoing natural recovery of Sydney Harbour and to a lesser extent because of the environmental mitigation protection measures implemented during remediation activities at the STPs. The lack of detection of most individual PAHs and PCBs, plus relatively low bio-accumulation of metals observed during baseline and remediation attest to the effectiveness of using mussels as monitoring tools for environmental quality.

  6. Are toxins from harmful algae a factor involved in the decline of harbour seal populations in Scotland?

    OpenAIRE

    Jensen, Silje-Kristin

    2015-01-01

    Firstly this study builds on the investigation initiated by Hall and Frame (2010), which found that Scottish harbour seals were exposed to domoic acid (DA), a potent natural neurotoxin produced by phytoplankton. Using the same sample collection technique to gather urine and faecal material from various populations around Scotland with differing population trajectories (Lonergan et al., 2007), the objective was to investigate not only exposure to DA, but also other groups of ...

  7. First case of bacteraemia due to Acinetobacter schindleri harbouring blaNDM-1 in an immunocompromised patient

    Directory of Open Access Journals (Sweden)

    S. Montaña

    2018-01-01

    Full Text Available Clinically significant NDM-1-producing Acinetobacter schindleri has not yet been described in the literature. We report the first case of bacteraemia due to an A. schindleri strain harbouring blaNDM-1 recovered from an immunocompromised patient. Our report reinforces the fact that NDM-1 can easily be acquired by Acinetobacter species. Keywords: Acinetobacter schindleri, bacteraemia, blaNDM-1, clinically significant isolate, immunocompromised patient

  8. Wave simulation for the design of an innovative quay wall: the case of Vlorë Harbour

    Science.gov (United States)

    Antonini, Alessandro; Archetti, Renata; Lamberti, Alberto

    2017-01-01

    Sea states and environmental conditions are basic data for the design of marine structures. Hindcasted wave data have been applied here with the aim of identifying the proper design conditions for an innovative quay wall concept. In this paper, the results of a computational fluid dynamics model are used to optimise the new absorbing quay wall of Vlorë Harbour (Republic of Albania) and define the design loads under extreme wave conditions. The design wave states at the harbour entrance have been estimated analysing 31 years of hindcasted wave data simulated through the application of WaveWatch III. Due to the particular geography and topography of the Bay of Vlorë, wave conditions generated from the north-west are transferred to the harbour entrance with the application of a 2-D spectral wave module, whereas southern wave states, which are also the most critical for the port structures, are defined by means of a wave generation model, according to the available wind measurements. Finally, the identified extreme events have been used, through the NewWave approach, as boundary conditions for the numerical analysis of the interaction between the quay wall and the extreme events. The results show that the proposed method, based on numerical modelling at different scales from macro to meso and to micro, allows for the identification of the best site-specific solutions, also for a location devoid of any wave measurement. In this light, the objectives of the paper are two-fold. First, they show the application of sea condition estimations through the use of wave hindcasted data in order to properly define the design wave conditions for a new harbour structure. Second, they present a new approach for investigating an innovative absorbing quay wall based on CFD modelling and the NewWave theory.

  9. Economic and marketing aspects of using food irradiation technology in treatment of Egyptian exports in domietta harbour

    International Nuclear Information System (INIS)

    EL-Khateeb, M.A.

    2004-01-01

    The present study discuss the economic and marketing aspects for the establishment of food irradiation facility in Domietta harbour and the effect of various parameters on unit processing costs. This study is concerned with carrying out an economic evaluation for the application of food exports from Domietta harbour. The study has been carried out according to the approach applied in the evaluation of economic projects and also considering the requirements of technology projects for food preservation.The study is divided into two sections.The first section: concerned with the marketing and technical aspects where the suitable commodity mix was determined for the agricultural crops which are proposed for irradiation. The marketing study comprised determination of the commodity mix, distributions of the commodity mix all over the year according to the harvest seasons and determination the type and capacity of the source. The second section: comprises the economic analysis according to the method adopted by the International Bank for Development taking into consideration the effect of applying radiation technology on the national income. It provides a model for calculating specific unit processing costs by correlating the known capital costs with the annual operation cost and annual throughputs. The cost benefit of the proposed food irradiation facility was analyzed taking into account the cost of the capital investment, operation cost and other additional parameters. The results of this study showed that there is no economic feasibility for the establishment of an irradiation facility for the radiation treatment of food commodities exported from Domietta harbour

  10. Fostering Ecological Literacy: A Case Study of the Saint John Harbour in Two High School English Language Arts Classrooms

    Science.gov (United States)

    Douglas, Velta

    Integrating environmental education into curriculum in a way that tackles the holistic and complicated nature of multi-dimensional issues continues to be a challenge for educators and administrators. There is potential in using ecological literacy to introduce local environmental case studies into English Language Arts high school classrooms. This research examines the experiences of two ELA classrooms in one Saint John, NB, high school with a two-week unit based on stakeholder relationships within the Saint John Harbour. Through presentations by guest speakers and research sourced from local community groups, students learned about the highly complex environmental issues that inform management decisions for the Harbour. Using these materials as background, students participated in a mock stakeholders meeting. Case study methodology was used to explore student learning in both a higher-level and a lower-level grade 10 ELA class. Data for the analysis included: cognitive mapping exercises; oral and written classroom assignments and activities; a videotape of the mock stakeholder meetings; a focus group interview with selected students; and researcher field notes. Data demonstrated significant student learning about environmental issues including increased sophistication in describing links between and among environmental issues affecting the harbour, and much more complex understandings of the positions and roles of the various stakeholder groups. Some important areas of resistance to new learning were also evident. Implications for practice and policy and recommendations for future research are discussed.

  11. Ionizing radiation modulates the exposure of the HUIV26 cryptic epitope within collagen type IV during angiogenesis

    International Nuclear Information System (INIS)

    Brooks, Peter C.; Roth, Jennifer M.; Lymberis, Stella C.; DeWyngaert, Keith; Broek, Daniel; Formenti, Silvia C.

    2002-01-01

    Purpose: The majority of the research on the biologic effects of ionizing radiation has focused on the impact of radiation on cells in terms of gene expression, DNA damage, and cytotoxicity. In comparison, little information is available concerning the direct effects of radiation on the extracellular microenvironment, specifically the extracellular matrix and its main component, collagen. We have developed a series of monoclonal antibodies that bind to cryptic epitopes of collagen Type IV that are differentially exposed during matrix remodeling and are key mediators of angiogenesis. We have hypothesized that ionizing radiation might affect the process of angiogenesis through a direct effect on the extracellular matrix and specifically on collagen Type IV. Methods and Materials: Angiogenesis was induced in a chick chorioallantoic membrane (CAM) model; 24 h later, a single-dose treatment with ionizing radiation (0.5, 5, and 20 cGy) was administered. Angiogenesis was assessed, and the exposure of two cryptic regulatory epitopes within collagen Type IV (HUI77 and HUIV26) was studied in vitro by solid-phase ELISA and in vivo by immunofluorescence staining. Results: A dose-dependent reduction of angiogenesis with maximum inhibition (85%-90%) occurring at 20 cGy was demonstrated in the CAM model. Exposure of the cryptic HUIV26 site, an angiogenesis control element, was inhibited both in vitro and in vivo by the same radiation dose, whereas little if any change was observed for the HUI77 cryptic epitope. Conclusions: A dose-dependent alteration of the functional exposure of the HUIV26 cryptic epitope is induced by radiation in vitro and in the CAM model in vivo. This radiation-induced change in protein structure and function may contribute to the inhibitory effects of ionizing radiation on new blood vessel growth and warrants further studies in other models

  12. Please mind the gap - Visual census and cryptic biodiversity assessment at central Red Sea coral reefs.

    Science.gov (United States)

    Pearman, John K; Anlauf, Holger; Irigoien, Xabier; Carvalho, Susana

    2016-07-01

    Coral reefs harbor the most diverse assemblages in the ocean, however, a large proportion of the diversity is cryptic and, therefore, undetected by standard visual census techniques. Cryptic and exposed communities differ considerably in species composition and ecological function. This study compares three different coral reef assessment protocols: i) visual benthic reef surveys: ii) visual census of Autonomous Reef Monitoring Structures (ARMS) plates; and iii) metabarcoding techniques of the ARMS (including sessile, 106-500 μm and 500-2000 μm size fractions), that target the cryptic and exposed communities of three reefs in the central Red Sea. Visual census showed a dominance of Cnidaria (Anthozoa) and Rhodophyta on the reef substrate, while Porifera, Bryozoa and Rhodophyta were the most abundant groups on the ARMS plates. Metabarcoding, targeting the 18S rRNA gene, significantly increased estimates of the species diversity (p < 0.001); revealing that Annelida were generally the dominant phyla (in terms of reads) of all fractions and reefs. Furthermore, metabarcoding detected microbial eukaryotic groups such as Syndiniophyceae, Mamiellophyceae and Bacillariophyceae as relevant components of the sessile fraction. ANOSIM analysis showed that the three reef sites showed no differences based on the visual census data. Metabarcoding showed a higher sensitivity for identifying differences between reef communities at smaller geographic scales than standard visual census techniques as significant differences in the assemblages were observed amongst the reefs. Comparison of the techniques showed no similar patterns for the visual techniques while the metabarcoding of the ARMS showed similar patterns amongst fractions. Establishing ARMS as a standard tool in reef monitoring will not only advance our understanding of local processes and ecological community response to environmental changes, as different faunal components will provide complementary information but

  13. The Hemiparasitic Plant Phtheirospermum (Orobanchaceae Is Polyphyletic and Contains Cryptic Species in the Hengduan Mountains of Southwest China

    Directory of Open Access Journals (Sweden)

    Wen-Bin Yu

    2018-02-01

    Full Text Available Phtheirospermum (Orobanchaceae, a hemiparasitic genus of Eastern Asia, is characterized by having long and viscous glandular hairs on stems and leaves. Despite this unifying character, previous phylogenetic analyses indicate that Phtheirospermum is polyphyletic, with Phtheirospermum japonicum allied with tribe Pedicularideae and members of the Ph. tenuisectum complex allied with members of tribe Rhinantheae. However, no analyses to date have included broad phylogenetic sampling necessary to test the monophyly of Phtheirospermum species, and to place these species into the existing subfamiliar taxonomic organization of Orobanchaceae. Two other genera of uncertain phylogenetic placement are Brandisia and Pterygiella, also both of Eastern Asia. In this study, broadly sampled phylogenetic analyses of nrITS and plastid DNA revealed hard incongruence between these datasets in the placement of Brandisia. However, both nrITS and the plastid datasets supported the placement of Ph. japonicum within tribe Pedicularideae, and a separate clade consisting of the Ph. tenuisectum complex and a monophyletic Pterygiella. Analyses were largely in agreement that Pterygiella, the Ptheirospermum complex, and Xizangia form a clade not nested within any of the monophyletic tribes of Orobanchaceae recognized to date. Ph. japonicum, a model species for parasitic plant research, is widely distributed in Eastern Asia. Despite this broad distribution, both nrITS and plastid DNA regions from a wide sampling of this species showed high genetic identity, suggesting that the wide species range is likely due to a recent population expansion. The Ph. tenuisectum complex is mainly distributed in the Hengduan Mountains region. Two cryptic species were identified by both phylogenetic analyses and morphological characters. Relationships among species of the Ph. tenuisectum complex and Pterygiella remain uncertain. Estimated divergence ages of the Ph. tenuisectum complex corresponding

  14. Cryptic, Sympatric Diversity in Tegu Lizards of the Tupinambis teguixin Group (Squamata, Sauria, Teiidae and the Description of Three New Species.

    Directory of Open Access Journals (Sweden)

    John C Murphy

    Full Text Available Tegus of the genera Tupinambis and Salvator are the largest Neotropical lizards and the most exploited clade of Neotropical reptiles. For three decades more than 34 million tegu skins were in trade, about 1.02 million per year. The genus Tupinambis is distributed in South America east of the Andes, and currently contains four recognized species, three of which are found only in Brazil. However, the type species of the genus, T. teguixin, is known from Bolivia, Brazil, Colombia, Ecuador, French Guyana, Guyana, Peru, Suriname, Trinidad and Tobago, and Venezuela (including the Isla de Margarita. Here we present molecular and morphological evidence that this species is genetically divergent across its range and identify four distinct clades some of which are sympatric. The occurrence of cryptic sympatric species undoubtedly exacerbated the nomenclatural problems of the past. We discuss the species supported by molecular and morphological evidence and increase the number of species in the genus Tupinambis to seven. The four members of the T. teguixin group continue to be confused with Salvator merianae, despite having a distinctly different morphology and reproductive mode. All members of the genus Tupinambis are CITES Appendix II. Yet, they continue to be heavily exploited, under studied, and confused in the minds of the public, conservationists, and scientists.

  15. Cryptic, Sympatric Diversity in Tegu Lizards of the Tupinambis teguixin Group (Squamata, Sauria, Teiidae) and the Description of Three New Species.

    Science.gov (United States)

    Murphy, John C; Jowers, Michael J; Lehtinen, Richard M; Charles, Stevland P; Colli, Guarino R; Peres, Ayrton K; Hendry, Catriona R; Pyron, R Alexander

    2016-01-01

    Tegus of the genera Tupinambis and Salvator are the largest Neotropical lizards and the most exploited clade of Neotropical reptiles. For three decades more than 34 million tegu skins were in trade, about 1.02 million per year. The genus Tupinambis is distributed in South America east of the Andes, and currently contains four recognized species, three of which are found only in Brazil. However, the type species of the genus, T. teguixin, is known from Bolivia, Brazil, Colombia, Ecuador, French Guyana, Guyana, Peru, Suriname, Trinidad and Tobago, and Venezuela (including the Isla de Margarita). Here we present molecular and morphological evidence that this species is genetically divergent across its range and identify four distinct clades some of which are sympatric. The occurrence of cryptic sympatric species undoubtedly exacerbated the nomenclatural problems of the past. We discuss the species supported by molecular and morphological evidence and increase the number of species in the genus Tupinambis to seven. The four members of the T. teguixin group continue to be confused with Salvator merianae, despite having a distinctly different morphology and reproductive mode. All members of the genus Tupinambis are CITES Appendix II. Yet, they continue to be heavily exploited, under studied, and confused in the minds of the public, conservationists, and scientists.

  16. Phylogenetic relationships of geckos of the Hemiphyllodactylus harterti group, a new species from Penang Island, Peninsular Malaysia, and a likely case of true cryptic speciation.

    Science.gov (United States)

    Cobos, Anthony; Grismer, L Lee; Wood, Perry L; Quah, Evan S H; Anuar, Shahrul; Muin, Mohd Abdul

    2016-05-03

    An integrative taxonomic analysis based on the mitochondrial gene ND2 and its flanking tRNAs, morphology, and color pattern indicates that a newly discovered gecko described herein as Hemiphyllodactylus cicak sp. nov. from Penang Hill on the Island of Penang, Peninsular Malaysia is a member of the H. harterti group. Hemiphyllodactylus cicak sp. nov. is most closely related to the clade composed of the sister species H. harterti from Bukit Larut, Perak in the Bintang Mountain Range and H. bintik from Gunung Tebu, Terengganu from the Timur Mountain Range. These three allopatric species form a monophyletic group that extends approximately 270 km across three isolated mountain ranges in northern Peninsular Malaysia. The molecular analysis also indicates that H. titiwangsaensis from the Titiwangsa Mountain Range is composed of three genetically distinct allopatric populations. The southern two populations from Fraser's Hill and Genting Highlands, Pahang have an uncorrected pairwise sequence divergence of 3.5% whereas these two populations have 12.4 and 12.8 % sequence divergences, respectively, from the northern population at Cameron Highlands, Pahang. Although the high sequence divergence clearly distinguishes the southern two populations from the former as a different species, all three populations are morphologically indistinguishable, leading to the hypothesis of a true, cryptic speciation event.

  17. Avoidance of wind farms by harbour seals is limited to pile driving activities.

    Science.gov (United States)

    Russell, Debbie J F; Hastie, Gordon D; Thompson, David; Janik, Vincent M; Hammond, Philip S; Scott-Hayward, Lindesay A S; Matthiopoulos, Jason; Jones, Esther L; McConnell, Bernie J

    2016-12-01

    As part of global efforts to reduce dependence on carbon-based energy sources there has been a rapid increase in the installation of renewable energy devices. The installation and operation of these devices can result in conflicts with wildlife. In the marine environment, mammals may avoid wind farms that are under construction or operating. Such avoidance may lead to more time spent travelling or displacement from key habitats. A paucity of data on at-sea movements of marine mammals around wind farms limits our understanding of the nature of their potential impacts.Here, we present the results of a telemetry study on harbour seals Phoca vitulina in The Wash, south-east England, an area where wind farms are being constructed using impact pile driving. We investigated whether seals avoid wind farms during operation, construction in its entirety, or during piling activity. The study was carried out using historical telemetry data collected prior to any wind farm development and telemetry data collected in 2012 during the construction of one wind farm and the operation of another.Within an operational wind farm, there was a close-to-significant increase in seal usage compared to prior to wind farm development. However, the wind farm was at the edge of a large area of increased usage, so the presence of the wind farm was unlikely to be the cause.There was no significant displacement during construction as a whole. However, during piling, seal usage (abundance) was significantly reduced up to 25 km from the piling activity; within 25 km of the centre of the wind farm, there was a 19 to 83% (95% confidence intervals) decrease in usage compared to during breaks in piling, equating to a mean estimated displacement of 440 individuals. This amounts to significant displacement starting from predicted received levels of between 166 and 178 dB re 1 μPa (p-p) . Displacement was limited to piling activity; within 2 h of cessation of pile driving, seals were distributed as

  18. Phylogeny of deepwater snappers (Genus Etelis) reveals a cryptic species pair in the Indo-Pacific and Pleistocene invasion of the Atlantic.

    Science.gov (United States)

    Andrews, Kimberly R; Williams, Ashley J; Fernandez-Silva, Iria; Newman, Stephen J; Copus, Joshua M; Wakefield, Corey B; Randall, John E; Bowen, Brian W

    2016-07-01

    Evolutionary genetic patterns in shallow coastal fishes are documented with dozens of studies, but corresponding surveys of deepwater fishes (>200m) are scarce. Here we investigate the evolutionary history of deepwater snappers (genus Etelis), comprised of three recognized Indo-Pacific species and one Atlantic congener, by constructing a phylogeny of the genus with two mtDNA loci and two nuclear introns. Further, we apply range-wide Indo-Pacific sampling to test for the presence and distribution of a putative cryptic species pair within E. carbunculus using morphological analyses and mtDNA cytochrome b sequences from 14 locations across the species range (N=1696). These analyses indicate that E. carbunculus is comprised of two distinct, non-interbreeding lineages separated by deep divergence (d=0.081 in cytochrome b). Although these species are morphologically similar, we identified qualitative differences in coloration of the upper-caudal fin tip and the shape of the opercular spine, as well as significant differences in adult body length, body depth, and head length. These two species have overlapping Indo-Pacific distributions, but one species is more widespread across the Indo-Pacific, whereas the other species is documented in the Indian Ocean and Western Central Pacific. The dated Etelis phylogeny places the cryptic species divergence in the Pliocene, indicating that the biogeographic barrier between the Indian and Pacific Oceans played a role in speciation. Based on historic taxonomy and nomenclature, the species more widespread in the Pacific Ocean is E. carbunculus, and the other species is previously undescribed (referred to here as E. sp.). The Atlantic congener E. oculatus has only recently (∼0.5Ma) diverged from E. coruscans in the Indo-Pacific, indicating colonization via southern Africa. The pattern of divergence at the Indo-Pacific barrier, and Pleistocene colonization from the Indian Ocean into the Atlantic, is concordant with patterns observed

  19. Background matching and evolution of cryptic colours of selected passerines in deciduous woodlands

    DEFF Research Database (Denmark)

    Bursell, Jens; Dyck, Jan

    2003-01-01

    Most drab plumage colours are probably cryptic. Crypsis (camouflage) occurs when the colour of a significant part of the plumage is similar to the colour of a significant part of the background against which the prey bird may be detected by a potential predator. In this study we compare back...... colours of tits and associated species with colour backgrounds in their habitat during a four-month period in winter. We test the hypothesis that in some of the species back colour is similar to one of the background colours. In addition to colour backgrounds, microhabitats and tree species were also...... recorded. Great Tit Parus major, Nuthatch Sitta europea and Treecreeper Certhia familiaris showed distinct preferences for different colour backgrounds, reflecting their choice of microhabitats and tree species. The data suggest that in the Great Tit the olivemoss green back colour has evolved as crypsis...

  20. Cryptic PML-RARα positive acute promyelocytic leukemia with unusual morphology and cytogenetics

    Directory of Open Access Journals (Sweden)

    Goyal Manu

    2010-10-01

    Full Text Available Acute Promyelocytic Leukemia (APL is different from other forms of acute myeloid leukemia (AML, to the reason being the potential devastating coagulopathy and the sensitivity to all-trans retinoic acid (ATRA and arsenic trioxide (As 2 O 3 . We hereby present a case of APL, morphologically distinct from the hypergranular APL; however, the flow cytometry revealed a characteristic phenotype showing dim CD45, bright CD13, bright CD33 and dim CD117 positivity. These were negative for CD34, HLA-DR, B-lymphoid and T-lymphoid lineage markers. Conventional cytogenetics revealed a distinct karyotype of a male with translocation t(4;15(q34.2:q26.3. However, interphase florescence-in-situ hybridization (FISH revealed PML/RARA fusion signal on chromosome 15 in 90% cells. The cryptic translocations may be missed on conventional cytogenetics, however, need to be picked by other techniques as FISH.

  1. Cryptic diversity in Australian stick insects (Insecta; Phasmida) uncovered by the DNA barcoding approach.

    Science.gov (United States)

    Velonà, A; Brock, P D; Hasenpusch, J; Mantovani, B

    2015-05-18

    The barcoding approach was applied to analyze 16 Australian morphospecies of the order Phasmida, with the aim to test if it could be suitable as a tool for phasmid species identification and if its discrimination power would allow uncovering of cryptic diversity. Both goals were reached. Eighty-two specimens representing twelve morphospecies (Sipyloidea sp. A, Candovia annulata, Candovia sp. A, Candovia sp. B, Candovia sp. C, Denhama austrocarinata, Xeroderus kirbii, Parapodacanthus hasenpuschorum, Tropidoderus childrenii, Cigarrophasma tessellatum, Acrophylla wuelfingi, Eurycantha calcarata) were correctly recovered as clades through the molecular approach, their sequences forming monophyletic and well-supported clusters. In four instances, Neighbor-Joining tree and barcoding gap analyses supported either a specific (Austrocarausius mercurius, Anchiale briareus) or a subspecific (Anchiale austrotessulata, Extatosoma tiaratum) level of divergence within the analyzed morphospecies. The lack of an appropriate database of homologous coxI sequences prevented more detailed identification of undescribed taxa.

  2. Cyanomargarita gen. nov. (Nostocales, Cyanobacteria): convergent evolution resulting in a cryptic genus.

    Science.gov (United States)

    Shalygin, Sergei; Shalygina, Regina; Johansen, Jeffrey R; Pietrasiak, Nicole; Berrendero Gómez, Esther; Bohunická, Markéta; Mareš, Jan; Sheil, Christopher A

    2017-08-01

    Two populations of Rivularia-like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase-Escalante National Monument, a desert park-land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies. We here name the new cryptic genus Cyanomargarita gen. nov., with type species C. melechinii sp. nov., and additional species C. calcarea sp. nov. We also name a new family for these taxa, the Cyanomargaritaceae. © 2017 Phycological Society of America.

  3. Occam’s Quantum Strop: Synchronizing and Compressing Classical Cryptic Processes via a Quantum Channel

    Science.gov (United States)

    Mahoney, John R.; Aghamohammadi, Cina; Crutchfield, James P.

    2016-02-01

    A stochastic process’ statistical complexity stands out as a fundamental property: the minimum information required to synchronize one process generator to another. How much information is required, though, when synchronizing over a quantum channel? Recent work demonstrated that representing causal similarity as quantum state-indistinguishability provides a quantum advantage. We generalize this to synchronization and offer a sequence of constructions that exploit extended causal structures, finding substantial increase of the quantum advantage. We demonstrate that maximum compression is determined by the process’ cryptic order-a classical, topological property closely allied to Markov order, itself a measure of historical dependence. We introduce an efficient algorithm that computes the quantum advantage and close noting that the advantage comes at a cost-one trades off prediction for generation complexity.

  4. Coral colonisation of an artificial reef in a turbid nearshore environment, Dampier Harbour, western Australia.

    Directory of Open Access Journals (Sweden)

    David Blakeway

    Full Text Available A 0.6 hectare artificial reef of local rock and recycled concrete sleepers was constructed in December 2006 at Parker Point in the industrial port of Dampier, western Australia, with the aim of providing an environmental offset for a nearshore coral community lost to land reclamation. Corals successfully colonised the artificial reef, despite the relatively harsh environmental conditions at the site (annual water temperature range 18-32°C, intermittent high turbidity, frequent cyclones, frequent nearby ship movements. Coral settlement to the artificial reef was examined by terracotta tile deployments, and later stages of coral community development were examined by in-situ visual surveys within fixed 25 x 25 cm quadrats on the rock and concrete substrates. Mean coral density on the tiles varied from 113 ± 17 SE to 909 ± 85 SE per m(2 over five deployments, whereas mean coral density in the quadrats was only 6.0 ± 1.0 SE per m(2 at eight months post construction, increasing to 24.0 ± 2.1 SE per m(2 at 62 months post construction. Coral taxa colonising the artificial reef were a subset of those on the surrounding natural reef, but occurred in different proportions--Pseudosiderastrea tayami, Mycedium elephantotus and Leptastrea purpurea being disproportionately abundant on the artificial reef. Coral cover increased rapidly in the later stages of the study, reaching 2.3 ± 0.7 SE % at 62 months post construction. This study indicates that simple materials of opportunity can provide a suitable substrate for coral recruitment in Dampier Harbour, and that natural colonisation at the study site remains sufficient to initiate a coral community on artificial substrate despite ongoing natural and anthropogenic perturbations.

  5. Analysis of seasonal changes in reproductive organs from Icelandic harbour porpoises (Phocoena phocoena

    Directory of Open Access Journals (Sweden)

    Sverrir Daníel Halldórsson

    2003-07-01

    Full Text Available In this study, we analyse some aspects of the macro- and microscopical appearance of gonads of harbour porpoises (Phocoena phocoena from Icelandic coastal waters. Sampling of animals bycaught in gillnets took place in the years 1991 to 1997 and covered the months from September to June. The differences in diameter of seminiferous tubules between samples from the peripheral and central parts of the testis indicate that histological changes associated with maturity begin in the core of the testis. The average tubule diameter was 49, 78 and 118 μm in immature, pubertal and mature animals respectively. The tubule size increased from 55 to 95 μm, coinciding with combined testis weight of 75 to 150 g, indicating the onset of puberty within this range of tubule size and testis weight. The estimated average diameter of tubules when an animal reaches maturity is 82.2 μm or 86.15 μm depending on the method used. The diameter of seminiferous tubules of mature and pubertal animals varies seasonally with a steady increase in the spring. However, lack of samples after mid-June makes estimation of the exact timing of mating impossible. In females, the follicle size of mature and immature animals of age 2 years and older shows seasonalvariation, increasing in late winter or spring. The corpus luteum increases in size during the late pregnancy. The average size of the corpus albicans as a function of the total number of corpora albicantia for each animal, diminishes following the logarithmic equation y = 4.49 – 0.447 · lnx (y = corpus size, x = number of corpora albicantia but apparently they never disappear completely from the ovary. Ovarian activity was almost confined to the left ovary. Our results indicate parturition and copulation in the summer months from late June to August.

  6. Possible causes of a harbour porpoise mass stranding in Danish waters in 2005.

    Directory of Open Access Journals (Sweden)

    Andrew J Wright

    Full Text Available An unprecedented 85 harbour porpoises stranded freshly dead along approximately 100 km of Danish coastline from 7-15 April, 2005. This total is considerably above the mean weekly stranding rate for the whole of Denmark, both for any time of year, 1.23 animals/week (ranging from 0 to 20 during 2003-2008, excluding April 2005, and specifically in April, 0.65 animals/week (0 to 4, same period. Bycatch was established as the cause of death for most of the individuals through typical indications of fisheries interactions, including net markings in the skin and around the flippers, and loss of tail flukes. Local fishermen confirmed unusually large porpoise bycatch in nets set for lumpfish (Cyclopterus lumpus and the strandings were attributed to an early lumpfish season. However, lumpfish catches for 2005 were not unusual in terms of season onset, peak or total catch, when compared to 2003-2008. Consequently, human activity was combined with environmental factors and the variation in Danish fisheries landings (determined through a principal component analysis in a two-part statistical model to assess the correlation of these factors with both the presence of fresh strandings and the numbers of strandings on the Danish west coast. The final statistical model (which was forward selected using Akaike information criterion; AIC indicated that naval presence is correlated with higher rates of porpoise strandings, particularly in combination with certain fisheries, although it is not correlated with the actual presence of strandings. Military vessels from various countries were confirmed in the area from the 7th April, en route to the largest naval exercise in Danish waters to date (Loyal Mariner 2005, 11-28 April. Although sonar usage cannot be confirmed, it is likely that ships were testing various equipment prior to the main exercise. Thus naval activity cannot be ruled out as a possible contributing factor.

  7. Terrestrial bryophytes as indicators of fluoride emission from a phosphorus plant, Long Harbour, Newfoundland, Canada

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, B.A.; Thompson, L.K.; Sidhu, S.S.

    1979-01-01

    A study of the effects of fluoride emissions (HF, SiF/sub 4/) on certain species of bryophytes was carried out in the vicinity of an industrial palnt producing elemental phosphorus at Long Harbour, Nfld. Damage symptoms varied from mild phyllid chlorosis (yellowing) to severe browning of up to 95% of the phyllids. Polytrichum commune Hedw. was the main bryophyte species used in the survey. Random collections from 45 sample sites were analysed for total fluoride. The fluoride concentrations in phyllid tissue ranged from a high of 6066 ppm (dry weight) at a distance of 1 km northeast of the emission source to 44 ppm (dry weight) 11.7 km northeast of the emission source in the direction of the prevailing wind. Control samples were obtained from similar sites in areas far removed from the industrial plant and contained, on average, 11.3 ppm (dry weight). The concentration of fluoride in the bryophyte phyllid tissue was inversely correlated with distance from the emission source, in the direction of the prevailing wind. The severity of acropetal scorching was found to be correlated with the concentration of fluoride in the bryophyte phyllid tissue, and in addition, samples high in fluoride had fewer sporophytes. Fluoride concentrations in bryophyte tissue are compared with concentrations of fluoride in the needles of balsam fir, Abies Balsamea I., in four damage zones, and also with available and total fluoride in soil humus and concentrations of fluoride in air. The total area affected by fluoride emissions was increased using bryophytes as the pollution indicator species, especially in areas far from the industrial plant.

  8. Malignant melanoma arising from a perianal fistula and harbouring a BRAF gene mutation: a case report

    Directory of Open Access Journals (Sweden)

    Tajahuerce Marcos

    2011-08-01

    Full Text Available Abstract Background Melanoma of the anal region is a very uncommon disease, accounting for only 0.2-0.3% of all melanoma cases. Mutations of the BRAF gene are usually absent in melanomas occurring in this region as well as in other sun-protected regions. The development of a tumour in a longstanding perianal fistula is also extremely rare. More frequent is the case of a tumour presenting as a fistula, that is, the fistula being a consequence of the cancerous process, although we have found only two cases of fistula-generating melanomas reported in the literature. Case Presentation Here we report the case of a 38-year-old male who presented with a perianal fistula of four years of evolution. Histopathological examination of the fistulous tract confirmed the presence of malignant melanoma. Due to the small size and the central location of the melanoma inside the fistulous tract, we believe the melanoma reported here developed in the epithelium of the fistula once the latter was already formed. Resected sentinel lymph nodes were negative and the patient, after going through a wide local excision, remains disease-free nine years after diagnosis. DNA obtained from melanoma tissue was analysed by automated direct sequencing and the V600E (T1799A mutation was detected in exon 15 of the BRAF gene. Conclusion Since fistulae experience persistent inflammation, the fact that this melanoma harbours a BRAF mutation strengthens the view that oxidative stress caused by inflammatory processes plays an important role in the genesis of BRAF gene mutations.

  9. St. John's Harbour's South Side Hills internal development concept: going underground for multi-use space

    Energy Technology Data Exchange (ETDEWEB)

    Kierans, T W

    1979-03-01

    The advantages of underground locations for space saving, security, stability, environmental, aesthetic, and weather protection reasons with regard to power plants, municipal transport facilities, liquid fuel storage, national defence structures, public utilities and parking garages have been recognized for many years. The municipal, provincial, and federal authorities responsible for the city and seaport of St. John's, Newfoundland should consider the short-, medium-, and long-term benefits of the comprehensive concept proposed in this paper for the internal development of the South Side Hills - the rocky, sandstone hills that rise steeply to over 220 m between the crowded St. John's Harbour and Freshwater Bay. This proposal outlines a plan of excavation, space utilization, organization, financing, rock support, ventilation, water and energy supply, transportation arrangements and, not of least of all, the important use of the excavated rock to create a system of bottom-founded and floating concrete breakwaters at the entrance to Freshwater Bay. The proposed breakwaters would make it possible for St. John's to claim one of the finest deep-water harbors on the eastern seaboard of North America. Its location close to the North Atlantic main shipping lanes and on the threshold of the potential energy corridor to the Easten Arctic makes it an outstanding and natural location for such a facility. Other benefits include environmental protection and conservation of the natural beauty of the Hills and much improved utilization of the existing harbor. The employment opportunities and the potential for substantial city growth using existing untapped natural resources appear fully to merit the detailed economic cost studies that the concept now requires.

  10. Patterns and processes in the genetic differentiation of the Brachionus calyciflorus complex, a passively dispersing freshwater zooplankton.

    Science.gov (United States)

    Xiang, Xian-ling; Xi, Yi-long; Wen, Xin-li; Zhang, Gen; Wang, Jin-xia; Hu, Ke

    2011-05-01

    Elucidating the evolutionary patterns and processes of extant species is an important objective of any research program that seeks to understand population divergence and, ultimately, speciation. The island-like nature and temporal fluctuation of limnetic habitats create opportunities for genetic differentiation in rotifers through space and time. To gain further understanding of spatio-temporal patterns of genetic differentiation in rotifers other than the well-studied Brachionus plicatilis complex in brackish water, a total of 318 nrDNA ITS sequences from the B. calyciflorus complex in freshwater were analysed using phylogenetic and phylogeographic methods. DNA taxonomy conducted by both the sequence divergence and the GMYC model suggested the occurrence of six potential cryptic species, supported also by reproductive isolation among the tested lineages. The significant genetic differentiation and non-significant correlation between geographic and genetic distances existed in the most abundant cryptic species, BcI-W and Bc-SW. The large proportion of genetic variability for cryptic species Bc-SW was due to differences between sampling localities within seasons, rather than between different seasons. Nested Clade Analysis suggested allopatric or past fragmentation, contiguous range expansion and long-distance colonization possibly coupled with subsequent fragmentation as the probable main forces shaping the present-day phylogeographic structure of the B. calyciflorus species complex. Copyright © 2011 Elsevier Inc. All rights reserved.

  11. Oxygen levels versus chemical pollutants: do they have similar influence on macrofaunal assemblages? A case study in a harbour with two opposing entrances

    International Nuclear Information System (INIS)

    Guerra-Garcia, J.M.; Garcia-Gomez, J.C.

    2005-01-01

    Generally, harbours are polluted zones characterised by low values of hydrodynamism and oxygen in the water column and high concentrations of pollutants in sediments. The harbour of Ceuta, North Africa, has an unusual structure; it is located between two bays connected by a channel, which increases the water movement and exchange in the harbour, maintaining moderate oxygen levels in the water-sediment interface. Nevertheless, high concentration of organic matter, nutrients and heavy metals were measured in sediments from this harbour. Under these unusual conditions (high levels of pollution but total saturation of oxygen in the water column) we studied the responses of soft-bottom macrobenthic communities using uni and multivariate analyses. The number of species was similar inside and outside the harbour but the species composition differed between internal and external stations; oxygen levels seem to control the 'quantity' of species whereas pollutants control the 'quality' of them. - A high diversity of benthic animals was found in a polluted harbour where high oxygen levels occurred

  12. Detecting cryptic speciation in the widespread and morphologically conservative carpet chameleon (Furcifer lateralis) of Madagascar.

    Science.gov (United States)

    Florio, A M; Ingram, C M; Rakotondravony, H A; Louis, E E; Raxworthy, C J

    2012-07-01

    Species delimitation within recently evolved groups can be challenging because species may be difficult to distinguish morphologically. Following the General Lineage Concept, we apply a multiple evidence approach to assess species limits within the carpet chameleon Furcifer lateralis, which is endemic to Madagascar and exported in large numbers for the pet trade. Cryptic speciation within F. lateralis was considered likely because this species (1) has a vast distribution, (2) occupies exceptionally diverse habitats and (3) exhibits subtle regional differences in morphology. Phylogenetic trees reconstructed using nuclear and mitochondrial genes recovered three well-supported clades corresponding with geography. Morphological results based on canonical variates analysis show that these clades exhibit subtle differences in head casque morphology. Ecological niche modelling results found that these phylogenetic groups also occupy unique environmental space and exhibit patterns of regional endemism typical of other endemic reptiles. Combined, our findings provide diverse yet consistent evidence for the existence of three species. Consequently, we elevate the subspecies F. lateralis major to species rank and name a new species distributed in northern and western Madagascar. Initial ecological divergence, associated with speciation of F. lateralis in humid eastern habitat, fits the Ecographic Constraint model for species diversification in Madagascar. By contrast, the second speciation event provides some support for the Riverine Barrier model, with the Mangoky River possibly causing initial isolation between species. These findings thus support two contrasting models of speciation within closely related species and demonstrate the utility of applying a combined-evidence approach for detecting cryptic speciation. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

  13. Cryptic extinction of a common Pacific lizard Emoia impar (Squamata, Scincidae) from the Hawaiian Islands.

    Science.gov (United States)

    Fisher, Robert; Ineich, Ivan

    2012-01-01

    Most documented declines of tropical reptiles are of dramatic or enigmatic species. Declines of widespread species tend to be cryptic. The early (1900s) decline and extinction of the common Pacific skink Emoia impar from the Hawaiian Islands is documented here through an assessment of literature, museum vouchers and recent fieldwork. This decline appears contemporaneous with the documented declines of invertebrates and birds across the Hawaiian Islands. A review of the plausible causal factors indicates that the spread of the introduced big-headed ant Pheidole megacephala is the most likely factor in this lizard decline. The introduction and spread of a similar skink Lampropholis delicata across the islands appears to temporally follow the decline of E. impar, although there is no evidence of competition between these species. It appears that L. delicata is spreading to occupy the niche vacated by the extirpated E. impar. Further confusion exists because the skink E. cyanura, which is very similar in appearance to E. impar, appears to have been introduced to one site within a hotel on Kaua'i and persisted as a population at that site for approximately 2 decades (1970s–1990s) but is now also extirpated. This study highlights the cryptic nature of this early species extinction as evidence that current biogeographical patterns of non-charismatic or enigmatic reptiles across the Pacific may be the historical result of early widespread invasion by ants. Conservation and restoration activities for reptiles in the tropical Pacific should consider this possibility and evaluate all evidence prior to any implementation.

  14. Species delimitation in the Gehyra nana (Squamata: Gekkonidae) complex: cryptic and divergent morphological evolution in the Australian Monsoonal Tropics, with the description of four new species.

    Science.gov (United States)

    Doughty, Paul; Bourke, Gayleen; Tedeschi, Leonardo G; Pratt, Renae C; Oliver, Paul M; Palmer, Russell A; Moritz, Craig

    2018-04-04

    Recent advances in molecular genetic techniques and increased fine scale sampling in the Australian Monsoonal Tropics (AMT) have provided new impetus to reassess species boundaries in the Gehyra nana species complex, a clade of small-bodied, saxicolous geckos which are widely distributed across northern Australia. A recent phylogenomic analysis revealed eight deeply divergent lineages that occur as a series of overlapping distributions across the AMT and which, as a whole, are paraphyletic with four previously described species. Several of these lineages currently included in G. nana are phenotypically distinct, while others are highly conservative morphologically. Here we use an integrated approach to explore species delimitation in this complex. We redefine G. nana as a widespread taxon with complex genetic structure across the Kimberley of Western Australia and Top End of the Northern Territory, including a lineage with mtDNA introgressed from the larger-bodied G. multiporosa. We describe four new species with more restricted distributions within the G. nana complex. The new species are phylogenetically divergent and morphologically diagnosable, and include the relatively cryptic G. paranana sp. nov. from the western Northern Territory, the large-bodied G. pseudopunctata sp. nov. from the southern Kimberley ranges, G. granulum sp. nov., a small-bodied form with granules on the proximal lamellae from the north-west and southern Kimberley ranges and the small-bodied G. pluraporosa sp. nov. restricted to the northern Kimberley. Our revision largely stabilises the taxonomy of the G. nana complex, although further analyses of species limits among the remaining mostly parapatric lineages of G. nana sensu stricto are warranted.

  15. Hybridization between two cryptic filamentous brown seaweeds along the shore: analysing pre- and postzygotic barriers in populations of individuals with varying ploidy levels.

    Science.gov (United States)

    Montecinos, Alejandro E; Guillemin, Marie-Laure; Couceiro, Lucia; Peters, Akira F; Stoeckel, Solenn; Valero, Myriam

    2017-07-01

    We aimed to study the importance of hybridization between two cryptic species of the genus Ectocarpus, a group of filamentous algae with haploid-diploid life cycles that include the principal genetic model organism for the brown algae. In haploid-diploid species, the genetic structure of the two phases of the life cycle can be analysed separately in natural populations. Such life cycles provide a unique opportunity to estimate the frequency of hybrid genotypes in diploid sporophytes and meiotic recombinant genotypes in haploid gametophytes allowing the effects of reproductive barriers preventing fertilization or preventing meiosis to be untangle. The level of hybridization between E. siliculosus and E. crouaniorum was quantified along the European coast. Clonal cultures (568 diploid, 336 haploid) isolated from field samples were genotyped using cytoplasmic and nuclear markers to estimate the frequency of hybrid genotypes in diploids and recombinant haploids. We identified admixed individuals using microsatellite loci, classical assignment methods and a newly developed Bayesian method (XPloidAssignment), which allows the analysis of populations that exhibit variations in ploidy level. Over all populations, the level of hybridization was estimated at 8.7%. Hybrids were exclusively observed in sympatric populations. More than 98% of hybrids were diploids (40% of which showed signs of aneuploidy) with a high frequency of rare alleles. The near absence of haploid recombinant hybrids demonstrates that the reproductive barriers are mostly postzygotic and suggests that abnormal chromosome segregation during meiosis following hybridization of species with different genome sizes could be a major cause of interspecific incompatibility in this system. © 2017 John Wiley & Sons Ltd.

  16. Reduction of excess sludge in a sequencing batch reactor by lysis-cryptic growth using quick lime for disintegration under low temperature.

    Science.gov (United States)

    Lv, Xiao-Mei; Song, Ju-Sheng; Li, Ji; Zhai, Kun

    2017-08-01

    In the present study, quick-lime-based thermal-alkaline sludge disintegration (SD) under low temperature was combined with cryptic growth to investigate the excess sludge reduction efficiency in the sequencing batch reactor (SBR). The optimized condition of SD was as follows: T = 80℃, pH = 11, t = 180 min, and the SD rate was about 42.1%. With 65.6% of excess sludge disintegrated and returned to the SBR, the system achieved sludge reduction rate of about 40.1%. The lysis-cryptic growth still obtained satisfactory sludge reduction efficiency despite the comparative low SD rate, which suggested that disintegration rate might not be the decisive factor for cryptic-growth-based sludge reduction. Lysis-cryptic growth did not impact the effluent quality, yet the phosphorus removal performance was enhanced, with effluent total phosphorus concentration decreased by 0.3 mg/L (33%). Crystal compounds of calcium phosphate precipitate were detected in the system by Fourier transform infrared spectroscopy and X-ray diffraction, which indicated the phosphorus removal potential of SD using lime. Moreover, endogenous dehydrogenase activity of activated sludge in the lysis-cryptic system was enhanced, which was beneficial for sludge reduction. SD and cryptic growth in the present study demonstrates an economical and effective approach for sludge reduction.

  17. Short-term effects of the construction of wind turbines on harbour porpoises at Horns Reef

    Energy Technology Data Exchange (ETDEWEB)

    Tougaard, J. [Hedeselskabet, Miljoe og Energi A/S, Viborg(Denmark); Carstensen, Jakob [National Environmental Res. Inst., Dept. of Marine Ecology, Roskidle (Denmark); Damsgaard Henriksen, O.; Teilmann, J. [National Environmental Res. Inst., Dept. of Arctic Biology, Roskilde (Denmark)

    2003-04-15

    In 2002 the Worlds largest offshore wind farm, consisting of 80 2MW wind turbines, was constructed on Horns Reef in the Danish North Sea. Ship based visual surveys and long-term deployment of acoustic dataloggers (PODs) were used to assess short term effects of construction on behaviour and abundance of harbour porpoises (Phocoena phocoena). Most focus was put on mounting of steel monopile foundations for the turbines, as they were rammed into the seabed. This type of operation is known to generate very loud underwater sound levels. Combined evidence from animal densities obtained from visual surveys, behavioural observations during surveys and acoustic activity data in and outside the construction area demonstrated effects on the behaviour and abundance of animals on both short-term (hours) and long term (entire construction period) scales. Acoustic activity by the porpoises decreased dramatically on the entire Horns Reef at the onset of ramming operations and returned to higher levels a few hours after each ramming operation was completed. A reduction in abundance close to ramming operations was anticipated, as deterring devices (pingers and seal scarers) were deployed prior to each ramming operation to deter marine mammals from the area and thus protect them from exposure to the loud sound levels generated by the ramming procedure. The changes in abundance and behaviour over large distances are unlikely to be explained by the deterring sounds, which have comparably lower intensities than the ramming sounds and these effects must be attributed to the ramming. A general effect on the behaviour of animals was seen during the construction period and at distances of up to 10-15 kilometers from the construction site. Compared to observations before and after construction there was a decrease in non-directional swimming, a behaviour assumed to correlate with feeding activity. Animal density estimates indicates that there were fewer animals present on the entire Horns

  18. Status, ecology and life history of harbour porpoise (Phocoena phocoena, in Danish waters

    Directory of Open Access Journals (Sweden)

    Christina Lockyer

    2003-07-01

    Full Text Available A review of historical harbour porpoise catches in Danish waters, together with current distribution, are provided. Most information on distribution is derived from historical catch data with a total of about 100,000 animals taken in Little Belt alone and 40,000 from Isefjord area during the 19th century. Recent sightings surveys and tagging indicate extensive movements of animals within and between Inner Danish Waters and the Skagerrak / North Sea. Biological information is reviewed for the region, drawing on directed catches, bycatches and strandings from a databasecomprising nearly 1,900 records from 1834 through 1998. Diet, parasites, pollutants, biological parameters (age and reproduction and body condition are reported, focusing mainly on the period 1996-98 when comprehensive data were collected. In 1980s samples, gadoids were the most important prey items (found in 62% of stomachs followed by clupeoids (35%, gobiids (30%, and ammodytids (30%. Some dietary differences were observed between North Sea and Inner Danish waters. Pollutant analyses indicated a decline in sumDDT concentrations yet an increase in sumPCB and HCH levels in Danish porpoises, with comparatively higher levels here than in Baltic and Norwegian waters. Heavy metal concentrations appear higher than in Baltic porpoises. Biological parameters indicate a longevity of up to 23 years in both sexes but with fewer than 5% living beyond 12 years. Sexual maturity occurred at slightly over age 3 years in both females and males, with corresponding lengths of about 135 cm in males and 143 cm in females. The dataindicate a size range at birth of 65 - 75 cm (weight 4.5 – 6.7 kg, with a minimum of 60 cm and 3.4 kg, and a likely gestation time of 10 months. Conception most likely occurs during August, with peak births in June. Directed catches comprised adult animals whereas bycaught and stranded porpoises comprised predominantly juveniles. In data from all sources, males outnumbered

  19. Short-term effects of the construction of wind turbines on harbour porpoises at Horns Reef

    International Nuclear Information System (INIS)

    Tougaard, J.; Carstensen, Jakob; Damsgaard Henriksen, O.; Teilmann, J.

    2003-04-01

    In 2002 the Worlds largest offshore wind farm, consisting of 80 2MW wind turbines, was constructed on Horns Reef in the Danish North Sea. Ship based visual surveys and long-term deployment of acoustic dataloggers (PODs) were used to assess short term effects of construction on behaviour and abundance of harbour porpoises (Phocoena phocoena). Most focus was put on mounting of steel monopile foundations for the turbines, as they were rammed into the seabed. This type of operation is known to generate very loud underwater sound levels. Combined evidence from animal densities obtained from visual surveys, behavioural observations during surveys and acoustic activity data in and outside the construction area demonstrated effects on the behaviour and abundance of animals on both short-term (hours) and long term (entire construction period) scales. Acoustic activity by the porpoises decreased dramatically on the entire Horns Reef at the onset of ramming operations and returned to higher levels a few hours after each ramming operation was completed. A reduction in abundance close to ramming operations was anticipated, as deterring devices (pingers and seal scarers) were deployed prior to each ramming operation to deter marine mammals from the area and thus protect them from exposure to the loud sound levels generated by the ramming procedure. The changes in abundance and behaviour over large distances are unlikely to be explained by the deterring sounds, which have comparably lower intensities than the ramming sounds and these effects must be attributed to the ramming. A general effect on the behaviour of animals was seen during the construction period and at distances of up to 10-15 kilometers from the construction site. Compared to observations before and after construction there was a decrease in non-directional swimming, a behaviour assumed to correlate with feeding activity. Animal density estimates indicates that there were fewer animals present on the entire Horns

  20. Characterization of the IncA/C plasmid pSCEC2 from Escherichia coli of swine origin that harbours the multiresistance gene cfr.

    Science.gov (United States)

    Zhang, Wan-Jiang; Xu, Xing-Ran; Schwarz, Stefan; Wang, Xiu-Mei; Dai, Lei; Zheng, Hua-Jun; Liu, Siguo

    2014-02-01

    To determine the complete nucleotide sequence of the multidrug resistance plasmid pSCEC2, isolated from a porcine Escherichia coli strain, and to analyse it with particular reference to the cfr gene region. Plasmid pSCEC2 was purified from its E. coli J53 transconjugant and then sequenced using the 454 GS-FLX System. After draft assembly, predicted gaps were closed by PCR with subsequent sequencing of the amplicons. Plasmid pSCEC2 is 135 615 bp in size and contains 200 open reading frames for proteins of ≥100 amino acids. Analysis of the sequence of pSCEC2 revealed two resistance gene segments. The 4.4 kb cfr-containing segment is flanked by two IS256 elements in the same orientation, which are believed to be involved in the dissemination of the rRNA methylase gene cfr. The other segment harbours the resistance genes floR, tet(A)-tetR, strA/strB and sul2, which have previously been found on other IncA/C plasmids. Except for these two resistance gene regions, the pSCEC2 backbone displayed >99% nucleotide sequence identity to that of other IncA/C family plasmids isolated in France, Chile and the USA. The cfr gene was identified on an IncA/C plasmid, which is well known for its broad host range and transfer and maintenance properties. The location on such a plasmid will further accelerate the dissemination of cfr and co-located resistance genes among different Gram-negative bacteria. The genetic context of cfr on plasmid pSCEC2 underlines the complexity of cfr transfer events and confirms the role that insertion sequences play in the spread of cfr.

  1. Personal exposure to benzene and 1,3-butadiene during petroleum refinery turnarounds and work in the oil harbour.

    Science.gov (United States)

    Akerstrom, M; Almerud, P; Andersson, E M; Strandberg, B; Sallsten, G

    2016-11-01

    Petroleum refinery workers' exposure to the carcinogens benzene and 1,3-butadiene has decreased during normal operations. However, certain occupational groups or events at the refineries still involve a risk of higher exposures. The aim of this study was to examine the personal exposure to benzene and 1,3-butadiene at refinery turnarounds and during work in the oil harbour. Personal exposure measurements of benzene and 1,3-butadiene were taken during work shifts, with a priori assumed higher benzene exposure, using PerkinElmer diffusive samplers filled with Carbopack X. Mean exposure levels were calculated, and repeated exposure measurements, when available, were assessed using mixed effect models. Group and individual compliance with the Swedish occupational exposure limit (OEL) was tested for the different exposure groups. Mean benzene exposure levels for refinery workers during the three measured turnarounds were 150, 610 and 960 µg/m 3 , and mean exposures for oil harbour workers and sewage tanker drivers were 310 and 360 µg/m 3 , respectively. Higher exposures were associated with handling benzene-rich products. Most occupational groups did not comply with the Swedish OEL for benzene nor did the individuals within the groups. The exposure to 1,3-butadiene was very low, between Work within the petroleum refinery industry, with potential exposure to open product streams containing higher fractions of benzene, pose a risk of personal benzene exposures exceeding the OEL. Refinery workers performing these work tasks frequently, such as contractors, sewage tanker drivers and oil harbour workers, need to be identified and protected.

  2. MULTIFUNCTIONAL LAND USE IN THE RENEWAL OF HARBOUR AREAS: PATTERNS OF PHYSICAL DISTRIBUTION OF THE URBAN FUNCTIONS

    Directory of Open Access Journals (Sweden)

    Antoni Remesar

    2004-09-01

    Full Text Available Being one of the most representative spatial processes of the last 30 years, which frequently occur in strategic parts of the cities and justify special financing investments, the operations of renewal of harbour areas can be seen as a laboratory of contemporary urban design. In the context of the activity developed by the IFHP Working Party on Multifunctional and Intensive Land Use, these operations are also an high potential field of research, justifying its closer analysis, as it has been done in the last two years with the technical visits to Amsterdam, Rotterdam, Oslo, and now to Barcelona. Focusing on the multifunctional use of spaces, this paper analyses several operations of renewal of harbour areas, trying to identify the urban design solutions adopted in those operations regarding the physical distribution of the proposed urban functions. The case-study comparative analysis is the applied method, based on which are identified: (1 the different urban functions present on these operations, and; (2 the concept under which these different functions are disposed in the area and combined between themselves. The hypothesis is that it can be established a general classification on the forms how different functions are combined in these operations. The paper previously distinguishes two types of functions, regarding the relative its importance in the area: the dominant urban functions and the located urban functions. The dominant urban functions are those functions that generally dominate an urban area, although it can contain located urban functions within its perimeter on specific locations, e.g., residential areas, offices and shopping areas, industrial areas, public equipment areas and special use areas. The located urban functions are those specific functions that aren’t dominating functions and exist within the perimeter of a dominant urban function, e.g., schools, museums, public services, local shopping’s and others. The papers

  3. Sources of ambient concentrations and chemical composition of PM 2.5-0.1 in Cork Harbour, Ireland

    Science.gov (United States)

    Hellebust, S.; Allanic, A.; O'Connor, I. P.; Jourdan, C.; Healy, D.; Sodeau, J. R.

    2010-02-01

    Particulate matter (PM 10-2.5 and PM 2.5-0.1) has been collected over a period of one year in Cork Harbour, Ireland, using a high-volume cascade impactor and polyurethane foam collection substrate. Collected PM 2.5-0.1 was analysed for water-soluble inorganic ions and metal content using ion chromatography and inductively coupled plasma-optical emission spectroscopy. On average approximately 50% by mass of the chemical content of PM was identified. The motivation for the study was to assess the potential impact of shipping emissions on air quality in Cork Harbour and City, with a view to informing public health impacts. The average ambient concentration of PM 10 between May 2007 and April 2008 was 4.6 µgm - 3 and the maximum concentration measured in one sample, representing a 4 day collection period, was 16 µgm - 3 . The major inorganic constituents identified in PM collected in Haulbowline Island in Cork Harbour were sulfate, ammonium, nitrate, chloride and sodium ions, which were mainly attributable to sea salt and secondary inorganic aerosols from regional sources. The results were analysed by principal component analysis for the purpose of source apportionment. Four factors were identified explaining over 80% of the data set variance. The factors were: shipping, sea salt, crustal material and secondary inorganic aerosols (SIA). The smaller size fraction was frequently observed to dominate, as the average concentration was 2.77 µgm - 3 for PM 2.5-0.1 compared to 1.9 µgm - 3 for PM 10-2.5. Fresh ship plumes were not found to make a significant contribution to primary PM 2.5-0.1 concentrations adjacent to the shipping channel. However, this was partially attributed to the ultrafine nature of ship emissions and the majority of the toxic metal content was attributed to emissions associated with heavy oil combustion sources, which include ship engines.

  4. CO2 emissions from a temperate drowned river valley estuary adjacent to an emerging megacity (Sydney Harbour)

    Science.gov (United States)

    Tanner, E. L.; Mulhearn, P. J.; Eyre, B. D.

    2017-06-01

    The Sydney Harbour Estuary is a large drowned river valley adjacent to Sydney, a large urban metropolis on track to become a megacity; estimated to reach a population of 10 million by 2100. Monthly underway surveys of surface water pCO2 were undertaken along the main channel and tributaries, from January to December 2013. pCO2 showed substantial spatio-temporal variability in the narrow high residence time upper and mid sections of the estuary, with values reaching a maximum of 5650 μatm in the upper reaches and as low as 173 μatm in the mid estuary section, dominated by respiration and photosynthesis respectively. The large lower estuary displayed less variability in pCO2 with values ranging from 343 to 544 μatm controlled mainly by tidal pumping and temperature. Air-water CO2 emissions reached a maximum of 181 mmol C m-2 d-1 during spring in the eutrophic upper estuary. After a summer high rainfall event nutrient-stimulated biological pumping promoted a large uptake of CO2 transitioning the Sydney Harbour Estuary into a CO2 sink with a maximum uptake of rate of -10.6 mmol C m-2 d-1 in the mid-section of the estuary. Annually the Sydney Harbour Estuary was heterotrophic and a weak source of CO2 with an air-water emission rate of 1.2-5 mmol C m-2 d-1 (0.4-1.8 mol C m-2 y-1) resulting in a total carbon emission of around 930 tonnes per annum. CO2 emissions (weighted m3 s-1 of discharge per km2 of estuary surface area) from Sydney Harbour were an order of magnitude lower than other temperate large tectonic deltas, lagoons and engineered systems of China, India, Taiwan and Europe but were similar to other natural drowned river valley systems in the USA. Discharge per unit area appears to be a good predictor of CO2 emissions from estuaries of a similar climate and geomorphic class.

  5. Cryptic species of Ponto-Caspian bighead goby of the genus Ponticola (Gobiidae)

    DEFF Research Database (Denmark)

    Vasil'eva, E. D.; Schwarzhans, Werner; Medvedev, D. A.

    2016-01-01

    . gorlap which inhabits the northern, western, and southern Caspian Sea. These three allopatric species have ctenoid scales to varying degrees on the crown and nape (100% presence in P. kessleri and complete absence in P. iljini), and there are small differences in the shape of the head, the thickness...... of the beginning of divergence of the considered three cryptic species, as well as isolating barriers that led to allopatric speciation, are discussed....

  6. Spatial distribution, territoriality and sound production by tropical cryptic butterflies (Hamadryas, Lepidoptera: Nymphalidae): implications for the "industrial melanism" debate

    OpenAIRE

    Julián Monge-Nájera; Francisco Hernández; María Isabel González; Javier Soley; José Araya; Stefano Zolla

    1998-01-01

    Neotropical butterflies of the genus Hamadryas, noted by the emission of sound, spend much time perching on trees and are believed to be cryptically patterned and colored with respect to tree trunks and branches they use as perching sites, but the subject had not been studied previously. This paper describes spatial distribution, territoriality and sound production in five species, under natural conditions: Hamadryas amphinome (Lucas, 1853), H. februa (Godart, 1824), H. feronia (Fruhstorfer, ...

  7. Cryptically patterned moths perceive bark structure when choosing body orientations that match wing color pattern to the bark pattern.

    Directory of Open Access Journals (Sweden)

    Chang-Ku Kang

    Full Text Available Many moths have wing patterns that resemble bark of trees on which they rest. The wing patterns help moths to become camouflaged and to avoid predation because the moths are able to assume specific body orientations that produce a very good match between the pattern on the bark and the pattern on the wings. Furthermore, after landing on a bark moths are able to perceive stimuli that correlate with their crypticity and are able to re-position their bodies to new more cryptic locations and body orientations. However, the proximate mechanisms, i.e. how a moth finds an appropriate resting position and orientation, are poorly studied. Here, we used a geometrid moth Jankowskia fuscaria to examine i whether a choice of resting orientation by moths depends on the properties of natural background, and ii what sensory cues moths use. We studied moths' behavior on natural (a tree log and artificial backgrounds, each of which was designed to mimic one of the hypothetical cues that moths may perceive on a tree trunk (visual pattern, directional furrow structure, and curvature. We found that moths mainly used structural cues from the background when choosing their resting position and orientation. Our findings highlight the possibility that moths use information from one type of sensory modality (structure of furrows is probably detected through tactile channel to achieve crypticity in another sensory modality (visual. This study extends our knowledge of how behavior, sensory systems and morphology of animals interact to produce crypsis.

  8. Cryptically patterned moths perceive bark structure when choosing body orientations that match wing color pattern to the bark pattern.

    Science.gov (United States)

    Kang, Chang-Ku; Moon, Jong-Yeol; Lee, Sang-Im; Jablonski, Piotr G

    2013-01-01

    Many moths have wing patterns that resemble bark of trees on which they rest. The wing patterns help moths to become camouflaged and to avoid predation because the moths are able to assume specific body orientations that produce a very good match between the pattern on the bark and the pattern on the wings. Furthermore, after landing on a bark moths are able to perceive stimuli that correlate with their crypticity and are able to re-position their bodies to new more cryptic locations and body orientations. However, the proximate mechanisms, i.e. how a moth finds an appropriate resting position and orientation, are poorly studied. Here, we used a geometrid moth Jankowskia fuscaria to examine i) whether a choice of resting orientation by moths depends on the properties of natural background, and ii) what sensory cues moths use. We studied moths' behavior on natural (a tree log) and artificial backgrounds, each of which was designed to mimic one of the hypothetical cues that moths may perceive on a tree trunk (visual pattern, directional furrow structure, and curvature). We found that moths mainly used structural cues from the background when choosing their resting position and orientation. Our findings highlight the possibility that moths use information from one type of sensory modality (structure of furrows is probably detected through tactile channel) to achieve crypticity in another sensory modality (visual). This study extends our knowledge of how behavior, sensory systems and morphology of animals interact to produce crypsis.

  9. Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales, Jungermanniopsida, including two reinstated and five new species

    Directory of Open Access Journals (Sweden)

    Matt Renner

    2013-10-01

    Full Text Available Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph. and R. notabilis sp. nov. are endemic to the Wet Tropics Bioregion of north-east Queensland, suggesting high diversity and high endemism might characterise the bryoflora of this relatively isolated wet-tropical region. Radula demissa sp. nov. is endemic to southern temperate Australasia, and like R. strangulata occurs on both sides of the Tasman Sea. Radula imposita sp. nov. is a twig and leaf epiphyte found in association with waterways in New South Wales and Queensland. Another species, R. pugioniformis sp. nov., has been confused with Radula buccinifera but was not included in the molecular phylogeny. Morphological data suggest it may belong to subg. Odontoradula. Radula buccinifera is endemic to Australia including Western Australia and Tasmania, and to date is known from south of the Clarence River on the north coast of New South Wales. Nested within R. buccinifera is a morphologically distinct plant from Norfolk Island described as R. anisotoma sp. nov. Radula australiana is resolved as monophyletic, sister to a species occurring in east coast Australian rainforests, and nesting among the R.buccinifera lineages with strong support. The molecular phylogeny suggests several long-distance dispersal events may have occurred. These include two east-west dispersal events from New Zealand to Tasmania and south-east Australia in R. strangulata, one east-west dispersal event from Tasmania to

  10. CTL escape mediated by proteasomal destruction of an HIV-1 cryptic epitope.

    Directory of Open Access Journals (Sweden)

    Sylvain Cardinaud

    2011-05-01

    Full Text Available Cytotoxic CD8+ T cells (CTLs play a critical role in controlling viral infections. HIV-infected individuals develop CTL responses against epitopes derived from viral proteins, but also against cryptic epitopes encoded by viral alternative reading frames (ARF. We studied here the mechanisms of HIV-1 escape from CTLs targeting one such cryptic epitope, Q9VF, encoded by an HIVgag ARF and presented by HLA-B*07. Using PBMCs of HIV-infected patients, we first cloned and sequenced proviral DNA encoding for Q9VF. We identified several polymorphisms with a minority of proviruses encoding at position 5 an aspartic acid (Q9VF/5D and a majority encoding an asparagine (Q9VF/5N. We compared the prevalence of each variant in PBMCs of HLA-B*07+ and HLA-B*07- patients. Proviruses encoding Q9VF/5D were significantly less represented in HLA-B*07+ than in HLA-B*07- patients, suggesting that Q9FV/5D encoding viruses might be under selective pressure in HLA-B*07+ individuals. We thus analyzed ex vivo CTL responses directed against Q9VF/5D and Q9VF/5N. Around 16% of HLA-B*07+ patients exhibited CTL responses targeting Q9VF epitopes. The frequency and the magnitude of CTL responses induced with Q9VF/5D or Q9VF/5N peptides were almost equal indicating a possible cross-reactivity of the same CTLs on the two peptides. We then dissected the cellular mechanisms involved in the presentation of Q9VF variants. As expected, cells infected with HIV strains encoding for Q9VF/5D were recognized by Q9VF/5D-specific CTLs. In contrast, Q9VF/5N-encoding strains were neither recognized by Q9VF/5N- nor by Q9VF/5D-specific CTLs. Using in vitro proteasomal digestions and MS/MS analysis, we demonstrate that the 5N variation introduces a strong proteasomal cleavage site within the epitope, leading to a dramatic reduction of Q9VF epitope production. Our results strongly suggest that HIV-1 escapes CTL surveillance by introducing mutations leading to HIV ARF-epitope destruction by proteasomes.

  11. Genetic and epigenetic variations induced by wheat-rye 2R and 5R monosomic addition lines.

    Science.gov (United States)

    Fu, Shulan; Sun, Chuanfei; Yang, Manyu; Fei, Yunyan; Tan, Feiqun; Yan, Benju; Ren, Zhenglong; Tang, Zongxiang

    2013-01-01

    Monosomic alien addition lines (MAALs) can easily induce structural variation of chromosomes and have been used in crop breeding; however, it is unclear whether MAALs will induce drastic genetic and epigenetic alterations. In the present study, wheat-rye 2R and 5R MAALs together with their selfed progeny and parental common wheat were investigated through amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP) analyses. The MAALs in different generations displayed different genetic variations. Some progeny that only contained 42 wheat chromosomes showed great genetic/epigenetic alterations. Cryptic rye chromatin has introgressed into the wheat genome. However, one of the progeny that contained cryptic rye chromatin did not display outstanding genetic/epigenetic variation. 78 and 49 sequences were cloned from changed AFLP and MSAP bands, respectively. Blastn search indicated that almost half of them showed no significant similarity to known sequences. Retrotransposons were mainly involved in genetic and epigenetic variations. Genetic variations basically affected Gypsy-like retrotransposons, whereas epigenetic alterations affected Copia-like and Gypsy-like retrotransposons equally. Genetic and epigenetic variations seldom affected low-copy coding DNA sequences. The results in the present study provided direct evidence to illustrate that monosomic wheat-rye addition lines could induce different and drastic genetic/epigenetic variations and these variations might not be caused by introgression of rye chromatins into wheat. Therefore, MAALs may be directly used as an effective means to broaden the genetic diversity of common wheat.

  12. Guidelines for collecting and maintaining archives for genetic monitoring

    Science.gov (United States)

    Jackson, Jennifer A.; Laikre, Linda; Baker, C. Scott; Kendall, Katherine C.; ,

    2012-01-01

    Rapid advances in molecular genetic techniques and the statistical analysis of genetic data have revolutionized the way that populations of animals, plants and microorganisms can be monitored. Genetic monitoring is the practice of using molecular genetic markers to track changes in the abundance, diversity or distribution of populations, species or ecosystems over time, and to follow adaptive and non-adaptive genetic responses to changing external conditions. In recent years, genetic monitoring has become a valuable tool in conservation management of biological diversity and ecological analysis, helping to illuminate and define cryptic and poorly understood species and populations. Many of the detected biodiversity declines, changes in distribution and hybridization events have helped to drive changes in policy and management. Because a time series of samples is necessary to detect trends of change in genetic diversity and species composition, archiving is a critical component of genetic monitoring. Here we discuss the collection, development, maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and DNA can be stored, and provides guidelines for proper practice.

  13. Characterization of contaminants in snapping turtles (Chelydra serpentina) from Canadian Lake Erie Areas of Concern: St. Clair River, Detroit River, and Wheatley Harbour

    Energy Technology Data Exchange (ETDEWEB)

    Solla, Shane R. de; Fernie, Kimberly J

    2004-11-01

    PCBs, organochlorine pesticides and dioxins/furans in snapping turtle eggs and plasma (Chelydra serpentina) were evaluated at three Areas of Concern (AOCs) on Lake Erie and its connecting channels (St. Clair River, Detroit River, and Wheatley Harbour), as well as two inland reference sites (Algonquin Provincial Park and Tiny Marsh) in 2001-2002. Eggs from the Detroit River and Wheatley Harbour AOCs had the highest levels of p,p'-DDE (24.4 and 57.9 ng/g) and sum PCBs (928.6 and 491.0 ng/g) wet weight, respectively. Contaminant levels in eggs from St. Clair River AOC were generally higher than those from Algonquin Park, but similar to those from Tiny Marsh. Dioxins appeared highest from the Detroit River. The PCB congener pattern in eggs suggested that turtles from the Detroit River and Wheatley Harbour AOCs were exposed to Aroclor 1260. TEQs of sum PCBs in eggs from all AOCs and p,p'-DDE levels in eggs from the Wheatley Harbour and the Detroit River AOCs exceeded the Canadian Environmental Quality Guidelines. Furthermore, sum PCBs in eggs from Detroit River and Wheatley Harbour exceeded partial restriction guidelines for consumption. Although estimated PCB body burdens in muscle tissue of females were well below consumption guidelines, estimated residues in liver and adipose were above guidelines for most sites.

  14. Characterization of contaminants in snapping turtles (Chelydra serpentina) from Canadian Lake Erie Areas of Concern: St. Clair River, Detroit River, and Wheatley Harbour.

    Science.gov (United States)

    de Solla, Shane R; Fernie, Kimberly J

    2004-11-01

    PCBs, organochlorine pesticides and dioxins/furans in snapping turtle eggs and plasma (Chelydra serpentina) were evaluated at three Areas of Concern (AOCs) on Lake Erie and its connecting channels (St. Clair River, Detroit River, and Wheatley Harbour), as well as two inland reference sites (Algonquin Provincial Park and Tiny Marsh) in 2001-2002. Eggs from the Detroit River and Wheatley Harbour AOCs had the highest levels of p,p'-DDE (24.4 and 57.9 ng/g) and sum PCBs (928.6 and 491.0 ng/g) wet weight, respectively. Contaminant levels in eggs from St. Clair River AOC were generally higher than those from Algonquin Park, but similar to those from Tiny Marsh. Dioxins appeared highest from the Detroit River. The PCB congener pattern in eggs suggested that turtles from the Detroit River and Wheatley Harbour AOCs were exposed to Aroclor 1260. TEQs of sum PCBs in eggs from all AOCs and p,p'-DDE levels in eggs from the Wheatley Harbour and the Detroit River AOCs exceeded the Canadian Environmental Quality Guidelines. Furthermore, sum PCBs in eggs from Detroit River and Wheatley Harbour exceeded partial restriction guidelines for consumption. Although estimated PCB body burdens in muscle tissue of females were well below consumption guidelines, estimated residues in liver and adipose were above guidelines for most sites.

  15. Characterization of contaminants in snapping turtles (Chelydra serpentina) from Canadian Lake Erie Areas of Concern: St. Clair River, Detroit River, and Wheatley Harbour

    International Nuclear Information System (INIS)

    Solla, Shane R. de; Fernie, Kimberly J.

    2004-01-01

    PCBs, organochlorine pesticides and dioxins/furans in snapping turtle eggs and plasma (Chelydra serpentina) were evaluated at three Areas of Concern (AOCs) on Lake Erie and its connecting channels (St. Clair River, Detroit River, and Wheatley Harbour), as well as two inland reference sites (Algonquin Provincial Park and Tiny Marsh) in 2001-2002. Eggs from the Detroit River and Wheatley Harbour AOCs had the highest levels of p,p'-DDE (24.4 and 57.9 ng/g) and sum PCBs (928.6 and 491.0 ng/g) wet weight, respectively. Contaminant levels in eggs from St. Clair River AOC were generally higher than those from Algonquin Park, but similar to those from Tiny Marsh. Dioxins appeared highest from the Detroit River. The PCB congener pattern in eggs suggested that turtles from the Detroit River and Wheatley Harbour AOCs were exposed to Aroclor 1260. TEQs of sum PCBs in eggs from all AOCs and p,p'-DDE levels in eggs from the Wheatley Harbour and the Detroit River AOCs exceeded the Canadian Environmental Quality Guidelines. Furthermore, sum PCBs in eggs from Detroit River and Wheatley Harbour exceeded partial restriction guidelines for consumption. Although estimated PCB body burdens in muscle tissue of females were well below consumption guidelines, estimated residues in liver and adipose were above guidelines for most sites

  16. Characterization of contaminants in snapping turtles (Chelydra serpentina) from Canadian Lake Erie Areas of Concern: St. Clair River, Detroit River, and Wheatley Harbour

    Energy Technology Data Exchange (ETDEWEB)

    Solla, Shane R. de; Fernie, Kimberly J

    2004-11-01

    PCBs, organochlorine pesticides and dioxins/furans in snapping turtle eggs and plasma (Chelydra serpentina) were evaluated at three Areas of Concern (AOCs) on Lake Erie and its connecting channels (St. Clair River, Detroit River, and Wheatley Harbour), as well as two inland reference sites (Algonquin Provincial Park and Tiny Marsh) in 2001-2002. Eggs from the Detroit River and Wheatley Harbour AOCs had the highest levels of p,p'-DDE (24.4 and 57.9 ng/g) and sum PCBs (928.6 and 491.0 ng/g) wet weight, respectively. Contaminant levels in eggs from St. Clair River AOC were generally higher than those from Algonquin Park, but similar to those from Tiny Marsh. Dioxins appeared highest from the Detroit River. The PCB congener pattern in eggs suggested that turtles from the Detroit River and Wheatley Harbour AOCs were exposed to Aroclor 1260. TEQs of sum PCBs in eggs from all AOCs and p,p'-DDE levels in eggs from the Wheatley Harbour and the Detroit River AOCs exceeded the Canadian Environmental Quality Guidelines. Furthermore, sum PCBs in eggs from Detroit River and Wheatley Harbour exceeded partial restriction guidelines for consumption. Although estimated PCB body burdens in muscle tissue of females were well below consumption guidelines, estimated residues in liver and adipose were above guidelines for most sites.

  17. A Method for Identifying Pollution Sources of Heavy Metals and PAH for a Risk-Based Management of a Mediterranean Harbour

    Directory of Open Access Journals (Sweden)

    Ombretta Paladino

    2017-01-01

    Full Text Available A procedure for assessing harbour pollution by heavy metals and PAH and the possible sources of contamination is proposed. The procedure is based on a ratio-matching method applied to the results of principal component analysis (PCA, and it allows discrimination between point and nonpoint sources. The approach can be adopted when many sources of pollution can contribute in a very narrow coastal ecosystem, both internal and outside but close to the harbour, and was used to identify the possible point sources of contamination in a Mediterranean Harbour (Port of Vado, Savona, Italy. 235 sediment samples were collected in 81 sampling points during four monitoring campaigns and 28 chemicals were searched for within the collected samples. PCA of total samples allowed the assessment of 8 main possible point sources, while the refining ratio-matching identified 1 sampling point as a possible PAH source, 2 sampling points as Cd point sources, and 3 sampling points as C > 12 point sources. By a map analysis it was possible to assess two internal sources of pollution directly related to terminals activity. The study is the prosecution of a previous work aimed at assessing Savona-Vado Harbour pollution levels and suggested strategies to regulate the harbour activities.

  18. Seven new species of Paleanotus (Annelida: Chrysopetalidae) described from Lizard Island, Great Barrier Reef, and coral reefs of northern Australia and the Indo-Pacific: two cryptic species pairs revealed between western Pacific Ocean and the eastern Indian Ocean.

    Science.gov (United States)

    Watson, Charlotte

    2015-09-18

    Morphological investigation into the paleate genus Paleanotus Schmarda 1861 of the family Chrysopetalidae from northern Australian coral reefs, primarily Lizard Island and outlying reefs, included a complex of very small, slender individuals (length < 5 mm). This complex resolved into 7 new species, described herein: Paleanotus inornatus n. sp., P. adornatus n. sp., P. chrysos n. sp., P. aquifolia n. sp., P. latifolia n. sp., P. silus n. sp., and P. silopsis n. sp. A key is provided to the new species and Paleanotus distinguished from Treptopale and Hyalopale, two closely related genera. Diagnostic features of the apical structure and shape of the notochaetal main paleae plus median paleae shape and raised rib pattern, differentiates each species from the other. Gametous states are described. Two cryptic species pairs (Paleanotus silopsis n. sp. and P. silus n. sp.; Paleanotus aquifolia n. sp. and P. latifolia n. sp.) were identified. In each case one species is restricted to either the NE or NW Australian coast. In each pair the most eastern point for the NW Australian species range occurs at Darwin, western Arnhemland, Northern Territory. Additional material for each species pair extends their respective ranges northwards: NW Australia to Thailand, Andaman Sea, eastern Indian Ocean or NE Australia, Great Barrier Reef to the Philippines, western Pacific Ocean. Cryptic morphology and potential genetic diversity is discussed in Paleanotus inornatus n. sp. and P. adornatus n. sp. that possess overlapping widespread distribution patterns across northern Australia and Indo-Pacific reefs. The smallest bodied taxon, Paleanotus chrysos n. sp. is the only species with a Coral Sea range encompassing Lizard Island, Heron Island and New Caledonia.

  19. Diffusion in coastal and harbour zones, effects of Waves,Wind and Currents

    Science.gov (United States)

    Diez, M.; Redondo, J. M.

    2009-04-01

    As there are multiple processes at different scales that produce turbulent mixing in the ocean, thus giving a large variation of horizontal eddy diffusivities, we use a direct method to evaluate the influence of different ambient parameters such as wave height and wind on coastal dispersion. Measurements of the diffusivity are made by digital processing of images taken from from video recordings of the sea surface near the coast. The use of image analysis allows to estimate both spatial and temporal characteristics of wave fields, surface circulation and mixing in the surf zone, near Wave breakers and inside Harbours. The study of near-shore dispersion [1], with the added complexity of the interaction between wave fields, longshore currents, turbulence and beach morphology, needs detailed measurements of simple mixing processes to compare the respective influences of forcings at different scales. The measurements include simultaneous time series of waves, currents, wind velocities from the studied area. Cuantitative information from the video images is accomplished using the DigImage video processing system [3], and a frame grabber. The video may be controlled by the computer, allowing, remote control of the processing. Spectral analysis on the images has also used n order to estimate dominant wave periods as well as the dispersion relations of dominant instabilities. The measurements presented here consist mostly on the comarison of difussion coeficients measured by evaluating the spread of blobs of dye (milk) as well as by measuring the separation between different buoys released at the same time. We have used a techniques, developed by Bahia(1997), Diez(1998) and Bezerra(2000)[1-3] to study turbulent diffusion by means of digital processing of images taken from remote sensing and video recordings of the sea surface. The use of image analysis allows to measure variations of several decades in horizontal diffusivity values, the comparison of the diffusivities

  20. Simulation-Augmented Methods for Safe and Efficient Manoeuvres in Harbour Areas

    Directory of Open Access Journals (Sweden)

    Knud Benedict

    2016-07-01

    Full Text Available Safety of navigation is especially challenging and critical when a ship approaches and manoeuvres in harbour areas. Improving the safety especially in the first and last phase of a voyage is crucial and requires measures addressing both the human and technical-technological elements including support systems that shall provide human operators with information relevant for decision making. The present situation is characterized by the introduction of numerous sophisticated technical and support systems often integrated with several components becoming increasingly complex. On the users end, changes are not that obvious and not that rapid as for technology. However, new approaches are under development or already in use. They are characterized by applying and adapting solutions from other transport modes. In this way, tasks and procedures on ships, that are highly safety-relevant and containing high portions of manoeuvring activities have been changed to high back-up procedures as in air planes. For port manoeuvres e.g. the system of pilot/co-pilot was introduced on ferries in a sense that one officer is operating and the other is monitoring and checking the safe performance. In cruise shipping, new structures replacing the traditional rank-based with a flexible system based on job functions. This system creates a kind of a safety net around the person conning the vessel. Each operation is cross checked before execution by one or two other persons. The first obvious consequence is higher costs due to doubling personnel. On the other hand there is also a need for a technology appropriately supporting the checking officer by enabling her or him to monitor what the conning officer is doing. “Fast-Time Manoeuvring Simulation Technology” (FTS developed at the Institute for Innovative Ship Simulation and Maritime Systems (ISSIMS has huge potential to fulfil this task. FTS calculates within one second of computing time up to 1000 seconds of real