DNA Barcodes最新文献

{"title":"DNA Barcoding Indonesian freshwater fishes: challenges and prospects","authors":"N. Hubert, Kadarusman, A. Wibowo, F. Busson, D. Caruso, S. Sulandari, N. Nafiqoh, L. Pouyaud, L. Rüber, J. Avarre, F. Herder, R. Hanner, P. Keith, R. Hadiaty","doi":"10.1515/DNA-2015-0018","DOIUrl":"https://doi.org/10.1515/DNA-2015-0018","url":null,"abstract":"With 1172 native species, the Indonesian ichthyofauna is among the world's most speciose. Despite that the inventory of the Indonesian ichthyofauna started during the eighteen century, the numerous species descriptions during the last decades highlight that the taxonomic knowledge is still fragmentary. Meanwhile, the fast increase of anthropogenic perturbations during","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"50 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120896321","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids?","authors":"S. Behrens-Chapuis, F. Herder, H. Esmaeili, J. Freyhof, N. Hamidan, M. Özuluğ, R. Šanda, M. Geiger","doi":"10.1515/DNA-2015-0020","DOIUrl":"https://doi.org/10.1515/DNA-2015-0020","url":null,"abstract":"DNA barcoding is a fast and reliable tool for species identification, and has been successfully applied to a wide range of freshwater fishes. The limitations reported were mainly attributed to effects of geographic scale, taxon-sampling, incomplete lineage sorting, or mitochondrial introgression. However, the metrics for the success of assigning unknown samples to species or genera also depend on a suited taxonomic framework. A simultaneous use of the mitochondrial COI and the nuclear RHO gene turned out to be advantageous for the barcode efficiency in a few previous studies. Here, we examine 14 cyprinid fish genera, with a total of 74 species, where standard DNA barcoding failed to identify closely related species unambiguously. Eight of the genera (Acanthobrama, Alburnus, Chondrostoma, Gobio, Mirogrex, Phoxinus, Scardinius, and Squalius) contain species that exhibit very low interspecific divergence, Research Article Open Access © 2015 S. Behrens-Chapuis et al. licensee De Gruyter Open. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License. S. Behrens-Chapuis*, F. Herder, H. R. Esmaeili, J. Freyhof, N. A. Hamidan, M. Özuluğ, R. Šanda, M. F. Geiger Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids? *Corresponding author: S. Behrens-Chapuis, Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany, E-mail: sichapuis@t-online.de F. Herder, M. F. Geiger, Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for Animal Biodiversity, Adenauerallee 160, 53113 Bonn, Germany H. R. Esmaeili, Ichthyology Research Laboratory, Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran J. Freyhof, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5a, 04103 Leipzig, Germany N. A. Hamidan, The Royal Society for the Conservation of Nature – Conservation Division, P.O. Box 1215, Jubaiha 11941, Jordan and Centre for Conservation Ecology and Environmental Science, School of Applied Sciences, Bournemouth University, Poole, BH12 5BB, U.K. M. Özuluğ, Istanbul University, Science Faculty, Department of Biology, 34134 Vezneciler, Istanbul, Turkey R. Šanda, National Museum, Václavské nám. 68, 115 79 Prague, Czech Republic Unauthenticated Download Date | 7/20/18 5:52 AM 188 S. Behrens-Chapuis, et al. has been considered that the mental disc in labeonine cyprinids has evolved and been reduced independently in several lineages [29]. This new hypothesis was supported by phylogenetic analyses of nuclear and mitochondrial genes in labeonines by Yang et al. [30]. Likewise, mtCOI-based findings in Hamidan et al. [31] and Geiger et al. [10] showed the same pattern with different labeonine genera (defined by the mental disc apparatus) to be nested within Garra, which could be explained by past hybridization e","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126758912","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A record of the Porbeagle, Lamna nasus, in coastal waters of Buenos Aires (Argentina) confirmed by DNA barcoding","authors":"E. Mabragaña, J. Astarloa, L. Lucifora","doi":"10.1515/DNA-2015-0017","DOIUrl":"https://doi.org/10.1515/DNA-2015-0017","url":null,"abstract":"A record of a juvenile Porbeagle, Lamna nasus, in the coastal waters of Argentina is confirmed by DNA barcoding, since the specimen lacked some external diagnostic features. We discuss the occurrence of this species in the coastal waters of Argentina, its molecular affinity with conspecifics from a broad range of the species, and relevant conservation issues.","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"97 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114478513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Use of DNA barcode in the identification of fish species from Ribeira de Iguape Basin and coastal rivers from São Paulo State (Brazil)","authors":"Jefferson Monteiro Henriques, G. J. D. C. Silva, F. Y. Ashikaga, R. Hanner, F. Foresti, Cláudio Oliveira","doi":"10.1515/DNA-2015-0015","DOIUrl":"https://doi.org/10.1515/DNA-2015-0015","url":null,"abstract":"Species identification is a difficult task, ranging from the definition of the species concept itself to the definition of the threshold for speciation. DNA Barcode technology uses a fragment of the Cytochrome Oxidase I (COI) gene as a molecular tool that many studies have already validated as a tool for species identification. DNA barcode sequences for COI were generated and analyzed from 805 specimens. The General Mixed Yule Coalescent (GMYC) analysis recognized 99 independent evolution units, and the Barcode Index Numbers (BIN) approach pointed to the existence of 104 BINs (interpreted as distinct species). By cross-tabulating the results of all approaches, we identified 109 Molecular Operational Taxonomic Units (MOTU) by at least one methodology. In most cases (89 MOTUs), the genetic approaches are in agreement with morphological identification, and the discrepant results of MOTUs are in the complex groups, which have many morphological similarities but may represent species complexes.","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127119418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Status of DNA Barcoding Coverage for the Tropical Western Atlantic Shorefishes and Reef Fishes","authors":"B. Victor, Martha Valdez-Moreno, L. Vásquez-Yeomans","doi":"10.1515/DNA-2015-0011","DOIUrl":"https://doi.org/10.1515/DNA-2015-0011","url":null,"abstract":"Background: Barcode coverage is difficult to assess for large regions due to incomplete species lists, inaccurate identifications, and cryptic diversity. However, as coverage approaches completion, it becomes possible to critically evaluate identifications and validate barcode lineages. We collate the results of the FISH-BOL barcode project and assess coverage for each family of bony shorefishes and reef fishes from the tropical western Atlantic Ocean. Methodology: We identify to species the public and private barcode lineages from the region on BOLD, confirming identifications by vouchers, phylogeographic deduction, and the process of elimination. The lineages and BINs are assigned to species from a comprehensive species list for the region. Results: We estimate 1029 of 1311 total bony shorefish species in the region are barcoded (78.5%). For reef-associated fishes, 902 of 1083 species are barcoded (83.3%). About 70 of the 181 species not yet barcoded are endemic species from Florida/ Gulf of Mexico or Venezuela, leaving about 90% of the central Caribbean reef fish species barcoded to date. Most species are represented by one barcode lineage, but among the gobioids and blennioids there are many more lineages (BINs) than species, indicating substantial cryptic diversity. Conclusions: As barcode coverage for a region approaches completion, a robust assessment of coverage can be made. The reef fish fauna of the tropical western Atlantic now has the highest coverage for a large marine area, from about 80 to 90% depending on definitions and geographic limits.","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"96 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120898415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA Barcoding, species delineation and taxonomy: a historical perspective","authors":"N. Hubert, R. Hanner","doi":"10.1515/DNA-2015-0006","DOIUrl":"https://doi.org/10.1515/DNA-2015-0006","url":null,"abstract":": DNA barcoding is a system designed to provide species identification by using standardized gene regions as internal species tag. Foreseen since its earlier development as a solution to speed up the pace of species discovery, DNA barcoding has established as a mature field of biodiversity sciences filing the conceptual gap between traditional taxonomy and different fields of molecular systematics. Initially proposed as a tool for species identification, DNA barcoding has also been applied in taxonomy routines for automated species delineation. Species identification and species delineation, however, should be considered as distinct activities relying on different theoretical and methodological backgrounds. The aim of the present review is to provide an overview of the use of DNA sequences in taxonomy, since the earliest development of molecular taxonomy until the development of DNA barcoding. We further present the differences between procedures of species identification and species delineation and highlight how DNA barcoding proposed a new paradigm that helps promote more sustainable practices in taxonomy.","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129186951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cods for sale Do we know what we are buying","authors":"Christian Lambarri, Héctor Espinosa, Armando J. Martínez, Ariana Hernández","doi":"10.1515/DNA-2015-0004","DOIUrl":"https://doi.org/10.1515/DNA-2015-0004","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116462186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular identification of Leporinus from the south portion of South America","authors":"G. S. Avelino, H. Britski, F. Foresti, C. Oliveira","doi":"10.1515/DNA-2015-0013","DOIUrl":"https://doi.org/10.1515/DNA-2015-0013","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125903778","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Standards for Conducting a DNA Barcoding Market Survey: Minimum Information and Best Practices","authors":"A. Naaum, Jason St.Jaques, Kimberly A. Warner, Linda Santschi, Ralph Imondi, R. Hanner","doi":"10.1515/DNA-2015-0010","DOIUrl":"https://doi.org/10.1515/DNA-2015-0010","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"25 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130563809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA barcoding increases resolution and changes structure in Canadian boreal shield lake food webs","authors":"T. Bartley, H. Braid, K. McCann, N. Lester, B. Shuter, R. Hanner","doi":"10.1515/DNA-2015-0005","DOIUrl":"https://doi.org/10.1515/DNA-2015-0005","url":null,"abstract":"Food webs are important in understanding the structure, function, and behaviour of ecosystems, but, due to methodological limitations, are often poorly resolved in ways that impact food-web properties. Although DNA barcoding has proven useful in determining the diet of consumers, few studies have used this technique to determine food-web structure. These studies report mixed impacts on various food-web properties, but are limited by their taxonomic focus and their failure to evaluate DNA barcoding for both diet analysis and food-web structure. In this study, we show that, when compared to a morphological approach, DNA barcoding increases foodweb resolution by increasing the number and frequency of prey species identified in the stomach contents of eight species of Canadian boreal shield predatory fishes. In addition, we observed differences in food-web structure, such as increased generalism, habitat coupling, and omnivory, that have strong implications for food-web stability and dynamics. We conclude that DNA barcoding is a powerful tool to evaluate how resolution impacts foodweb properties and can help further our understanding of how food webs are structured by identifying feeding Research Article Open Access © 2015 Timothy J. Bartley et al. licensee De Gruyter Open. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License. Timothy J. Bartley*, Heather E. Braid, Kevin S. McCann, Nigel P. Lester, Brian J. Shuter, Robert H. Hanner DNA barcoding increases resolution and changes structure in Canadian boreal shield lake food webs *Corresponding author:Timothy J. Bartley, Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1, E-mail: timothy.bartley@gmail. com Heather E. Braid, Institute for Applied Ecology New Zealand, Auckland University of Technology, Private Bag 92006, Auckland, New Zealand 1010 Kevin S. McCann, Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1 Nigel P. Lester, Brian J. Shuter, Science and Research Branch, Ontario Ministry of Natural Resources, Peterborough, Ontario, Canada K9J 7B8 Brian J. Shuter, Department of Ecology and Evolution, University of Toronto, Toronto, Ontario, Canada M5S 3G5 Robert H. Hanner, Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1 Unauthenticated Download Date | 12/4/15 10:11 PM Lake food web resolution and DNA barcoding 31 highly refined picture of feeding interactions required to address issues surrounding food-web resolution. DNA barcoding is increasingly recognized as an effective means for identifying trophic interactions [15, 16, 17], making it a potentially powerful tool to parse out food-web structure [18, 19]. Barcoding uses a short, standardized DNA sequence and a molecular reference library (i.e., the Barcode of Life Data Systems, BOLD [20]) to identify species [21]. The efficacy of","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"129 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122231997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}