DNA Barcodes最新文献

{"title":"A test of sequence-matching algorithms for a DNA barcode database of invasive grasses","authors":"A. Syme, F. Udovicic, V. Stajsic, D. Murphy","doi":"10.2478/DNA-2012-0002","DOIUrl":"https://doi.org/10.2478/DNA-2012-0002","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"176 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121322757","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":"Sympatry and colour variation disguised well-differentiated sister species: Suphrodytes revised with integrative taxonomy including 5 kbp of housekeeping genes (Coleoptera: Dytiscidae)","authors":"J. Bergsten, G. Brilmyer, Alex Crampton-Platt, A. Nilsson","doi":"10.2478/DNA-2012-0001","DOIUrl":"https://doi.org/10.2478/DNA-2012-0001","url":null,"abstract":"The genus Suphrodytes, is currently regarded as a monobasic Palearctic genus with one colour-variable species, S. dorsalis. Here we show with >5 kbp of nuclear and mitochondrial genes and quantitative morphological characters that Suphrodytes consists of two well-defined species, albeit each with variable colour pattern. The primary barcode gene CO1, showed consistent signs of multiple copies, therefore a range of alternative housekeeping genes were screened for information. The two species were reciprocally monophyletic in genetrees from 12S, 16S, CO1, CO2, CytB, H3 and 18S. Explicit species delimitation tests based on the coalescent process model rejected the null hypothesis that the genealogies originated from a single panmictic species. The mitochondrial proteincoding genes were proportionally richest in information followed by 12S and Histone 3. Conservative nuclear 18S had a single fixed diagnostic character. The two species were significantly different in total bodylength, bodyshape, shape of the male aedeagus and parameres. We review the taxonomic literature of Suphrodytes and find S. dorsalis (Fabricius, 1787) and S. figuratus (Gyllenhal, 1826) to be the oldest available names for the respective species, and for which we designate lectotypes. Synonyms are established for both species which are broadly sympatric across the Palearctic and frequently even collected at the same locality.","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"30 1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117049603","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":"Extending DNA barcoding coverage for Lake Whitefish (Coregonus clupeaformis) across the three major basins of Lake Huron","authors":"Lauren M. Overdyk, H. Braid, S. Crawford, R. Hanner","doi":"10.1515/DNA-2015-0007","DOIUrl":"https://doi.org/10.1515/DNA-2015-0007","url":null,"abstract":"DNA barcoding is a useful tool for both species identification and discovery, but the latter requires denser sampling than typically used in barcode studies. Lake Whitefish (Coregonus clupeaformis) is a valuable species, fished traditionally, commercially, and recreationally in Lake Huron. Based on the natural geographic and bathymetric separation of the three major basins in Lake Huron, the potential separation of Lake Whitefish within these basins, and the variation among life history (early and late spawning), we predicted that Lake Huron might harbour cryptic lineages of Lake Whitefish at the basin level. To test this prediction, DNA barcodes of the mitochondrial 5’ cytochrome c oxidase subunit I (COI) gene sequences were recovered from spawning phase Lake Whitefish (n = 5 per site), which were collected from sites (n = 28) around Lake Huron during Fall 2012. These sequences, combined with other publically available DNA barcodes from the Barcode of Life Data System (BOLD), revealed twelve unique haplotypes across North America, with seven unique to Lake Huron. The dominant haplotype was found throughout Lake Huron and east to the St. Lawrence River. No deep divergences were revealed. This comprehensive lake-wide sampling effort offers a new perspective on C. clupeaformis, and Research Article Open Access © 2015 Lauren M. Overdyk et al. licensee De Gruyter Open. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License. Lauren M. Overdyk*, Heather E. Braid, Stephen S. Crawford, Robert H. Hanner Extending DNA barcoding coverage for Lake Whitefish (Coregonus clupeaformis) across the three major basins of Lake Huron *Corresponding author:Lauren M. Overdyk, Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1, E-mail: loverdyk@uoguelph.ca Stephen S. Crawford, Robert H. Hanner: Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1 Heather E. Braid: Institute for Applied Ecology New Zealand, Auckland University of Technology, Private Bag 92006, Auckland, New Zealand 1010 Stephen S. Crawford: Chippewas of Nawash, Unceded First Nation, 135 Lakeshore Blvd, Nevaashiinigmiing, Ontario, Canada N1G 2W1 Robert H. Hanner: Biodiversity Institute of Ontario, University of Guelph, 50 Stone Road East, Guelph, Ontario, Canada N1G 2W1 10.1515/dna-2015-0007 Downloaded from De Gruyter Online at 09/12/2016 11:31:59PM via free access 60 L.M. Overdyk et al. 2 Materials and Methods 2.1 Specimen Collection A lake-wide sampling effort for adult Lake Whitefish was undertaken in the fall of 2012 in Lake Huron (Figure 1; Table 1). Spawning-phase Lake Whitefish were sampled from twenty-eight locations across the three basins of Lake Huron: the Main Basin (n = 16), the North Channel (n = 4), and Georgian Bay (n = 8). Early and late samples were taken from Sites 16-18 (Cape Hurd, Stokes Bay, and Howdenvale) along the Western shor","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"2012 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":"114587674","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":"COI gene geographic variation of Gypsy moth (Lepidoptera: Lymantriidae) and a TaqMan PCR diagnostic assay","authors":"Lu Qian, Yulin An, Jun-Young Song, Mei Xu, Jian-Zhong Ye, Cuiping Wu, Bin Li, D. Hao","doi":"10.2478/DNA-2014-0002","DOIUrl":"https://doi.org/10.2478/DNA-2014-0002","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"52 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":"131589571","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":"Mitochondrial markers for identification and phylogenetic studies in insects - A Review","authors":"S. Mandal, Liansangmawii Chhakchhuak, G. Gurusubramanian, N. S. Kumar","doi":"10.2478/DNA-2014-0001","DOIUrl":"https://doi.org/10.2478/DNA-2014-0001","url":null,"abstract":"Similar morphology and high genetic diversity poses problems in phylogenetic studies of insects. To solve these problems, mitochondrial based markers have been adopted and are increasingly used as molecular markers for phylogenetic studies. Varied markers have been used for different species of insects, viz., markers for 16S r RNA, 12S r RNA, ND (1-6 genes), ATPase and control regions. Among which protein coding gene, CO-1 is found to be best because of its advantage over others whereas, AT rich region of mitochondrial DNA is the least used marker. A recent advanced technology in phylogenetic analysis; namely mitogenomics have greatly improved this research field. This short review attempted to summarize recent studies on the application of vari ous mitochondrial molecular markers for phylogenetic study of insects.","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"1 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":"124948468","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":"The applicability of DNA barcoding for dietary analysis of sika deer","authors":"Fumiko Nakahara, H. Ando, Hideyuki Ito, A. Murakami, Naoki Morimoto, M. Yamasaki, A. Takayanagi, Y. Isagi","doi":"10.1515/DNA-2015-0021","DOIUrl":"https://doi.org/10.1515/DNA-2015-0021","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"1999 11","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114129985","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":"An exploration of sufficient sampling effort to describe intraspecific DNA barcode haplotype diversity: examples from the ray-finned fishes (Chordata: Actinopterygii)","authors":"Jarrett D Phillips, R. Gwiazdowski, D. Ashlock, R. Hanner","doi":"10.1515/DNA-2015-0008","DOIUrl":"https://doi.org/10.1515/DNA-2015-0008","url":null,"abstract":"Estimating appropriate sample sizes to measure species abundance and richness is a fundamental problem for most biodiversity research. In this study, we explore a method to measure sampling sufficiency based on haplotype diversity in the ray-finned fishes (Animalia: Chordata: Actinopterygii). To do this, we use linear regression and hypothesis testing methods on haplotype accumulation curves from DNA barcodes for 18 species of fishes, in the statistics platform R. We use a simple mathematical model to estimate sampling sufficiency from a sample-number based prediction of intraspecific haplotype diversity, given an assumption of equal haplotype frequencies. Our model finds that haplotype diversity for most of the 18 fish species remains largely unsampled, and this appears to be a result of small sample sizes. Lastly, we discuss how our overly simple model may be a useful starting point to develop future estimators for intraspecific sampling sufficiency in studies using DNA barcodes.","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"1 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":"116096802","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":"Knodus moenkhausii (Characiformes: Characidae): one fish species, three hydrographic basins - a natural or anthropogenic phenomenon?","authors":"C. Souza, C. Oliveira, L. H. Pereira","doi":"10.1515/DNA-2015-0016","DOIUrl":"https://doi.org/10.1515/DNA-2015-0016","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"9 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":"123978553","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":"Community engagement in seafood identification using DNA barcoding reveals market substitution in Canadian seafood","authors":"A. Naaum, R. Hanner","doi":"10.1515/DNA-2015-0009","DOIUrl":"https://doi.org/10.1515/DNA-2015-0009","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"52 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":"124349097","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":"Species delimitation in Neoplecostomus (Siluriformes: Loricariidae) using morphologic and genetic approaches","authors":"F. F. Roxo, L. Ochoa, Guilherme J. Costa-Silva, C. Oliveira","doi":"10.1515/DNA-2015-0014","DOIUrl":"https://doi.org/10.1515/DNA-2015-0014","url":null,"abstract":"","PeriodicalId":446240,"journal":{"name":"DNA Barcodes","volume":"16 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":"117309566","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}