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      Identifying Canadian Freshwater Fishes through DNA Barcodes

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          Abstract

          Background

          DNA barcoding aims to provide an efficient method for species-level identifications using an array of species specific molecular tags derived from the 5′ region of the mitochondrial cytochrome c oxidase I (COI) gene. The efficiency of the method hinges on the degree of sequence divergence among species and species-level identifications are relatively straightforward when the average genetic distance among individuals within a species does not exceed the average genetic distance between sister species. Fishes constitute a highly diverse group of vertebrates that exhibit deep phenotypic changes during development. In this context, the identification of fish species is challenging and DNA barcoding provide new perspectives in ecology and systematics of fishes. Here we examined the degree to which DNA barcoding discriminate freshwater fish species from the well-known Canadian fauna, which currently encompasses nearly 200 species, some which are of high economic value like salmons and sturgeons.

          Methodology/Principal Findings

          We bi-directionally sequenced the standard 652 bp “barcode” region of COI for 1360 individuals belonging to 190 of the 203 Canadian freshwater fish species (95%). Most species were represented by multiple individuals (7.6 on average), the majority of which were retained as voucher specimens. The average genetic distance was 27 fold higher between species than within species, as K2P distance estimates averaged 8.3% among congeners and only 0.3% among concpecifics. However, shared polymorphism between sister-species was detected in 15 species (8% of the cases). The distribution of K2P distance between individuals and species overlapped and identifications were only possible to species group using DNA barcodes in these cases. Conversely, deep hidden genetic divergence was revealed within two species, suggesting the presence of cryptic species.

          Conclusions/Significance

          The present study evidenced that freshwater fish species can be efficiently identified through the use of DNA barcoding, especially the species complex of small-sized species, and that the present COI library can be used for subsequent applications in ecology and systematics.

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          Most cited references57

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          DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.

          DNA barcoding and DNA taxonomy have recently been proposed as solutions to the crisis of taxonomy and received significant attention from scientific journals, grant agencies, natural history museums, and mainstream media. Here, we test two key claims of molecular taxonomy using 1333 mitochondrial COI sequences for 449 species of Diptera. We investigate whether sequences can be used for species identification ("DNA barcoding") and find a relatively low success rate (< 70%) based on tree-based and newly proposed species identification criteria. Misidentifications are due to wide overlap between intra- and interspecific genetic variability, which causes 6.5% of all query sequences to have allospecific or a mixture of allo- and conspecific (3.6%) best-matching barcodes. Even when two COI sequences are identical, there is a 6% chance that they belong to different species. We also find that 21% of all species lack unique barcodes when consensus sequences of all conspecific sequences are used. Lastly, we test whether DNA sequences yield an unambiguous species-level taxonomy when sequence profiles are assembled based on pairwise distance thresholds. We find many sequence triplets for which two of the three pairwise distances remain below the threshold, whereas the third exceeds it; i.e., it is impossible to consistently delimit species based on pairwise distances. Furthermore, for species profiles based on a 3% threshold, only 47% of all profiles are consistent with currently accepted species limits, 20% contain more than one species, and 33% only some sequences from one species; i.e., adopting such a DNA taxonomy would require the redescription of a large proportion of the known species, thus worsening the taxonomic impediment. We conclude with an outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy.
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            The promise of DNA barcoding for taxonomy.

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              Sequence-based species delimitation for the DNA taxonomy of undescribed insects.

              Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2008
                18 June 2008
                : 3
                : 6
                : e2490
                Affiliations
                [1 ]Département de biologie, Pavillon Charles-Eugène-Marchand, Université Laval, Sainte-Foy, Québec, Canada
                [2 ]Canadian Barcode of Life Network, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
                [3 ]Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada
                [4 ]Great Lakes Laboratory for Fisheries and Aquatic Sciences, Fisheries and Oceans Canada, Burlington, Ontario, Canada
                [5 ]Department of Zoology, Vancouver, British Columbia, Canada
                [6 ]Fisheries and Oceans Canada, Central & Arctic Region, Freshwater Institute, Winnipeg, Manitoba, Canada
                [7 ]Ministère des Ressources naturelles et de la faune du Québec, Direction de l'aménagement de la faune de Montréal, de Laval et de la Montérégie, Longueuil, Québec, Canada
                [8 ]Fish and Wildlife Research Unit, University of New Brunswick, Fredericton, New Brunswick, Canada
                [9 ]Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
                University of Uppsala, Sweden
                Author notes

                Conceived and designed the experiments: LB RH NH. Performed the experiments: LB NH JA. Analyzed the data: ET LB RH NH EH NM DW JA. Contributed reagents/materials/analysis tools: ET LB PB NH EH NM MB DW AC JZ JA PD. Wrote the paper: ET LB RH NH NM.

                Article
                07-PONE-RA-02932R2
                10.1371/journal.pone.0002490
                3278308
                22423312
                4f80f7d8-0eb4-40d5-9a5c-8fa0c0b2e8fc
                Hubert et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 5 December 2007
                : 19 May 2008
                Page count
                Pages: 8
                Categories
                Research Article
                Evolutionary Biology/Evolutionary and Comparative Genetics
                Genetics and Genomics/Animal Genetics

                Uncategorized
                Uncategorized

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