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Barcoding Atlantic Canada’s mesopelagic and upper bathypelagic marine fishes

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      Abstract

      DNA barcode sequences were developed from 557 mesopelagic and upper bathypelagic teleost specimens collected in waters off Atlantic Canada. Confident morphological identifications were available for 366 specimens, of 118 species and 93 genera, which yielded 328 haplotypes. Five of the species were novel to the Barcode of Life Database (BOLD). Most of the 118 species conformed to expectations of monophyly and the presence of a “barcode gap”, though some known weaknesses in existing taxonomy were confirmed and a deficiency in published keys was revealed. Of the specimens for which no firm morphological identification was available, 156 were successfully identified to species, and a further 11 to genus, using their barcode sequences and a combination of distance- and character-based methods. The remaining 24 specimens were from species for which no reference barcode is yet available or else ones confused by apparent misidentification of publicly available sequences in BOLD. Addition of the new sequences to those previously in BOLD contributed support to recent taxonomic revisions of Chiasmodon and Poromitra, while it also revealed 18 cases of potential cryptic speciation. Most of the latter appear to result from genetic divergence among populations in different ocean basins, while the general lack of strong horizontal environmental gradients within the deep sea has allowed morphology to be conserved. Other examples of divergence appear to distinguish individuals living under the sub-tropical gyre of the North Atlantic from those under that ocean’s sub-polar gyre. In contrast, the available sequences for two myctophid species, Benthosema glaciale and Notoscopelus elongatus, showed genetic structuring on finer geographic scales. The observed structure was not consistent with recent suggestions that “resident” populations of myctophids can maintain allopatry despite the mixing of ocean waters. Rather, it indicates that the very rapid speciation characteristic of the Myctophidae is both on-going and detectable using barcodes.

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      Clustal W and Clustal X version 2.0.

      The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++. This will facilitate the further development of the alignment algorithms in the future and has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems. The programs can be run on-line from the EBI web server: http://www.ebi.ac.uk/tools/clustalw2. The source code and executables for Windows, Linux and Macintosh computers are available from the EBI ftp site ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
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        Biological identifications through DNA barcodes.

        Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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          Universal primer cocktails for fish DNA barcoding

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            Author and article information

            Affiliations
            [1 ] Department of Fisheries and Oceans, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
            [2 ] Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
            Chang Gung University, TAIWAN
            Author notes

            Competing Interests: The authors have declared that no competing interests exist.

            Contributors
            ORCID: http://orcid.org/0000-0003-3784-4533, Role: Conceptualization, Role: Data curation, Role: Formal analysis, Role: Writing – original draft, Role: Writing – review & editing
            Role: Formal analysis, Role: Writing – review & editing
            Role: Investigation, Role: Methodology, Role: Writing – original draft, Role: Writing – review & editing
            Role: Conceptualization, Role: Resources, Role: Writing – original draft, Role: Writing – review & editing
            Role: Editor
            Journal
            PLoS One
            PLoS ONE
            plos
            plosone
            PLoS ONE
            Public Library of Science (San Francisco, CA USA )
            1932-6203
            20 September 2017
            2017
            : 12
            : 9
            28931082
            5607201
            10.1371/journal.pone.0185173
            PONE-D-17-23160
            (Editor)
            © 2017 Kenchington 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.

            Counts
            Figures: 2, Tables: 3, Pages: 20
            Product
            Funding
            The authors received no specific funding for this work.
            Categories
            Research Article
            Biology and Life Sciences
            Evolutionary Biology
            Evolutionary Processes
            Speciation
            Cryptic Speciation
            Biology and Life Sciences
            Taxonomy
            Computer and Information Sciences
            Data Management
            Taxonomy
            Biology and Life Sciences
            Organisms
            Eukaryota
            Animals
            Vertebrates
            Fish
            Marine Fish
            Biology and Life Sciences
            Marine Biology
            Marine Fish
            Earth Sciences
            Marine and Aquatic Sciences
            Marine Biology
            Marine Fish
            Biology and Life Sciences
            Evolutionary Biology
            Evolutionary Systematics
            Phylogenetics
            Phylogenetic Analysis
            Biology and Life Sciences
            Taxonomy
            Evolutionary Systematics
            Phylogenetics
            Phylogenetic Analysis
            Computer and Information Sciences
            Data Management
            Taxonomy
            Evolutionary Systematics
            Phylogenetics
            Phylogenetic Analysis
            Research and Analysis Methods
            Database and Informatics Methods
            Biological Databases
            Sequence Databases
            Research and Analysis Methods
            Database and Informatics Methods
            Bioinformatics
            Sequence Analysis
            Sequence Databases
            Biology and life sciences
            Molecular biology
            Molecular biology techniques
            DNA barcoding
            Research and analysis methods
            Molecular biology techniques
            DNA barcoding
            Biology and life sciences
            Evolutionary biology
            Evolutionary systematics
            Molecular systematics
            DNA barcoding
            Biology and life sciences
            Taxonomy
            Evolutionary systematics
            Molecular systematics
            DNA barcoding
            Computer and information sciences
            Data management
            Taxonomy
            Evolutionary systematics
            Molecular systematics
            DNA barcoding
            Research and Analysis Methods
            Database and Informatics Methods
            Bioinformatics
            Sequence Analysis
            Sequence Alignment
            Earth Sciences
            Marine and Aquatic Sciences
            Bodies of Water
            Oceans
            Custom metadata
            All relevant data are within the paper and its Supporting Information files. S1 Table contains Process Reference Codes for the BOLD database and GenBank accession numbers for each specimen.

            Uncategorized

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