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      Molecular tools for identification of shark species involved in depredation incidents in Western Australian fisheries

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          Abstract

          Shark depredation is an issue of concern in some Western Australian recreational and commercial fisheries where it can have economic, social and ecological consequences. Knowledge of the shark species involved is fundamental to developing effective management strategies to mitigate the impacts of depredation. Identification of the species responsible is difficult as direct observation of depredation events is uncommon and evaluating bite marks on fish has a high degree of uncertainty. The use of trace DNA techniques has provided an alternative method for species identification. We demonstrate proof of concept for a targeted DNA barcoding approach to identify shark species using trace DNA found at bite marks on recovered remains of hooked fish. Following laboratory validation, forensic analysis of swabs collected from samples of bitten demersal fish, led to the definitive identification of shark species involved in 100% of the incidences of depredation (n = 16).

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          Most cited references39

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          Bias in template-to-product ratios in multitemplate PCR.

          Martin F. Polz, Colleen Cavanaugh (1998)
          Bias introduced by the simultaneous amplification of specific genes from complex mixtures of templates remains poorly understood. To explore potential causes and the extent of bias in PCR amplification of 16S ribosomal DNAs (rDNAs), genomic DNAs of two closely and one distantly related bacterial species were mixed and amplified with universal, degenerate primers. Quantification and comparison of template and product ratios showed that there was considerable and reproducible overamplification of specific templates. Variability between replicates also contributed to the observed bias but in a comparatively minor way. Based on these initial observations, template dosage and differences in binding energies of permutations of the degenerate, universal primers were tested as two likely causes of this template-specific bias by using 16S rDNA templates modified by site-directed mutagenesis. When mixtures of mutagenized templates containing AT- and GC-rich priming sites were used, templates containing the GC-rich permutation amplified with higher efficiency, indicating that different primer binding energies may to a large extent be responsible for overamplification. In contrast, gene copy number was found to be an unlikely cause of the observed bias. Similarly, amplification from DNA extracted from a natural community to which different amounts of genomic DNA of a single bacterial species were added did not affect relative product ratios. Bias was reduced considerably by using high template concentrations, by performing fewer cycles, and by mixing replicate reaction preparations.
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            Shark interactions in pelagic longline fisheries

            Eric Gilman, Shelley Clarke, Nigel Brothers … (2008)
            Article 0 comments Cited 87 times – based on 0 reviews     Review now
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              Identification of shark species composition and proportion in the Hong Kong shark fin market based on molecular genetics and trade records.

              Shelley C Clarke, Jennifer E Magnussen, Debra L Abercrombie … (2006)
              The burgeoning and largely unregulated trade in shark fins represents one of the most serious threats to shark populations worldwide. In Hong Kong, the world's largest shark fin market, fins are classified by traders into Chinese-name categories on the basis of market value, but the relationship between market category and shark species is unclear preventing identification of species that are the most heavily traded. To delineate these relationships, we designed a sampling strategy for collecting statistically sufficient numbers of fins from traders and categories under conditions of limited market access because of heightened trader sensitivities. Based on information from traders and morphological inspection, we hypothesized matches between market names and shark taxa for fins within 11 common trade categories. These hypotheses were tested using DNA-based species identification techniques to determine the concordance between market category and species. Only 14 species made up approximately 40% of the auctioned fin weight. The proportion of samples confirming the hypothesized match, or concordance, varied from 0.64 to 1 across the market categories. We incorporated the concordance information and available market auction records for these categories into stochastic models to estimate the contribution of each taxon by weight to the fin trade. Auctioned fin weight was dominated by the blue shark (Prionace glauca), which was 17% of the overall market. Other taxa, including the shortfin mako (Isurus oxyrinchus), silky (Carcharhinus falciformis), sandbar (C. obscurus), bull (C. leucas), hammerhead (Sphyrna spp.), and thresher (Alopias spp.), were at least 2-6% of the trade. Our approach to marketplace monitoring of wildlife products isparticularly applicable to situations in which quantitative data at the source of resource extraction are sparse and large-scale genetic testing is limited by budgetary or other market access constraints.
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                Author and article information

                Contributors
                Seema Fotedar:
                ORCID: http://orcid.org/0000-0002-7488-0608
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Sherralee Lukehurst: Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Gary Jackson: Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: ResourcesRole: Writing – original draftRole: Writing – review & editing
                Michael Snow: Role: ConceptualizationRole: Formal analysisRole: Project administrationRole: ResourcesRole: Writing – original draftRole: Writing – review & editing
                Heather M. Patterson: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 11 January 2019
                Publication date Collection: 2019
                Volume: 14
                Issue: 1
                Electronic Location Identifier: e0210500
                Affiliations
                [1 ] Department of Primary Industries and Regional Development, Government of Western Australia, Hillarys, Western Australia, Australia
                [2 ] Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
                Department of Agriculture and Water Resources, AUSTRALIA
                Author notes

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

                Author information
                http://orcid.org/0000-0002-7488-0608
                Article
                Publisher ID: PONE-D-18-22553
                DOI: 10.1371/journal.pone.0210500
                PMC ID: 6329513
                PubMed ID: 30633772
                SO-VID: f8459b8d-3e88-45dd-9829-e79b8af1d3d2
                Copyright © © 2019 Fotedar et al
                License:

                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
                Date received : 6 August 2018
                Date accepted : 23 December 2018
                Page count
                Figures: 4, Tables: 5, Pages: 14
                Funding
                The authors received no specific funding for this work.
                Categories
                Subject: Research Article
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Eukaryota
                Subject: Animals
                Subject: Vertebrates
                Subject: Fish
                Subject: Chondrichthyes
                Subject: Elasmobranchii
                Subject: Sharks
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Biological Databases
                Subject: Sequence Databases
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Bioinformatics
                Subject: Sequence Analysis
                Subject: Sequence Databases
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Bioinformatics
                Subject: Sequence Analysis
                Subject: Sequence Alignment
                Subject: Research and analysis methods
                Subject: Extraction techniques
                Subject: DNA extraction
                Subject: Biology and Life Sciences
                Subject: Molecular Biology
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Subject: Research and Analysis Methods
                Subject: Molecular Biology Techniques
                Subject: Artificial Gene Amplification and Extension
                Subject: Polymerase Chain Reaction
                Subject: Research and Analysis Methods
                Subject: Database and Informatics Methods
                Subject: Database Searching
                Subject: Sequence Similarity Searching
                Subject: Biology and Life Sciences
                Subject: Agriculture
                Subject: Fisheries
                Subject: Biology and life sciences
                Subject: Molecular biology
                Subject: Molecular biology techniques
                Subject: DNA barcoding
                Subject: Research and analysis methods
                Subject: Molecular biology techniques
                Subject: DNA barcoding
                Subject: Biology and life sciences
                Subject: Evolutionary biology
                Subject: Evolutionary systematics
                Subject: Molecular systematics
                Subject: DNA barcoding
                Subject: Biology and life sciences
                Subject: Taxonomy
                Subject: Evolutionary systematics
                Subject: Molecular systematics
                Subject: DNA barcoding
                Subject: Computer and information sciences
                Subject: Data management
                Subject: Taxonomy
                Subject: Evolutionary systematics
                Subject: Molecular systematics
                Subject: DNA barcoding
                Custom metadata
                Data Availability All relevant data are within the paper or available from the GenBank database (accession numbers MG811816-MG811828; MG811803-MG811815; MK092067-MK092076).

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                ScienceOpen disciplines: Uncategorized

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