DNA-based identification methods of prey fish from stomach contents of 12 species of eastern North Pacific groundfish |
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| Affiliation: | 1. Freshwater Institute, Fisheries and Oceans Canada, 501 University Crescent, Winnipeg, Canada MB R3T 2N6;2. Institute of Ocean Sciences, Fisheries and Oceans Canada, 9860 West Saanich Road, Sidney, Canada BC V8L 4B2;1. UR 03AGRO1 Ecosystèmes et Ressources Aquatiques, Institut National Agronomique de Tunisie, 43 Avenue Charles Nicolle, 1082 Tunis, Tunisie;2. UMR 6539 Laboratoire des Sciences de l''Environnement Marin (CNRS/UBO/IRD/Ifremer), Institut Universitaire Européen de la Mer, Technopôle Brest-Iroise, Rue Dumont d''Urville, 29280 Plouzané, France;3. Université du Littoral Côte d⿿Opale, Laboratoire d⿿Océanologie et de Géosciences, UMR 8187 LOG CNRS, 32 Avenue Foch, 62930 Wimereux, France;4. IRD, UMR 248 MARBEC, Université de Montpellier, Bat. 24 ⿿ CC 093 Place Eugène Bataillon, 34095 Montpellier Cedex 5, France;5. University of Cape Town, Marine Research Institute and Department of Biological Sciences, Private Bag X3, Rondebosch 7701, South Africa;6. UR FRE 3498 ÿcologie et Dynamique des Systèmes Anthropisés, CNRS-UPJV, Université de Picardie Jules Verne, Amiens, France;7. Instituto del Mar del Perú (IMARPE), Gamarra y General Valle s/n Chucuito, Callao, Peru;8. Aix Marseille Université, CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM110, 13288, Marseille, France;1. University of Washington, School of Aquatic and Fisheries Sciences, 1122 NE Boat St, Seattle WA 98105, United States;2. Fisheries Resource and Monitoring Division, Northwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E., Seattle, WA 98112, United States;3. Institute of Ocean Sciences, Fisheries and Oceans Canada, 9860 W. Saanich Rd. Sidney, B.C V8L 5T5, Canada;4. Fisheries and Oceans Canada, School of Resource and Environmental Management, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada;5. Center for Quantitative Science, Ocean Teaching Building, Suite 300, Box 357941, Seattle, WA 98195, United States;6. Auke Bay Laboratories, Alaska Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration, 17101 Pt. Lena Loop Rd., Juneau, AK 99801, United States;1. Department of Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, Canada V8W 2Y2;2. Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC, Canada V9T 6N7;3. National Marine Fisheries Service, Northwest Fisheries Science Center, 2725 Montlake Blvd. East, Seattle 98112, WA, USA;4. Fisheries and Oceans Canada, 9860 W. Saanich Rd., Sidney, BC, Canada V8L 4B2;5. Fisheries and Oceans Canada, Emeritus, Pacific Biological Station, 3190 Hammond Bay Rd, Nanaimo, BC, Canada V9T 6N7;6. Washington Department of Fish and Wildlife, 1111 Washington St SE, 6th Floor, Olympia, WA 98504-3150, USA;7. Salmoforsk International Environmental Consulting, 2280 Brighton Ave, Victoria, BC, Canada V8S 2G2;8. Washington Department of Fish and Wildlife, 16018 Mill Creek Boulevard, Mill Creek, WA 98012-1541, USA;9. Fisheries and Oceans Canada, St. Andrews Biological Station, 125 Marine Science Driver, St. Andrews, NB, Canada E5B 0E4 |
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| Abstract: | Stomach content analysis of eastern North Pacific groundfish has been conducted routinely by researchers interested in understanding trophic interactions between key predator species and their prey. Identification of prey by traditional morphological methods has limitations however, due to the loss of identifiable characters from digestion and morphological similarities between taxa. Furthermore, some forage fish (e.g., osmerids, ammodytids, and juvenile gadids), common prey of Bering Sea and Gulf of Alaska groundfish, are difficult to distinguish because of their slender or fusiform shape, disarticulating easily during digestion. DNA-based identification methods were developed to differentiate among 18 fish species, some that are found at depths greater than 200 m, from four taxonomic families: Ammodytidae and Osmeridae (forage fish), Pleuronectidae (flatfish), and Gadidae (gadid fish). Polymerase chain reaction (PCR) amplification of a 739 basepair section of mitochondrial DNA cytochrome c oxidase I and an 862 basepair section of mitochondrial DNA cytochrome b was followed by restriction digest assays and resulted in species level resolution for 16 of 18 species of interest. PCR restriction digest assays applied to fish prey from stomach contents of groundfish indicated the presence of several target species, eulachon (Thaleichthys pacificus), walleye pollock (Gadus chalcogrammus), searcher (Bathymaster signatus), rock sole (Lepidopsetta bilineata), yellowfin sole (Limanda aspera) and either Bering flounder (Hippoglossoides robustus) or flathead sole (H. elassodon). The PCR restriction digest protocols improved the identification rate of predated fish from stomach contents compared to identification by conventional taxonomic methods alone, and DNA sequence analysis further resolved identification of unknown prey fish samples. |
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| Keywords: | Groundfish Stomach contents Prey fish Restriction digest Genetics Alaska |
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