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Resource Ecology & Fisheries Management (REFM) Division

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Resource Ecology and Ecosystem Modeling Program

DNA-based Identification of Stomach Contents

Fast identification of prey species using morphological characteristics is not always possible because some common prey species found in stomach contents disarticulate at the head and tail fairly rapidly, and the remains consist of an incomplete vertebral column with some flesh attached.

In collaboration with Melanie Paquin and Mike Canino (RACE Divison) we are developing rapid and cost-effective methods of molecular identification to apply to groups of difficult-to-distinguish species. The polymerase chain reaction (PCR) method and restriction fragment length polymorphisms (RFLP) were used to develop protocols for the identification of forage fish prey found in fish stomachs. Taxonomic identifications of the forage fish prey were made to species using the physical characteristics of the fish remains. Tissue samples from each of the forage fish prey were collected for molecular analysis using the PCR-RFLP protocols.

We found 100% concordance in species identifications using the PCR-RFLP protocol and identifications using remaining physical characteristics. In addition, six taxonomically unidentifiable fish prey were sequenced, providing identification of a Pacific sand lance (Ammodytes hexapterus), a northern smoothtongue (Leuroglossus schmidti), a northern rock sole (Lepidopsetta polyxystra), and three sculpins (family Cottidae).

By Troy Buckley and Richard Hibpshman


Fish Stomach Collection and Lab Analysis

During the fourth quarter of 2010 Resource Ecology and Ecosystem Modeling (REEM) Program staff focused primarily on the analysis of fish stomachs from the Bering Sea. The contents of 4,106 stomach samples from 15 species were analyzed from the Bering Sea, and 189 walleye pollock stomach samples from the Gulf of Alaska were analyzed.

Detailed analysis with high taxonomic resolution of prey has begun on small-mouthed flatfish for an essential fish habitat (EFH) project and on walleye pollock for the Bering Sea Integrated Ecosystem Research Program (BSIERP) project.

Both of these projects incorporate independent information on the available prey community. Laboratory personnel also dried 474 tissue samples in preparation for stable isotope analysis. Fisheries observers returned stomach samples from 462 walleye pollock and 1 arrowtooth flounder from the eastern Bering Sea, and 149 walleye pollock from the Gulf of Alaska. In total, 15,905 records were added to the REEM food habits database.

By Troy Buckley and Geoff Lang
 

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