title: Molecular identification of prey in the stomach contents of Harp Seals (Pagophilus groenlandicus) using species-specific oligonucleotides.
abstract: All methods of diet analysis in marine mammals, including hard part analysis (HPA), have biases affecting the accuracy of prey-species identification and frequency in the estimated diet due to differential consumption, digestion and retention. Using PCR amplification of specific prey DNA with species-specific primers, we developed a DNA-based method that complements HPA and provides an alternative means to detect prey from stomach contents of Harp Seals (Pagophilus groenlandicus). The target size that could be reliably amplified was determined using a digestion time-series of Atlantic Cod (Gadus morhua) tissue in simulated seal stomachs. Various target lengths were trialed using general teleost primers; amplicons of approximately 800 bp or less were consistently obtained. Prey species-specific PCR primers for Atlantic Cod, Arctic Cod (Boreogadus saida) and Capelin (Mallotus villosus) were designed and tested with DNA from the stomach contents of 31 Harp Seals. Amplicons were obtained for all three species-specific primer sets. Amplification results compared with HPA revealed: (i) Atlantic Cod hard parts were found in five stomachs where no Atlantic Cod DNA amplified, suggesting that Atlantic Cod may be over-represented in the estimated diet, (ii) amplification of Arctic Cod DNA occurred for 17 stomachs, including all 12 stomachs with, and five stomachs without, Arctic Cod hard parts, and (iii) Capelin DNA amplified for four of five stomachs with Capelin hard parts and for one stomach without Capelin hard parts. We conclude that PCR amplification of specific prey DNA provides a viable means to complement Harp Seal diet analysis by HPA, but suggest that valuable information for quantitative diet analysis rests in a quantitative PCR approach.
authors.affiliation: Department of Biology, Memorial University of Newfoundland, St. John's, NF, Canada A1B 3X9 Genomics and Proteomics Facility, CREAIT Network, Memorial University of Newfoundland, St. John's, NF, Canada A1B 3X9 Science Branch, Department of Fisheries and Oceans, Northwest Atlantic Fisheries Centre, PO Box 5667, St. John's, NF, Canada A1C 5X1 Department of Psychology, Memorial University of Newfoundland, St. John's, NF, Canada A1B 3X9.
authors.forename: H D
authors.initials: HD
authors.lastname: Marshall
authors.forename: K A
authors.initials: KA
authors.lastname: Hart
authors.forename: E S
authors.initials: ES
authors.lastname: Yaskowiak
authors.forename: G B
authors.initials: GB
authors.lastname: Stenson
authors.forename: D
authors.initials: D
authors.lastname: McKinnon
authors.forename: E A
authors.initials: EA
authors.lastname: Perry