Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 8528
Title: Estimation of a killer whale (Orcinus orca) populations diet using sequencing analysis of DNA from feces
Author: Michael J. Ford, Jennifer Hempelmann, M. B. Hanson, Katherine L. Ayres, Robin W. Baird, Candice K. Emmons, Jessica I. Lundin, Gregory S. Schoor, S. K. Wasser, Linda K. Park
Publication Year: 2016
Journal: PLoS ONE
Volume: 11
Issue: 1
Pages: e0144956
Keywords: diet,DNA,killer whale,feces,Salish Sea

Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function.  The diet of many species, however, is difficult to observe directly.  Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets.  In this study, we used high–throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their summer range in the Salish Sea. We combined 175 fecal samples collected between May and September from five years between 2006 and 2011 into 13 sample groups.  Two known DNA composition control groups were also created.  Each group was sequenced at a ~330bp segment of the 16s gene in the mitochondrial genome using an Illumina MiSeq sequencing system.  After several quality controls steps, 4,987,107 individual sequences were aligned to a custom sequence database containing 19 potential fish prey species and the most likely species of each fecal–derived sequence was determined.  Based on these alignments, salmonids made up >98.6% of the total sequences and thus of the inferred diet.  Of the six salmonid species, Chinook salmon made up 79.5% of the sequences, followed by coho salmon (15%).  Over all years, a clear pattern emerged with Chinook salmon dominating the estimated diet early in the summer and coho salmon contributing an average of >40% of the diet in late summer.  Sockeye salmon appeared to be occasionally important, at >18% in some sample groups.  Non–salmonids were rarely observed.  Our results are consistent with earlier results based on surface prey remains, and confirm the importance of Chinook salmon in this populations summer diet. 

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Theme: Ecosystem approach to improve management of marine resources
Foci: Characterize ecological interactions (e.g. predation, competition, parasitism, disease, etc.) within and among species.