Data from: Estimation of a killer whale (Orcinus orca) population’s diet using sequencing analysis of DNA from feces

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 population’s
summer diet.