10.5061/DRYAD.DS6GC
Ford, Michael J.
Northwest Fisheries Science Center
Hempelmann, Jennifer
Northwest Fisheries Science Center
Hanson, M. Bradley
Northwest Fisheries Science Center
Ayres, Katherine L.
University of Washington
Baird, Robin W.
Cascadia Research
Emmons, Candice K.
Northwest Fisheries Science Center
Lundin, Jessica I.
University of Washington
Schorr, Gregory S.
Cascadia Research
Wasser, Samuel K.
University of Washington
Park, Linda K.
Northwest Fisheries Science Center
Data from: Estimation of a killer whale (Orcinus orca) population’s diet
using sequencing analysis of DNA from feces
Dryad
dataset
2016
16s ribosomal RNA
Oncorhynchus
DNA sequence
killer whale
Holocene
Orcinus orca
2016-01-25T18:54:49Z
2016-01-25T18:54:49Z
en
https://doi.org/10.1371/journal.pone.0144956
88753241 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Mitochondrial 16s ribosomal gene fragment sequences from killer whale
fecesThere are 15 fasta files containing DNA sequences from a ~330bp
fragment of the mitochondrial 16s ribosomal RNA gene. These sequences were
amplified from 175 killer whale feces collected from the wild. The samples
are pooled into 13 experimental groups; the numbers in the file names
correspond to the sample pools described in Table S1 of the associated
publication which contains sampling information (time, location, whale ID
if known). Samples 23 and 24 are controls, as described in the
publication. Methodological details including primers and sequencing
methods are described in the associated publication.16s fecal summer prey
sequences for dryad.zip
USA
San Juan Islands
Salish Sea
Washington