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

Mitochondrial 16s ribosomal gene fragment sequences from killer whale feces

There 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

Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whales.

Understanding diet is critical for conservation of endangered predators. Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily along the outer coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of their seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook salmon (Oncorhynchus tshawytscha), despite that species' rarity compared to some other salmonids. During other times of the year, when occurrence patterns include other portions of their range, their diet remains largely unknown. To address this data gap, we collected feces and prey remains from October to May 2004-2017 in both the Salish Sea and outer coast waters. Using visual and genetic species identification for prey remains and genetic approaches for fecal samples, we characterized the diet of the SRKWs in fall, winter, and spring. Chinook salmon were identified as an important prey item year-round, averaging ~50% of their diet in the fall, increasing to 70-80% in the mid-winter/early spring, and increasing to nearly 100% in the spring. Other salmon species and non-salmonid fishes, also made substantial dietary contributions. The relatively high species diversity in winter suggested a possible lack of Chinook salmon, probably due to seasonally lower densities, based on SRKW's proclivity to selectively consume this species in other seasons. A wide diversity of Chinook salmon stocks were consumed, many of which are also at risk. Although outer coast Chinook samples included 14 stocks, four rivers systems accounted for over 90% of samples, predominantly the Columbia River. Increasing the abundance of Chinook salmon stocks that inhabit the whales' winter range may be an effective conservation strategy for this population

Sampling locations of fecal material.

<p>Each dot represents one sampling event, color coded to represent sampling occurring in early (May-July 25), mid (July 26-September 4), and late (September 5–30) summer.</p

Temporal distribution of fecal samples included in the analysis and of the approximated daily abundance of Chinook, sockeye and coho salmon in the San Juan Islands area.

<p>Each dot represents fecal samples collected on a specific day, with the area of the dot proportional to the number of samples on that day (smallest size = 1 sample). The dots are color-coded to indicate the within-year pools of samples that were combined for sequencing analysis, for a total of 13 year-by-season sample pools. Smoothed daily salmon abundance was estimated by local polynomial regression of daily catch-per-unit-effort data scaled by total annual run size (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0144956#pone.0144956.s005" target="_blank">S1 Text</a> for details).</p