Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces

Abstract

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.

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

“…In their killer whale study, Ford et al. () analysed known percentages of DNA extracted from four fish species and the RRA of each fish corresponded well to input (generally within 5% of expected values) providing confidence in their conclusions. Using prey species of harbour seals, Thomas, Deagle, Eveson, Harsch, and Trites () carried out a detailed study on sequence recovery from blended tissue mixtures.…”

“…This effect can be illustrated in metabarcoding data from a population‐level diet study of killer whales (Figure ). This study concluded that the whale population's diet consisted primarily of Chinook salmon (~80%) based on high RRA of this species in most samples (Ford et al., ). If we consider the killer whales’ diet as occurrence (POO; each food species occurrence given equal value), the view changes considerably because other salmon species and halibut frequently detected at low levels become important prey.…”

“…Both mitochondrial and chloroplast DNA markers are present in multiple copies in each cell, and copy number varies between tissue types (e.g., leaves versus roots; Ma & Li, ) and physiological state (e.g., juvenile vs. gravid adult; Veltri, Espiritu, & Singh, ). Getting a thoroughly homogeneous mix of tissues in a small volume suitable for DNA extractions is challenging; therefore, mixtures made from DNA extracted separately for each taxa are sometimes used (e.g., Ford et al., ; Krehenwinkel, Wolf, et al., ; Piñol, Mir, Gomez‐Polo, & Agustí, ). However, results from purified genomic DNA mixture may have little biological meaning because differences in cell density and genome size will confound results (i.e., low recovery from a species could be a bias, or the species may have a large genome and therefore fewer markers are in the fixed amount of DNA added to the mixture) (Piñol et al., ).…”

“…While the effort needed to justify the RRA approach may be challenging, the possibility of obtaining more accurate diet estimates will make it worthwhile in many situations. We have seen such effort undertaken in papers addressing broad ecological questions (Kartzinel et al., ; Willerslev et al., ), and in diet studies of marine predators, where population consumption has significant fisheries management implications (Ford et al., ; Thomas et al., ). This approach should also be possible in monitoring programmes, such as those carried out on seabird diet (Jarman et al., ; Sydeman et al., ), where the long‐term investment warrants the development of robust DNA‐based methods that provide the best possible data.…”

Ecological implications of changing hatchery practices for Chinook salmon in the Salish Sea

“…Reduced diversity in these stocks has likely reduced the ecosystem's hatchery portfolio, and it is hypothesized that this could have a destabilizing effect on recruitment (Sturrock et al 2019). Maintaining diversity-and the stability it may confer-in the composite of Chinook stocks along the west coast of North America could be a critical factor for the recovery of southern resident killer whales, which depend heavily on Chinook salmon for prey (Ford et al 2016). Thus, other regions along the west coast that provide large contributions of hatchery Chinook salmon (e.g., Columbia River, Washington, and Oregon coast) might consider the findings presented in this study relevant, as future hatchery practices are designed.…”