Data on the diets of Salish Sea harbour seals from DNA metabarcoding

Abstract

Marine trophic ecology data are in high demand as natural resource agencies increasingly adopt ecosystem-based management strategies that account for complex species interactions. Harbour seal (Phoca vitulina) diet data are of particular interest because the species is an abundant predator in the northeast Pacific Ocean and Salish Sea ecosystem that consumes Pacific salmon (Oncorhynchus spp.). A multi-agency effort was therefore undertaken to produce harbour seal diet data on an ecosystem scale using, 1) a standardized set of scat collection and analysis methods, and 2) a newly developed DNA metabarcoding diet analysis technique designed to identify prey species and quantify their relative proportions in seal diets. The DNA-based dataset described herein contains records from 4,625 harbour seal scats representing 52 haulout sites, 7 years, 12 calendar months, and a total of 11,641 prey identifications. Prey morphological hard parts analyses were conducted alongside, resulting in corresponding hard parts data for 92% of the scat DNA samples. A custom-built prey DNA sequence database containing 201 species (192 fishes, 9 cephalopods) is also provided.

Fine‐scale diversity of prey detected in humpback whale feces

“…The species of fish and the animal's gut transition time are therefore relevant to the extent of bone erosion prior to the animal defecating (Tollit et al, 2007 ). Food transit time through the digestive system of captive harbor seals ( Phoca vitulina ), for example, is between 2 and 6 h (Markussen, 1993 ), and salmonid bones have been identified in free‐ranging harbor seal feces in BC and Washington State (Thomas et al, 2022 ), in which the fragile otoliths of juvenile salmonids are often severely eroded (Thomas et al, 2017 ). Compared to seals, digestion time in rorqual whales is estimated to be considerably longer, possibly 15–18 h in fin whales (Víkingsson, 1997 ), though inter‐ and intraspecific variability in food passage time in rorquals remains unknown.…”

First Diet Description of the Harbor Seal (Phoca Vitulina) in the Northwest Corner of the Olympic Peninsula, Washington State

“…Albeit based on a small sample size and acknowledging limitations in estimating relative biomass consumed, these prey groups together comprised 45.1% of the diet of Harbor Seals overall, results with which the SSFO largely concurred. The common denominator between this diet composition and those described overall for Washington State (Steingass 2017; Thomas and others 2022) is the frequent consumption of Pacific Herring. Harbor Seals in other regions of the state frequently consume Pacific Hake ( Merluccius productus ), Shiner Perch ( Cymatogaster aggregata ), and Chum Salmon ( Oncorhynchus keta ) (Thomas and others 2011; Lance and others 2012; Howard and others 2013).…”

“…Steingass (2017) summarized the diet data of Harbor Seals from studies conducted during 1931–2013 based on hard-parts analysis (identification of otoliths, bones, cartilaginous structures, and beaks) of 12,993 scats and 95 stomach contents, including samples from the coast of Washington State and the Salish Sea (the inland marine waters of Washington State and British Columbia, Canada). More recently, Thomas and others (2022) published the diet data of Harbor Seals based on DNA metabarcoding and hard parts analyses of 4625 scats collected during 2011–2019 throughout the Salish Sea. Despite the wealth of information, there are clear spatial gaps: only 1 study has described the diet of Harbor Seals from the northwestern coast of the Olympic Peninsula (Gearin and others 1998), and only 1 study has examined their diet at the western end of the Strait of Juan de Fuca off Vancouver Island, Canada (Olesiuk and others 1990).…”

“…As such, we avoided direct comparisons of RRA, SSFO and FO results. For RRA especially, we were able to compare estimates among the prey items in our study, given that under certain conditions they reflect relative biomass consumed (Deagle and others 2019; Thomas and others 2022).…”

Quantifying impacts of harbor seal Phoca vitulina predation on juvenile Coho Salmon in the Strait of Georgia, British Columbia

“…Unsurprisingly, the observed trends in harbor seal abundances have prompted increased interest in the foraging ecology of these generalist predators (Thomas et al. 2011, 2022; Howard et al. 2013), especially since the abundances of valuable fishes like salmon and rockfish have declined severely over the same time period (Palsson et al.…”