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

Austen C Thomas,Benjamin W Nelson,Michael Schmidt,Andrew W Trites,Hassen Allegue,Steven Jeffries,Amelia Louden,Alejandro Acevedo-Gutiérrez,Chad Nordstrom,Jed Moore,Sheena Majewski,Scott Pearson,Bruce Deagle

doi:10.1038/s41597-022-01152-5

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.

Highlights

Background & SummaryIn recent years the fisheries and ecosystem modelling communities have expressed increased interest in harbour seal (Phoca vitulina) diet information to help inform prey consumption estimates and ecosystem models[1–3]
In 2011, collaborating researchers at the University of British Columbia (UBC) and the Australian Antarctic Division undertook an effort to create a new diet analysis method capable of providing both the salmon species and the proportional biomass of prey contained in harbour seal scat samples
In previous studies of harbour seal impacts to juvenile salmonids in the Salish Sea[1,2,8,34], these diagnostic hard structures were combined with DNA extracted from each scat sample to estimate the proportion of juvenile and adult salmon in the seal diet

Summary

Background & Summary

In recent years the fisheries and ecosystem modelling communities have expressed increased interest in harbour seal (Phoca vitulina) diet information to help inform prey consumption estimates and ecosystem models[1–3]. In 2011, collaborating researchers at the University of British Columbia (UBC) and the Australian Antarctic Division undertook an effort to create a new diet analysis method capable of providing both the salmon species and the proportional biomass of prey contained in harbour seal scat samples. Between the years of 2011 and 2019, over four-thousand regional harbour seal scat samples were collected and processed using our standardized DNA metabarcoding diet analysis method This is the product of a collaborative transboundary research effort including two universities (University of British Columbia, Western Washington University), three government agencies (Washington Department of Fish and Wildlife, Fisheries and Oceans Canada, Australian Antarctic Division), a native American tribe (Nisqually Indian Tribe), a non-profit organization (Long Live the Kings) and private corporation (Smith-Root Inc.).

Methods

Findings

Code availability