Harbor seal diet data from the Olympic Peninsula, WA 2020-2021

Description

In this submission, we share data collected on harbor seals (Phoca vitulina) from the Olympic Peninsula in northwest Washington from 2020-2021. Our primary objectives were to characterize the diets of harbor seals in the winter and spring to determine their consumption on Pacific salmon (Onchorhynchus sp.) and other important fisheries species. To determine diet we collected scat samples between December 2020 and May 2021 from 7 harbor seal haulout sites in two regions: four along the northwestern coast of the Olympic Peninsula (hereafter Pacific coast) and three along the Strait of Juan de Fuca. We used traditional hard parts identification, DNA metabarcoding, and qPCR to describe the diet and determine the sex of the seals. Despite our low sample size and narrow collection time frame, we found differences in prey species consumed between regions and sexes. A manuscript of our results has been submitted to Northwestern Naturalist in November 2022.

Steps to reproduce

All research was conducted along the Olympic Peninsula in northwest Washington. Harbor seal haulouts sampled included 3 sites in the Strait of Juan de Fuca (Waadah Island, Seal Rock, Eagle Point) and 4 sites on the Pacific Coast (Tatoosh Island, Wa'atch Point, Father and Son, Cooke Rock). Our goal was to collect 30 harbor seal scat per month for the winter (December, January, February) and spring (March, April, May) seasons. Scat samples were collected following Thomas et al. (2017) and Voelker et al. (2020) and frozen prior to analysis. Frozen scats were thawed in ethanol and manually homogenized within fine (0.25 mm mesh) nylon paint strainer bags to separate hard parts from the DNA matrix. Hard parts were cleaned by washing the sealed paint strainer bags in a commercial style washing machine followed by additional cleaning using nested sieves (0.5 mm, 1mm, and 2 mm). Hard remains were preserved in ~50% isopropyl alcohol and, excluding cephalopod beaks and pens, and crab parts, were dried prior to identification. Prey hard parts, including bones, cartilagenous structures, beaks, and shells, were identified to the lowest possible taxonomic level (Lance et al. 2001, 2012). Occasionally, prey items were confidently identified to family, with a strong likelihood of species level identification. These were reported in the tables separately from prey species with the indicator “Cf”. DNA metabarcoding analysis was performed following standard protocols to quantify the diet proportions of each prey species consumed (Thomas et al. 2016, 2017). DNA was extracted via the QIAGEN stool kit following adapted protocols for pinniped scat (Deagle et al. 2005). After extraction, quantitative PCR (qPCR) was used to determine sex of the seal (see Rothstein 2015, Schwarz et al. 2018, Voelker et al. 2020). Deviations from standard protocols are described in Lewis (2022). 16S rRNA was used as the metabarcoding marker for fish and cephalopod prey species and salmonid species were determined using the Cytochrome Oxidase subunit I (COI) region. Prey species were identified by nucleotide BLAST using a custom reference library (taxonomy database) of fish and cephalopod DNA sequences. Decontamination was performed as described in Lewis (2022) and sequences were assigned to species based on the best match (threshold BLASTN e-value < 1e-20 and a minimum identity of 0.99). We used relative read abundances (RRA in %) to quantify the proportions of each prey species determined via DNA metabarcoding. RRA is calculated by the number of reads from a prey species divided by the total number of prey reads within an individual sample (Thomas et al. 2006). To generate the RRA for individual salmon species, the total salmon RRA was divided by the COI RRA values for each species. For samples that did not detect salmon via COI analysis, but did detect salmon via 16S analysis, the RRA for that salmon species is based on the original read count and RRA from the 16S analysis only.

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