2.1 Collection and processing of scat samples
Scat collections were conducted by multiple researcher groups at five
harbor seal haul-outs in the Salish Sea over a period of four
non-sequential years (Figure 1). Haul-outs varied in seal population
size as well as by habitat type (Table S1). Not all sites were visited
every year and the months during which each site was visited varied
between years (Table S1). Collections at Belle Chain, Cowichan, Comox,
and Fraser River were conducted by teams from University of British
Columbia under Fisheries and Oceans Canada’s Marine Mammal Research
Licenses (MML 2011-10 and MML 2014-07) and University of British
Columbia’s Animal Care Permits (A11-0072 and A14-0068) awarded to
University of British Columbia Marine Mammal Research Unit. Collections
at Baby Island were conducted by a team from Western Washington
University under Federal Permit 18002 from the United States Office of
Protected Resources, National Marine Fisheries Service, and a Western
Washington University’s Animal Care and Use Committee exception awarded
to Alejandro Acevedo-Gutiérrez.
Collection of scat followed the general procedure described in Thomas,
Deagle, Eveson, Harsch, and Trites (2016). Briefly, upon arrival at a
haul-out we searched the entire area for scat. When scat was found, the
entire scat was collected into a 126 μl nylon strainer inside
of a 500 ml sealable container using a wooden tongue dispenser and
plastic spoon. The container was then stored in a cooler with ice until
transfer to a -20 freezer later that day. At Baby Island and
Cowichan Bay in 2014 the entire outside of the scat was swabbed before
collection. Swabbing focused on any mucus material, as it likely
contains higher proportions of seal DNA (Rothstein, 2015). The swab was
then placed in a vial of ethanol and stored in a cooler with ice until
transfer to a -20 freezer later that day.
A DNA slurry of homogenized scat in ethanol was prepared for each sample
to obtain a representative set of DNA following the procedure described
in Thomas et al. (2016). Briefly, the entire scat was thawed in ethanol
and homogenized within the mesh bag. After homogenization, a
representative sample of DNA slurry was allowed to pass through the bag.
The mesh bag was then removed, zip-tied, and stored at -20 for later
use in prey hard part analysis. We then let the DNA slurry settle in the
containers on the bench top overnight. The next day we pipetted the
settled slurry into 20 mL scintillation vials that were subsequently
stored at -20 until further analysis.