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Sex‐specific diet information is important in the determination of
predator impacts on prey populations. Unfortunately, the diet of males and
females can be difficult to describe, particularly when they are marine
predators. We combined two molecular techniques to describe haul‐out use
and prey preferences of male and female harbor seals (Phoca vitulina) from
Comox and Cowichan Bay (Canada) during 2012–2013. DNA metabarcoding
quantified the diet proportions comprised of prey species in harbor seal
scat, and qPCR determined the sex of the individual that deposited each
scat. Using 287 female and 260 male samples, we compared the monthly sex
ratio with GLMs and analyzed prey consumption relative to sex, season,
site, and year with PERMANOVA. The sex ratio between monthly samples
differed widely in both years (range = 12%–79% males) and showed different
patterns at each haul‐out site. Male and female diet differed across both
years and sites: Females consumed a high proportion of demersal fish
species while males consumed more salmonid species. Diet composition was
related to both sex and season (PERMANOVA: R2 = 27%, p < 0.001; R2
= 24%, p < 0.001, respectively) and their interaction (PERMANOVA:
R2 = 11%, p < 0.001). Diet differences between males and females
were consistent across site and year, suggesting fundamental foraging
differences, including that males may have a larger impact on salmonids
than females. Our novel combination of techniques allowed for both prey
taxonomic and spatiotemporal resolution unprecedented in marine predators.
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