14 
Fishery Bulletin 111(1) 
abundance, although overexploitation has likely played 
a prominent role (e.g., Levin et al., 2006). Predation 
may have contributed to historic declines or may be 
inhibiting recovery, because the abundance of Salish 
Sea pinnipeds has been increasing and is thought to be 
near carrying capacity (Jeffries et al., 2003). Although 
pinnipeds have the potential to deplete local fish stocks 
or hinder management actions that would promote 
the recovery of depleted stocks (Harwood and Croxall, 
1988; Bowen et al., 1993; Fu et al., 2001; Bjprge et al., 
2002; Boyd, 2002; MacKenzie et al., 2011), there is no 
direct evidence to that effect in the Salish Sea. Conse- 
quently, an improved understanding of the role of pin- 
niped predation in regulation of prey abundance would 
enhance our knowledge of marine ecosystem dynam- 
ics and potentially inform the effective management of 
fish stocks. 
The diets of harbor seals in this region are thought 
to be composed primarily of adult salmon (Oncorhyn- 
chus spp.), Pacific herring, and gadids (Scheffer and 
Slipp, 1944; Olesiuk, 1993; Tollit et al., 1997; Browne 
et al., 2002; Wright et al., 2007; Thomas et al., 2011; 
Lance et al., 2012). However, seals are considered op- 
portunistic predators that target locally abundant prey 
and switch between prey species in response to chang- 
es in prey abundance — a type-III functional response 
(Holling, 1959; Middlemas et al., 2006). Such predatory 
behavior, in combination with local and seasonal diver- 
sity in the availability of prey (Stasko et al., 1976; Will- 
son and Womble, 2006; Therriault et al., 2009; Thomas 
et al., 2011), implies harbor seal diet composition will 
vary both spatially and temporally, and thus compli- 
cate accurate diet assessment. 
Prior investigations of harbor seal diets in the Pa- 
cific Northwest have relied primarily on observational 
studies, stomach content analyses, and especially scat 
analyses (Scheffer and Slipp, 1944; Everitt et al., 1981; 
Brown and Mate, 1983; Olesiuk, 1993; Zamon, 2001; 
Orr et al., 2004; Wright et al., 2007; Thomas et al., 
2011; Lance et al., 2012). Such methods provide im- 
portant insights into predatory behavior and document 
the presence of particular prey species in predator di- 
ets; however, several well-known factors can limit their 
utility in quantitative investigations of diet (Phillips 
and Harvey, 2009; Klare et al., 2011). For example, scat 
analyses frequently are compromised by unequal prob- 
abilities of detecting prey classes, as well as by dif- 
ficulty in derivation of quantitative estimates of diet 
composition from frequency-of-occurrence data. In ad- 
dition, results pertain only to a short period of time, 
ranging from the last predatory event in observational 
studies to 1-2 days in scat-based investigations (Har- 
vey, 1989; Cottrell and Trites, 2002; Tollit et al., 2004; 
Trites and Joy, 2005; Hauser et al., 2008; Phillips and 
Harvey, 2009). 
Quantitative fatty acid signature analysis (QFASA; 
Iverson et al., 2004) has important advantages over 
other methods of diet assessment. Perhaps, most im- 
portant, the method produces statistical estimates of 
diet composition and measures of precision. The num- 
ber of fatty acids that can be biosynthesized by animals 
is limited (Ackman, 1989); therefore, the presence of 
some compounds can be attributed to diet alone. This 
fact, in combination with the large number of fatty 
acid compounds present in adipose tissue, particular- 
ly in marine ecosystems, enables QFASA to estimate 
the contribution of a large number of prey classes to 
diets, limited primarily by the diversity of fatty acids 
among prey classes. In addition, although most meth- 
ods of diet assessment provide information only on re- 
cent consumption, sampling of adipose deposits may 
provide insights into diets over a period of weeks to 
months (Iverson et al., 2004; Budge et al., 2006). QFA- 
SA requires the development of comprehensive data on 
the fatty acid composition of potential prey, work that 
may be costly or otherwise difficult. Although predators 
must be captured and handled, only a small incision 
is required for sampling and predators can be quickly 
released. Overall, QFASA presents predators with lim- 
ited negative consequences and can produce diet com- 
position estimates that largely avoid potential biases 
characteristic of other methods. 
We used QFASA to investigate the diets of harbor 
seals captured from haul-out sites among the San Juan 
Islands of Washington State and the southern Gulf Is- 
lands of British Columbia; both island groups are with- 
in the Salish Sea. Blubber samples were collected from 
captured harbor seals and representative specimens 
of known or potential prey species also were collected. 
Samples from both predators and potential prey were 
analyzed to determine their fatty acid composition, and 
diet compositions of sampled harbor seals were esti- 
mated with QFASA mixture modeling. The resulting 
estimates provide new insights into harbor seal preda- 
tion on depressed fish populations and reveal dietary 
heterogeneity on spatial, demographic, and individual 
scales. 
Materials and methods 
Study area 
The San Juan Islands and the southern Gulf Islands 
lie in the transboundary waters of Washington State 
and British Columbia between the Strait of Georgia, 
Strait of Juan de Fuca, and Puget Sound (Fig. 1). This 
area is characterized by hundreds of large and small 
islands, rocky intertidal reefs, protected bays and estu- 
aries, and rich marine life. Harbor seals use more than 
150 haul-out locations in the study area, including 
intertidal sandbars and numerous small islands and 
rocky reefs distributed throughout the region. Harbor 
seals are abundant throughout the Salish Sea (Jeffries 
et al., 2003). 
