Howard et at: Fish consumption by harbor seals (Phoca vitulina) in the San Juan Islands, Washington 
31 
Diet 
Collection of scat samples Scat samples were collect- 
ed at 23 sites that represented regional variation in 
habitat in the San Juan Islands from 2005 to 2008 as 
part of a larger harbor seal diet study conducted in 
the northern Puget Sound (Fig. 1) (Lance et al., 2012). 
Samples collected during seal breeding and nonbreed- 
ing seasons in 2007-08 were used in our study. De- 
tailed scat sample processing, collection information, 
and analysis of frequency occurrence of prey items in 
harbor seal diet are summarized in Lance et al. (2012). 
Briefly, samples for the diet study were collected from 
harbor seal haul-out locations during daytime low 
tides, placed in plastic bags, and then frozen until they 
were processed. Scat samples were processed following 
Lance et al. 3 and Orr et al. (2003). Otoliths were mea- 
sured and graded according to the methods of Tollit et 
al. (2007). On otoliths that were graded as good (no or 
minimal erosion) and fair (small amount of erosion), 
the width and length were measured with an ocular 
micrometer. For our study, scat samples were pooled 
by seal breeding and nonbreeding seasons for further 
analyses. 
Reconstruction of wet biomass To choose appropriate 
input values for diet in the model, a wet biomass re- 
construction technique (Laake et al., 2002) was used to 
estimate the proportion by wet weight of prey items in 
harbor seal diet. This technique focuses on energetic 
content of seal diet, rather than on frequency of items 
in diet, by accounting for the number and size of prey 
consumed in a diet sample. The proportion of wet bio- 
mass of a prey item (jt ( ) in harbor seal diet was calcu- 
lated by (Laake et al., 2002): 
where n t = the corrected number of items of prey item /; 
and 
w t = the average weight (in grams) of all prey 
items i. 
The corrected number of “items” (n,, number of in- 
dividuals in the sample) was calculated by applying 
a species-specific (or closest proxy) correction factor 
to account for otolith loss during digestion. We used 
otoliths to enumerate all species except Shiner Perch, 
for which we used the number of pharyngeal plates to 
derive a more reliable passage rate. We lacked otolith- 
loss correction factors for herring (Clupeidae) and Wall- 
eye Pollock; therefore, we considered the correction fac- 
tors for Pacific Sardine (Sardinops sagax) and Pacific 
Hake in Phillips and Harvey (2009), respectively, to 
Lance, M. M., Orr A. J., Riemer S. D., Weise M. J., and Laake 
J. L. 2001. Pinniped food habits and prey identification 
techniques protocol. AFSC Processed Report 2001-04, 41 
p. Alaska Fisheries Science Center, Seattle, WA. [Available 
from http://access.afsc.noaa.gov/pubs/search.cfm.! 
be reasonable proxies because these species are simi- 
lar in size and structure (M. M. Lance, personal com- 
mun.l. We used a Pink Salmon ( Oncorhynchus gorbus- 
cha) otolith-loss correction factor for all salmonids, a 
Shortbelly Rockfish ( Sebastes jordani) correction factor 
for all rockfish species, and species-specific correction 
factors for Shiner Perch and Pacific Staghorn Sculpin 
( Leptocottus armatus) (Harvey, 1989; Phillips and Har- 
vey, 2009). 
Length correction factors were applied to measure- 
ments from otoliths scored as being in good or fair con- 
dition to account for otolith erosion during digestion. 
Corrected otolith lengths then were used to calculate 
the fish size with species-specific length-weight regres- 
sions (Harvey et al., 2000). When we lacked species- 
specific correction factors or length-weight regressions, 
we used estimated body sizes of prey items. 
Otoliths of juvenile and adult salmonids were distin- 
guished on the basis of otolith and bone sizes. Otoliths 
that were graded in good enough condition to measure 
and reconstruct salmonid size were uncommon in scat 
samples; therefore, for salmonid adults that were not 
identified to species, we used an approximate average 
size (1589 g) for Pink Salmon, the species most com- 
monly consumed by harbor seals (Lance et al., 2012). 
An average estimated size of 35 g was used for all sal- 
monid juveniles. We also lacked otolith-length correc- 
tion factors for herring and Walleye Pollock; therefore, 
we used Pacific Sardine and Pacific Hake as proxies. 
The remaining length correction factors that we used 
were a Shortbelly Rockfish correction factor for all 
rockfish species, and species-specific correction factors 
for Shiner Perch and Pacific Staghorn Sculpin. 
It should be noted that reconstruction was not pos- 
sible for all species in the diet samples because of the 
diversity of harbor seal diet and lack of appropriate 
correction factors as noted previously and in Table 2. 
Given the complexity of harbor seal diet and lack of 
reconstruction techniques for several species, we recon- 
structed the proportion in the sample only for prey spe- 
cies of conservation concern or for prey species whose 
frequency of occurrence was >5.0 in the broader study 
of harbor seal diet (Lance et al., 2012). Our goal was 
to set a reasonable range of values for model input in 
addition to describing diet composition; therefore, we 
make here a distinction between diet sample results 
and the parameter values used in the model to calcu- 
late consumption. When there was great uncertainty 
in percent contribution by wet weight to harbor seal 
diet because of the use of proxy correction factors or 
omission of some species from biomass reconstruction, 
confidence intervals were increased (see Model uncer- 
tainty and parameter estimation section). 
Consumption rates 
We calculated consumption (as biomass) for 5 key 
prey species or groups that are species of conserva- 
tion concern or most common in harbor seal diet: her- 
