364 
Fishery Bulletin 107(3) 
Scale (km) 
-o- shrimp (mixed spp.) 
-*-crab (mixed spp.) 
~x northern anchovy 
Pacific herring 
~s~ jacksmelt 
plainfin midshipman 
+ Chinook salmon 
-a- Pacific staghorn sculpin 
-a- English sole 
-o- white croaker 
yellowfin goby 
Figure 2 
The effects of scale on the analyses of spatial overlap between distribution of Pacific harbor seals ( Phoca vitulina richardii) 
and their prey species in San Francisco Bay, CA, 2001-05. Potential prey species included Pacific herring ( Clupea palla- 
sii), northern anchovy ( Engraulis mordax ), plainfin midshipman (Porichthys notatus). Pacific staghorn sculpin (Leptocot- 
tus armatus), white croaker ( Genyonemus lineatus), yellowfin goby (Acanthogobius flavimanus), jacksmelt ( Atherinopsis 
californiensis), English sole ( Pleuronectes vetulus ), Chinook salmon {Oncorhynchus tshawytscha), shrimp (mixed species, 
primarily Crangon spp.), and crab (mixed species, primarily Dungeness crab. Cancer magister). Graphs show the change 
in strength of Pearson’s correlations (r) between seal and prey locations with changes in analysis scale from 1 km to 
10 km, for each season. Only statistically significant (P< 0.05) correlations are shown. 
Correlation analyses 
According to our analyses, three benthic species — plain- 
fin midshipman, English sole, and Pacific staghorn scul- 
pin — are important prey of harbor seals in SFB (Fig. 
2). Spatial overlap between distribution of harbor seals 
and abundance of primary harbor seal prey species was 
greatest in central SFB, and in waters around Castro 
Rocks (Fig. 3). Although harbor seals used areas in the 
north and south SFB in all seasons, waters of central 
SFB and surrounding the primary haul-out site, Castro 
Rocks, were used most frequently. Correlations revealed 
both year-round consistency in the identity of harbor seal 
prey species and seasonal differences between primary 
prey species. 
Spring (March-May): During the spring pupping 
season, harbor seal locations were most highly cor- 
related with English sole and crab (Figs. 2A and 
3A). In all seasons, there were strong correlations 
between the distribution of crab and harbor seals 
(Fig. 4). In contrast to the fall and summer, there 
was no significant correlation between harbor seal 
locations and abundance of Pacific staghorn scul- 
pin during the spring. 
Summer (June-August): During the summer molt- 
ing season, harbor seal locations were most highly cor- 
related with English sole and Pacific staghorn sculpin 
(Figs. 2B and 3B). Harbor seals in SFB frequently 
visited areas where high numbers of Pacific staghorn 
sculpin were found in the 2001-05 CDFG trawls, most 
notably in the waters around the Castro Rocks haul- 
out site. 
Fall (September-November): During the fall, harbor 
seal locations were most highly correlated with plain- 
fin midshipman, white croaker, and Pacific staghorn 
sculpin (Figs. 2C and 30. Across spatial scales, cor- 
relations with plainfin midshipman were particularly 
strong (often >0.8) during the fall. 
Winter (December-February): During the winter, 
harbor seal locations were most highly correlated 
with plainfin midshipman, English sole, and Pacific 
herring (Figs. 2D and 3D). Harbor seals foraged in 
Pacific herring spawning areas, and correlations be- 
tween Pacific herring and harbor seals were greatest 
during this season. No significant correlation was 
found between the distribution of harbor seals and 
Chinook salmon. There was little correlation between 
the frequency of use of an area by harbor seals and 
the distribution of yellowfin goby, a non-native spe- 
cies that was found to be an important prey species 
in an earlier study of the diet of SFB harbor seals 
(Torok, 1994). 
