Wildes et at: Genetic variation in outer-coastal and fjord populations of Clupea pallasii in the eastern Gulf of Alaska 
383 
Table 1 
Location and dates for Pacific herring (Clupea pallasii) collections from Southeast and Prince William Sound (PWS), Alaska. 
Sample size ( n ) reflects the number of individuals successfully genotyped and used in analyses. The two Lynn Canal collections 
in the early spring of 2008 are noted as Lynn Canal 08, a and b. 
Sample 
Latitute (N) 
Longitude (W) 
Sampling date 
n 
Spawning fish 
Berners Bay 07 
58°40.9' 
134°59.r 
4/5/2007 
52 
Berners Bay 08 
58°40.9' 
134°59.1' 
5/3/2008 
126 
Berners Bay 09 
58°39.3' 
134°58.5' 
5/5/2009 
148 
Hobart Bay 08 
57°27.6' 
133°21.1' 
5/9/2008 
128 
Hoonah Sound 08 
57°36.6' 
135°21.5' 
4/23/2008 
100 
Sitka Sound 07 
57°05.1' 
135°30.4' 
3/29/2007 
75 
Sitka Sound 08 
57°08.9' 
135°28.7' 
4/4/2008 
131 
Nonspawning fish 
Lynn Canal 07 
58°27.2' 
134°47.0' 
11/10/2007 
97 
Lynn Canal 08a 
58°27.2' 
134°49.0' 
2/23/2008 
98 
Lynn Canal 08b 
58°29.6' 
134°49.2' 
2/25/2008 
98 
Nichols Bay 07 
54°43.8' 
132°08.3' 
6/14/2007 
97 
Western PWS07 
60°13.6' 
148°11.0' 
7/15/2007 
99 
Eastern PWS07 
60°39.2' 
134°49.2' 
12/2/2007 
92 
as threatened or endangered under the Endangered 
Species Act is a stock’s discreteness or uniqueness. To 
date, four genetic studies have been completed in the 
eastern GOA. One study of allozymes indicated that, 
in general, GOA populations are genetically distinct 
from those to the south in British Columbia, Canada 
and west of Kodiak Island, (Grant and Utter, 1984): 
one locus in that study indicated heterogeneity among 
populations within the GOA. In more recent studies 
of microsatellite DNA variation, genetically discrete 
stocks of herring were detected in British Columbia 
(Beacham et ah, 2008) and in Puget Sound in Washing- 
ton State (Small et ah, 2005). In both studies, genetic 
divergence among these discrete stocks was attributed 
to different spawning times, geographic isolation, or 
both. In the fourth study, O’Connell et al. (1998a) con- 
firmed genetic differentiation between Prince William 
Sound and western Alaska Pacific herring populations, 
using microsatellites. 
This study was conducted to determine whether 
Lynn Canal Pacific herring (hereafter, herring) in 
Southeast Alaska are genetically distinct from other 
eastern Gulf of Alaska herring and whether overwin- 
tering Lynn Canal herring spawn in Berners Bay. We 
evaluated 22 existing microsatellite loci developed 
for Pacific and Atlantic herring (Clupea harengus ) 
(Miller et al., 2001; McPherson et al., 2001; Olsen et 
al., 2002; O’Connell et al., 1998b) for their ability to 
distinguish herring populations in the eastern Gulf of 
Alaska. Our results indicate that this class of highly 
polymorphic nuclear DNA markers, combined with 
adequate sample sizes, can resolve spatial patterns of 
genetic heterogeneity consistent with discrete stocks 
of Pacific herring. 
Materials and methods 
Sample collections 
Thirteen collections of herring were made in seven loca- 
tions in Southeast Alaska from 2007 to 2009 (Table 1, 
Fig. 1). These samples included three collections of 
nonspawning, overwintering herring in Lynn Canal 
and three collections of spawning herring in associated 
Berners Bay, which is located on the eastern side of 
Lynn Canal and hosts a high concentration of spring 
spawning herring. Three consecutive years of spawn- 
ing fish were sampled in Berners Bay: about two weeks 
before spawning in 2007 (Berners07) and during the 
spawning season in 2008 and 2009 (Berners08 and 
Berners09, respectively). Three samples of overwinter- 
ing fish were collected in Lynn Canal during the winter 
of 2007-08. The Lynn07 collection was made in early 
winter (November), whereas collections from along the 
shoreline (Lynn08a) and from a deep trench offshore 
(Lynn08b) were made several days apart, approximately 
two months (late February) before the spawning season. 
In 2008, samples of spawning fish were also collected 
in Hobart Bay, approximately 200 km south of Berners 
Bay on the mainland in central Southeast Alaska, and 
in Hoonah Sound, on northern Chichagof Island. Two 
collections were made in Sitka Sound, on the outer 
coast of Baranof Island, during the spawning season 
in 2007 and 2008, and one collection of immature fish 
was obtained from Nichols Bay located at southern 
Prince of Wales Island in 2007. Two additional collec- 
tions were made in Prince William Sound; one from a 
postspawning group in Whale Bay in 2007, located on 
the western side of the sound (wPWS), and one from an 
