388 
Fishery Bulletin 109(4) 
our collections from 2008 were about two years younger 
(on average 4.6 years for Berners Bay herring and 6 
years for Sitka Sound herring) than those in the ADFG 
database for that year. Analysis by year class may be 
beneficial in future studies in order to examine allele 
frequencies by age and possible heterogeneity among 
year classes or spawning waves. 
Genetic differences were significant between South- 
east Alaska (collectively) and the two collections from 
Prince William Sound, although no inference about 
population structure within Prince William Sound is 
made here, because both of the collections comprised 
nonspawning fish obtained from a single year. Larger 
sample sizes and multiyear collections and the use of 
microsatellite markers may be useful for further genetic 
studies within Prince William Sound. 
Large numbers of alleles at some of the microsatel- 
lites and the large effective population size of herring 
necessitate analysis of adequate numbers of samples to 
detect population structure. Accordingly, samples sizes 
were increased during the course of the present study, 
effectively increasing the power of the analyses. Results 
of earlier analyses after one and two years of sampling 
did not reveal significant genetic differences among col- 
lections in our study, and notably the number of alleles 
at several loci exceeded the number of individuals in 
a collection — an important consideration when using 
highly polymorphic markers. Low F gT values might be 
expected because highly polymorphic loci negatively cor- 
relate with F st values (O’Reilly et al., 2004). Berners07 
was generally homogeneous with all other collections in 
pairwise tests of differentiation (homogeneity and F ST ), 
possibly owing to small sample size, which reduces the 
reliability of the estimate. 
Low F st values, weak bootstrap support for some of 
the branches of the neighbor-joining tree, and an AMO- 
VA illustrating high genetic variation within individual 
samples, indicate that population structure among re- 
gional groups of herring in Southeast Alaska is detect- 
able but weak. This inference would further indicate 
low-level or episodic gene flow among these regions. 
Conclusion 
In conclusion, Pacific herring from Berners Bay and 
over-wintering fish in Lynn Canal, in the archipelago of 
Southeast Alaska, were genetically divergent from the 
spawners along the outer coast of the eastern Gulf of 
Alaska. Lack of recovery of the Berners Bay population 
despite closure of the fisheries, may be due to spatial 
isolation and adaptation to local environmental condi- 
tions. Other potential causes for the lack of recovery 
may be increased predation from expanding popula- 
tions of sea lions and humpback whales (Rice et al. 4 ) 
or water disturbance in spawning areas and water pol- 
lution. Additional pressures on this stock could lead to 
substantial declines in Lynn Canal herring abundance 
and in the abundances of fish and marine mammals 
that forage on them. 
Acknowledgments 
We thank all who contributed samples: R. Brenner, D. 
Harris, S. Moffitt (ADFG); C. Gabriele (Glacier Bay 
National Park); S. Johnson, J. Thedinga, F. Sewall, A. 
Eller, and K. Cox (Alaska Fisheries Science Center- 
[AFSC]). We thank C. Marvin (AFSC), N. Rutecki, 
and L. Miller for their assistance in the laboratory. M. 
Canino, M. Carls, C. Kondzela, A. Moles, T. McCraney, 
J. Rice (AFSC), D. Tallmon (University of Alaska Fair- 
banks), Stew Grant (ADFG) and Jeff Olsen (United 
States Fish and Wildlife Service [USFWS]) for early 
reviews of the manuscript, R. Waples (Northwest Fisher- 
ies Science Center) and J. Maselko (AFSC) for technical 
assistance, and J. Hudson (USFWS) for aging fish. 
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