Genetic variation between 
outer-coastal and fjord populations 
of Pacific herring (Cl u pea pa I la si i) 
in the eastern Gulf of Alaska 
Harthvan T. Nguyen 
Jeffrey R. Guyon 
Email address for contact author: Sharon.Wildes@noaa.gov 
Auke Bay Laboratories 
Alaska Fisheries Science Center 
National Marine Fisheries Service 
National Oceanic and Atmospheric Administration 
17109 Point Lena Loop Rd. 
Juneau, Alaska, 99801-8344 
Abstract — Pacific herring (Clupea 
pallasii ) from the Gulf of Alaska 
were screened for temporal and spa- 
tial genetic variation with 15 mic- 
rosatellite loci. Thirteen collections 
were examined in this study: 11 from 
Southeast Alaska and 2 from Prince 
William Sound, Alaska. Although F ST 
values were low, a neighbor-joining 
tree based on genetic distance, homo- 
geneity, and F st values revealed that 
collectively, the Berners Bay and 
Lynn Canal (interior) collections 
were genetically distinct from Sitka 
Sound and Prince of Wales Island 
(outer-coastal) collections. Tempo- 
ral genetic variation within regions 
(among three years of Berners Bay 
spawners and between the two Sitka 
Sound spawners) was zero, whereas 
0.05% was attributable to genetic 
variation between Berners Bay and 
Sitka Sound. This divergence may be 
attributable to environmental differ- 
ences between interior archipelago 
waters and outer-coast habitats, 
such as differences in temperature 
and salinity. Early spring collections 
of nonspawning Lynn Canal herring 
were nearly genetically identical to 
collections of spawning herring in 
Berners Bay two months later — an 
indication that Berners Bay spawners 
over-winter in Lynn Canal. Southeast 
Alaskan herring (collectively) were 
significantly different from those in 
Prince William Sound. This study 
illustrates that adequate sample size 
is needed to detect variation in pelagic 
fish species with a large effective 
population size, and microsatellite 
markers may be useful in detecting 
low-level genetic divergence in Pacific 
herring in the Gulf of Alaska. 
Manuscript submitted 31 August 2010. 
Manuscript, accepted 22 June 2011. 
Fish. Bull. 109:382-393 (2011). 
The views and opinions expressed 
or implied in this article are those of the 
author (or authors) and do not necessarily 
reflect the position of the National Marine 
Fisheries Service, NOAA. 
Sharon L. Wildes (contact author) 
Johanna J. Vollenweider 
Defining the population structure of 
a species is fundamental for fishery 
management and resource conserva- 
tion. Sustainable management of com- 
mercially harvested stocks depends 
on a clear understanding of the extent 
of fish movements and migratory 
behavior, spawning-site fidelity, and 
degree of immigration and emigra- 
tion. One means to assess population 
structure is through genetic analysis. 
Armed with the knowledge of genetic 
stock structure, managers can use the 
appropriate spatial scale to under- 
stand life history, essential habitat, 
migration patterns, distribution, 
connectivity and isolation of stocks, 
recruitment, and spawning behav- 
ior. Understanding genetic diversity, 
which allows for adaptation to chang- 
ing environmental conditions, is vital 
information for conserving a species. 
Detecting genetic divergence within 
pelagic fish species, however, is often 
difficult because of large population 
sizes that retard genetic drift and 
gene flow among cohorts through dis- 
persal and migration (Shaklee and 
Bentzen 1998; Waples, 1998). Even 
small numbers of migrants or episodic 
straying events can lead to increased 
genetic connectivity among otherwise 
isolated stocks. Genetic divergence 
may occur if gene flow is interrupted 
by a single factor or combination of 
factors such as physical barriers, 
temporal variation (time of spawn- 
ing), and spawning-site and natal-site 
fidelity. 
A particularly large void of genetic 
information exists for forage fishes 
in the Gulf of Alaska. These species 
play a role of great consequence in 
marine ecosystems, as prey for most 
commercially important fish species. 
Without these nutritionally rich fish, 
many higher trophic level species 
might lack the resources to overwin- 
ter. Yet the amount of genetic infor- 
mation available for forage species 
is minimal at best. One example of 
a forage species is the Pacific her- 
ring (Clupea pallasii), which pro- 
vides a critical link between lower 
and higher trophic levels. Herring 
typically eat crustaceans and small 
fish, and serve as forage for whales, 
sea lions, birds, larger fish, (Bakun, 
2006; Hart, 1973; Hourston and Hae- 
gele, 1980), and humans. 
There are few genetic studies of 
Pacific herring in Alaska, particu- 
larly in regions that have experi- 
enced a recent decline in stocks, 
such as Prince William Sound in the 
central Gulf of Alaska (GOA), and 
Lynn Canal in southeast Alaska. 
Herring abundance in Lynn Canal 
has declined since the late 1970s and 
has not recovered to pre-1980 levels, 
despite the closure of the fishery in 
1981. One criterion for listing a stock 
