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Discussion 
Genetic structure was evident among herring 
populations in the eastern Gulf of Alaska. 
Collections from the fjord system of Berners 
Bay and Lynn Canal were significantly dif- 
ferentiated from the outer coast collections 
(Sitka Sound). The level of differentiation 
was surprising given the small geographical 
separation of approximately 235 km between 
the two areas and the higher genetic con- 
nectivity typical among marine pelagic spe- 
cies such as herring. Spawning fish from 
three years of collection in Berners Bay and 
overwintering fish from Lynn Canal con- 
sistently grouped together, indicating these 
fish may be overwintering in Lynn Canal 
and spawning in Berners Bay. Early spring 
collections in Lynn Canal in 2008 (Lynn08a 
and Lynn08b) were particularly homoge- 
neous with the spring spawning group in 
Berners Bay (Berners08). These three col- 
lections grouped together in the neighbor- 
joining tree and remained together more 
than 50% of the time in the consensus tree 
with both loci replacement and allele replace- 
ment bootstrapping methods. Hobart Bay, 
located several hundred km to the south of 
Berners Bay in the interior waters of South- 
east Alaska, was not genetically distinct from 
either the fjord group of Berners Bay and 
Lynn Canal or outer-coastal Sitka Sound, 
indicating that either there is more extensive 
gene flow between these regions — Hobart Bay 
is an interior water body but located along 
the main waterway that bisects southeast 
Alaska — or that the sample size of the single 
collection at Hobart Bay (n = 100) may not be 
large enough for detection of differentiation 
as statistical power decreases considerably if 
sample sizes are unbalanced (Goudet, 1996; 
Waples and Gaggiotti, 2006). Pacific herring 
from Hoonah Sound, however, were geneti- 
cally distinct from herring in Berners Bay 
and Lynn Canal interior collections. Herring 
from this region also had a unique fatty acid 
signature differing from those at all other 
locations tested in Southeast Alaska (Otis 1 ). 
Results of our genetic study tend to verify 
previous morphological, tagging, and genetic 
studies that have indicated reduced gene 
flow among regions within Southeast Alas- 
1 Otis, T., R. Heintz, and J. Maselko. 2010. Inves- 
tigation of Pacific herring (Clupea pallasii ) stock 
structure in Alaska using otolith microchemistry 
and heart tissue fatty acid composition. Final 
Rept. submitted to EVOS-TC (Exxon Valdez Oil 
Spill Trustee Council). [Available at http:// 
w w w/evostc. state, ak. us/Files. cfm?doc=/Store/ 
FinalReports/2007- 07769 -Final, pdf] 
