Clemento et al.: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Oncorhynchus tshawytscha 121 
Significant deviations from HWE (P<0.0001) were ob- 
served at various loci in 17 populations but represented 
<0.3% of all observations. Only the Butte Creek spring- 
run, Trinity River Hatchery spring-run, and Smith Riv- 
er populations were not in HWE at more than 2 loci, 
with 5, 5, and 4 significant tests, respectively. Similarly, 
only 3 loci deviated from HWE in more than 2 popu- 
lations: Ots_u07_07.161 in 3 populations, Ots_111312- 
435 in 6 populations, and Ots_111666-408 in 4 popula- 
tions. Only 1 population (Trinity River Hatchery spring 
run) displayed significant LD (P<0.001) at more than 
1% of locus comparisons (1.14%), and, over all popu- 
lations, the percentage of significant comparisons was 
0.16%. Only 2 locus pairs were significant in more than 
5 populations: Ots_AldBl-122 and Ots_AldoB4-183, 
known to be in the same gene complex, were in LD 
in 42 populations, and Ots_Myc-366 and Ots_unk-526 
displayed LD in 8 populations. 
A large range in the degree of differentiation be- 
tween populations was observed (Table 1). Mean F st 
across all populations (excluding Coho Salmon) was 
0.183, indicating that approximately 18% of genetic 
variation was partitioned between population samples. 
Within reporting units that contained more than one 
population (N=18), pairwise Fst was between 0.000 
and 0.152 and had a mean value of 0.018. Ten pair- 
wise comparisons, all within reporting units, were not 
significantly different from zero (P<0.01). Between re- 
porting units, Fgj values ranged from 0.005 to 0.411 
and had a mean value of 0.188. The least differentiated 
populations were the fall-run populations from Califor- 
nia’s Central Valley, as has been observed with other 
genetic data sets (Williamson and May, 2005; Seeb et 
ah, 2007). 
Genetic structure of the Chinook Salmon popula- 
tions in the baseline is displayed in an unrooted neigh- 
bor-joining dendrogram (Fig. 1). Relationships are in 
strong agreement with expectations that were based 
on geography and previous studies (Waples et al., 2004; 
Beacham et ah, 2006; Templin et ah, 2011; Moran et 
ah, 2013); populations generally are organized north 
to south along the main branch, and populations from 
within the same drainage usually cluster together. 
Populations from California’s Central Valley are 
monophyletic in relation to the remainder of the popu- 
lations but are characterized by short branch lengths, 
small distances between nodes, and low bootstrap sup- 
port. Central Valley spring-run and fall-run popula- 
tions also are monophyletic, with the exception of the 
Feather River Hatchery spring run, which is included 
in the fall-run reporting unit because of a history of 
substantial mtrogression between the runs and the 
consequent difficulty of genetically distinguishing this 
stock from fall-run fish (Garza et al. 8 ). Sacramento 
Garza, J. C., S. M. Blankenship, C. Lemaire, and G. Char- 
rier. 2008. Genetic population structure of Chinook Salm- 
on ( Oncorhynchus tshawytscha) in California's Central Val- 
ley. Final report for CalFed project “Comprehensive evalua- 
tion of population structure and diversity for Central Valley 
River winter-run fish are quite distinct as a result of 
a well-documented recent bottleneck (Hedrick et al., 
1995) and have one of the longest branches on the 
tree, with bootstrap support of 100%. Fish from rivers 
in northern California and coastal Oregon also form 
a monophyletic group. Columbia River populations are 
dispersed throughout the tree, although populations 
from the same reporting unit generally share a com- 
mon branch, as do populations from Alaska. 
Accuracy of assignment and mixture estimations 
The 7669 individuals that remained after removal of 
training-set fish were subjected to self-assignment 
with gsi_sim (Table 1). Correct assignment to popu- 
lation ranged from 13% for the Butte Creek fall-run 
population to 100% for 5 different populations. The 
following reporting units had the lowest correct as- 
signment rates to population: Central Valley fall run, 
Upper Columbia River summer/fall run, and Western 
Alaska, Lower Kuskokwim River, averaging 28%, 36%, 
and 40%, respectively. The lowest rate of correct as- 
signment to reporting unit was for the Siuslaw River 
population from the Mid Oregon Coast reporting unit, 
with over half of the individuals assigning to popula- 
tions in the North Oregon coast reporting unit. The 
largest change in correct assignment percentage from 
population to reporting unit was for the Central Valley 
fall run, which increased to 91%. 
The results of the mixture simulations for the 9 re- 
porting units most frequently found in California and 
Oregon fisheries appear in Figure 2. Results for the 
remaining reporting units are not shown because they 
are relatively uninformative as a result of the rar- 
ity with which populations from north of the Colum- 
bia River are encountered at the southern end of the 
California Current marine ecosystem, an observation 
corroborated by historical CWT data: in the 3 decades 
since 1983, only 0.5% of all CWTs recovered from 
Chinook Salmon in California ocean fisheries were 
from stocks outside of California or Oregon (Regional 
Mark Information System, Regional Mark Process- 
ing Center, http://www.rmpc.org). Accurate estimates 
of the mixing proportions were obtained for fishery 
samples simulated either by CV-GC or by K-fold. The 
mean maximum likelihood estimate of the proportion 
of each reporting unit was generally highly correlated 
with the true proportion, indicating that any bias was 
very small. 
For 6 reporting units (Central Valley fall run, Sac- 
ramento River winter run, Klamath River, California 
Coast, Rogue River, and North Oregon Coast), the 5% 
and 95% quantiles for reporting-unit mixing propor- 
tions corresponded closely with the quantiles one would 
obtain with perfect identification of all fish (see the 
gray regions in Fig. 2). The somewhat wider GSI quan- 
Salmon,” 54 p. [Available from http://swfsc.noaa.gov/publia- 
tions/FED/OlllO.pdf.J 
