124 
Fishery Bulletin 112(2-3) 
Table 3 
Genetic stock identification (GSI) results from assignment of samples of Chinook Salmon ( Oncorhyn - 
chus tshawytscha) collected in 2010 from the California fishery to their source populations through 
the use of a single nucleotide polymorphism baseline, as well as concordance with recoveries of coded 
wire tags (CWTs). N.=North; S.=South. 
Stock 
Number 
from GSI 
Number 
with CWT 
Number of 
GSI-CWT 
matches 
GSI-CWT 
agreement (%) 
California Coast 
30 
1 
0 
0.00% 
Central Valley fall 
1581 
958 
957 
99.90% 
Central Valley spring 
7 
1 
0 
0.00% 
Klamath River 
108 
50 
49 
98.00% 
Lower Columbia spring 
1 
0 
0 
- 
Mid Columbia Tule fall 
7 
2 
2 
100.00% 
Mid Oregon Coast 
14 
1 
0 
0.00% 
N. California/S. Oregon Coast 
58 
25 
25 
100.00% 
Rogue River 
154 
11 
5 
45.45% 
Snake River fall 
1 
1 
1 
100.00% 
Upper Columbia summer/fall 
8 
2 
2 
100.00% 
Total 
1969 
1052 
1041 
98.95% 
tile intervals observed for the Central Valley spring- 
run reporting unit were likely due to its similarity to 
the Central Valley fall-run reporting unit, combined 
with the fact that the spring run is typically at much 
lower abundance than is the fall run. Likewise, the 
genetic similarity of fish from the Mid Oregon Coast 
reporting unit and the Northern California/Southern 
Oregon Coast reporting unit made it difficult to ac- 
curately estimate mixing proportions for these report- 
ing units; however, the estimates were still quite good 
and largely unbiased. Therefore, despite the enlarged 
quantile intervals for Central Valley spring-run and 
the Mid Oregon Coast reporting units versus Northern 
California-Southern Oregon reporting unit, the results 
from both simulation methods indicated that the SNP 
baseline is capable of providing estimates of the true 
mixing proportions for most reporting units that are 
nearly as accurate as one would expect given perfect 
identification of each fish. 
Fishery samples 
Of the 2090 samples collected from California fisher- 
ies in 2010, 85 samples were excluded because they 
did not yield acceptable genotypes (<60 successfully 
genotyped loci) and 2 samples were excluded because 
they were duplicates of 2 other samples in the data 
set. Eight fish exceeded the iHz threshold of 0.56 and 
were removed because of potential contamination. Sev- 
en fish were identified as Coho Salmon through both 
GSI assignment and with the species-diagnostic assay. 
Another 18 samples did not meet assignment confi- 
dence criteria (mean 2 -score of -3.99 and a mean of 
75 successfully genotyped loci) and were also excluded. 
For the remaining 1969 fish, assignment probabilities 
to reporting unit ranged from 36.4% to 100% (mean 
98.5%) and z-scores ranged from -4.12 to 2.68 (mean 
-0.04). Centra] Valley fall-run fish dominated the stock 
composition, accounting for more than 80% of sampled 
fish, followed by the Rogue River (7.79%) and Klam- 
ath River (5.46%) reporting units and 8 other stocks 
with <5% (Table 3). Of the assigned fish, 1052 retained 
CWTs that were recovered. Genetic assignment to re- 
porting unit disagreed with CWT origin for only 11 fish 
(1.05%), and, of these mismatches, 6 were fish with 
Klamath or Smith River tags that were assigned to the 
genetically similar Rogue River reporting unit. 
Discussion 
Here we describe one of the first large-scale SNP base- 
lines for genetic stock identification of Chinook Salmon 
and the first designed for use with fisheries in the Cali- 
fornia Current large marine ecosystem off the contigu- 
ous United States. Chinook Salmon are an economi- 
cally and ecologically important species and are a ma- 
jor component of fisheries in the North Pacific Ocean. 
We genotyped more than 8000 individual fish from 69 
distinct populations at 96 SNP loci to construct the 
baseline. The reporting units included in the baseline 
represent the likely sources for more than 99% of the 
fish typically encountered in PFMC fisheries off Cali- 
fornia and Oregon. 
Furthermore, results from mixture analyses and 
self-assignment indicate that the baseline has near 
maximum possible power for discrimination of Chinook 
Salmon stocks at the reporting unit level. Estimates of 
