Van Doornik et al.: Stock-specific distribution of juvenile Oncorhynchus mykiss during early marine migration 
101 
Table 2 
Percentage of individuals correctly assigned to their stock of origin, determined by using leave-one-out simulations, for 7 ge¬ 
netic stock groups of steelhead f Oncorhynchus mykiss), ranging from the Central Valley of California to Puget Sound, Wash¬ 
ington. The genetic stock groups in the left column represent the groups from which fish originated, and the genetic stock 
groups in the column heads identify the genetic stock group to which fish were assigned by using genetic stock identification. 
Genetic stock group 
Puget Sound 
Strait of 
Juan de Fuca 
Washington 
coast 
Columbia 
River 
Oregon 
coast 
Northern 
California 
Klamath 
Mountains 
Province 
Central 
Valley, 
California 
Puget Sound/Strait of Juan de Fuca 
90.3% 
6.6% 
2.3% 
0.8% 
0.0% 
0.0% 
0.0% 
Washington coast 
8.1% 
84.1% 
6.4% 
1.3% 
0.0% 
0.0% 
0.0% 
Columbia River 
0.3% 
0.3% 
99.2% 
0.1% 
0.0% 
0.0% 
0.0% 
Oregon coast 
2.3% 
4.7% 
6.3% 
86.7% 
0.0% 
0.0% 
0.0% 
Northern California 
0.0% 
0.0% 
0.0% 
0.0% 
100.0% 
0.0% 
0.0% 
Klamath Mountains Province 
0.0% 
0.0% 
0.0% 
0.0% 
0.0% 
100.0% 
0.0% 
Central Valley, California 
0.0% 
0.0% 
0.0% 
0.0% 
0.0% 
0.0% 
100.0% 
Table 3 
Percentage of individuals correctly assigned to their stock of origin, determined by using leave-one-out simulations, for 4 
Columbia River genetic stock groups of steelhead (Oncorhynchus mykiss ). The genetic stock groups in the left column rep¬ 
resent the groups from which fish originated, and the genetic stock groups in the column heads identify which genetic stock 
groups fish were assigned to by using genetic stock identification. 
Middle and 
Lower Columbia 
Lower Columbia 
Upper Columbia 
Middle and 
River 
River 
River/Lower 
Upper 
Genetic stock group 
summer run 
winter run 
Snake River 
Snake River 
Lower Columbia River summer run 
89.2% 
10.8% 
0.0% 
0.0% 
Lower Columbia River winter run 
5.4% 
93.4% 
1.0% 
0.2% 
Middle and Upper Columbia River/Lower Snake River 
0.1% 
0.1% 
91.4% 
8.4% 
Middle and Upper Snake River 
0.0% 
0.0% 
7.6% 
92.4% 
required under the Endangered Species Act (Busby et 
al., 1996; NWFSC, 2015). The first-tier baseline, with 
131 loci from 148 coast-wide populations, had high 
self-assignments within each reporting group (Table 2). 
The overall within-group self-assignment average was 
94.1%. The least accurate group for this configuration 
was the Washington coast group, with an average of 
84.1%. The majority of the incorrect assignments for 
this group were made to the Columbia River group. 
The second-tier baseline, with 180 loci from 109 pop¬ 
ulations of the Columbia River, had an overall within- 
group self-assignment accuracy of 91.9% (Table 3). The 
least accurate group for this baseline was the Lower 
Columbia River summer-run group, with an average of 
89.2% and the majority of incorrect assignments made 
to the Lower Columbia River winter-run group. 
Of our ocean-caught samples, 34 fish had been 
tagged previously with coded-wire tags, which pro¬ 
vided identification of their hatchery of origin. These 
fish originated from 4 of our genetic stock groups and 
provided a further means to assess the accuracy of our 
baselines and genetic stock groups. Our GSI estimates 
agreed 100% with the stock origins indicated by the 
tags for those samples. 
Genetic stock identification 
During the surveys conducted in May, 490 steelhead 
were caught, with high variation in the number of fish 
caught among years (Table 4). The majority (68.8%) of 
the fish caught were marked, indicating that they had 
a hatchery origin. This proportion is an underestimate 
of the true proportion of fish with a hatchery origin 
in our sample, given that the marking rate of steel¬ 
head from hatcheries in the Columbia River was 83.2% 
during our sampling period (Regional Mark Processing 
Center, Regional Mark Information Database, available 
from website, accessed July 2017). Steelhead captured 
in the trawl hauls originated from 8 of the 10 genetic 
reporting groups, but the vast majority of them were 
from the Columbia River (78.3%). Only one steelhead 
was identified as having originated from any of the 3 
