112 
Abstract— Chinook Salmon ( Oncorhyn - 
chus tshawytsclia) is an economically 
and ecologically important species, 
and populations from the west coast 
of North America are a major compo- 
nent of fisheries in the North Pacific 
Ocean. The anadromous life history 
strategy of this species generates 
populations (or stocks) that typically 
are differentiated from neighboring 
populations. In many cases, it is de- 
sirable to discern the stock of origin 
of an individual fish or the stock com- 
position of a mixed sample to monitor 
the stock-specific effects of anthropo- 
genic impacts and alter management 
strategies accordingly. Genetic stock 
identification (GSI) provides such dis- 
crimination, and we describe here a 
novel GSI baseline composed of geno- 
types from more than 8000 individual 
fish from 69 distinct populations at 96 
single nucleotide polymorphism (SNP) 
loci. The populations included in this 
baseline represent the likely sources 
for more than 99% of the salmon en- 
countered in ocean fisheries of Cali- 
fornia and Oregon. This new genetic 
baseline permits GSI with the use of 
rapid and cost-effective SNP genotyp- 
ing, and power analyses indicate that 
it provides very accurate identifica- 
tion of important stocks of Chinook 
Salmon. In an ocean fishery sample, 
GST assignments of more than 1000 
fish, with our baseline, were highly 
concordant (98.95%) at the reporting 
unit level with information from the 
physical tags recovered from the same 
fish. This SNP baseline represents an 
important advance in the technologies 
available to managers and researchers 
of this species. 
Manuscript submitted 13 February 2013. 
Manuscript accepted 10 February 2014. 
Fish. Bull. 112:112-130 (2014). 
doi:10.7755/FB. 112.2-3.2 
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. 
Evaluation of a single nucleotide polymorphism 
baseline for genetic stock identification of 
Chinook Salmon ( Oncorhynchus tshawytscha ) in 
the California Current large marine ecosystem 
Anthony J. Clemento 
Eric D. Crandall 
John Carlos Garza 
Eric C. Anderson (contact author) 
Email address for contact author: eric.anderson@noaa.gov 
Fisheries Ecology Division 
Southwest Fisheries Science Center 
National Marine Fisheries Service, NOAA 
1 10 Shaffer Road 
Santa Cruz, California 95060 
Institute of Marine Sciences 
University of California, Santa Cruz 
1 10 Shaffer Road 
Santa Cruz, California 95060 
Chinook Salmon ( Oncorhynchus 
tshawytscha) are found in rivers 
from central California around the 
North Pacific Rim and the Bering 
Sea to Russia and are the target of 
valuable commercial and recreation- 
al fisheries. A key aspect of the life 
history of Chinook Salmon is natal 
homing, whereby each fish of this 
anadromous species typically returns 
to spawn in the same river in which 
it was born. This homing generates 
populations (or stocks) that may be 
genetically differentiated from neigh- 
boring populations and can exhibit 
local adaption (Utter et ah, 1989; 
Taylor, 1991). Recent population de- 
clines, particularly at the southern 
end of the native range of this spe- 
cies, have resulted in the listing of 
many stocks under the U.S. Endan- 
gered Species Act (ESA; Federal Reg- 
ister, 1990, 1999) and have highlight- 
ed the need to refine the manage- 
ment and conservation of Chinook 
Salmon. However, such refinements 
are challenging because the migra- 
tory life history of salmon means 
that the many effects from anthropo- 
genic sources that occur in rivers or 
in the ocean (e.g., fisheries, water di- 
version, or turbine entrainment) may 
affect multiple, intermingled stocks. 
In such cases, it may be necessary to 
discern the stock of origin of affected 
fish to monitor stock-specific impacts 
and design management strategies 
accordingly. 
The use of pre-existing biological 
markers to distinguish salmon stocks 
has a long history. The traits used 
in these efforts have included mor- 
phometric and meristic characters 
(Fournier et ah, 1984; Claytor and 
MacCrimmon, 1988), scale patterns 
(Cook, 1982), parasite assemblages 
(Boyce et al., 1985), and stable iso- 
tope ratios (Barnett-Johnson et ah, 
2008). However, the most universally 
applicable methods have involved the 
use of genetic markers because every 
fish has a unique genetic makeup. 
The first genetic markers widely 
used for identification in salmon 
were electrophoretically detectable 
protein polymorphisms known as al- 
lozymes (Milner et ah, 1985; Shak- 
lee and Phelps, 1990; Tessier et ah, 
1995; Allendorf and Seeb, 2000). 
With the advent of polymerase chain 
reaction (PCR), many more types of 
genetic markers became available to 
