Clemento et al.: Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Oncorhynchus tshawytscha 119 
Table 2 
List of the 96 single nucleotide polymorphism (SNP) loci used to construct the baseline for genetic stock identification of 
Chinook Salmon ( Oncorhynchus tshawytscha ) from the west coast of North America, with dbSNP accession numbers (from 
the National Center for Biotechnology Information online repository for short genetic variations; https://www.ncbi.nlm.nih. 
gov/snp) and source reference (Sr) where available: l=Clemento et al., 2011; 2=Smith et al., 2005a; 3=Campbell and Narum, 
2008; 4=Smith et al., 2005b. 
Locus 
dbSNP 
Sr 
Locus 
dbSNP 
Sr 
Locus 
dbSNP 
Sr 
Ots_94857-232 
ss2755 18685 
1 
Ots_l 10495-380 
ss275518741 
1 
Ots_131906-141 
ss275518787 
1 
Ots_96222-525 
ss275518688 
1 
Ots_110551-64 
ss275518742 
1 
Ots_AldBl-122 
ss275518788 
1 
0ts_96500-180 
ss2755 18689 
1 
OkiOts_120255-113 
unpubl. 
- 
Ots_AldoB4-183 
ss275518789 
1 
Ots^97077-179 
ss275518691 
1 
Ots_l 11.312-435 
ss275518746 
1 
Ots Myc-366 
ss275518795 
1 
Ots_99550-204 
ss275518695 
1 
Ots_l 11666-408 
ss275518747 
1 
Ots_ALDBINTl-SNPl 
ss275518796 
1 
Ots 100884-287 
ss275518696 
1 
Ots„l 11681-657 
ss275518748 
1 
Ots_NAML12-SNPl 
ss275518798 
1 
Ots_101119-381 
ss275518697 
1 
Ots_112208-722 
ss275518749 
1 
Ots_ ARNT-195 
unpubl. 
- 
Ots_101704-143 
ss275518699 
1 
Ots_112301-43 
ss275518750 
1 
Ots_RAG3 
unpubl. 
- 
Ots_102213-210 
ss275518702 
1 
Ots_l 12419-131 
ss275518751 
1 
Ots_AsnRS-60 
ss48398657 
2 
Ots_102414-395 
ss275518703 
1 
Ots_l 12820-284 
ss275518752 
1 
Ots_aspat-196 
ss65917744 
3 
Ots_102420-494 
ss275518704 
1 
Ots_l 12876-371 
ss275518753 
1 
Ots_CD59-2 
unpubl 
- 
Ots_102457-132 
ss275518705 
1 
Ots_l 13242-216 
ss275518754 
1 
Ots_CD63 
unpubl. 
- 
0ts._102801-308 
ss275518706 
1 
Ots_113457-40 
ss275518755 
1 
Ots_EP-529 
unpubl. 
- 
Ots. 102867-609 
ss275518707 
1 
Ots_l 17043-255 
ss275518757 
1 
Ots_GDH-81x 
ss65917741 
3 
Ots. 103041-52 
ss275518708 
1 
OtsH 17242-136 
ss275518759 
1 
Ots„HSP90B-385 
ss65713207 
2 
OtsJ 04063-132 
ss275518711 
1 
Ots_l 17432-409 
ss275518762 
1 
Ots_MHCl 
ss49851328 
4 
Ots 104569-86 
ss275518714 
1 
Ots_l 18175-479 
ss275518763 
1 
Ots_mybp-85 
unpubl 
- 
Ots_105105-613 
ss275518715 
1 
Ots_ 118205-61 
ss275518764 
1 
Ots_myoD-364 
ss65917726 
3 
Ots^ 105132-200 
ss275518716 
1 
Ots_118938-325 
ss275518765 
1 
Ots_Ots311-101x 
ss65917748 
3 
Ots_105401-325 
ss275518718 
1 
Ots.l 22414-56 
ss275518767 
1 
Ots_PGK-54 
unpubl. 
- 
Ots_105407-117 
ss275518719 
1 
Ots_123048-521 
ss275518768 
1 
Ots_Prl2 
ss49851322 
4 
Ots_106499-70 
ss275518724 
1 
Ots_123921-lll 
ss275518770 
1 
Ots_.RFC2-558 
ss48398670 
2 
Ots_106747-239 
ss275518725 
1 
Ots_124774-477 
ss275518771 
1 
Ots_SClkF2R2-135 
ss48398694 
2 
Ots_107074-284 
ss275518726 
1 
Ots„127236-62 
ss275518773 
1 
Ots_SWSlop-182 
ss48398635 
2 
Ots_107285-93 
ss275518728 
1 
Ots„128302-57 
ss275518775 
1 
Ots_TAPBP 
unpubl. 
- 
Ots_107806-821 
ss275518730 
1 
Ots_128693-461 
ss275518777 
1 
Ots_u07-07.161 
unpubl. 
- 
0ts_108007-208 
ss275518731 
1 
Ots_128757-61 
ss275518778 
1 
Ots_u07-49.290 
unpubl. 
- 
Ots_108390-329 
ss275518732 
1 
Ots_129144-472 
ss275518779 
1 
Ots_u4-92 
ss48398636 
2 
Ots_108735-302 
ss275518733 
1 
Ots_129170-683 
ss275518780 
1 
Ots_BMP2-SNPl 
ss275518800 
1 
Ots_109693-392 
ss275518737 
1 
Ots_129458-451 
ss275518782 
1 
Ots_TFl-SNPl 
ss275518802 
1 
Ots_l 10064-383 
ss275518738 
1 
Ots_130720-99 
ss275518784 
1 
Ots_S71-336 
unpubl. 
- 
Ots_l 10201-363 
ss275518739 
1 
Ots_131460-584 
ss275518785 
1 
Ots_unk_526 
unpubl. 
abilities, employing a leave-one-out procedure that ex- 
cludes the gene copies of the individual being assigned 
and recalculates population allele frequencies before 
assignment. Analogous to the THL procedure of An- 
derson (2010), both the training and holdout sets were 
included for estimation of population allele frequencies. 
However, assignments of individuals in the training set 
were excluded from the results to avoid any high-grad- 
ing bias of assignment accuracy (Anderson, 2010). 
Analysis of simulated mixed fisheries is a common 
method for evaluation of the resolving power of a base- 
line for stock identification (Fournier et al., 1984; Wood 
et al., 1987; Kalinowski, 2004; Beacham et al., 2006). 
In many studies, samples from simulated fisheries that 
consist entirely of fish from one population are ana- 
lyzed in so called “100% simulations.” However, such 
simulations typically do not assess how well the base- 
line will perform on samples from fisheries that exploit 
more than one stock. Therefore, we conducted simula- 
tions with 20 different mixing proportion vectors. The 
population composition of these mixtures was deter- 
mined by using the baseline to estimate the relative 
proportions of reporting units present in 20 different 
month-by-area strata sampled from commercial fisher- 
ies off the coast of California and Oregon in 2010 and 
2011 (E. Crandall et al., unpubl. data). 
These vectors reflect mixing proportions that are 
expected to be encountered in PFMC fisheries. For a 
given value of the mixing proportion vector of all pop- 
ulations, a replicate simulation consisted of 1) simu- 
lating the number of fish from each population in a 
sample size of 200 by drawing a multinomial ran- 
dom variable with cell probabilities equal to the mix- 
ing proportion vector; 2) simulating the genotypes of 
