128 
Fishery Bulletin 112(2-3) 
a hatchery population of steelhead ( Oncorhynchus 
mykiss). Mol. Ecol. 22:4733-4746. 
Aguilar, A., and J. C. Garza. 
2008. Isolation of 15 single nucleotide polymorphisms 
from coastal steelhead, Oncorhynchus mykiss (Salmoni- 
dae). Mol. Ecol. Resour. 8:659-662. 
Allendorf, F., and L. W. Seeb. 
2000. Concordance of genetic divergence among sockeye 
salmon populations at allozyme, nuclear DNA, and mi- 
tochondrial DNA markers. Evolution 54:640-51. 
Anderson, E. C. 
2010. Assessing the power of informative subsets of loci 
for population assignment: standard methods are up- 
wardly biased. Mol. Ecol. Resour. 10:701-710. 
2012. Large-scale parentage inference with SNPs: an ef- 
ficient algorithm for statistical confidence of parent pair 
allocations. Stat. Appl. Genet. Mol. Biol. 11:12. doi: 
10.1515/1544-6115.1833 
Anderson, E. C., and J. C. Garza. 
2006. The power of single-nucleotide polymorphisms 
for large-scale parentage inference. Genetics 
172:2567-2582. 
Anderson, E. C., R. S. Waples, and S. T. Kalinowski. 
2008. An improved method for predicting the accuracy 
of genetic stock identification. Can. J. Fish. Aquat. Sci. 
65:1475-1486. 
Banks, M. A., V. K. Rashbrook, M. Calavetta, C. Dean, and D. 
Hedgecock. 
2000. Analysis of microsatellite DNA resolves genetic 
structure and diversity of Chinook salmon ( Oncorhyn- 
chus tshawytscha) in California’s Central Valley. Can. 
J. Fish. Aquat. Sci. 57:915-927. 
Barnett-Johnson, R., T. E. Pearson, F. C. Ramos, C. Grimes, 
and R. B. MacFarlane. 
2008. Tracking natal origins of salmon using isotopes, 
otoliths, and landscape geology. Limnol. Oceanogr. 
53:1633-1642. 
Beacham, T. D., R. E. Withler, and T. Stevens. 
1996. Stock identification of chinook salmon ( Oncorhyn- 
chus tshawytscha) using minisatellite DNA varia- 
tion. Can. J. Fish. Aquat. Sci. 53:380-394. 
Beacham, T. D., J. R. Candy, K. L. -Jonsen, -J. Supernault, 
M. Wetklo, L. Deng, K. M. Miller, R. E. Withler, and N. 
Varnavskaya. 
2006. Estimation of stock composition and individual 
identification of Chinook salmon across the Pacific Rim 
by use of microsatellite variation. Trans. Am. Fish. 
Soc. 135:861-888. 
Beacham, T. D., I. Winther, K. L. Jonsen, M. Wetklo, L. Deng, 
and J. R. Candy. 
2008. The application of rapid microsatellite-based stock 
identification to management of a Chinook Salmon troll 
fishery off the Queen Charlotte Islands, British Colum- 
bia. N. Am. J. Fish. Manage. 28:849-855. 
Bernatchez, L., and P. Duchesne. 
2000. Individual-based genotype analysis in studies of 
parentage and population assignment: how many loci, 
how many alleles? Can. J. Fish. Aquat. Sci. 57:1-12. 
Boyce, N. P., Z. Kabata, and L. Margolis. 
1985. Investigations of the distribution, detection, and 
biology of Henneguya salminicola (Protozoa, Myxozoa), 
a parasite of the flesh of Pacific salmon. Can. Tech. 
Rep. Fish. Aquat. Sci. 1405, 55 p. 
Buckland-Nicks, J. A., M. Gillis, and T. E. Reimchen. 
2012. Neural network detected in a presumed vestigial 
trait: ultrastructure of the salmonid adipose fin. Proc. 
R. Soc. Lond., Ser. B: Biol. Sci. 279:553-563 
Campbell, N., and S. R. Narum. 
2008. Identification of novel single-nucleotide polymor- 
phisms in Chinook salmon and variation among life his- 
tory types. Trans. Am. Fish. Soc. 137:96-106. 
Cavalli-Sforza, L. L., and A. W. F. Edwards. 
1967. Phylogenetic analysis: models and estimation pro- 
cedures. Am. J. Hum. Genet. 19:233-257. 
Claytor, R., and H. MacCrimmon. 
1988. Morphometric and meristic variability among 
North American Atlantic salmon (Salmo salar). Can. 
J. Zool. 66:310-317. 
Clemento, A. J., A. Abadia-Cardoso, H. A. Starks, and J. C. 
Garza. 
2011. Discovery and characterization of single nucleo- 
tide polymorphisms in Chinook salmon, Oncorhynchus 
tshawytscha . Mol. Ecol. Resour. 11 (suppl. sl):50-66. 
Cook, R. C. 
1982. Stock identification of sockeye salmon ( Oncorhyn- 
chus nerka ) with scale pattern recognition. Can. J. 
Fish. Aquat. Sci. 39:611-617. 
Cornuet, J., S. Piry, G. Luikart, A. Estoup, and M. Solignac. 
1999. New methods employing multilocus genotypes to 
select or exclude populations as origins of individuals. 
Genetics 153:1989-2000. 
Cronin, M. A., W. J. Spearman, and R. L. Wilmot. 
1993. Mitochondrial DNA variation in Chinook ( On- 
corhynchus tshawytscha ) and chum salmon (O. keta ) 
detected by restriction enzyme analysis of polymerase 
chain reaction (PCR) products. Can. J. Fish. Aquat. 
Sci. 50:708-715. 
Elliott, D. G., and R. J. Pascho. 
2001. Evidence that coded-wire-tagging procedures can 
enhance transmission of Renibacterium salmoninarum 
in Chinook salmon. J. Aquat. Anim. Health 13:181-193. 
Federal Register. 
1990. Endangered and threatened wildlife and plants; 
listing of the Sacramento River winter-run Chinook 
salmon as threatened. Vol. 55(231):4962. GPO, Wash- 
ington, DC. 
1999. Endangered and threatened species; threatened 
status for three Chinook Salmon Evolutionarily Signifi- 
cant Units (ESUs) in Washington and Oregon, and en- 
dangered status for one Chinook Salmon ESU in Wash- 
ington. Vol. 64(56):14308-14328. GPO, Washington, 
DC. 
Fisher, F. W. 
1994. Past and present status of Central Valley Chinook 
salmon. Conserv. Biol. 8:870-873. 
Flannery, B. G., J. K. Wenburg, and A. J. Gharrett. 
2007. Variation of amplified fragment length polymor- 
phisms in Yukon River chum salmon: population struc- 
ture and application to mixed-stock analysis. Trans. 
Am. Fish. Soc. 136:911-925. 
Fournier, D. A., T. D. Beacham, B. E. Riddell, and C. A. Busack. 
1984. Estimating stock composition in mixed stock fish- 
eries using morphometric, meristic, and electrophoretic 
characteristics. Can. J. Fish. Aquat. Sci. 41:400-408. 
Habicht, C., S. Sharr, D. Evans, and J. E. Seeb. 
1998. Coded wire tag placement affects homing ability of 
pink salmon. Trans. Am. Fish. Soc. 127:652-657. 
