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Fishery Bulletin 103(3) 



senior author). We identified these types as Sebastes 

 aleutianus and Sebastes sp. cf. aleutianus (a species that 

 has putatively not been described but is similar to S. 

 aleutianus). The S. aleutianus type is characterized by 

 individuals with genomes of predominately ACP *100; 

 IDDH*100, and *500; MP/*129; PGM-2*100, *83, *91, 

 and *117; and XO*100. The Sebastes sp. cf. aleutianus 

 type is characterized by individuals with genomes of 

 predominately ACPM6; IDDH*500 and *750; MPI *100; 

 PGM-2 *83, *74, and *63; and XO* 109. We used 25 

 loci to perform multidimensional scaling analysis of 

 individual rougheye genotypes to illustrate separation 

 of the two types. 



We chose STRUCTURE, a Bayesian clustering model 

 (Pritchard et al., 2000) to gain greater statistical rigor 

 in identifying individual types and possible hybrids of 

 rougheye rockfish. This model seeks to identify popula- 

 tions in a mixture without the availability of baseline 

 samples from the separate populations. The proportions 

 of each individual's genome belonging to the population 

 identified by the model and the separate population al- 

 lele frequencies are simultaneously estimated. A 907c 

 probability interval is computed for each individual's 

 inferred genome source proportions. For this analysis, 

 we used 25 loci, 100,000 iterations, and a 10,000 burn- 

 in period. This model assumes that loci are in Hardy- 



