Single-Nucleotide Polymorphisms (SNPs) under Diversifying Selection Provide Increased Accuracy and Precision in Mixed-Stock Analyses of Sockeye Salmon from the Copper River, Alaska

Genetic markers are increasingly being used to ascertain the population of origin of individuals or mixtures of individuals in complex aggregations of Pacific salmon Oncorhynchus spp. Multilocus genotype data from single-nucleotide polymorphisms (SNPs) are especially useful for admixture analyses. Single-nucleotide polymorphisms can be discovered in nonmodel organisms with relative ease and can be characterized in the coding and regulatory regions of the genome influenced by selection. Those influenced by diversifying selection may show atypically high levels of differentiation among populations and thus be particularly valuable for genetic stock identification in cases where neutral loci show little difference among populations of interest. We identified four SNP loci from a panel of 42 as candidates for diversifying selection (referred to here as nonneutral SNPs) in sockeye salmon O. nerka from the Copper River and adjacent coastal drainages in south-central Alaska. We evaluated the information content of the four nonneutral loci for use in genetic stock identification and assessed their ability to improve the accuracy and precision of composition estimates. The average measure of informativeness for assignment (In) for neutral loci was 0.019, and the average I-n for nonneutral loci was 0.064. A simulation-based approach indicated that the addition of the nonneutral SNP loci to a neutral marker panel provided significantly higher resolution in the assignment of individuals to their populations of origin than would have been accomplished by adding an equal number of neutral loci. Nonneutral SNP loci improved the ability to identify the origin of individual fish and to estimate the composition of Pacific salmon populations in mixed fisheries.