Mixed stock and landscape genetics analyses of sockeye salmon in the Copper River, Alaska using SNPs

Genetic markers are increasingly used for ascertaining the population of origin of individuals or mixtures of individuals in Pacific salmon mixed stock fisheries. Multilocus genotype data from single nucleotide polymorphisms (SNPs) are especially useful for admixture analyses. SNPs can be discovered in non-model organisms with relative ease and may be characterized in coding regions of the genome influenced by selection. SNPs influenced by selection may show atypically high levels of differentiation among populations, and thus be particularly valuable for genetic stock identification if neutral loci show no differences between geographically proximate populations. We identified four SNP loci from a panel of 45 as candidates for diversifying selection in sockeye salmon from the Copper River and adjacent coastal drainages in southcentral Alaska. We evaluated the information content of these four 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 In for non-neutral loci was 0.064. A simulation-based approach indicated that the addition of non-neutral SNP loci to a neutral marker panel provided significantly higher resolution to assign individuals to population of origin than would have been accomplished by adding an equal number of neutral loci. SNP loci influenced by selection improved the ability to identify straying by individual fish and estimate the composition of Pacific salmon populations in mixed fisheries.