Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of Chinook salmon in the Columbia River Basin

Genetic stock identification (GSI) is an important tool in fisheries management. Microsatellites (µSATs) have been the dominant genetic marker for GSI, however increasing availability and numerous advantages of single nucleotide polymorphism (SNP) markers make them an appealing alternative. We tested performance of 13 µSAT versus 92 SNP loci in a fine-scale application of GSI, using a new baseline for Chinook salmon consisting of 49 collections (n=4014) distributed across the Columbia River Basin. In GSI, baseline genotypes for both marker sets were used independently to analyze a real fishery mixture (n=2731) representing the total run of Chinook salmon passing Bonneville Dam in the Columbia River. Marker sets were evaluated using three criteria: 1) ability to differentiate reporting groups, 2) proportion of correct assignment in mixture simulation tests and baseline leave-one-out analyses, and 3) individual assignment and confidence intervals around estimated stock proportions of...