Pacific Rim Chinook salmon genetic stock identification baseline of SNP genotypes

Genetic stock identification (GSI) can be an effective tool for fisheries
management, but development of reference baselines can be challenging for
species with broad geographic distributions. Mixed stock fisheries of
Chinook salmon (Oncorhynchus tshawytscha) have utilized GSI analyses for
decades with various genetic baselines, but these have largely become
outdated with advances in technology that enable more efficient
genotyping. In this study, we compiled a large genetic baseline of single
nucleotide polymorphism (SNP) markers for 391 populations that encompass
the entire geographic range of Chinook salmon. Using cross validation
simulations, we demonstrated that a multi-tiered assignment approach can
provide high accuracy at both tier 1 (broad scale with three coastwide
reporting groups; 97.8% mean accuracy) and tier 2 (fine scale regional
reporting groups; up to 97.7% mean accuracy) levels. Realistic mixture
simulations showed that this multi-tiered approach can provide highly
effective GSI results for several common mixed stock fisheries
applications in the Pacific Ocean. This new SNP baseline and multi-tiered
assignment approach provides the most comprehensive GSI range-wide
baseline for Chinook salmon over any previous applications and enables
highly efficient genotyping solutions for these scenarios.