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tshawytscha) have utilized GSI analyses for decades with various genetic baselines, but these have largely become outdated with advances in technology that enable more efficient genotyping.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.

Methods
We assembled SNP data that was provided by the genetics laboratories of several different agencies. The data has been tested for its ability to perform genetic stock identification estimates.