Evaluation of a single nucleotide polymorphism baseline for genetic stock identification of Chinook salmon (Oncorhynchus tshawytscha) in the California current large marine ecosystem

Abstract

Chinook Salmon (Oncorhyn- chus tshawytscha) is an economically and ecologically important species, and populations from the west coast of North America are a major compo-nent of fisheries in the North Pacific Ocean. The anadromous life history strategy of this species generates populations (or stocks) that typically are differentiated from neighboring populations. In many cases, it is de-sirable to discern the stock of origin of an individual fish or the stock com- position of a mixed sample to monitor the stock-specific effects of anthropo-genic impacts and alter management strategies accordingly. Genetic stock identification (GSI) provides such dis-crimination, and we describe here a novel GSI baseline composed of geno-types from more than 8000 individual fish from 69 distinct populations at 96 single nucleotide polymorphism (SNP) loci. The populations included in this baseline represent the likely sources for more than 99% of the salmon en- countered in ocean fisheries of Cali-fornia and Oregon. This new genetic baseline permits GSI with the use of rapid and cost-effective SNP genotyp-ing, and power analyses indicate that it provides very accurate identifica-tion of important stocks of Chinook Salmon. In an ocean fishery sample, GSI assignments of more than 1000 fish, with our baseline, were highly concordant (98.95%) at the reporting unit level with information from the physical tags recovered from the same fish. This SNP baseline represents an important advance in the technologies available to managers and researchers of this species.