Single nucleotide polymorphisms provide rapid and accurate estimates of the proportions of US and Canadian Chinook salmon caught in Yukon River fisheries

As anadromous Chinook salmon Oncorhynchus tshawytscha bound for U.S. and Canadian spawning grounds migrate through the U.S. portion of the Yukon River, they are targeted by several fisheries. To fulfill treaty obligations between the two countries, fishery managers need to know what portion of fish caught in the United States are of Canadian origin. Allozyme markers have been used to assign individuals in mixed fishery samples to U.S. and Canadian portions of the Yukon River; however, these markers are limited by sampling difficulties and by the number of available loci. Microsatellite DNA markers have been considered as an alternative; however, microsatellite data are not readily transportable among laboratories or countries. Here we present the use of single nucleotide polymorphism (SNP) markers that combine the ease of sampling and large potential number of loci of other DNA markers with universally transportable data. Simulations and analyses of known fish suggest that the SNP baseline can be used to assign fish to country of origin with more than 95% accuracy. Assignments based on SNP data are largely concordant with those based on allozyme data. The SNP baseline described here may be used to provide rapid and accurate estimates of the proportions of U.S. and Canadian Chinook salmon caught in Yukon River fisheries.