Managing mixed-stock fisheries: genotyping multi-SNP haplotypes increases power for genetic stock identification

Assignment methods that use genetic data to allocate migrating fish to population of origin are a powerful tool to help manage the harvest of mixed-stock fisheries. A common challenge for fishery applications is resolving the relative contribution of closely related populations where assignment accuracy may be limited. An overlooked method for increasing assignment accuracy is the use of multi-SNP haplotypes rather than single-SNP genotypes. Haplotypes increase power for detecting population structure, and loci derived from next-generation sequencing methods often contain multiple SNPs. We evaluated the utility of multi-SNP haplotyping for mixture analysis in Western Alaska Chinook salmon. Multi-SNP haplotype data increased the accuracy of mixture analysis for closely related populations by up to seven percentage points relative to single-SNP genotype data for a set of 500 loci; 90% accuracy was achievable with as few as 150 loci with multi-SNP haplotypes but required at least 300 loci with single-SNP genotypes. Individual assignment to reporting groups showed an even greater increase in accuracy of up to 17 percentage points when multi-SNP haplotypes were used. Haplotyping multiple SNPs shows promise to improve the accuracy of assigning unknown fish to population of origin whenever haplotype data are available.

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