Application of molecular markers to mixed-stock analysis of Yukon River fall chum salmon

Abstract

Country of origin provides the basis for allocating harvests of Yukon River chum salmon. The genetic divergence among Yukon River chum salmon populations adjacent to the international border as revealed by allozyme and micro satellite variation is insufficient to determine the country of origin of returning fish using mixed-stock analysis (MSA). Consequently, we investigated the resolution provided by alternative genetic markers in an attempt to detect levels of divergence that would be sufficient for MSA. We analyzed 10 Yukon River chum salmon populations for variation at 30 variable amplified fragment length polymorphism (AFLP) loci and for mitochondrial DNA (mtDNA) restriction site variation. We assessed these markers for their utility in MSA and, for mtDNA, phylogeographic analysis. The AFLP results show that MSA was most successful when mixtures were allocated to regions. The AFLP data were able to provide improved country of origin MSA estimates for the border populations with a 6.5% improvement for the Canadian populations over micro satellite analysis. No divergence in mtDNA haplotype frequency distributions was detected (P>0.05) within the Yukon River. Lack of mtDNA divergence likely resulted from a Pleistocene bottleneck that led to panmixia of the mtDNA genome.