Evolution of Mitochondrial DNA Variation within and among Yukon River Chum Salmon Populations

Abstract

AbstractWe surveyed seven regions of the mitochondrial DNA (mtDNA) genome for restriction site variation to investigate the evolution of genetic variability in chum salmon Oncorhynchus keta from the Yukon River. Chum salmon from other Alaska regions were also analyzed to provide context for mtDNA variation. No divergence was observed in mtDNA haplotype frequency distributions among Yukon River populations, but divergence was observed across Alaska. The haplotype genealogy identified two lineages, and nested clade analysis revealed significant relationships between the geographical distribution of haplotypes and their genealogy for a two‐step clade (which predominates in the Yukon River), a three‐step clade, and for the total cladogram. The demographic signal detected for the two‐step clade was consistent with isolation by distance, whereas contiguous range expansion was identified for the three‐step clade and the total cladogram. The absence of signals of historical fragmentation suggests that incomplete lineage sorting is responsible for paraphyly within the Yukon River. Mismatch analysis reveals either that an ancestral Yukon River population underwent a post‐Pleistocene expansion followed by subdivision or that expansion and subdivision coincided. Although restriction site analysis of mtDNA is of limited use for Yukon River chum salmon fishery management applications (e.g., mixed‐stock analysis), it is useful for separating population history from contemporary processes and aids our understanding of Yukon River chum salmon evolution.