Phylogeographic analysis of mitochondrial DNA variation in Alaskan coho salmon, Oncorhynchus kisutch

Mitochondrial DNA (mtDNA) haplotypes of coho salmon (Oncorhynchus kisutch) sampled from northern Pacific Ocean and Bering Sea drainages formed two mon ophyletic clades between which nucleotide divergences averaged 2.95 substit utions per 1000 nucleotides. These data were obtained from restriction endo nuclease digestions of PCR products that included over 97% of the mtDNA gen ome and resolved 16 different haplotypes in 258 fish from 13 locations. Com parisons. of haplotype compositions of populations indicated that the Berin g Sea drainages and one Kodiak Island population clustered separately from nine other Gulf of Alaska populations, including one from Asia. Rates of ge ne flow among populations estimated from haplotype frequencies (assuming an equilibrium between gene flow and random drift) were low (about one female per generation between drainages within regions) in relation to allozyme-b ased estimates of gene flow for other Pacific salmon species. Much of the h aplotype frequency variation was within-region variation. Haplotypes from b oth clades occur in many extant populations, suggesting that gene flow, pop ulation movements, or recolonization followed divergence of refugial isolat es. Nested clade analysis of the geographic distribution of mtDNA haplotype s, indicated that coho salmon demographic history has been influenced by re cent isolation by distance and that historic population fragmentation was p receded by range expansion. These observations are consistent with effects expected from Pleistocene glacial advances and retreats.