Genetic variation and structure of Chinook salmon life history types in the Snake River

We evaluated 25 inland populations of Chinook salmon Oncorhynchus tshawytscha in the Snake River with 13 microsatellite loci to test for contemporary genetic differentiation at three scales: between life history types, among regions within life history types, and among populations within regions. The genetic distance and diversity of natural Chinook salmon populations were also contrasted with those of Chinook salmon from several hatcheries. The results provide strong evidence for reproductive isolation among ocean-and stream-type life histories (F-ST range, 0.080-0.120). Regional structuring of stream-type Chinook salmon within subbasins was also significant, as all populations were differentiated (F-ST range, 0.017-0.045), but populations generally clustered together by region in a neighbor-joining dendrogram. This evidence suggests high levels of philopatry to natal areas in stream-type Chinook salmon, but ocean-type collections were not significantly different from one another (F-ST range, 0.001-0.002). Higher levels of genetic diversity in ocean-type (306 total alleles; allelic richness, 16.5) than in stream-type collections (206 total alleles; allelic richness, 12.2) may also reflect variable levels of gene flow within each life history type and colonization history. The genetic similarity of populations within regions suggests gene flow not only from transplanted stocks but also from natural dispersal that provides metapopulation structure. None of the 25 populations in this study offered significant evidence for a genetic bottleneck (M ratio < 0.68) despite apparent demographic bottlenecks in several populations throughout the Snake River drainage in the last century. The combination of dispersal through metapopulation dynamics and transfers of hatchery stocks may be responsible for reducing the genetic bottleneck signal.