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 oceanand 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 oceantype (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. Chinook salmon Oncorhynchus tshawytscha are a diverse species of Pacific salmon with at least two distinct life history types, ocean and stream (Healey 1991). Ocean-type adult Chinook salmon begin their freshwater migration in early fall, spawning in warmer water near tidewaters or main-stem sections of large rivers. Conversely, stream-type adult Chinook salmon begin migrating in spring, using colder headwater tributaries for spawning. Further, due to early emergence and rapid juvenile growth, ocean-type juveniles migrate to estuaries within 3 months, while stream-type juveniles postpone migration to the sea for 1 year or more. However, each of these life history types includes a wide array of variation throughout their life cycles (e.g., reservoir-type Chinook salmon; Connor et al. 2005). The geographic distribution of ocean-type Chinook salmon is predominantly below 568N, whereas stream-type salmon are found more commonly north of this latitude (Healey 1991; Brannon et al. 2004). Both of these life history types occur widely throughout the Columbia River basin in the Pacific Northwest of the United States and have overlapping distributions. Historically, populations of Chinook salmon have been structured through philopatry to natal streams (Quinn and Dittman 1990), geological processes (i.e., the Wisconsin Glaciation; Teel et al. 2000), metapopulation dynamics (Cooper and Mangel 1999), and life history characteristics (Waples et al. 2004). Previous studies have shown that temporal variation within populations is small relative to geographic variation (Utter et al. 1989; Beacham et al. 2003), and populations within drainages tend to be more genetically similar than those in other major watersheds (e.g., Waples et al. 2004). Exceptions to this pattern of geographic structure include strong differentiation of sympatric oceanand stream-type life histories in the Columbia River (Narum et al. 2004; Waples et al.