Steelhead Genetic Diversity at Multiple Spatial Scales in a Managed Basin: Snake River, Idaho

We investigated the genetic diversity of steelhead Oncorhynchus mykiss in 74 wild populations and 5 hatchery stocks in Idaho's Snake River basin at the drainage, watershed, and population spatial scales using 11 microsatellite loci. We found significant genetic diversity at multiple spatial scales. Analysis of molecular variance showed that genetic diversity was greater among watersheds within drainages (3.66%) than among drainages (1.97%). Over 94% of the genetic diversity found in the Clearwater, Salmon, and Snake River drainages occurred within individual populations. Estimated effective population sizes ranged from 213 to 486.6 at the drainage scale, from 81.2 to 610.4 at the watershed scale, and from 8.4 to 4,845 at the population scale. The Middle Fork Salmon, South Fork Salmon, Lochsa, and Selway rivers—watersheds managed for wild fish—formed distinct groups in our consensus neighbor-joining (NJ) trees. At the watershed scale our analyses support differentiation of all hatchery and wild stocks. However, this was not the case for analyses at the population scale, where 236 FST pairwise comparisons out of 3,081 (wild and hatchery) were not significantly different. The distribution of genetic diversity across the landscape does not appear to be organized by the A run or B run management designations for anadromous steelhead. The Dworshak hatchery stock was significantly different from all but one population (O'Hara Creek, Selway River) in pairwise F ST comparisons and grouped with other Clearwater River drainage populations in our NJ trees. The Oxbow, Sawtooth, and Pahsimeroi hatchery stocks were indistinguishable from each other based on F ST analysis. Currently, this study represents the most comprehensive evaluation of genetic diversity in Idaho's steelhead populations across multiple scales with different management histories.