Microgeographic genetic diversity of wild steelhead trout (Oncorhynchus mykiss) in a conservation hatchery operated coastal river: How wild are they?

Allelic variation at 10 microsatellite loci was assayed in potentially wild Oncorhynchus mykiss 32 collected from 11 tributaries and three upper main stem river sites (n=547), and compared to steelhead 33 trout from the hatchery operated in the lower main stem river (n=333). The objective was to investigate 34 microgeographic genetic structure of wild O. mykiss , in the face of large-scale hatchery stocking since 35 1984. Measures of genetic diversity within wild samples indicated diversity were similar to what has 36 previously been documented for wild populations. The level of microgeographic site subdivision (θ) was 37 significant (θ = 0.031), indicating moderate structure, and much higher than among sites located in the 38 lower river where the hatchery operates (θ = 0.004). Bayesian assignment clustering was used to infer 39 genetic ancestry without relying on prior information about sampling sites of individuals, and indicated 40 the existence of five or more, wild O. mykiss populations. The overall spatial pattern, however, identified 41 no clearly separate sites, but what appeared as an overlapping mosaic of modestly genetically divergent 42 localities. We conclude that wild O. mykiss populations exist in the tributaries and the upper main stem 43 river and its tributaries. These upper river populations appear to have retained genetic diversity and 44 differentiation in the face of extensive hatchery releases. 45