Fine-scale population structure of rainbow trout (Oncorhynchus mykiss) in the Spokane River drainage in relation to hatchery stocking and barriers

We examined population structure in rainbow trout (Oncorhynchus mykiss) collected from 20 tributaries and three mainstems in the greater Spokane River drainage using 13 microsatellite loci. Populations displayed some excess homozygosity and linkage disequilibrium, which was more pronounced in upper tributary collections and likely the result of small effective population sizes or structuring within tributaries. In general, population structure followed geographic structure: collections from creeks within sub-drainages were most closely related and collections from different tributaries were genetically distinct. Comparisons to cutthroat trout (O. clarki) indicated little to no introgression. Comparisons to steelhead, coastal, and inland rainbow trout from hatcheries suggested introgression by hatchery fish into some wild populations. Introgression was suspected in populations from stocked tributaries and where the tributary lacked barriers to escaped hatchery fish. Populations from tributaries above barriers that had not been stocked were genetically distinct from hatchery fish and appeared to be native inland redband rainbow trout.