Genetic Relationships Among Tucannon, Touchet, and Walla Walla River Summer Steelhead (Oncorhynchus mykiss) Receiving Mitigation Hatchery Fish From Lyons Ferry Hatchery

Limited information is available on the temporal stability of population allele frequencies. In salmonids, recent empirical studies provide conflicting results regarding the consistency of genetic variation over time within populations. Additionally, since many salmonid populations are of conservation concern and reduced in size, knowledge about effective population size (Ne) and the degree of temporal stability in gene frequencies becomes particularly important as a device for assessing the potential effects of genetic drift. We conduct a temporal analysis of allele frequencies at 14 microsatellite loci for sample collections replicated over a period of eight brood years. We compare the triad of two natural-origin summer steelhead (Oncorhynchus mykiss) populations (Tucannon and Touchet rivers) with a single hatchery population (Lyons Ferry Hatchery (LFH) stock) that is used for harvest augmentation within both rivers. We report that allele frequencies for the two natural summer steelhead populations are stable over seven brood years, and the phylogenetic relationships are constant for temporally stratified samples from a single location. In contrast, yearly allele frequency estimates from LFH samples are generally divergent from each other. Evidence suggests that LFH samples may have a lower Ne, as compared to the natural population samples. We also report on several management specific questions, 1) are steelhead caught in the lower and upper Tucannon River trap genetically different, 2) are steelhead that migrate after 1 year in freshwater divergent from those that chose to migrate after 2 or more years in freshwater, and 3) is there evidence for LFH introgression into the Tucannon, Touchet, and Walla Walla Rivers? We find no evidence that steelhead trapped in the lower or upper trap are different genetically. We find no evidence that freshwater age 1 individuals are more related to LFH steelhead, or are genetically different from freshwater age 2-3 steelhead. Based on phylogenetic data and individual assignment analysis we find evidence for LFH introgression into the Tucannon River, but not the Touchet or Walla Walla Rivers. Additionally, there was specific concern for introgression of LFH steelhead into Coppei Creek (Touchet tributary). We found no evidence for LFH introgression to this population. This report also incorporates genetic data from other steelhead studies, which results in the first comparison of lower Columbia River, Walla Walla River, Snake River, and Grand Ronde River steelhead. We report that Kalama River steelhead are approximately twice as differentiated from Tucannon, Touchet, and Walla Walla Rivers (between region FST ~ 0.04) than they are to themselves (Within region FST ~ 0.02). We report that Cougar Creek steelhead are quite differentiated from Tucannon, Touchet, and Walla Walla Rivers (between region FST ~ 0.05). The amount of genetic variance partitioned among groups is similarly different comparing either Rattlesnake Creek or Wallowa stock to the Tucannon, Touchet, and Walla Walla Rivers (between region FST ~ 0.02)