Subpopulation structure of steelhead trout (Oncorhynchus mykiss) in the Middle Fork Eel River as determined by microsatellite DNA polymorphisms

Polymorphic microsatellite markers were employed to explore fine-­scale genetic differences between adult summer steelhead trout and juvenile Oncorhynchus mykiss samples collected from the upper Middle Fork Eel River, California. Sampling locations were chosen to capture spatial variation among juveniles within the watershed, and sampling over multiple years allowed estimation of temporal genetic variation for the adult summer steelhead trout group. Tests for Hardy­-Weinberg and linkage equilibrium were used to identify significant deviations for each locus and sample population. Kinship and family structure, as estimated by the relatedness coefficient (rxy), effectively explained observed genetic disequilibrium. Analysis revealed minimal genetic variation between the three sample years of adult summer steelhead trout, suggesting that the summer life-­history phenotype has a heritable component. Significant genetic differences among juvenile collections from upper Middle Fork Eel tributaries indicated the presence of small, isolated, resident populations. Although closely related to the summer steelhead trout population, these resident groups did not appear to be exchanging migrants with the anadromous form at this time. Within the adult holding habitat, many juveniles assigned to the summer steelhead trout lineage, while others appeared to represent unique groups possibly due to family structure. Comparisons with outgroups from the Eel River, Mendocino Coast and Smith River revealed significant distinctions between groups of O. mykiss sampled at the drainage scale. Overall, sampled populations showed varying degrees of differentiation, indicative of a complex history of gene flow and genetic drift in the Middle Fork Eel.