Influences of Hatchery Supplementation, Spawner Distribution, and Habitat on Genetic Structure of Chinook Salmon in the South Fork Salmon River, Idaho

We evaluated the genetic influence of hatchery supplementation on distinct naturally spawning populations of Chinook salmon Oncorhynchus tshawytscha in the South Fork Salmon River (SFSR), Idaho. Genetic tissue samples were collected from unmarked natural-origin and McCall Fish Hatchery (MFH)-reared Chinook salmon carcasses, and fish were identified by an adipose fin clip at five main-stem sites located both upstream and downstream of a seasonal exclusionary weir in the upper SFSR. We evaluated allele frequency data across 95 single-nucleotide polymorphism loci to determine the extent of genetic differentiation among collections. Genetic distance analyses and homogeneity tests indicated little subpopulation distinction in the upper SFSR. The weak overall genetic structure (global FST = 0.010) is likely reflective of a population diversity similar to the historical structure with introgression by MFH stock in the naturally spawning population of the upper SFSR. Further analyses were conducted to evaluate the genetic structure among the upper SFSR and spawning aggregates in two adjacent SFSR tributaries: the Secesh River, which is devoid of any hatchery stocking, and Johnson Creek, where a discrete supplementation program has been implemented using only Johnson Creek fish. Our results indicated variable abundances of SFSR hatchery spawners distributed spatially among the three main watersheds. Gene flow appears to be restricted and genetic differentiation to be relatively large despite substantial hatchery releases in the upper SFSR. Three historical aggregates of Chinook salmon appear to persist in the SFSR metapopulation, where variable hatchery influences are coincident with the distribution of suitable spawning habitat and watershed-specific management objectives.