AbstractThe Mad River Hatchery supports one of the most important fisheries for steelhead Oncorhynchus mykiss in California. Although the Mad River Hatchery has stated goals of operating an integrated hatchery program that addresses demographic and genetic risks, very little monitoring of these goals has taken place. We applied parentage‐based tagging methods to assess the origin (wild versus hatchery), age structure, and spawn‐date heritability of steelhead returning to the Mad River Hatchery. We generated single nucleotide polymorphism genotypes at 96 loci for all adult steelhead broodstock spawned at Mad River Hatchery over a 9‐year period (2009–2017; N = 1,572) and identified 965 trios (mother, father, and offspring) using parentage analysis. Although the hatchery attempts to release 100% adipose‐fin‐clipped hatchery steelhead, our analysis uncovered a large difference in the proportion of hatchery‐origin broodstock individuals as estimated by pedigrees (0.87) and traditional adipose fin clipping (0.58). This difference presumably resulted from failure to clip or identify a clip in 100% of hatchery‐produced fish. Our analysis revealed the complete age structure of six cohorts of hatchery broodstock and showed substantial differences in different years for Mad River Hatchery steelhead. Pedigree‐based estimates of narrow‐sense heritability for spawn date were 0.242 to 0.470, indicating moderate to high heritability, and highlighting the opportunity for a strong response to selection on this trait imposed by hatchery spawning. The application of parentage‐based tagging provided critical information for understanding life history variation and the efficacy of management actions for Mad River Hatchery steelhead and provides a framework for minimizing domestication selection and associated reductions in fitness for naturally spawning fish in this integrated population.
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