Restricted inclusion of wild broodstock at a large hatchery does not result in detectable genetic differentiation in a supplemented coho salmon (<i>Oncorhynchus kisutch</i>) population

Hatchery production is common in salmonid management for harvest and conservation. Many hatcheries employ integrated broodstock programs, where wild-origin fish are included as broodstock and uni- or bi-directional gene flow between wild and hatchery components of the population is encouraged. Such approaches often assume that opportunistically obtained wild fish meet the genetic goals of minimizing hatchery–wild differentiation and maintaining genetic diversity. This may be incorrect if fine-scale spatial genetic structure exists. Here we investigate the population genetic consequences of such hatchery operations in coho salmon ( Oncorhynchus kisutch) in a small river system featuring a large integrated broodstock program. We do so using 11 082 SNPs scored in wild-origin and hatchery-origin fish collected throughout the system. We found no evidence for genetic differentiation between hatchery-origin and wild-origin fish, no evidence of lowered genetic diversity in hatchery-origin fish, and no evidence for genetic differentiation among fish sampled throughout the river system. In addition, we did not detect inbreeding. Collectively, these results are consistent with current practices meeting integrated hatchery program goals of adequately sampling the genetic diversity present in wild-origin fish, although they may slightly reduce the effective population size of the combined population.