Genetic population structure of introduced and native lineages of Oncorhynchus nerka in a large impounded watershed

Abstract Kokanee, the non‐anadromous life‐history form of Oncorhynchus nerka , use lacustrine habitat in watersheds draining into the north Pacific Ocean. Kokanee also have been widely introduced into reservoirs following impoundment of rivers consequent to the construction of hydroelectric dams. Genetically divergent subpopulations of Kokanee should be identified and evaluated when implementing watershed‐level fishery management strategies. We analyzed the genetic population structure of Kokanee in the Williston watershed, north‐central British Columbia, where native populations were present in the reservoir and headwater lakes prior to stocking Columbia River‐origin fish in the 1990s. Using microsatellite markers, we determined that native Williston Reservoir Kokanee were divergent from only one of the headwater lake populations. Native populations in headwater lakes remain entirely separate from the reservoir populations, and there was no indication of past or current introgression with the introduced stock. We identified all fish collected from 2006 to 2019 as introduced Columbia River‐origin genotypes, and there was no evidence of genetic divergence by spawning location. As native Williston Kokanee have not been sampled from the reservoir in survey efforts since 2000, it is likely that this population has been extirpated from the reservoir perhaps through competition with the introduced Columbia River‐origin lineage.