Genome-wide assessment of kokanee salmon stock diversity, population history and hatchery representation at the northern range margin

Freshwater fisheries represent important natural resources, yet a vast majority are threatened by anthropogenic stressors. Accurate baseline information on stock diversity, population history and hatchery representation are required for implementing effective conservation and management strategies for mitigating declines. Genetic tools have played key roles for informing fisheries management, including for kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka), particularly in the southern portion of its North American range. Here, we investigated stock diversity, population history and hatchery representation of kokanee at the northern extent of its range in Canada in Kluane National Park and Reserve (KNPR) in the Yukon that underwent a 12-year population crash followed by a rapid increase in numbers. Using restriction-site associated DNA sequencing, we genotyped individuals at 11,442 single nucleotide polymorphisms (SNPs) that were sampled from putative reproductive ecotypes spawning on the shore of Sockeye Lake (n = 26), within Sockeye Creek (n = 20) or near an outlet in between (n = 2), as well as broodstock from the Whitehorse Rapids Fish Hatchery (n = 29). We found no evidence of ecotype differentiation based on neutral SNPs nor outlier loci. Within-population genetic diversity and effective population size were substantially higher in the wild population relative to the hatchery and significant differentiation was detected, suggesting the hatchery population was not representative of wild stock diversity. Overall, our results indicate that separate management of kokanee in KNPR based on ecotype is not warranted at this time and that supplementation with the existing hatchery stock is not appropriate.