Data from: 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 Hatchery (n=29). We found no
evidence of wild stock diversity or 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 suggest 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.