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Setzke, Christopher

University of British Columbia

Freshwater fisheries are 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) located in the Yukon. In addition, we reconstructed the genetic consequences of a recent 12-year population crash followed by a rapid increase in numbers this population underwent. First using restriction-site associated DNA sequencing, we genotyped individuals at 11,442 single nucleotide polymorphisms (SNPs) that were sampled from putative reproductive shore- and stream-spawning ecotypes in KNPR as well as broodstock from the Whitehorse Rapids Hatchery. We found no evidence of wild stock diversity or ecotype differentiation based on neutral SNPs nor previously identified 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. Then using Genotyping-in-Thousands by sequencing we genotyped the previously mentioned individuals, as well as pre-crash archival samples from KNPR and the nearby extirpated Frederick Lake, at 271 SNPs. We observed similar diversity metrics and low differentiation between pre- and post-crash individuals in KNPR. We also found that the Frederick Lake population had lower diversity metrics than that observed in KNPR, a possible factor in its extirpation. This population was highly differentiated from the one in KNPR, constituting the loss of a unique population. Overall, our results suggest that the kokanee population in KNPR retained the majority of its genetic diversity despite the population crash experienced, should be managed as a single population, and that hatchery supplementation with the existing stock is not appropriate.

Text

2021-07-21

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/79068

Biology

University of British Columbia

UBCO

http://creativecommons.org/licenses/by-nc-nd/4.0/