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

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Abstract

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.

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Availability of data and material

All Illumina raw reads are available from the NCBI sequence read archive (BioProject ID: PRJNA761341); RAD loci sequences and SNP genotypic data are deposited in DRYAD (https://doi.org/10.5061/dryad.ffbg79cvz).

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Acknowledgements

We thank Parks Canada staff for collecting samples from Sockeye Lake in Kluane National Park and Reserve, Lawrence Vano and Warren Kapaniuk at the Whitehorse Rapids Fish Hatchery for providing hatchery samples, Laura Grieve for GIS help in the generation of Figure 1, and Lorne LaRocque for background on the establishment of the Whitehorse Rapids Fish Hatchery population. Computational resources were made available by Compute Canada through the Resources for Research Groups program. Funding for this work was provided by Parks Canada Conservation and Restoration Program agreement # GC-1160 and the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant # RGPIN‐2019‐04621 to MAR.

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  1. Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC, V1V 1V7, Canada

    Christopher Setzke & Michael A. Russello

  2. Parks Canada Agency, Yukon Field Unit, Suite 205 - 300 Main St, Whitehorse, YT, Y1A 2B5, Canada

    Carmen Wong

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Setzke, C., Wong, C. & Russello, M.A. Genome-wide assessment of kokanee salmon stock diversity, population history and hatchery representation at the northern range margin. Conserv Genet 23, 243–253 (2022). https://doi.org/10.1007/s10592-021-01418-2

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