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Chang, Sarah Lu

University of British Columbia

The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the resident freshwater form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Additionally, stocking programs have been implemented to re-establish extirpated species to their historical ranges and can affect recipient ecosystems. Here, we developed and applied two Genotyping-in-Thousands by Sequencing (GT-seq) panels with targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada, as well as further investigation of the genetic outcomes of an anadromous sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia. The broad-scale GT-seq panel exhibited high self-assignment accuracy (93.3%), perfect assignment of individuals not included in the baseline to their geographic basin and life history form. The panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays and improving resolution, extending a long-term time series, and demonstrating the scalability of this approach for this system and others. The O. nerka hybrid panel exhibited high efficiency, accuracy, and power (>94.5%) of assignment to pure-stock sockeye/kokanee, F₁ F₂ and B₂ backcross-sockeye/kokanee. We genetically re-assigned 91 individuals that had previously been assessed with otolith microchemistry analysis and TaqMan® SNP assay genetic assignment to evaluate panel power with known individuals and found that our panel was able to reclassify individuals previously assigned as F₁ hybrids to pure-stock and B₂ backcross classes. We then estimated hybrid proportions and the progression of introgression in 2019, revealing that hybrids now comprise of 31% of the population. Our results expand upon previous evidence of hybridization and intermediate morphology between O. nerka migratory forms, as well as providing a novel genomic tool able to detect advanced introgression for continued monitoring of the Skaha Lake restocking initiative.

Text

2021-07-02

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/78849

Biology

University of British Columbia

UBCO

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