Abstract
Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake, British Columbia as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of O. nerka, but were restricted to assigning individuals to pure-stock or “hybrid”. Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F1, F2, and B2 backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan® assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B2 backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~ 74% of which were B2 backcross or F2. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.
Highlights
Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives
Despite differences in spawning behavior, kokanee males are known to sneak on spawning sockeye salmon females[24], and size-selective mating has been observed between male sockeye salmon and female k okanee[25], allowing for gene flow between migratory forms
The accurate identification of advanced hybrid classes is valuable for monitoring the extent of introgression and potential fitness impacts between multiple reproductive forms of a single species or where hybridization between species is possible
Summary
Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Previous research examining hybridization between sockeye salmon and kokanee found O. nerka hybrids occupy intermediate morphologies and exhibit a largely resident life history, this latter finding requires further investigation[12,29] These studies employed genetic marker sets that were effective at differentiating pure-stock from hybrid, they had limited power for the identification of advanced hybrid classes that has become increasingly important for genetic monitoring as the reintroduction program matures. A previous simulation-based sensitivity analysis found that a panel comprised of 300 highly differentiated SNPs has the resolution needed to detect advanced hybrid classes between sockeye salmon and kokanee in Skaha L ake[36] With this in mind, advancements in massively parallel sequencing can be leveraged to improve the identification of hybridization in systems by pooling barcoded amplicons to increase the power of genetic panels for classification[37]; Genotyping-in-Thousands by sequencing (GT-seq) is a useful approach in cases where large sample sizes need to be cost-effectively genotyped[38]
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