Genotyping-in-Thousands by sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon

www.nature.com/scientificreports OPEN Genotyping‑in‑Thousands by sequencing panel development and application for high‑resolution monitoring of introgressive hybridization within sockeye salmon Sarah L. Chang1, Hillary G. M. Ward2, Lucas D. Elliott1,3 & Michael A. Russello1* 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 Genotypingin-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 backcrosssockeye/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 intraspecific hybridization are important management parameters. Global fish populations are in decline due to agricultural development, rapidly rising riverine water temperatures, and reduced c onnectivity1–6. In particular, 80% of salmonid populations in the Columbia River have experienced losses linked to hydroelectric development and the destruction of spawning and rearing habitat7,8. In response, management strategies have included incorporating fish passage at dams to mitigate impacts to migratory fish life histories and supplementing populations in decline with hatchery fry for stock enhancement. For example, Coho salmon (Oncorhynchus kisutch) have been restored in the lower Columbia River using hatchery stocking, resulting in the establishment of local naturalized p opulations5,9. Additionally, the enhancement of spawning habitat has been an effective strategy to restore fish populations, where the replacement of river substrate improved water velocities, dissolved oxygen, and usage of the site by spawning Chinook salmon (O. tshawytscha)10. Ultimately, the success of fish stocking programs that target species with diverse migratory and resident forms should include careful consideration of resulting hybridization dynamics and corresponding outcomes on recovery initiatives. 1 Department of Biology, University of British Columbia, Kelowna, BC, Canada. 2Lands and Natural Resource Operations and Rural Development, British Columbia Ministry of Forests, Penticton, BC, Canada. 3UiT The Arctic University of Norway, Tromsø, Norway. *email: Scientific Reports | (2022) 12:3441 | https://doi.org/10.1038/s41598-022-07309-x 1 Vol.:(0123456789) www.nature.com/scientificreports/ Hybridization in fish species is well documented, including inter-specific hybrids such as rainbow (Oncorhynchus mykiss) and cutthroat trout (O. clarkii)11, as well as within-species hybrids between different life history forms, such as the case between anadromous sockeye salmon and freshwater resident kokanee12. The longterm effects of hybridization are often complex, with the potential for both positive and negative outcomes13. Hybridization can be a powerful conservation tool harnessed to rescue populations with low genetic diversity and increase fitness through the integration of favorable traits such as larger body size, more offspring, and longer lifespans13–16. On the other hand, detrimental effects have been observed such as introgression with maladapted gene c omplexes17, decrease in reproductive s uccess18, and negative impacts on g rowth19, with hybrid fitness theorized to decrease as the divergence between parental phenotypes i ncreases20. Overall, the impacts of intra-specific hybridization in the wild are still not well understood, warranting further study, especially when observed as part of an active management program. Oncorhynchus nerka provides an excellent system for investigating the genetic and physiological outcomes of hybridization as it exhibits tremendous life history variation, shows natal homing behavior, and represents a valuable species targeted for population restoration through r estocking21. This species exhibits two main migratory forms, including anadromous sockeye salmon (hereafter referred to as “sockeye salmon”) and freshwater resident kokanee (hereafter referred to as “kokanee”). Kokanee are much smaller than sockeye salmon (26 cm versus > 45 cm average adult fork length) and occur sympatrically in many lakes, but tend to exhibit different spawning habitat preferences and spawning periods22,23. Despite differences in spawning behavior, kokanee males are known to sneak on spawning sockeye salmon females24, and size-selective mating has been observed between male sockeye salmon and female k okanee25, allowing for gene flow between migratory forms. Sockeye-kokanee hybridization can lead to an increase in body size of resident hybrids that can increase angler satisfaction19 and bolster the overall genetic diversity of O. nerka in the system16. Conversely, hybrids can also experience negative impacts such as lower swimming capabilities than pure sockeye s almon26, medial seawater a daptabilities27, intermediate maturation time23, decreased egg survival rate28, and the loss of the iconic red coloration that is key in sexual s election25. With a broad range of potential outcomes, accurate assessment of the extent of introgression is critical for elucidating the long-term effects of hybridization associated with supplementation and reintroduction programs. To address large-scale declines in sockeye salmon populations in the Columbia River, an experimental reintroduction program was initiated in Skaha Lake within the Okanagan Basin of the Southern Interior of British Columbia, Canada. This program provides an excellent opportunity to investigate the extent and outcomes of intra-specific hybridization be (...truncated)