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

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.

A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples

“…We designed our SNP selection and validation workflow to construct a GT‐seq panel for effectively identifying and sexing individuals, as well as estimating pairwise kinship up to third‐order relationships. Other recent applications of multi‐scaled GT‐seq panels include identifying individuals and reconstructing population structure in polar bears (Hayward et al, 2022 ) and rattlesnakes (Schmidt, Govindarajulu, et al, 2020 ), and identifying life history forms, assigning stock, and reconstructing population history in kokanee salmon (Chang et al, 2022 ; Setzke et al, 2021 ).…”

“…Genotyping‐in‐Thousands by sequencing (GT‐seq; Campbell et al, 2015 ) is a MTAS approach currently available that has seen widespread utility across studies in ecology, evolution, and conservation (Chang et al, 2021 , 2022 ; Hayward et al, 2022 ; Jo et al, 2021 ; Natesh et al, 2019 ; Schmidt et al, 2020 ; Setzke et al, 2021 ; Sjodin et al, 2020 ). Here, we employed a scalable workflow to develop a GT‐seq panel for invasive Sitka black‐tailed deer in Gwaii Haanas.…”

“…Deer have disrupted ecosystem structure and dynamics due to their unconstrained browsing of native vegetation, preventing temperate rainforest regeneration; these impacts have been observed on numerous islands with deer present, which exhibit lower species richness compared to deer-free islands across several taxa Stockton et al, 2005). In addition, the Haida Nation have longstanding practical and Genotyping-in-Thousands by sequencing (GT-seq; Campbell et al, 2015) is a MTAS approach currently available that has seen widespread utility across studies in ecology, evolution, and conservation (Chang et al, 2021(Chang et al, , 2022Hayward et al, 2022;Jo et al, 2021;Natesh et al, 2019;Setzke et al, 2021;Sjodin et al, 2020). Here, we employed a scalable workflow to develop a GT-seq panel for invasive Sitka black-tailed deer in Gwaii Haanas.…”

The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid

“…Recent genome‐wide studies based on reduced‐representation approaches have identified a handful of single nucleotide polymorphisms (SNPs) exhibiting putative signatures of divergent selection among O. nerka migratory and reproductive ecotypes (Christensen et al, 2020; Larson et al, 2017; Lemay & Russello, 2015; Nichols et al, 2016; Veale & Russello, 2017a), with perhaps the most notable being an SNP in LRRC9 on LG12 showing a strong association with stream/river‐spawning and shore/beach‐spawning in both sockeye and kokanee (Veale & Russello, 2017b). These previous studies, however, were limited to the analysis of sequence variation and by their sparse coverage of the genome, constraining their ability to more fully characterize the genomic basis and architecture of these life history traits, including SVs that could maintain reproductive and migratory life history differentiation among ecotypes in the presence of gene flow (Chang et al, 2022; Elliott et al, 2020; Veale & Russello, 2016, 2017a). In fact, testing the role of SVs in life history variation in sockeye/kokanee is particularly timely as evidence for an important contribution of SVs in maintaining ecotypic differentiation in salmonids varies by species: for example, while a well‐characterized double‐inversion is associated with sex‐specific migratory tendency in rainbow trout ( Oncorhynchus mykiss ; Pearse et al, 2019), a block of highly differentiated SNPs spanning ~140 kb and controlling migratory timing in Chinook salmon ( Oncorhynchus tshawytscha ) does not appear to be maintained by an inversion or other SVs (Thompson et al, 2020).…”

“…Here, we analysed sequence and structural variation from short‐ and long‐read whole genome resequencing data to investigate the genomic basis and architecture of reproductive and migratory behaviour, focusing on a system where sockeye and kokanee populations share recent common ancestry (Beacham & Withler, 2017; Taylor et al, 1996; Veale & Russello, 2017a) and where stream‐spawning and shore‐spawning kokanee co‐occur (Okanagan Lake/River, British Columbia, Canada). Given the complexity of the traits under divergent selection and evidence of gene flow among O. nerka ecotypes (Chang et al, 2022; Elliott et al, 2020; Veale & Russello, 2016), we hypothesized the following: (i) the genetic basis of ecotypic differentiation involves many genes of different functions; (ii) the underlying genetic architecture is polygenic, with numerous, tightly linked variants (SNPs and/or SVs); and (iii) large SVs maintain clusters of differentiated loci associated with migratory and reproductive behaviour.…”