Long‐distance migration is a major factor driving local adaptation at continental scale in Coho salmon

Abstract

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with longdistance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

Re‐evaluating Coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data

“…Here, we observed a distinct genetic split between the Thompson populations and all other populations, a pattern which is consistent with previous studies using SNP markers (Beacham et al, 2020), microsatellite and MHC markers (Beacham et al, 2001;, and mitochondrial DNA haplotypes (Smith et al, 2001). Furthermore, Rougemont et al (2022) identified evidence for local adaptation to conditions related to The definition of CUs for Pacific salmon was an important first step in the implementation of the WSP in Canada (DFO, 2005). The intent of these units was to represent biologically meaningful entities of diversity for standardized monitoring of the status of all five wild salmon species and assessing impacts of actions taken to conserve and manage wild populations (DFO, 2009).…”

“…Previous studies identified a strong signal of latitudinal isolation by distance (IBD) across the entire North American distribution of Coho salmon due to the northward postglacial population expansion (Rougemont et al, 2020(Rougemont et al, , 2022. Similarly, we evaluated the relationship between genetic diversity (H s ) and genetic differentiation (β ST ) and the distance from the southernmost site to assess the potential confounding effect of latitude on subsequent genotypeenvironment association (GEA) analyses.…”

“…Type I errors compared with other GEA methods (Capblancq & Forester, 2021;Forester et al, 2018). Given the strong signal of IBD along the south-north axis in BC (see Section 3.1), we used the same approach as in Rougemont et al (2022) to control for the potential confounding effect of geography in GEAs by including latitude as a conditioning variable in the model (see also Meirmans, 2012).…”

A Homology Guide for Pacific Salmon Genus Oncorhynchus resolves patterns of Duplicate Retention, Rediploidization and Local Adaptation Following the Salmonid Specific Whole Genome Duplication Event

“…These declines have prompted intense interest in understanding the genetic basis of ecologically important traits as well as the development of genome editing technology to aid in conservation efforts (Phelps, Seeb, & Seeb, 2020;Waples, Naish, & Primmer, 2020). However, the variation of gene copy number produced by differential rediploidization between species and inconsistent gene naming complicates these efforts (Limborg, Larson, Seeb, & Seeb, 2017;Rougemont et al, 2022) mykiss gardeneri) (Chen, Farrell, Matala, & Narum, 2018). Through our investigation we produced a gene family-based homology guide for Oncoryhynchus which includes both gene name (NCBI ID) and copy number that we hope we will serve as an easy to use resource for the salmonid community to address the issue of homolog identification.…”

“…These declines have prompted intense interest in understanding the genetic basis of ecologically important traits as well as the development of genome editing technology to aid in conservation efforts (Phelps, Seeb, & Seeb, 2020; Waples, Naish, & Primmer, 2020). However, the variation of gene copy number produced by differential rediploidization between species and inconsistent gene naming complicates these efforts (Limborg, Larson, Seeb, & Seeb, 2017; Rougemont et al, 2022) by making the identification of homologous genes, a prerequisite for either genetic analysis or genome editing efforts extremely challenging.…”