title: Landscape genomics in Atlantic salmon (Salmo salar): searching for gene-environment interactions driving local adaptation.
abstract: A growing number of studies are examining the factors driving historical and contemporary evolution in wild populations. By combining surveys of genomic variation with a comprehensive assessment of environmental parameters, such studies can increase our understanding of the genomic and geographical extent of local adaptation in wild populations. We used a large-scale landscape genomics approach to examine adaptive and neutral differentiation across 54 North American populations of Atlantic salmon representing seven previously defined genetically distinct regional groups. Over 5500 genome-wide single nucleotide polymorphisms were genotyped in 641 individuals and 28 bulk assays of 25 pooled individuals each. Genome scans, linkage map, and 49 environmental variables were combined to conduct an innovative landscape genomic analysis. Our results provide valuable insight into the links between environmental variation and both neutral and potentially adaptive genetic divergence. In particular, we identified markers potentially under divergent selection, as well as associated selective environmental factors and biological functions with the observed adaptive divergence. Multivariate landscape genetic analysis revealed strong associations of both genetic and environmental structures. We found an enrichment of growth-related functions among outlier markers. Climate (temperature-precipitation) and geological characteristics were significantly associated with both potentially adaptive and neutral genetic divergence and should be considered as candidate loci involved in adaptation at the regional scale in Atlantic salmon. Hence, this study significantly contributes to the improvement of tools used in modern conservation and management schemes of Atlantic salmon wild populations.
authors.affiliation: Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, 1030 avenue de la Médecine, Québec, Québec G1V 0A6, Canada. vincent.bourret.1@ulaval.ca.
authors.forename: Bourret
authors.initials: B
authors.lastname: Vincent
authors.forename: Mélanie
authors.initials: M
authors.lastname: Dionne
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Kent
authors.forename: Sigbjørn
authors.initials: S
authors.lastname: Lien
authors.forename: Louis
authors.initials: L
authors.lastname: Bernatchez
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000818:Animals; D017753:Ecosystem; D059647:Gene-Environment Interaction; D016678:Genome; D008957:Models, Genetic; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D020317:Salmo salar / Q000235:genetics*
keywords: Conservation; local adaptation; population genetics; salmonids; single nucleotide polymorphism