Conservation Genomics and Adaptive Divergence of Atlantic Salmon in High Definition

In this new era of genomic innovations, a growing number of studies are examining the drivers of historical and contemporary evolution in wild populations. While allowing for more reliable estimates of population structure parameters than smaller panels of anonymous non-coding markers, the advent of large single nucleotide polymorphism (SNP) array also offers the opportunity to examine unresolved query. The application of SNP panels to understanding the extent of local adaptation in wild populations, particularly in salmonids, has the potential to provide key information in conservation planning and resource management. Recent landscape genetics studies of Atlantic salmon in Québec have shown that populations are regionally structured in wide groups and that these regional differences are likely driven by the distinct environmental conditions faced by populations, thus suggesting a regional scale of local adaptation in this species. However, relatively little is known about the genomics of adaptive divergence underlying these patterns. In this study, we utilized an innovative large-scale landscape genomics approach to concurrently examine adaptive and neutral differentiation across 25 populations of Atlantic salmon. Over 6000 genome-wide SNPs were genotyped in 624 individuals. Genome scans, along with landscape analysis and linkage map information, provided us with valuable knowledge on the genomic basis of local adaptation. In particular, we were able to identify over 100 markers potentially under divergent and balancing selection, as well as showing potential selective agents from environmental conditions and biological functions/processes associated with adaptive divergence. Thus, in addition to significantly contributing to the improvement of tools available in conservation and management of Atlantic salmon wild populations, our results also shed light on the genomic basis of adaptive divergence.