Genomic Basis and Climate Change Vulnerability of Migration Timing in Atlantic Salmon (Salmo salar)

With global environmental change, mismatches between seasonal movements of species and environmental conditions are increasingly impacting survival and persistence. Atlantic salmon (Salmo salar) perform long-distance marine migrations culminating in a return to natal rivers, the timing of which varies among and within populations. Global declines of salmon raise the possibility that phenological mismatches could be a contributing factor; however, the underlying genetic architecture of run timing remains poorly understood. Here, we use a 220 K SNP Array to examine the association of genetic variation with run timing at a population level for 11 North American rivers. We also ask what the potential vulnerability of run timing is to future climate change by estimating trait-specific genomic offsets, i.e., predicted shifts in allele frequencies at loci associated with run timing under projected climate change, yielding relative estimates for each population. Detected associations suggest a polygenic basis for run timing, including a large structural variant and maturation-associated genes previously characterised in Atlantic salmon (six6, vgll3), and ppfia2, a migration-timing gene conserved across vertebrates. Genomic offsets associated with climate change impacts for run timing were highest in more northern populations, suggesting potential maladaptation in future migrations. By describing the genetic architecture of run timing in North American Atlantic salmon and possible impacts of climate change on the persistence of life-history strategies, results from this study contribute towards a better understanding of this complex life-history trait to inform future conservation management.