A large-effect locus underlies migration timing in North American Atlantic salmon (Salmo salar).

The timing of migration often aligns with predictable seasonal or environmental cues, allowing populations to maximise fitness by moving between habitats at optimal times. However, rapid environmental change is disrupting this predictability, leading to mismatches between expected and observed conditions with potential demographic consequences. Atlantic salmon are long-distance migrators that travel between freshwater and oceanic habitats and are experiencing widespread declines across their range. Our understanding of the genetic basis of run timing in Atlantic salmon has been limited to European populations, or at a coarse population level. We combine whole-genome sequencing of 498 individuals from seven North American populations with individual migration timing data to explore the genomic basis of adult return timing. We identify a large-effect region on chromosome 17 associated with migration timing (unimodal or bi-model), with ppfia2 explaining a substantial proportion of the variation, as well as an underlying polygenic basis to this complex life-history trait. These findings demonstrate a clear genomic basis for migration timing in Atlantic salmon, with the associated ppfia2 gene also playing a role in other long-distance migratory vertebrates. This suggests a potentially conserved evolutionary mechanism underlying migration timing across species and highlights the importance of genetic insights for understanding population resilience and declines in Atlantic salmon.