Genomic signatures of adaptation to novel environments: hatchery and life history-associated loci in landlocked and anadromous Atlantic salmon (Salmo salar)

Abstract

The adaptation of marine and anadromous fishes to novel, freshwater environments requires major physiological shifts in functions related to osmoregulation, immunity, and metabolism. For Atlantic salmon (Salmo salar) populations, such changes have occurred independently in many landlocked populations that were formed as a result of extensive hydrological shifts in North America around 10 000 years ago. We compared patterns of genetic variation between two landlocked and one anadromous population of Atlantic salmon to identify loci that may have played an important evolutionary role in facilitating the transition from an anadromous to an entirely freshwater life history. Outlier loci included single nucleotide polymorphisms (SNPs) in genes related to functions including immunity, growth, and osmoregulation. We also used these same populations to characterize loci associated with distinct hatchery rearing environments. This additional comparison identified outlier SNPs annotated to genes related to wound healing, consistent with findings from other genetic studies of domestication selection in fishes. Together, our results highlight putative responses to both natural selection imposed by major environmental changes and artificial selection levied by differing hatchery environments.