Introgression and Potential Outbreeding Depression Following Anthropogenically-Induced Secondary Contact Between Anadromous and Resident Atlantic Salmon (Salmo salar).

The evolution of alternative migratory strategies can lead to the establishment of ecologically and genetically distinct morphs; however, the forces that maintain these differences are often unclear. Here we assessed how migratory strategy may affect gene flow and adaptation in Atlantic Salmon (Salmo salar) in a setting where a migratory barrier was removed, and migratory and non-migratory salmon have been brought into contact through a program to initiate a migratory population. We used whole genome sequencing to characterize genetic variation in resident and anadromous salmon in this experimental system, as well as in the original source of the migratory individuals and a proximate source of strays into the system. Our results suggest that resident and anadromous salmon populations are highly divergent genetically, but that introgression from the resident population into the introduced migratory morph is widespread. However, despite a general trend of introgression into the migratory form, localized genomic regions appear resistant to gene flow, potentially highlighting adaptive divergence between resident and anadromous salmon. Additionally, we compared how the proportion of ancestry associated with migratory type changed between out migrating smolts and returning adults across two cohorts. Our results show a significant reduction in resident ancestry consistent with outbreeding depression during the marine migratory phase. Genomic comparisons between smolts and adults also identify several localized regions potentially under selection in the marine environment, possibly related to immune function. Together, these results suggest that introgression between divergent migratory forms in this system is unidirectional and is resulting in outbreeding depression and reduced migratory success. In the context of supplementation, our results suggest that enhancement activities aimed at boosting anadromous Atlantic Salmon populations could be impacted by introgression with resident populations. Additionally, interbreeding may present a demographic threat to resident populations, as anadromous-resident hybrids appear to follow a migratory life history.