Compounding Impacts—Genomic Exploration of the Potential Effect of Domestic Introgression on Climate Adaptation in Atlantic Salmon (Salmo salar)

Abstract

Predicting population, species, and community responses to climate change is critical for the successful management of wild ecosystems. However, climate change does not act alone. Interactions among climate change and other anthropogenic threats could significantly complicate predictions of global change yet have rarely been examined. Salmo salar (Atlantic salmon) are an increasingly at-risk northern diadromous fish, exposed to multiple threats including a changing climate and introgression from net-pen aquaculture escapees. Introgression from aquaculture escapees could alter wild salmon climate change responses through the introduction of maladaptive climate-associated variation. Here we conducted a genome-environment association analysis for wild Atlantic salmon throughout North America (n = 5208 samples) using a 220 K SNP array and explored differences between wild and aquaculture salmon at climate-associated loci. Environmental associations suggest a polygenic basis to climate adaptation which includes a large chromosomal translocation, previously implicated in climate-associated adaptation. Genomic differences between wild and domestic salmon generally increase with increasing geographic distance from the southern source location of North American salmon aquaculture. Wild salmon populations differed more genetically from aquaculture salmon (F_ST ~ two-fold higher) at climate-associated loci than genome-wide, suggesting introgression may erode climate adaptation in the wild, and further amplify the negative impacts of climate change on these populations. The results suggest a more encompassing view of anthropogenic impacts which explicitly considers interactions among environmental and anthropogenic threats is needed to better understand and conserve wild populations in a changing world.