Farmed Escapees Threaten MHC Diversity in Wild Atlantic Salmon

ABSTRACT Wild Atlantic salmon populations in Norway and elsewhere are experiencing long‐term declines driven by reduced marine survival, climate change, impacts from aquaculture, introduction of alien species, and environmental degradation. Understanding how immune diversity is affected by these declines, and thus the ability of Atlantic salmon to combat current and future invading pathogens, is essential for the success of conservation programs such as gene banks. Major histocompatibility complex (MHC) genes, some of the most polymorphic genes known to date, are essential in the host immune defense against invading pathogens. Here we investigate MHC class I and class II diversity in escaped farmed salmon and in eight wild Atlantic salmon populations defined as being at risk. The study demonstrates that rare alleles can be found in single closely related wild populations within a fjord, and collectively, the populations hold a large immune diversity. Moreover, our study found that a broad spatial and temporal collection of escaped farmed salmon had an MHC‐diversity at the same level as individual wild salmon populations, while escaped farmed salmon from single escape events had lower diversity. Overall, the wild salmon had considerably higher MHC diversity than escaped farmed salmon. Accumulated genetic introgression of escaped farmed salmon is therefore a major threat as it can compromise the MHC diversity within and among the wild populations. Conservation of MHC diversity in the ongoing gene bank program for Norwegian Atlantic salmon is important, and our observation emphasizes that a large number of founders to the gene bank are needed to conserve the many rare MHC alleles and that genotyping of potential founders may be useful in broodfish selection.