Overruled by nature: A plastic response to an ecological regime shift disconnects a gene and its trait

In Atlantic salmon, age at maturation represents a life history trait with a sex-specific trade-off between reproductive success and survival, mediated by the vgll3 gene through sex-specific dominance. By genotyping ~1500 historical and contemporary samples of salmon from the river Etne with a 50k SNP-array, we identified three loci significantly associated with sea-age. These included vgll3 and six6, which collectively explained 50% and 36% of the age of maturation for males and females in the 1983-1984 period respectively. In the same period, we also observed sex-specific epistasis, where the six6 genotype only influenced age at maturation in males carrying the late-maturation vgll3 allele. Strikingly, the combined influence of these genes was nearly absent in all samples from 2013-2016, while allelic frequencies at vgll3 remained unchanged. Many salmon populations in the northeast Atlantic, including that from Etne, have been exposed to a major ecological regime shift in the marine environment in 2005. Because this is associated with consistently slower growth and higher age at maturation, we conclude that the regime shift has led to the sudden bypassing of the influence of vgll3 and six6 on maturation through growth-driven plasticity. ### Competing Interest Statement The authors have declared no competing interest.