Code from: Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation

Large effects loci often contain genes with critical developmental
functions with potentially broad effects across life-stages. However, the
life-stage-specific fitness consequences are rarely explored. In Atlantic
salmon, variation in two large-effect loci, six6 and vgll3, is linked to
age at maturity, and several physiological and behavioural traits in early
life. By genotyping the progeny of wild Atlantic salmon that were planted
into natural streams with nutrient manipulations, we tested if genetic
variation in these loci is associated with survival in early life. We
found that higher early life survival was linked to the genotype
associated with late maturation in the vgll3, but with early maturation in
the six6 locus. These effects were significant in high-nutrient, but not
in in low-nutrient streams. The differences in early survival were not
explained by additive genetic effects in the offspring generation, but by
maternal genotypes in the six6 locus, and by both parents’ genotypes in
the vgll3 locus. Our results suggest that indirect genetic effects by
large-effect loci can be significant determinants of offspring fitness.
This study demonstrates an intriguing case of how large-effect loci can
exhibit complex fitness associations across life stages in the wild and
indicates that predicting evolutionary dynamics is difficult.