Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution

Chromosomal inversions have been shown to play a major role in local
adaptation by suppressing recombination between alternative arrangements
and maintaining beneficial allele combinations. However, so far, their
importance relative to the remaining genome remains largely unknown.
Understanding the genetic architecture of adaptation requires better
estimates of how loci of different effect sizes contribute to phenotypic
variation. Here, we used three Swedish islands where the marine snail
Littorina saxatilis has repeatedly evolved into two distinct ecotypes
along a habitat transition. We estimated the contribution of inversion
polymorphisms to phenotypic divergence while controlling for polygenic
effects in the remaining genome using a quantitative genetics framework.
We confirmed the importance of inversions but showed that contributions of
loci outside inversions are of similar magnitude, with variable
proportions dependent on the trait and the population. Some inversions
showed consistent effects across all sites, whereas others exhibited
site-specific effects, indicating that the genomic basis for replicated
phenotypic divergence is only partly shared. The contributions of sexual
dimorphism as well as environmental factors to phenotypic variation were
significant but minor compared to inversions and polygenic background.
Overall, this integrated approach provides insight into the multiple
mechanisms contributing to parallel phenotypic divergence.