Abstract
Across its Holarctic range, Arctic charr (Salvelinus alpinus)
populations have diverged into distinct trophic specialists across
independent replicate lakes. The major aspect of divergence between
ecomorphs is in head shape and body shape, which are ecomorphological
traits reflecting niche use. However, whether the genomic underpinnings
of these parallel divergences are consistent across replicates was
unknown but key for resolving the substrate of parallel evolution. We
investigated the genomic basis of head shape and body shape morphology
across four benthivore-planktivore ecomorph pairs of Arctic charr in
Scotland. Through genome-wide association analyses, we found genomic
regions associated with head shape (89 SNPs) or body shape (180 SNPs)
separately and 50 of these SNPs were strongly associated with both body
and head shape morphology. For each trait separately, only a small
number of SNPs were shared across all ecomorph pairs (3 SNPs for head
shape and 10 SNPs for body shape). Signs of selection on the associated
genomic regions varied across pairs, consistent with evolutionary
demography differing considerably across lakes. Using a comprehensive
database of salmonid QTLs newly augmented and mapped to a charr genome,
we found several of the head and body shape associated SNPs were within
or near morphology QTLs from other salmonid species, reflecting a shared
genetic basis for these phenotypes across species. Overall, our results
demonstrate how parallel ecotype divergences can have both
population-specific and deeply shared genomic underpinnings across
replicates, influenced by differences in their environments and
demographic histories.