Running title: Genomics of charr head and body
shape
Abstract:
Across its Holarctic range, Arctic charr (Salvelinusalpinus ) 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.
Keywords: parallel evolution, ecomorphology, QTL, genomics, fish,
population genomics