Conclusion:
Our results indicate differences in head and body shape responses to
ecological selection regimes across four replicate lakes. These
differing responses are likely enabled through the use of largely
different genetic bases across independent replicate ecomorph pairs.
Specifically, we found that only a small number of SNPs were shared
across all four pairs, suggesting limited genetic parallelism with these
shared SNPs under varying selective pressures across lakes. We found
that head and body shape morphology have a level of shared genetic
underpinnings in Arctic charr and that the genetics of these phenotypes
is shared to an extent across different salmonid species. Our analyses
highlight the complexity of the evolutionary genetics that underlie
parallel phenotypes across replicates. Further it we demonstrate the
power of using population replicates to resolve fundamental genetic and
evolutionary patterns from the noise of local variation.