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.