Conclusions
Our results provide evidence for substantial genetic variation underlying functionally relevant traits, and suggest adaptive divergence in face of gene flow in a large, panmictic population inhabiting a heterogeneous lake. In particular, gene-phenotype-environment association analyses allowed us to identify genomic signatures of selection by testing which phenotypic traits and genomic variants are associated with putative selective agents. Whilst we found evidence for genome-phenotype-environment correlations for spine length, we also found evidence for phenotypic divergence in body size (total length) and trophic morphology (gut length, gill raker length and gill raker number) without apparent genomic divergence – despite substantial additive genetic variation in these traits. The lack of genomic trait divergence across environments could reflect a combination of phenotypic plasticity and/or habitat choice , both of which can constrain or accelerate adaptive divergence . Our study sets the stage for a holistic understanding of patterns of divergence and the maintenance of genomic and phenomic variation in spatiotemporally varying wild populations.