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.