Abstract
A recent sequencing study has shown that two common Caribbean corals, Montastraea cavernosa and Siderastrea siderea , each consist of four genetically distinct lineages in the Florida Keys. These lineages are specialised to a certain depth and, to a lesser extent, to nearshore or offshore habitats. We hypothesised that the lineages' environmental specialisation is at least in part due to regulatory evolution, which would manifest as the emergence of groups of coregulated genes (‘modules’) demonstrating lineage‐specific responses to different reef environments. Our hypothesis also predicted that genes belonging to such modules would show greater genetic divergence between lineages than other genes. Contrary to these expectations, responses of cryptic lineages to natural environmental variation were essentially the same at the genome‐wide gene coexpression network level, with much fewer differences in gene expression between lineages compared to between habitats. Moreover, none of the identified coregulated gene expression modules exhibit elevated genetic divergence between lineages. Possible explanations of these unexpected results range from the leading role of algal symbionts and/or microbiome in adaptation to strong action of spatially varying selection equalising gene expression patterns despite different genetic background. We discuss how future studies could assist in discriminating between these possibilities.