Gene expression divergence in <i>Poephila </i>finches highlights the role of sex chromosomes in speciation

<p dir="ltr">Changes to gene expression can occur rapidly and underpin much of the phenotypic divergence between species. The complexity of gene regulatory networks means that changes in gene expression between populations can be vulnerable to the evolution of incompatibilities between multiple loci during species divergence. Using RNAseq data from three recently diverged taxa in the Australian grass-finch genus <i>Poephila </i>and their experimentally generated F1 hybrids, we show how the pattern of gene expression evolution has differed between the sexes and between somatic and gonadal tissues. We find strong evidence for a fast-Z effect in regulatory divergence consistent with a combination of the evolutionary processes of stabilising selection and genetic drift. Gene expression divergence in this system shows a predominant pattern of compensatory evolution in gene regulatory systems, with most divergence occurring on the sex chromosomes and attributable to additive <i>cis</i>-regulatory changes under relaxed selective constraint. In hybrid individuals, patterns of transgressive gene expression differ markedly between tissue types and sexes, demonstrating the impact of context-specific sexual selection and its consequences for general patterns in reproductive isolation, such as Haldane’s Rule. This study provides an empirical demonstration of key predictions of speciation theory in one of the most comprehensive studies of non-model vertebrates to date.</p>