Predominance of cis-regulatory changes in parallel expression divergence of sticklebacks. Threespine stickleback fish, Gasterosteus aculeatus

Adaptive evolution of gene expression may proceed via mutations influencing cis-regulatory elements such as promoters or enhancers or trans-acting factors such as transcription factors. There are conflicting predictions for the relative roles of cis- and trans-regulation in the early stages adaptive divergence-with-gene-flow. Populations that have evolved in parallel provide a powerful opportunity to look for general patterns and rules governing the evolution of gene expression. Here we show that parallel expression divergence in threespine stickleback fish is primarily driven by differences in cis-acting (allele-specific) gene regulation such as mutations in enhancers and promoters. We show that cis-regulation is predominantly additive and stable across genetic backgrounds and different environmental conditions enabling cis-regulatory mutations to act as a motor for the evolution of traits in the early stages of divergence-with-gene-flow.