Functional Evolution of a <em>cis-</em>Regulatory Module

<div><p>Lack of knowledge about how regulatory regions evolve in relation to their structure–function may limit the utility of comparative sequence analysis in deciphering <em>cis-</em>regulatory sequences. To address this we applied reverse genetics to carry out a functional genetic complementation analysis of a eukaryotic <em>cis-</em>regulatory module—the <em>even-skipped</em> stripe 2 enhancer—from four <em>Drosophila</em> species. The evolution of this enhancer is non-clock-like, with important functional differences between closely related species and functional convergence between distantly related species. Functional divergence is attributable to differences in activation levels rather than spatiotemporal control of gene expression. Our findings have implications for understanding enhancer structure–function, mechanisms of speciation and computational identification of regulatory modules.</p>