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Phenotypes that appear to be conserved could be maintained not only by strong purifying selection on the underlying genetic systems, but also by stabilizing selection acting via compensatory mutations with balanced effects. Such coevolution has been invoked to explain experimental results, but has rarely been the focus of study. Conserved expression driven by the  unc-47  promoters of  Caenorhabditis elegans  and  C. briggsae  persists despite divergence  within  a  cis -regulatory element and  between  this element and the  trans -regulatory environment. Compensatory changes in  cis  and  trans  are revealed when these promoters are used to drive expression in the other species. Functional changes in the  C. briggsae  promoter, which has experienced accelerated sequence evolution, did not lead to alteration of gene expression in its endogenous environment. Coevolution among promoter elements suggests that complex epistatic interactions within  cis -regulatory elements may facilitate their divergence. Our results offer a detailed picture of regulatory evolution in which subtle, lineage-specific, and compensatory modifications of interacting  cis  and  trans  regulators together maintain conserved gene expression patterns.

Coevolution within and between Regulatory Loci Can Preserve Promoter Function Despite Evolutionary Rate Acceleration