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Correct gene expression is often critical and consequently stabilizing selection on expression is widespread. Yet few genes possess highly conserved regulatory DNA, and for the few enhancers that have been carefully characterized, substantial functional reorganization has often occurred. Given that natural selection removes mutations of even very small deleterious effect, how can transcription factor binding evolve so readily when it underlies a conserved phenotype? As a first step toward addressing this question, I combine a computational model for regulatory function that incorporates many aspects of our present biological knowledge with a model for the fitness effects of misexpression. I then use this model to study the evolution of enhancers. Several robust behaviors emerge: First, the selective effects of mutations at a site change dramatically over time due to substitutions elsewhere in the enhancer, and even the overall degree of constraint across the enhancer can change considerably. Second, many of the substitutions responsible for changes in binding occur at sites where previously the mutation would have been strongly deleterious, suggesting that fluctuations in selective effects at a site are important for functional turnover. Third, most substitutions contributing to the repatterning of binding and constraint are effectively neutral, highlighting the importance of genetic drift-even for enhancers underlying conserved phenotypes. These findings have important implications for phylogenetic inference of function and for interpretations of selection coefficients estimated for regulatory DNA.

Changes in Selective Effects Over Time Facilitate Turnover of Enhancer Sequences