A general prediction of evolutionary genetics is that gene regulation should evolve largely through changes in independent cis-regulatory “modules” that segregate developmental roles while minimizing deleterious pleiotropic side effects of mutation ( 10, 11). Population genetic scans and comparative gene expression studies suggest that cis-regulatory differences underlie adaptive variation of red color patterns, and recent work has sought to characterize the specific noncoding regions around optix responsible for this ( Fig. Incredibly, red color pattern diversity in the genus Heliconius is largely controlled by divergent expression of a single gene, optix, making Heliconius an important case study of how variation at a single major effect locus can drive adaptation of a complex trait both within and between species ( Fig. Approximately 10 to 15 MYA, Heliconius spread across Central and South America, evolving red, black, and yellow aposematic wing patterns to warn predators of their toxicity ( 6). These butterflies are one of the defining examples of Müllerian mimicry, where local populations have evolved warning coloration to mimic other local toxic butterfly and moth species ( 4, 5). Neotropical Heliconius butterflies are a classic example of an adaptive radiation driven by few genes of large effect ( 1– 3). Our results support a model of color pattern evolution in Heliconius where changes to ancient, multifunctional cis-regulatory elements underlie adaptive radiation. Remarkably, we found orthologous cis-regulatory elements associate with wing pattern convergence of distantly related comimics, suggesting that parallel coevolution of ancestral elements facilitated pattern mimicry. We were surprised to find that the cis-regulatory architecture of optix is characterized by pleiotropy and regulatory fragility, where deletion of individual cis-regulatory elements has broad effects on both color pattern and wing vein development. Here we combine chromatin assays, DNA sequence associations, and genome editing to functionally characterize 5 cis-regulatory elements of the color pattern gene optix. Association studies have linked color pattern variation to a handful of noncoding regions, yet the presumptive cis-regulatory elements (CREs) that control color patterning remain unknown. Color pattern mimicry in Heliconius butterflies is a classic case study of complex trait adaptation via selection on a few large effect genes.
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