Ancient regulatory genetic elements underlie the evolution of butterfly wing patterns

Ancient and deeply conserved multifunctional gene regulatory elements play a crucial role in creating the diverse patterns that adorn butterfly wings, according to a new study. The evolution of phenotypic traits frequently occurs through sequence divergence in non-coding regions of the genome that control gene expression. However, few studies have characterized the history of the regulatory systems that underlie rapidly evolving traits. Transcription factors that bind to DNA at sites called cis-regulatory elements (CREs) can turn gene expression on or off and influence where, when, and to what extent a gene is expressed. Over an evolutionary timescale, variation in CREs may modify the expression of neighboring genes and thus modulate the phenotype of an organism. Butterfly wing patterns provide a good model for evaluating the development and genetic regulation underlying these evolutionary changes because slight shifts in gene expression of a few key master genes, like WntA, affect the expression of several other genes which directly result in variations of wing color and pattern across thousands of closely related species. Using comparative sequence analysis, ATAC-seq and a CRISPR knockouts for 46 CREs across five species of butterflies of the family Nymphalidae, Anyi Mazo-Vargas and colleagues found that major aspects of this ground plan are determined by an ancient array of deeply conserved non-coding DNA sequences. They show that although some species in this family have very different wing patterns than others, they all share the same regulatory elements as those also displaying the conserved nymphalid ground plan. “Mazo-Vargas et al. demonstrate that although the regulatory landscape surrounding a gene may be stable over a long time, the loss or gain of CREs may suddenly enable evolutionary change,” write Marianne Espeland and Lars Podsiadlowski in a related Perspective. “The approach to manipulate CREs and observe the phenotypic changes opens possibilities for examining other gene regulatory questions in developmental biology, such as those relevant for understanding invertebrate and vertebrate body plans.”