Researchers at the University of Chicago have published a study in PNAS that examines how a “supergene” called doublesex enables swallowtail butterflies (Papilio alphenor) to mimic the wing patterns of other, toxic butterfly species. This mimicry helps protect them from predators.
The team used genomic sequencing and CRISPR gene-editing techniques to investigate how the doublesex supergene evolved its role in controlling wing color and pattern. Their findings show that while most supergenes are groups of neighboring genes, in this case, the doublesex supergene consists of just one gene. Only female Papilio alphenor butterflies develop alternate wing patterns—adding orange spots to their white patches—while males retain standard coloring.
“Males and females of these butterflies can have totally different color patterns with pretty much the same genome—but somehow one piece of DNA encodes those different phenotypes,” said Nicholas VanKuren, research scientist in the Department of Ecology and Evolution at UChicago and lead author of the study.
“What’s great about this study is that we identified not only the differences between the two versions of that gene,” he said, “but also how those differences affected how the gene functions and turns these wing patterns on or off.”
Marcus Kronforst, professor of ecology and evolution at UChicago and senior author, explained: “This female-limited polymorphism in Papilio alphenor is a classic example of a supergene. That’s why we got interested in studying this so we can figure out what is responsible molecularly for creating a supergene. Historically, the problem of how they evolved has been kind of intractable, but now we have the tools to dissect them.”
The researchers found few differences in protein structure between two versions (alleles) of doublesex. Instead, they discovered that nearby non-coding DNA segments known as cis-regulatory elements were altering gene expression. The new allele had acquired six such elements whose function depended on the doublesex protein itself; together, these switched on the gene differently to create new mimetic wing patterns. This indicates that doublesex may regulate its own activity—a notable evolutionary development.
Further analysis showed that this allele could control color patterns by influencing several other genes involved in body plan development and wing patterning.
“These results are pretty exciting, because for the first time, we know where in the genome to look for these genetic switches that turn on color patterns,” VanKuren said. “And the fun thing is, it's not just this one species, Papilio alphenor, that has this female limited polymorphism. There are multiple, closely related species that have the same sort of mimicry switch, and they're controlled by the same gene too.”
Kronforst added: “Butterflies are a fantastic system for studying this, because they're just so incredibly diverse. There are so many species, and on top of that, within a species there are so many different color patterns. That kind of diversity gives us another tool to study where genetic variation comes from and how biodiversity evolves.”
The research was supported by funding from the National Institutes of Health. Other authors include Sofia I. Sheikh, Claire L. Fu, Darli Massardo, Namiko N. Service and Wei Lu from UChicago.