Using forest and prairie ecotypes of deer mice, scientists from Harvard University have generated new insights into the mechanisms that establish and maintain ecotypes, reporting their findings in this week's Science. Wide-ranging species that occupy diverse habitats often evolve distinct ecotypes, which frequently differ in multiple locally adaptive phenotypes. But how differences in multiple traits are maintained between ecotypes when migration acts as a homogenizing force remains a question. Using the mice, the researchers characterized the genetic basis of variation in two defining traits — tail length and coat color — and find a 41-megabase chromosomal inversion linked to both. In dark, long-tailed forest deer mice, the inversion frequency is 90 percent, and it decreases across a habitat transition to become absent in the light, short-tailed prairie ecotype. The study's authors further implicate divergent selection in maintaining the inversion at frequencies observed in the wild despite high levels of gene flow. "Our results thus underscore the important and perhaps widespread role of inversions in local adaptation, including in mammals, and highlight how selection acting on inversion polymorphisms may maintain intraspecific divergence in multiple traits in the wild," they write.