Large-scale mutation in the evolution of a gene complex for cryptic coloration

The types of mutations affecting adaptation in the wild are only beginning to be understood. In particular, whether structural changes shape adaptation by suppressing recombination or by creating new mutations is unresolved. Here we show that multiple, linked but recombining loci underlie cryptic color morphs of Timema chumash stick insects. In a related species, these loci are found in a region of suppressed recombination, forming a supergene. However, in seven species of Timema we find that a mega-base size ‘supermutation’ has deleted color loci in green morphs. Moreover, we find that balancing selection likely contributes more to maintaining this mutation than does introgression. Our results show how suppressed recombination and large-scale mutation can help package gene complexes into discrete units of diversity, such as morphs, ecotypes, or species.