Supergenes are tight clusters of loci that facilitate the co-segregation of adaptive variation, providing integrated control of complex adaptive phenotypes. Polymorphic supergenes, in which specific combinations of traits are maintained within a single population, were first described for 'pin' and 'thrum' floral types in Primula and Fagopyrum, but classic examples are also found in insect mimicry and snail morphology. Understanding the evolutionary mechanisms that generate these co-adapted gene sets, as well as the mode of limiting the production of unfit recombinant forms, remains a substantial challenge. Here we show that individual wing-pattern morphs in the polymorphic mimetic butterfly Heliconius numata are associated with different genomic rearrangements at the supergene locus P. These rearrangements tighten the genetic linkage between at least two colour-pattern loci that are known to recombine in closely related species, with complete suppression of recombination being observed in experimental crosses across a 400-kilobase interval containing at least 18 genes. In natural populations, notable patterns of linkage disequilibrium (LD) are observed across the entire P region. The resulting divergent haplotype clades and inversion breakpoints are found in complete association with wing-pattern morphs. Our results indicate that allelic combinations at known wing-patterning loci have become locked together in a polymorphic rearrangement at the P locus, forming a supergene that acts as a simple switch between complex adaptive phenotypes found in sympatry. These findings highlight how genomic rearrangements can have a central role in the coexistence of adaptive phenotypes involving several genes acting in concert, by locally limiting recombination and gene flow.

Key Words aposematism, Batesian mimicry, Müllerian mimicry, defensive coloration, predator behavior s Abstract Mimicry and warning color are highly paradoxical adaptations. Color patterns in both Müllerian and Batesian mimicry are often determined by relatively few pattern-regulating loci with major effects. Many of these loci are "supergenes," consisting of multiple, tightly linked epistatic elements. On the one hand, strong purifying selection on these genes must explain accurate resemblance (a reduction of morphological diversity between species), as well as monomorphic color patterns within species. On the other hand, mimicry has diversified at every taxonomic level; warning color has evolved from cryptic patterns, and there are mimetic polymorphisms within species, multiple color patterns in different geographic races of the same species, mimetic differences between sister species, and multiple mimicry rings within local communities. These contrasting patterns can be explained, in part, by the shape of a "number-dependent" selection function first modeled by Fritz Müller in 1879: Purifying selection against any warning-colored morph is very strong when that morph is rare, but becomes weak in a broad basin of intermediate frequencies, allowing opportunities for polymorphisms and genetic drift. This Müllerian explanation, however, makes unstated assumptions about predator learning and forgetting which have recently been challenged. Today's "receiver psychology" models predict that classical Müllerian mimicry could be much rarer than believed previously, and that "quasi-Batesian mimicry," a new type of mimicry intermediate between Müllerian and Batesian, could be common. However, the new receiver psychology theory is untested, and indeed it seems to us unlikely; alternative assumptions could easily lead to a more traditional Müllerian/Batesian mimicry divide.