Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

Abstract

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.

Figure 1. Supergene alleles and mimicry polymorphism in H. numata

Polymorphic forms of H. numata each mimic different models in the distantly related genus Melinaea (Nymphalidae: Danainae). Each form is controlled by a specific allele of the supergene P, with increasing dominance shown from left to right^,. Two parapatric regions of northeastern Peru (T, Tarapoto and Andean valleys; Y, Yurimaguas and Amazon lowlands) harbour different mimicry assemblages; dominance (<) is nearly complete between forms within each region, but is incomplete (~) between certain pairs of alleles from parapatric regions. In all other species studied in the genus Heliconius, wing pattern is controlled by several large-effect loci on different chromosomes. In H. melpomene the HmYb–HmSb–HmN complex is situated in the orthologous position to the H. numata P supergene. LG, linkage group.

Figure 2. Fine-scale mapping and nucleotide variation at the P supergene in H. numata

a, Fine-scale linkage mapping of the supergene P (indicated by red arrows) to the interval bounded by genes HN00020 and HN00041. Recombinants were observed in crosses totalling 366 individuals. Blue arrows indicate the position of the recombining loci HmYb and HmSb in H. melpomene. HmN, which is known to be part of this cluster of loci, is not fine-mapped in H. melpomene^,. Coloured blocks represent annotated gene regions on forward and reverse strands (see Supplementary Fig. 1 and Supplementary Table 3 for details). b, Association of SNP variation with mimicry polymorphism in a sample of 25 silvana and 34 aurora/arcuella individuals from a single population. Markers genotyped across rearrangements BP1 (pink) and BP2 (blue) show perfect association of SNP variation with wing pattern. No association was found in the flanking region from markers Fox (Hn00106) to BmSuc (Hn00019), or at 12 unlinked loci (green). The association decays more slowly in the direction of loci Bm5536 (GCP), Bm5586 (NudC) and Bm5593 (Srp68). c, LD heat map. Perfect LD (genotypic correlation coefficient r² = 1) is found across 580 kb spanning the BP1 and BP2 rearrangements (n = 59). LD decays rapidly outside this interval, although strong within-marker LD remains at HN00021. Markers that are unlinked to P show little LD with each other or with P. d, Haplotype network for marker LRR (Hn00024) in the Yurimaguas population, coloured according to wing-pattern phenotype. Haplotype clades separated by seven fixed differences are in complete association with wing pattern, taking into account dominance relationships. Similar haplotype clades were found for all loci genotyped within P, and across the Amazon basin, but not for genes flanking P or in unlinked regions (Supplementary Figs 4 and 6).

Figure 3. Chromosomal rearrangements associated with the supergene in natural populations

a, Comparison of the gene orders found in the H. numata BAC library and wild populations. The rearrangements involve the 400-kb segment from genes HM00023 to HM00040 (ERCC6) (BP1, clones 24I10 and 45B17), and the adjacent 180-kb segment from gene HN00041 (penguin) and HN00053 (lethal (2) giant larvae homologue) (BP2, clone 38G4). Genes closest to the breakpoints are shown. b, Long-range PCR assays across alternative breakpoints (BP0, BP1 and BP2) in wild populations show a perfect association of the polymorphic gene orders with mimicry variation in four morphs from natural populations of Eastern Peru, following the dominance relationships (Fig. 1). The Yurimaguas population segregates primarily for silvana and aurora/arcuella forms, associated with BP0 and BP2, respectively. The Tarapoto population segregates mainly for tarapotensis and bicoloratus forms, associated with BP2 and BP1, respectively. This population also harbours recessive illustris alleles associated with BP0 (Supplementary Table 6).