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Abstract Supergenes, regions of the genome with suppressed recombination between sets of functional mutations, contribute to the evolution of complex phenotypes in diverse systems. Excluding sex chromosomes, most supergenes discovered so far appear to be young, being found in one species or a few closely related species. Here, we investigate how a chromosome harbouring an ancient supergene has evolved over about 30 million years (Ma). TheFormicasupergene underlies variation in colony queen number in at least five species. We expand previous analyses of sequence divergence on this chromosome to encompass about 90 species spanning theFormicaphylogeny. Within the nonrecombining region, the geneknockoutcontains 22 single nucleotide polymorphisms (SNPs) that are consistently differentiated between two alternative supergene haplotypes in divergent EuropeanFormicaspecies, and we show that these same SNPs are present in mostFormicaclades. In these clades, including an early diverging NearcticFormicaclade, individuals with alternative genotypes atknockoutalso have higher differentiation in other portions of this chromosome. We identify hotspots of SNPs along this chromosome that are present in multipleFormicaclades to detect genes that may have contributed to the emergence and maintenance of the genetic polymorphism. Finally, we infer three gene duplications on one haplotype, based on apparent heterozygosity within these genes in the genomes of haploid males. This study strengthens the evidence that this supergene originated early in the evolution ofFormicaand that just a few loci in this large region of suppressed recombination retain strongly differentiated alleles across contemporaryFormicalineages.
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This content will become publicly available on February 28, 2026
Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly colour pattern supergene
Supergenes can evolve when recombination-suppressing mechanisms like inversions promote co-inheritance of alleles at two or more polymorphic loci that affect a complex trait. Theory shows that such genetic architectures can be favoured under balancing selection or local adaptation in the face of gene flow, but they can also bring costs associated with reduced opportunities for recombination. These costs may in turn be offset by rare ‘gene flux’ between inverted and ancestral haplotypes, with a range of possible outcomes. We aimed to shed light on these processes by investigating the ‘BC supergene’, a large genomic region comprising multiple rearrangements associated with three distinct wing colour morphs inDanaus chrysippus, a butterfly known as the African monarch, African queen and plain tiger. Using whole-genome resequencing data from 174 individuals, we first confirm the effects of BC on wing colour pattern: background melanism is associated with SNPs in the promoter region ofyellow, within an inverted subregion of the supergene, while forewing tip pattern is most likely associated with copy-number variation in a separate subregion of the supergene. We then show that haplotype diversity within the supergene is surprisingly extensive: there are at least six divergent haplotype groups that experience suppressed recombination with respect to each other. Despite high divergence between these haplotype groups, we identify an unexpectedly large number of natural recombinant haplotypes. Several of the inferred crossovers occurred between adjacent inversion ‘modules’, while others occurred within inversions. Furthermore, we show that new haplotype groups have arisen through recombination between two pre-existing ones. Specifically, an allele for dark colouration in the promoter ofyellowhas recombined into distinct haplotype backgrounds on at least two separate occasions. Overall, our findings paint a picture of dynamic evolution of supergene haplotypes, fuelled by incomplete recombination suppression.
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- Award ID(s):
- 2311366
- PAR ID:
- 10655954
- Editor(s):
- Khila, Abderrahman
- Publisher / Repository:
- PLOS
- Date Published:
- Journal Name:
- PLOS Biology
- Volume:
- 23
- Issue:
- 2
- ISSN:
- 1545-7885
- Page Range / eLocation ID:
- e3003043
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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