An ancient and eroded supergene underlies social organization across Formica ants

We uncover 20-30 MY of evolutionary history of a supergene controlling polymorphic social organization in Formica ants. We show that five Formica species exhibit homologous divergent haplotypes, each associated with either single- or multiple- queen colonies, spanning 11 Mbp on chromosome 3. Despite the size of the supergene, only 142 single nucleotide polymorphisms (SNPs) consistently distinguish alternative supergene haplotypes across all five species. These conserved trans- species SNPs are localized in a small number of disjunct clusters that are distributed across the supergene.