A novel supergene controls queen size and colony social organization in the ant Myrmica ruginodis

In some ant species, the size of queens is dimorphic, with larger queens dispersing to form single-queen colonies and smaller queens remaining in natal colonies as part of multiple-queen societies. These alternative reproductive strategies influence colony kin structure and worker behavior, and their many independent origins make them ideal systems to study parallel evolution of genome organization and adaptability. We investigate the genetic basis of alternative reproductive strategies in the queen-size dimorphic ant Myrmica ruginodis by sampling 95 queens from 31 colonies in southern Finland. Whole-genome sequencing revealed a novel 9 Mb supergene associated with both queen size and social organization. Queens homozygous for the AA haplotype were larger and found only in single-queen colonies, while queens in multiple-queen colonies were smaller and contained only AB and BB genotypes. This supergene is not homologous to previously identified supergenes in ants, suggesting it was formed by a unique evolutionary pathway.