Abstract
Large independently evolved supergenes control colony social organization and queen reproductive strategies in several ant lineages. Their independent origins, as well as the similarities of the associated phenotypes, make ant supergenes a promising system for studying the parallel evolution of genome organization and adaptability. However, the genetic basis of differences in social organization and queen phenotypes remains unknown in many ant species, limiting the potential power of this system for comparative studies. We investigated the genetic basis of colony social organization 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 carried only AB and BB genotypes. This supergene is not homologous to previously identified supergenes in ants, suggesting it arose through a distinct evolutionary pathway.