In this research project, funded by my recently awarded VR Starting Grant, we investigate the structure, function, and evolutionary dynamics of a 9 Mb supergene in Myrmica ants. In Myrmica ruginodis, we have established that this supergene controls queen size and colony social organization. We will extend these analyses by characterizing patterns of genomic differentiation, structural variation, recombination suppression, and gene content associated with alternative supergene haplotypes. In the sister species Myrmica rubra, the same genomic region appears to underlie a balanced lethal system, in which only supergene heterozygous queens reach sexual maturity. Further genomic analyses are required to understand the origin and long-term maintenance of this system, which is likely driven in part by the accumulation of recessive deleterious mutations on both haplotypes. These objectives require extensive whole-genome read mapping, variant calling, structural variant detection, and population genomic analyses, necessitating substantial computational resources.