The fire ant social supergene is characterized by extensive gene and transposable element duplication

In this study we characterized genes with copy number variation between SB and Sb-carrying individuals in the fire ant Solenopsis invicta. In S. invicta, a supergene composed of ~600 genes and having two variants, SB and Sb, regulates colony social form. In single queen colonies all individuals carry only the SB allele, while in multiple queen colonies, some individuals carry the Sb allele. We showed extensive acquisition of gene duplicates in Sb genomes, with some likely involved in polygyne-related phenotypes. We observed TE accumulation on Sb, likely due to the accumulation of repetitive elements on the non-recombining chromosome. Among the 115 non-TE genes with higher copy in Sb, enzymes responsible for cuticular hydrocarbon synthesis were highly represented. Overall, our results suggest that gene duplications may be an important factor leading to monogyne and polygyne ant societies.