Genomic architecture and evolutionary conflict drive allele-specific expression in the social supergene of the red fire ant

Supergenes are genomic regions of suppressed recombination that underlie complex polymorphisms. Despite the importance of such regions, our empirical understanding of their early evolution is limited. The young "social" supergene of the fire ant Solenopsis invicta provides a powerful system for disentangling the roles of evolutionary conflict and the implications of suppressed recombination. We used population genomics to identify genetic differences between supergene variants and we used gene expression analyses across, castes and body parts to characterize allelic expression differences for the hundreds of genes in the supergene. We find that the expression of most genes is independent of social form or supergene variant, in line with the young age of this system. However, many of the genes with allelic expression differences show a pattern consistent with gene degeneration due to suppressed recombination. In contrast, a small portion of the genes has the signature of evolutionary conflict between social forms.