  Supergenes are genomic regions containing sets of tightly linked loci that
control multi-trait phenotypic polymorphisms under balancing selection. Recent
advances in genomics have uncovered significant variation in both the genomic
architecture as well as the mode of origin of supergenes across diverse
organismal systems. Although the role of genomic architecture for the origin of
supergenes has been much discussed, differences in the genomic architecture
also subsequently affect the evolutionary trajectory of supergenes and the rate
of degeneration of supergene haplotypes. In this review, we synthesize recent
genomic work and historical models of supergene evolution, highlighting how the
genomic architecture of supergenes affects their evolutionary fate. We discuss
how recent findings on classic supergenes involved in governing ant colony
social form, mimicry in butterflies, and heterostyly in flowering plants relate
to theoretical expectations. Furthermore, we use forward simulations to
demonstrate that differences in genomic architecture affect the degeneration of
supergenes. Finally, we discuss implications of the evolution of supergene
haplotypes for the long-term fate of balanced polymorphisms governed by
supergenes.
