Figure Box 1.

Signatures of divergence and degeneration as a result of suppressed recombination have been used to pinpoint the location of supergenes. Different strategies can be applied depending on the extent of differentiation between the recombining and non-recombining allele. (A) Haplotypes remain homomorphic but mutations accumulate in the non-recombining one, such that genetic differentiation (e.g., F_ST) between morphs, or divergence (d_xy) between haplotypes can aid supergene identification (Tuttle et al. 2016). (B) The non-recombining haplotype has expanded through the accumulation of repetitive elements, such that frequent and large insertions can indicate the occurrence of long-term suppressed recombination (Stolle et al. 2019). (C) If there is hemizygosity at the supergene, analyses based on the detection of regions showing consistently reduced read depth relative to the rest of the genome in relevant morphs can aid in identification of the supergene (Li et al. 2016).