coalescent with epistasis

Kelly JK & Wade MJ 2000 Molecular evolution near a two-locus balanced polymorphism. J Theor Biol 204:83-101.

• the three loci are sufficiently close so that at most one recombination event in the region spanning A, B, and C is possible per generation per sequence
• when the neutral locus is between the selected loci, then r_AB = r_AC + r_BC

• when the recombination rates between neutral and selected loci are sufficiently low, the expected coalescent time for two neutral alleles depends on the frequency of their associated haplotype
• we develop the coalescent theory for neutral alleles conditional on their associated haplotype