Figure 2. Lineages at a Locus under Long-Term Balancing Selection.

Two haplotypes with different alleles, A_x and A_y, which diverged before the common ancestor of two species (1 and 2), are denoted by black and grey lines and boxes, respectively (denoting genes). Variants in the regions in and around the selected locus will remain associated with the haplotype in which they arose until recombination occurs with a different haplotype, even after the species become isolated. Species–specific differences (shown as thin horizontal lines in the tree and vertical lines in the haplotypes) will also accumulate. Recombination between different haplotypes (indicated by mixed black–grey haplotypes) will mean that sites close to the selected sites will be most differentiated between alleles (see Figure 1).