Figure 1.

Expected gene tree topologies and coalescence times under ILS only. For a rooted triplet, four topologies are possible (top row): two concordant with the species tree, which can result either from lineage sorting or ILS (top left), and two that are discordant with the species tree and arise from ILS only (top right). The two concordant trees must be at least as frequent as the two discordant trees, which are equally frequent to each other. For nonsister pairs of taxa—either P2–P3 (bottom left) or P1–P3 (bottom right)—coalescence is expected to occur at one of two times, depending on whether they coalesce first or second in a gene tree (gray dotted lines). These expected times are symmetrical across gene trees, and so pairwise divergences between the nonsister lineages are expected to be equal when averaged across loci.