Figure 3.

Biallelic site patterns are informative of underlying gene tree topologies. Except for low levels of homoplasy, such patterns can only arise from mutations (blue) on internal branches of the local genealogy. The occurrence of the incongruent site patterns “ABBA” (top middle) and “BABA” (top right) are therefore expected to reflect the frequency of discordant gene tree topologies. With introgression between a specific nonsister species pair, one incongruent pattern (bottom) can increase in frequency over the other due to the underlying asymmetry in gene tree frequencies.