10.2 Inferring introgression from phylogenetic trees

One test for introgression – called the \(\textbf{D}\) statistic, or ABBA-BABA test – compares the phylogenetic tree of species-level relationships with the tree for a specific genetic variant.

We expect the species-level tree for Neanderthals and humans to look like the white bars of the tree in Fig. 2, where any two human populations are more similar to each other than they are to Neanderthals or chimpanzees (the outgroup).

If a genetic variant differs between humans and Neanderthals, we generally expect it to segregate according to the species-level tree, in an AABB pattern (Fig. 2).

Fig. 2. A variant concordant with the species-level tree for modern humans and Neanderthals.