Phylogenomic methods for examining species relationship and admixture. The methods involve a rooted four-taxon phylogeny, specifically with three species (P1, P2, and P3) and an outgroup (O). P1 and P2 are most closely related to each other while P3 is an in-group taxon that is equally distant to both P1 and P2. (A) Gene tree topology test. T1, T2, and T3 represent total number of genes supporting Topology 1, 2, and 3, respectively. In this hypothetical example, Topology 1 is assumed to be the major topology. (B) ABBA-BABA test. N_ABBA and N_BABA represent total number of sites with the “ABBA” and “BABA” conformation, respectively.