Detection and polarization of introgression in a five-taxon phylogeny

When multiple speciation events occur rapidly in succession, discordant genealogies due to incomplete lineage sorting (ILS) can complicate the detection of introgression. A variety of methods, including the D-statistic (a.k.a. the “ABBA–BABA test”), have been proposed to infer introgression in the presence of ILS for a four-taxon clade. However, no integrated method exists to detect introgression using allelic patterns for more complex phylogenies. Here we explore the issues associated with previous systems of applying D-statistics to a larger tree topology, and propose new DFOIL tests as an integrated framework to infer both the taxa involved in and the direction of introgression for a symmetric five-taxon phylogeny. Using theory and simulations, we show that the DFOIL statistics correctly identify the introgression donor and recipient lineages, even at low rates of introgression. DFOIL is also shown to have extremely low false-positive rates. The DFOIL tests are computationally inexpensive to calculate and can easily be applied to phylogenomic data sets, both genome-wide and in windows of the genome. In addition, we explore both the principles and problems of introgression detection in even more complex phylogenies.