Detection and Polarization of Introgression in a Five-Taxon Phylogeny

Pease, James B.
Hahn, Matthew W.

¹Department of Biology, Indiana University, 1001 E. Third St., Bloomington, IN 47405, USA and ²School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA

*Correspondence to be sent to: Department of Biology, Indiana University, 1001 E. Third St., Bloomington, IN, 47405, USA. E-mail: [email protected]

Associate Editor: Laura Kubatko

Received February 9, 2015

Accepted April 10, 2015

Systematic Biology 64(4):p 651-662, July 2015. | DOI: 10.1093/sysbio/syv023

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 -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 -statistics to a larger tree topology, and propose new 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 statistics correctly identify the introgression donor and recipient lineages, even at low rates of introgression. is also shown to have extremely low false-positive rates. The 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.