TY - JOUR T1 - Evaluating the use of ABBA-BABA statistics to locate introgressed loci JF - bioRxiv DO - 10.1101/001347 SP - 001347 AU - Simon H. Martin AU - John W. Davey AU - Chris D. Jiggins Y1 - 2013/01/01 UR - http://biorxiv.org/content/early/2013/12/11/001347.abstract N2 - Several methods have been proposed to test for introgression across genomes. One method identifies an excess of shared derived alleles between taxa using Patterson’s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Smith and Kronforst (2013) propose that, at loci identified as outliers for the D statistic, introgression is indicated by a reduction in absolute genetic divergence (dXY) between taxa with shared ancestry, whereas ancestral structure produces no reduction in dXY at these loci. Here, we use simulations and Heliconius butterfly data to investigate the behavior of D when applied to small genomic regions. We find that D imperfectly identifies loci with shared ancestry in many scenarios due to a bias in regions with few segregating sites. A related statistic, f, is mostly robust to this bias but becomes less accurate as gene flow becomes more ancient. Although reduced dXY does indicate introgression when loci with shared ancestry can be accurately detected, both D and f systematically identify regions of lower dXY in the presence of both gene flow and ancestral structure, so detecting a reduction in dXY at D or f outliers is not sufficient to infer introgression. However, models including gene flow produced a larger reduction in dXY than models including ancestral structure in almost all cases, so this reduction may be suggestive, but not conclusive, evidence for introgression. ER -