Evaluating the use of ABBA-BABA statistics to locate introgressed loci

Mol Biol Evol. 2015 Jan;32(1):244-57. doi: 10.1093/molbev/msu269. Epub 2014 Sep 22.


Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide 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. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole-genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic ƒ(d), a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. ƒ(d) is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and ƒ(d) outliers tend to cluster in regions of low absolute divergence (d(XY)), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

Keywords: ABBA–BABA; Heliconius; gene flow; introgression; population structure; simulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Butterflies / genetics*
  • Computer Simulation*
  • Evolution, Molecular
  • Gene Flow
  • Genome, Insect*
  • Models, Statistical

Associated data

  • Dryad/10.5061/dryad.J1RM6