Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

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…

• LT
  Leverhulme Trust
• BA
  Biotechnology and Biological Sciences Research Council

  Awards: BB/H01439X/1, H01439X/1