Data from: 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 to cluster in genomic regions of reduced diversity. As an
alternative, we propose a related statistic f̂d, a modified version of a
statistic originally developed to estimate the genome-wide fraction of
admixture. f̂d is not subject to the same biases as D, and is better at
identifying introgressed loci. Finally, we show that both D and f̂d
outliers tend to cluster in regions of low absolute divergence (dXY),
which can confound a recently proposed test for differentiating
introgression from shared ancestral variation at individual loci.