RT Journal Article
SR Electronic
T1 Evaluating the use of ABBA-BABA statistics to locate introgressed loci
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 001347
DO 10.1101/001347
A1 Simon H. Martin
A1 John W. Davey
A1 Chris D. Jiggins
YR 2014
UL http://biorxiv.org/content/early/2014/06/02/001347.abstract
AB 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. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D when applied to small genomic regions, as has been attempted in several recent studies. We find that D is unreliable 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 fd, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. fd is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f outliers tend to cluster in regions of low genetic divergence, which can confound analyses aimed at differentiating introgression from shared ancestral variation at individual loci.