PT  - JOURNAL ARTICLE
AU  - Simon H. Martin
AU  - John W. Davey
AU  - Chris D. Jiggins
TI  - Evaluating the use of ABBA-BABA statistics to locate introgressed loci
AID  - 10.1101/001347
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 001347
4099  - http://biorxiv.org/content/early/2014/06/02/001347.short
4100  - http://biorxiv.org/content/early/2014/06/02/001347.full
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.