title: Evaluating the use of ABBA-BABA statistics to locate introgressed loci.
abstract: 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.
authors.affiliation: Department of Zoology, University of Cambridge, Cambridge, United Kingdom shm45@cam.ac.uk.
authors.forename: Simon H
authors.initials: SH
authors.lastname: Martin
authors.affiliation: Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: John W
authors.initials: JW
authors.lastname: Davey
authors.affiliation: Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Chris D
authors.initials: CD
authors.lastname: Jiggins
mesh_terms: D000465:Algorithms; D000818:Animals; D002080:Butterflies / Q000235:genetics*; D003198:Computer Simulation; D019143:Evolution, Molecular; D051456:Gene Flow; D049750:Genome, Insect; D015233:Models, Statistical
keywords: ABBA–BABA; Heliconius; gene flow; introgression; population structure; simulation