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Mol Biol Evol. 2015 Jan;32(1):244-57. doi: 10.1093/molbev/msu269. Epub 2014 Sep 22.

Evaluating the use of ABBA-BABA statistics to locate introgressed loci.

Author information

1
Department of Zoology, University of Cambridge, Cambridge, United Kingdom shm45@cam.ac.uk.
2
Department of Zoology, University of Cambridge, Cambridge, United Kingdom.

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.

KEYWORDS:

ABBA–BABA; Heliconius; gene flow; introgression; population structure; simulation

PMID:
25246699
PMCID:
PMC4271521
DOI:
10.1093/molbev/msu269
[Indexed for MEDLINE]
Free PMC Article

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