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bioRxiv · 10.1101/001347

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

Simon H. Martin·John W. Davey·Chris D. Jiggins
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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 Pattersons 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 [Formula] a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. [Formula] is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and [Formula] 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.

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Simon H. Martin, John W. Davey, Chris D. Jiggins. 2013-12-11. Evaluating the use of ABBA-BABA statistics to locate introgressed loci. https://doi.org/10.1101/001347

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