A Rarefaction Approach to Identify Local Introgression in a Three Population Tree

Patterson’s D statistic, also known as the ABBA − BABA statistic, is widely used to detect the presence of archaic genome-wide introgression between two non-sister taxa. Requiring only a single lineage from each of four taxa where one taxon acts as an outgroup to determine the ancestral allele, Patterson’s D , counts the imbalance between the number of biallelic sites where either the second and third taxa (ABAB site) or the first and third taxa (BABA site). When there is no introgression, these counts are expected to be equal, and a discordance between counts suggests introgression from the third taxon into either the first or second. Patterson’s D is limited to the detection of genome-wide introgression and exhibits a high false-positive rate when applied to smaller genomic segments. Here, we present a new method, D STatistic with Allelic Rarefaction ( D ^∗ ), to address these limitations. D ^∗ uses multiple lineages and does not require an outgroup to calculate the imbalance between the number of alleles found exclusively in the second and third taxa and the number of alleles found exclusively in the first and third taxa. D ^∗ employs a rarefaction technique to correct for unequal sample-size and allows multiallelic sites. We use simulations to show that D ^∗ has better precision and recall for detecting introgressed segments of DNA when compared to similar methods under a wide variety of model parameters and in the presence of technical artifacts common to ancient DNA analyses. We conclude with an analysis of Denisovan DNA introgression in modern day Papuans. Precompiled executables, the manual, and source code can be found at https://github.com/TQ-Smith/DSTAR