RT Journal Article
SR Electronic
T1 Estimates of Introgression as a Function of Pairwise Distances
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 154377
DO 10.1101/154377
A1 Bastian Pfeifer
A1 Durrell D. Kapan
YR 2017
UL http://biorxiv.org/content/early/2017/06/23/154377.abstract
AB We introduce a new method to detect introgressed loci by combining two widely used statistics: dxy (the average pairwise nucleotide diversity between population x and y) and the four-taxon Patterson’s D statistic. The result is a statistic that takes into account genetic distance across possible topologies named the Bdf and is designed to detect and at the same time to quantify introgression. We also relate this new method to the recently published fd estimate and incorporate all statistics into the powerful genomics R-package PopGenome. The updated PopGenome version is freely available on CRAN. The supplement material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework.