Dsuite - fast D-statistics and related admixture evidence from VCF files

Patterson’s D, also known as the ABBA-BABA statistic, and related
statistics such as the f4-ratio, are commonly used to assess evidence of
gene flow between populations or closely related species. Currently
available implementations often require custom file formats, implement
only small subsets of the available statistics, and are impractical to
evaluate all gene flow hypotheses across datasets with many populations or
species due to computational inefficiencies. Here we present a new
software package Dsuite, an efficient implementation allowing genome scale
calculations of the D and f4-ratio statistics across all combinations of
tens or hundreds of populations or species directly from a variant call
format (VCF) file. Our program also implements statistics suited for
application to genomic windows, providing evidence of whether
introgression is confined to specific loci and it can also aid in
interpretation of a system of f4-ratio results with the use of the
‘f-branch’ method. Dsuite is available at
https://github.com/millanek/Dsuite, is straightforward to use,
substantially more computationally efficient than comparable programs, and
provides a convenient suite of tools and statistics, including some not
previously available in any software package. Thus, Dsuite facilitates the
assessment of evidence for gene flow, especially across larger genomic
datasets.