Dsuite ‐ Fast <i>D</i>‐statistics and related admixture evidence from VCF files

<jats:title>Abstract</jats:title><jats:p>Patterson's <jats:italic>D</jats:italic>, also known as the ABBA‐BABA statistic, and related statistics such as the <jats:italic>f</jats:italic><jats:sub>4</jats:sub>‐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 data sets with many populations or species due to computational inefficiencies. Here, we present a new software package <jats:styled-content>Dsuite</jats:styled-content>, an efficient implementation allowing genome scale calculations of the <jats:italic>D</jats:italic> and <jats:italic>f</jats:italic><jats:sub>4</jats:sub>‐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 <jats:italic>f</jats:italic><jats:sub>4</jats:sub>‐ratio results with the use of the “<jats:italic>f</jats:italic>‐branch” method. <jats:styled-content>Dsuite</jats:styled-content> is available at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="https://github.com/millanek/Dsuite">https://github.com/millanek/Dsuite</jats:ext-link>, 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, <jats:styled-content>Dsuite</jats:styled-content> facilitates the assessment of evidence for gene flow, especially across larger genomic data sets.</jats:p>