Comp-D: a program for comprehensive computation of D-statistics and population summaries of reticulated evolution
Computation of Patterson’s D-statistic and its five-taxon derivatives are important phylogenetic methods for the quantification of reticulated evolution, yet are limited in application by the lack of a single, comprehensive program to efficiently perform all necessary calculations from common phylogenetic and population genetic program file formats. To increase accessibility for a broad range of researchers, we present a user-friendly program (COMP-D) that provides flexibility for incorporating heterozygous sites, implements multiple statistical methods, and aggregates results from multiple tests. Program augmentations also facilitate the detection of population-level introgression. COMP-D provides a threefold increase in speed relative to comparable software. It is implemented in C++ and released under the GNU General Public License v3.0. Source code is available for Linux/Mac OS X from: https://github.com/stevemussmann/Comp-D_MPI.
KeywordsRADseq Introgression SNP analysis Next-generation sequencing
The Arkansas High Performance Computing Center (AHPCC) provided technical assistance and computational resources. Tyler K. Chafin and Bradley T. Martin promoted software development by testing an early version of the program. This research was conducted in partial fulfillment of the Ph.D. degree in Biological Sciences at University of Arkansas (SMM). It was supported by generous University of Arkansas endowments: The Bruker Professorship in Life Sciences (MRD), the twenty-first Century Chair in Global Change Biology (MED), and a Doctoral Academy Fellowship (SMM). Three anonymous reviewers provided comments that greatly improved the manuscript.
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Conflict of interest
The authors have nothing to disclose.