quaint: An R Package for detecting introgression across a phylogeny using discordant gene tree topologies

Abstract

Premise: Hybrid speciation and introgressive hybridization are increasingly recognized as important evolutionary phenomena across the tree of life. One widely used class of methods to detect introgression includes D statistics and related methods which employ the ABBA-BABA test using nucleotide site patterns. Recent studies have applied this theoretical framework to phylogenomic datasets using gene tree topologies instead, but no software packages using this method have been developed. Methods and Results: An R package was developed to facilitate the inference of introgression given a set of gene trees and a species tree. Using an ABBA-BABA framework, this package summarizes patterns of gene tree discordance to infer introgression across large phylogenies. Conclusions: Using gene tree topologies, quaint overcomes the limitations of site-based methods, enabling the detection of introgression across broad phylogenomic contexts. This R package provides an accessible and reproducible tool for researchers investigating reticulate evolution.