SiPhyNetwork: An R package for simulating phylogenetic networks

Abstract

Abstract Gene flow is increasingly recognized as an important macroevolutionary process. The many mechanisms that contribute to gene flow (e.g. introgression, hybridization, lateral gene transfer) uniquely affect the diversification of dynamics of species, making it important to be able to account for these idiosyncrasies when constructing phylogenetic models. Existing phylogenetic‐network simulators for macroevolution are limited in the ways they model gene flow. We present SiPhyNetwork, an R package for simulating phylogenetic networks under a birth–death‐hybridization process. Our package unifies the existing birth–death‐hybridization models while also extending the toolkit for modelling gene flow. This tool can create patterns of reticulation such as hybridization, lateral gene transfer, and introgression. Specifically, we model different reticulate events by allowing events to either add, remove or keep constant the number of lineages. Additionally, we allow reticulation events to be trait dependent, creating the ability to model the expanse of isolating mechanisms that prevent gene flow. This tool makes it possible for researchers to model many of the complex biological factors associated with gene flow in a phylogenetic context.