SiPhyNetwork: An R package for Simulating Phylogenetic Networks

Abstract

O_LIGene 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. C_LIO_LIWe present SiPhyNetwork, an R package for simulating phylogenetic networks under a birth-death-hybridization process. C_LIO_LIOur package unifies the existing birth-death-hybridization models while also extending the toolkit for modeling gene flow. This tool can create patterns of reticulation such as hybridization, lateral gene transfer, and introgression. C_LIO_LISpecifically, 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. C_LI