TreeSimGM: Simulating phylogenetic trees under general Bellman-Harris models with lineage-specific shifts of speciation and extinction in R.

Abstract

Understanding macroevolutionary processes using phylogenetic trees is a challenging and complex process that draws on mathematics, computer science and biology. Given the development of complex mathematical models and the growing computational processing power, simulation tools are becoming increasingly popular.In order to simulate phylogenetic trees, most evolutionary biologists are forced to build their own algorithms or use existing tools built on different platforms and/or as standalone programmes. The absence of a simulation tool accommodating for user‐chosen model specifications limits, amongst others, model testing and pipelining with approximate Bayesian computation methods or other subsequent statistical analysis.We introduce “TreeSimGM,” an r‐package simulation tool for phylogenetic trees under a general Bellman and Harris model. This package allows the user to specify any desired probability distribution for the waiting times until speciation and extinction (e.g. age‐dependent speciation/extinction). Upon speciation, the user can specify whether one descendant species corresponds to the ancestor species inheriting its age or whether both descendant species are new species of age 0. Moreover, it is possible to scale the waiting time to speciation/extinction for newly formed species. Thus, “TreeSimGM” not only allows the user to simulate stochastic phylogenetic trees assuming several popular existing models, such as the Yule model, the constant‐rate birth–death model, and proportional to distinguishable arrangement models, but it also allows the user to formulate new models for exploration. A short explanation of the supported models and a few examples of how to use our package are presented here.As an r‐package, “TreeSimGM” allows flexible and powerful stochastic phylogenetic tree simulations. Moreover, it facilitates the pipelining of outputs or inputs with other functions in r. “TreeSimGM” contributes to the tools available to the r community in the fields of ecology and evolution, is freely available under the GPL‐2 licence and can be downloaded at https://cran.r-project.org/web/packages/TreeSimGM.