Abstract
Most living organisms that ever existed on Earth have left no descendants. Because introgressions and lateral gene transfers are frequent, some of these extinct lineages have impacted the evolution of extant species and their ancestors. As a consequence, ignoring extinct lineages in evolutionary studies can lead to spurious conclusions. Here we present Zombi, a platform to simulate the evolution of species, genes and genomes taking extinct lineages into account. We demonstrate its utility by testing a statistical inference method used to detect introgression and show that ignoring the presence of extinct lineages yields inconsistent results.
New Approaches Zombi is a platform designed to simulate evolutionary processes at different levels ranging from the species tree to the genomes and its constituent genes and their sequences, that evolve along it. Zombi considers explicitly the evolution of genomes in extinct lineages and thus the possibility for lateral gene transfers and introgressions to occur between species that are not represented in the extant phylogeny. Zombi provides the user with a clear and detailed output of the complete evolutionary process simulated. Zombi is written in Python 3.6 using the ETE 3 toolkit (Huerta-Cepas, Serra, & Bork, 2016) and the Pyvolve package (Spielman & Wilke, 2015). It is freely available at https://github.com/AADavin/ZOMBI.