Zombi: A simulator of species, genes and genomes that accounts for extinct lineages.

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.