Which Random Processes Describe the Tree of Life? A Large-Scale Study of Phylogenetic Tree Imbalance

Abstract

The explosion of phylogenetic studies not only provides a clear snapshot of biodiversity, but also makes it possible to infer how the diversity has arisen (see, for example, Purvis and Hector, 2000; Harvey et al., 1996; Nee et al., 1996; Mace et al., 2003). To this aim, variation in speciation and extinction rates have been investigated through their signatures in the shapes of phylogenetic trees (Mooers and Heard, 1997). This issue is of great importance, as fitting stochastic models to tree data would help to understand underlying macroevolutionary processes. Although the prevailing view is that it does not represent phylogenies so well, the most popular model of phylogenetic trees is a branching process introduced by Yule, in which lineages split at random (Yule, 1924). Here we report the study of one major database of published phylogenies using the Yule model as well as several other models. Our results confirm the previous observation that the Yule model is inadequate to describe phylogenetic tree data. In addition, they support the hypothesis that many trees are consistent with a simple branch split model first considered by Aldous in 1996.