Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

• Published in: Proceedings of the Royal Society B: Biological Sciences
• Main Authors: Etienne, Rampal S., Haegeman, Bart, Stadler, Tanja, Aze, Tracy, Pearson, Paul N., Purvis, Andy, Phillimore, Albert B.
• Other Authors: Centre for Ecological and Evolutionary studies Groningen, University of Groningen Groningen, Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Water Resource Modeling (MERE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Institut fur Integrative Biologie, School of Earth and Ocean Sciences Cardiff, Cardiff University, Division of Biology London, Imperial College London
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2012
• Subjects: birth-death model; diversification; missing species; [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH]; Planktonic foraminifera
• Online Access: https://hal.inria.fr/hal-00859543; https://doi.org/10.1098/rspb.2011.1439

aeres : ACL International audience The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there are often limits to diversity. Here, we present a general approach to evaluate the likelihood of a phylogeny under a model that accommodates diversity-dependence and extinction. We find, by likelihood maximization, that extinction is estimated most precisely if the rate of increase in the number of lineages in the phylogeny saturates towards the present or first decreases and then increases. We demonstrate the utility and limits of our approach by applying it to the phylogenies for two cases where a fossil record exists (Cetacea and Cenozoic macroperforate planktonic foraminifera) and to three radiations lacking fossil evidence (Dendroica, Plethodon and Heliconius). We propose that the diversity-dependence model with extinction be used as the standard model for macro-evolutionary dynamics because of its biological realism and flexibility.