title: Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record.
abstract: 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.
authors: Community and Conservation Ecology, Centre for Ecological and Evolutionary Studies, PO Box 11103, 9700 CC, Groningen, The Netherlands. r.s.etienne@rug.nl
authors: Rampal S
authors: RS
authors: Etienne
authors: Bart
authors: B
authors: Haegeman
authors: Tanja
authors: T
authors: Stadler
authors: Tracy
authors: T
authors: Aze
authors: Paul N
authors: PN
authors: Pearson
authors: Andy
authors: A
authors: Purvis
authors: Albert B
authors: AB
authors: Phillimore
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D053476:Extinction, Biological; D056908:Foraminifera / Q000145:classification / Q000235:genetics; D005580:Fossils; D014644:Genetic Variation; D007915:Lepidoptera / Q000145:classification / Q000235:genetics; D008957:Models, Genetic; D046109:Passeriformes / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D014562:Caudata / Q000145:classification / Q000235:genetics