title: Quantifying variation in speciation and extinction rates with clade data.
abstract: High-level phylogenies are very common in evolutionary analyses, although they are often treated as incomplete data. Here, we provide statistical tools to analyze what we name "clade data," which are the ages of clades together with their numbers of species. We develop a general approach for the statistical modeling of variation in speciation and extinction rates, including temporal variation, unknown variation, and linear and nonlinear modeling. We show how this approach can be generalized to a wide range of situations, including testing the effects of life-history traits and environmental variables on diversification rates. We report the results of an extensive simulation study to assess the performance of some statistical tests presented here as well as of the estimators of speciation and extinction rates. These latter results suggest the possibility to estimate correctly extinction rate in the absence of fossils. An example with data on fish is presented.
authors.affiliation: Institut de Recherche pour le Développement, ISEM UMR 226/5554 - UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta, 12730, Indonesia. Emmanuel.Paradis@ird.fr.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Paradis
authors.forename: Pablo A
authors.initials: PA
authors.lastname: Tedesco
authors.forename: Bernard
authors.initials: B
authors.lastname: Hugueny
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D053476:Extinction, Biological; D005399:Fishes / Q000235:genetics; D049810:Genetic Speciation; D014644:Genetic Variation; D008957:Models, Genetic
keywords: Birth-death models; extinction; maximum likelihood; speciation; stem ages