QUANTIFYING VARIATION IN SPECIATION AND EXTINCTION RATES WITH CLADE DATA |
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Authors: | Emmanuel Paradis Pablo A. Tedesco Bernard Hugueny |
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Affiliation: | 1. Institut de Recherche pour le Développement, ISEM UMR 226/5554 – UM2/CNRS/IRD, , Jakarta, 12730 Indonesia;2. UMR Biologie des ORganismes et des écosystémes Aquatiques (UMR BOREA, IRD 207‐CNRS 7208‐UPMC‐MNHN), Département Milieux et Peuplements Aquatiques, Muséum National d'Histoire Naturelle, , 75231 Paris, cedex, France |
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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. |
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Keywords: | Birth– death models extinction maximum likelihood speciation stem ages |
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