Paradis Emmanuel auteur aut IRD text journalArticle eng text/pdf born digital access Molecular phylogenies contribute to the study of the patterns and processes of macroevolution even though past events (fossils) are not recorded in these data. In this article, I consider the general time-dependent birth-death model to fit any model of temporal variation in speciation and extinction to phylogenies. I establish formulae to compute the expected cumulative distribution function of branching times for any model, and, building on previous published works, I derive maximum likelihood estimators. Some limitations of the likelihood approach are described, and a fitting procedure based on least squares is developed that alleviates the shortcomings of maximum likelihood in the present context. Parametric and nonparametric bootstrap procedures are developed to assess uncertainty in the parameter estimates, the latter version giving narrower confidence intervals and being faster to compute. I also present several general algorithms of tree simulation in continuous time. I illustrate the application of this approach with the analysis of simulated datasets, and two published phylogenies of primates (Catarrhinae) and lizards (Agamidae). specialized Birth-death diversification extinction phylogeny speciation 020 021 65 3 661-672 2011 0014-3820 https://www.documentation.ird.fr/hor/fdi:010053197 10.1111/j.1558-5646.2010.01179.x 0014-3820 [F B010053197] https://www.documentation.ird.fr/hor/fdi:010053197 https://www.documentation.ird.fr/intranet/publi/2011/03/010053197.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2011-04-07 2018-07-02 fdi:010053197 fre