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Estimating a time-calibrated phylogeny of fossil and extant taxa using RevBayes

Abstract : The fossil record is the primary source of time-stamped information useful for dating phylogenetic trees; and many statistical approaches are available for integrating data from fossil and living species. In this tutorial, we demonstrate how to perform joint inference of divergence times and phylogenetic relationships of fossil and extant taxa from morphological data using the program RevBayes. RevBayes (http://revbayes.com) is a flexible and powerful tool for Bayesian phylogenetic inference. Statistical models in RevBayes are built using probabilistic graphical models and described via an interpreted programming language. As a result, RevBayes offers a wide range of statistical models—ranging from very simple models with few parameters to hierarchical models describing complex biological processes—that are useful in many biological applications. The exercise described here provides instructions on how to construct a phylogenetic model combining the fossilized birth-death process and models describing the generation of morphological data, which is then used to execute an analysis that unites modern and extinct taxa in a dated phylogenetic tree. The content and associated files for this tutorial are kept up-to-date at: http://revbayes.com/tutorials/fbd_simple.
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Joëlle Barido-Sottani, Joshua A. Justison, April M. Wright, Rachel C.M. Warnock, Walker Pett, et al.. Estimating a time-calibrated phylogeny of fossil and extant taxa using RevBayes. Céline Scornavacca; Frédéric Delsuc; Nicolas Galtier. Phylogenetics in the Genomic Era, No commercial publisher | Authors open access book, pp.5.2:1--5.2:23, 2020. ⟨hal-02536394⟩

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