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Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data

Silvestro, Daniele ; Schnitzler, Jan ; Liow, Lee Hsiang ; Antonelli, Alexandre ; Salamin, Nicolas

In: Systematic Biology, 2014, vol. 63, no. 3, p. 349-367

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    Titre
    • Bayesian Estimation of Speciation and Extinction from Incomplete Fossil Occurrence Data
    Auteur
    • Silvestro, Daniele. Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
    • Schnitzler, Jan. Biodiversity and Climate Research Centre & Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
    • Liow, Lee Hsiang. Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway; and
    • Antonelli, Alexandre. Department of Plant and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, 413 19 Gothenburg, Sweden
    • Salamin, Nicolas. Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Systematic Biology, 2014, vol. 63, no. 3, p. 349-367. Oxford University Press
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:291929
    Summary
    The temporal dynamics of species diversity are shaped by variations in the rates of speciation and extinction, and there is a long history of inferring these rates using first and last appearances of taxa in the fossil record. Understanding diversity dynamics critically depends on unbiased estimates of the unobserved times of speciation and extinction for all lineages, but the inference of these parameters is challenging due to the complex nature of the available data. Here, we present a new probabilistic framework to jointly estimate species-specific times of speciation and extinction and the rates of the underlying birth-death process based on the fossil record. The rates are allowed to vary through time independently of each other, and the probability of preservation and sampling is explicitly incorporated in the model to estimate the true lifespan of each lineage. We implement a Bayesian algorithm to assess the presence of rate shifts by exploring alternative diversification models. Tests on a range of simulated data sets reveal the accuracy and robustness of our approach against violations of the underlying assumptions and various degrees of data incompleteness. Finally, we demonstrate the application of our method with the diversification of the mammal family Rhinocerotidae and reveal a complex history of repeated and independent temporal shifts of both speciation and extinction rates, leading to the expansion and subsequent decline of the group. The estimated parameters of the birth-death process implemented here are directly comparable with those obtained from dated molecular phylogenies. Thus, our model represents a step towards integrating phylogenetic and fossil information to infer macroevolutionary processes.[BDMCMC; biodiversity trends; Birth-death process; incomplete fossil sampling; macroevolution; species rise and fall.]