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A model with many small shifts for estimating species-specific diversification rates

Nature Ecology & Evolution volume 3, pages 1086–1092 (2019)Cite this article

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Abstract

Understanding how and why diversification rates vary through time and space and across species groups is key to understanding the emergence of today’s biodiversity. Phylogenetic approaches aimed at identifying variations in diversification rates during the evolutionary history of clades have focused on exceptional shifts subtending evolutionary radiations. While such shifts have undoubtedly affected the history of life, identifying smaller but more frequent changes is important as well. We developed ClaDS—a new Bayesian approach for estimating branch-specific diversification rates on a phylogeny that relies on a model with changes in diversification rates at each speciation event. We show, using Monte Carlo simulations, that the approach performs well at inferring both small and large changes in diversification. Applying our approach to bird phylogenies covering the entire avian radiation, we find that diversification rates are remarkably heterogeneous within evolutionarily restricted species groups. Some groups such as Accipitridae (hawks and allies) cover almost the full range of speciation rates found across the entire bird radiation. As much as 76% of the variation in branch-specific rates across this radiation is due to intraclade variation, suggesting that a large part of the variation in diversification rates is due to many small, rather than few large, shifts.

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Fig. 1: Illustration of the ClaDS model.
Fig. 2: Recovery of ClaDS parameters.
Fig. 3: ClaDS performs well in recovering branch-specific speciation rates.
Fig. 4: Patterns of diversification across 42 bird clades.

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Data availability

The simulated phylogenies used to test the method are available at https://github.com/OdileMaliet/ClaDS/tree/master/Simulations in a file named trees.zip. All of the empirical data used for the analysis were obtained from the Jetz et al.4 study, and are available from https://www.nature.com/articles/nature11631.

Code availability

The R functions used to simulate and fit the model are available in the RPANDA R package. All of the codes used to test our method are available from the GitHub repository at https://github.com/OdileMaliet/ClaDS.git.

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Acknowledgements

The authors are very grateful to L. Arístide, J. Clavel, J. Drury, C. Fruciano, S. Lambert, E. Lewitus, M. Manceau, O. Missa, B. Perez, A. Catarina Silva and G. Sommeria-Klein for their helpful comments on an earlier version of this manuscript. This work was supported by an AMX grant (from École Polytechique) and the LabEx MemoLife (to O.M.), PROCOPE Mobility Grant 57134817 (to F.H. and H.M.) and the European Research Council (ERC 616419-PANDA to H.M.).

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Authors and Affiliations

  1. Institut de Biologie de l’École Normale Supérieure, École Normale Supérieure, CNRS, INSERM, PSL Research University, Paris, France

    Odile Maliet & Hélène Morlon

  2. Theoretical Ecology, Faculty of Biology and Preclinical Medicine, University of Regensburg, Regenburg, Germany

    Florian Hartig

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  1. Odile Maliet
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Contributions

O.M., F.H. and H.M. designed the study and performed research. O.M. contributed new analytical tools and analysed the data. O.M., F.H. and H.M. wrote the paper.

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Correspondence to Odile Maliet.

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Supplementary Methods, Results and Figs. 1–34

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Maliet, O., Hartig, F. & Morlon, H. A model with many small shifts for estimating species-specific diversification rates. Nat Ecol Evol 3, 1086–1092 (2019). https://doi.org/10.1038/s41559-019-0908-0

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