Daniele Silvestro, Rachel C. M. Warnock, Alexandra Gavryushkina & Tanja Stadler
Nature Communications volume 9, Article number: 5237 (2018)
Abstract
Measuring the pace at which speciation and extinction occur is fundamental to understanding the origin and evolution of biodiversity. Both the fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results. Despite its implications, the theoretical reasons for this discrepancy remain unknown. Here, we reveal a conceptual and methodological basis able to reconcile palaeontological and molecular evidence: discrepancies are driven by different implicit assumptions about the processes of speciation and species evolution in palaeontological and neontological analyses. We present the “birth-death chronospecies” model that clarifies the definition of speciation and extinction processes allowing for a coherent joint analysis of fossil and phylogenetic data. Using simulations and empirical analyses we demonstrate not only that this model explains much of the apparent incongruence between fossils and phylogenies, but that differences in rate estimates are actually informative about the prevalence of different speciation modes.
Acknowledgements
We thank David Bapst and Charles Marshall for providing valuable feedback on the manuscript. In addition, we thank Ziheng Yang, Andreas Steingötter and the ETH Seminar for Statistics group for providing advice on model testing and Carl Simpson for providing data. D.S. received funding from the Swedish Research Council (2015-04748) and from the Swedish Foundation for Strategic Research. R.C.M.W. was funded by the ETH Zürich Postdoctoral Fellowship and Marie Curie Actions for People COFUND programme. T.S. is supported in part by the European Research Council under the Seventh Framework Programme of the European Commission (PhyPD: grant agreement number 335529). A.G. was funded by the Bioprotection Research Centre. Part of the analyses were run at the high-performance computing centre Vital-IT of the Swiss Institute of Bioinformatics (Lausanne, Switzerland).
Author information
Author notes
These authors contributed equally: Daniele Silvestro, Rachel C. M. Warnock.
Affiliations
Department of Biological and Environmental Sciences, University of Gothenburg, 41319, Gothenburg, Sweden
Daniele Silvestro
Global Gothenburg Biodiversity Centre, 41319, Gothenburg, Sweden
Daniele Silvestro
Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland
Daniele Silvestro
Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
Daniele Silvestro
, Rachel C. M. Warnock
& Tanja Stadler
Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, 4058, Basel, Switzerland
Rachel C. M. Warnock
& Tanja Stadler
Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
Alexandra Gavryushkina
Contributions
D.S., R.C.M.W., A.G., and T.S. designed the study and developed the methods. D.S. and R.C.M.W. wrote the manuscript with contributions from all authors. R.C.M.W. implemented the maximum likelihood tests and ran the simulations. D.S. implemented the Bayesian version of the BDC model and analysed the empirical data sets.
Nature Communications volume 9, Article number: 5237 (2018)
Speciation modes reflecting the difference in phylogenetic and stratigraphic interpretations of speciation and extinction rates.
Measuring the pace at which speciation and extinction occur is fundamental to understanding the origin and evolution of biodiversity. Both the fossil record and molecular phylogenies of living species can provide independent estimates of speciation and extinction rates, but often produce strikingly divergent results. Despite its implications, the theoretical reasons for this discrepancy remain unknown. Here, we reveal a conceptual and methodological basis able to reconcile palaeontological and molecular evidence: discrepancies are driven by different implicit assumptions about the processes of speciation and species evolution in palaeontological and neontological analyses. We present the “birth-death chronospecies” model that clarifies the definition of speciation and extinction processes allowing for a coherent joint analysis of fossil and phylogenetic data. Using simulations and empirical analyses we demonstrate not only that this model explains much of the apparent incongruence between fossils and phylogenies, but that differences in rate estimates are actually informative about the prevalence of different speciation modes.
Acknowledgements
We thank David Bapst and Charles Marshall for providing valuable feedback on the manuscript. In addition, we thank Ziheng Yang, Andreas Steingötter and the ETH Seminar for Statistics group for providing advice on model testing and Carl Simpson for providing data. D.S. received funding from the Swedish Research Council (2015-04748) and from the Swedish Foundation for Strategic Research. R.C.M.W. was funded by the ETH Zürich Postdoctoral Fellowship and Marie Curie Actions for People COFUND programme. T.S. is supported in part by the European Research Council under the Seventh Framework Programme of the European Commission (PhyPD: grant agreement number 335529). A.G. was funded by the Bioprotection Research Centre. Part of the analyses were run at the high-performance computing centre Vital-IT of the Swiss Institute of Bioinformatics (Lausanne, Switzerland).
Author information
Author notes
These authors contributed equally: Daniele Silvestro, Rachel C. M. Warnock.
Affiliations
Department of Biological and Environmental Sciences, University of Gothenburg, 41319, Gothenburg, Sweden
Daniele Silvestro
Global Gothenburg Biodiversity Centre, 41319, Gothenburg, Sweden
Daniele Silvestro
Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland
Daniele Silvestro
Swiss Institute of Bioinformatics (SIB), 1015, Lausanne, Switzerland
Daniele Silvestro
, Rachel C. M. Warnock
& Tanja Stadler
Department of Biosystems Science & Engineering, Eidgenössische Technische Hochschule Zürich, 4058, Basel, Switzerland
Rachel C. M. Warnock
& Tanja Stadler
Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
Alexandra Gavryushkina
Contributions
D.S., R.C.M.W., A.G., and T.S. designed the study and developed the methods. D.S. and R.C.M.W. wrote the manuscript with contributions from all authors. R.C.M.W. implemented the maximum likelihood tests and ran the simulations. D.S. implemented the Bayesian version of the BDC model and analysed the empirical data sets.
Competing interests
The authors declare no competing interests.
Corresponding author
Correspondence to Daniele Silvestro.
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About this article
Publication history
Received 19 December 2017 Accepted 13 November 2018
Published 07 December 2018
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