Methodology article
A Bayesian framework to estimate diversification rates and their variation through time and space
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* Corresponding author: Daniele Silvestro dsilvestro@senckenberg.de
- † Equal contributors
1 Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
2 Department of Botany and Molecular Evolution, Senckenberg Research Institute, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
3 Diversity and Evolution of Higher Plants, Institute of Ecology, Evolution and Diversity, Goethe University, Senckenberganlage 31, 60325 Frankfurt am Main, Germany
BMC Evolutionary Biology 2011, 11:311 doi:10.1186/1471-2148-11-311
Published: 21 October 2011Additional files
Additional file 1:
Marginal Likelihoods for different models of diversification. Marginal Likelihoods for simulated data sets calculated under birth-death (BD), pure-birth (PB), and pure-birth with rate shift (PB2-PB4) models based on thermodynamic integration.
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Additional file 2:
Posterior rate estimates. Parameter estimates, 95% credibility intervals and ESS values for all data sets simulated. All simulations settings are provided in Additional file 4.
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Additional file 3:
Effect of sequential estimation of divergence times and diversification rates. The potential impact of specifying priors on the birth-death parameters in both the molecular clock analysis and the subsequent rate estimation is assessed through generating a starting tree, simulating a molecular alignment on it, and run BEAST analyses on the alignment. The rate are then estimated on both the starting tree and the BEAST posterior trees, and compared.
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Additional file 4:
List of the simulation settings. Simulations were obtained from birth-death (BD), pure-birth (PB), pure-birth with rate shift (PB2-PB4), and (approximately) continuously decreasing speciation rates (SPVAR). The parameters included are speciation rates (λ), extinction rate (μ), time of rate shift (s), sampling fraction (ρ), and the shape parameter of the exponential transformation of λ through time (k). The continuously decreasing rates (SPVAR model) were approximated by imposing nine equally spaced rate shifts where speciation rates follow an exponential decrease. The value of λ reported for the SPVAR model represents the initial speciation rate (λ0).
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