Fast and accurate estimation of species-specific diversification rates using data augmentation
Data files
Nov 03, 2020 version files 877.59 MB
-
clads_Birds.jld2
877.27 MB
-
SI_ClaDS_DA_v1.pdf
319.33 KB
Abstract
Methods
These additionnal data contains supplementary figures supporting the paper, as well as a tutorial for the use of the Julia package.
The .jld2 file is the result of the run of ClaDS on the complete bird phylogeny computed with molecular data from Jetz (2012) with the Hackett backbone, containing 6670 species. We use TreeAnnotator from the software Beast with the Common Ancestor option for node height (Bouckaert 2019) to obtain a Maximum Clade Credibility (MCC) tree computed from a sample of 1000 trees from the posterior distribution. We fix the sampling fractions for each of the subtrees of the tree from Jetz (2012) as the ratio between the number of species in the molecular phylogeny over that in the phylogeny including all bird species. We attach the results of this analysis as a supplementary material to this paper.
Bouckaert, R., T. G. Vaughan, J. Barido-Sottani, S. Duchêne, M. Fourment, A. Gavryushkina,
J. Heled, G. Jones, D. Kühnert, N. De Maio, et al. 2019. Beast 2.5: An advanced software
platform for bayesian evolutionary analysis. PLoS computational biology 15:e1006650.
Jetz, W., G. Thomas, J. Joy, K. Hartmann, and A. Mooers. 2012. The global diversity of birds in
space and time. Nature 491:444.