Summary
CladeAge is an add-on package for the Bayesian software BEAST 2 which allows time calibration of phylogenetic trees based on probability densities for clade ages, calculated from a model of constant diversification and fossil sampling.
Background
In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. CladeAge overcomes this limitation by calculating optimal calibration densities for clades with fossil records, based on estimates for diversification rates and the so-called fossil sampling rate. This rate characterizes the frequency, with which fossils are preserved along branches of a phylogeny, and only fossils that are ultimately sampled (and published) by researchers used for this measure. A variety of tools are available to estimate this sampling rate for individual clades (e.g. TRiPS or PyRate), and the same is the case for the estimation of diversification rates (e.g. MEDUSA or BAMM).
How CladeAge works
Like other add-on packages for BEAST 2, CladeAge can be installed through the package manager that's built into BEAUti, a utility tool that comes with the BEAST 2 download. To install CladeAge, open BEAUti, and select "Manage packages" from the File menu. Then select the "CA" package from the list and click the Install/Upgrade button. Restart BEAUti, and a new panel for "Fossil Priors" should appear. This is where you can specify rate estimates for speciation, extinction, and fossil sampling, and optimal calibration densities for these parameters will be automatically calculated. You may then prepare the BEAST 2 XML file just like you would with other calibration densities. When you then run this XML file with BEAST 2, the CladeAge calibration densities will be used for divergence time estimation.
Further information
To find out more about CladeAge, you might find the Rough Guide for CladeAge and/or the CladeAge tutorial on the Taming the BEAST website useful.
How to cite CladeAge
Matschiner M, Musilová Z, Barth JMI, Starostová Z, Salzburger W, Steel M, Bouckaert R (2017) Bayesian phylogenetic estimation of clade ages supports trans-Atlantic dispersal of cichlid fishes. Systematic Biology, 66:3-22.
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