Relaxed phylogenetics and dating celestial dating
We used ν = 0.01 because it led to a rate density concentrated within the region 0.05–0.015 substitutions/site/unit time, which would appear reasonable.
Trees with more clock-like evolution (ν = 0.001) were also generated/analyzed, but results were similar and thus not shown.
Data were analyzed using Bayesian Markov chain Monte Carlo methods in which the prior on divergence times was specified from a birth–death process with species sampling (BDS) or a Dirichlet distribution using the programs MCMCTREE and MULTIDIVTIME.
The programs generally performed well on shallow phylogenies, but posterior mean node ages were biased and 95% posterior intervals included true ages in fewer than 95% of trees in some analyses.
The joint prior density of divergence times, conditional on root age, and other time constraints are derived from the BDS model.