Bayesian evolutionary rate estimate and dated trees
A root-to-tip regression analysis was undertaken using TempEst to
establish the temporal signal of datasets II-VII. The GTR+G+I model was
selected as the evolutionary model using JmodelTest, v. 2.1.7, while the
mean evolutionary rate and the dated trees were made using a Bayesian
Markov Chain Monte Carlo approach implemented in BEAST, v.1.10.4
(Suchard et al., 2018). Two coalescent priors (constant population size
and exponential growth) and strict vs relaxed molecular clock models
were tested by means of path sampling (PS) and stepping stone (SS)
sampling. Convergence was assessed by estimating the effective sampling
size (ESS) after a 10% burn-in, using Tracer software
(http://tree.bio.ed.ac.uk/software/tracer/), and accepting ESS values of
200 or more. Uncertainty in the estimates was indicated by 95% highest
posterior density (95% HPD) intervals. Posterior probability was used
as statistical support for specific clades and clusters. The trees were
summarized in Tree Annotator, and the tree with the maximum product of
posterior probabilities (maximum clade credibility or MCC), after a 10%
burn-in, chosen.