The Bayesian phylogenetic analysis ran four simultaneous chains for 2.0 × 106 total generations, each using a random tree as a starting point, the default heating scheme, and saving a tree every 100 generations for a total 20,000 trees.
Bayesian analysis (MrBayes V3.0b4 [ 48]) was initiated using a random tree from the combined dataset with four chains running simultaneously for 5,000,000 generations, and trees sampled every 100 generations.
To facilitate our analyses, we use a random tree T b,d) that has mean branching factor b, depth d, and node costs that are the sum of the costs of the edges from the root to the nodes.
For each replicate, we ran one cold chain and three hot chains of the Markov Chain Monte Carlo method, using a random starting tree and sampling trees every 100 generations.
Since in theory we can update the contingency tables in any exploration order, in the table, we also show the pruning effect of using a random spanning tree and a linear spanning tree to guide the updating process.
An independent analysis of the same dataset but including no calibrations and using a random starting tree was also run to test the effect of a starting tree on the final topology.
Bayesian analysis was performed by MrBayes (version 3.2.3), using a random starting tree, running eight chains for 4,000,000 generations, sampling every 250 trees (Ronquist et al., 2012).
As suggested, Bayesian analysis was performed by MrBayes (version 3.2.3), using a random starting tree, running eight chains for 4,000,000 generations, sampling every 250 trees.
Bayesian analyses were undertaken using four independent runs, each using a random starting tree and 1,000,000 generations with one cold and three heated chains, sampling trees every 100 generations.
The analyses were run using a random starting tree for 10 generations sampling every 10 generations under the uncorrelated lognormal relaxed clock model, a birth-death tree prior and the selected models of substitution for different partitions.
Two independent analyses were run using a random starting tree with three heated chains and one cold chain over 400,000 generations, with sampling every 100 generations.
