Table 3.

Moves used during Markov chain Monte Carlo (MCMC) analyses

Function in RevBayes	Description	Parameter to change	Weight
mvNNI	Nearest-neighbor interchange move	Ψ	num. of taxa (e.g. 16, 64)
mvSPR	Subtree prune-and-regraft move	Ψ	num. of taxa x 0.1 (e.g. 1.6, 6.4)
mvBranchLengthScale	Scaling move on the branch lengths	bl	num. of taxa (e.g. 16, 64)
mvBetaSimplex	Scaling move on nucleotide frequencies	π	2.0
mvDirichletSimplex	Scaling move on nucleotide frequencies	π	1.0
mvBetaSimplex	Scaling move on exchangeabilities	er	3.0
mvDirichletSimplex	Scaling move on exchangeabilities	er	1.5
mvScale	Scaling move on shape parameter	α	2.0
mvBetaProbability	Scaling move on proportion of invariable sites	I	2.0

JC analyses used only the first three moves