MrBayes_Analyses

NEXUS input file for analyses in MrBayes. Three approaches to calibration are included: Tip Calibration; Node Calibration; Tip and Node Combined Calibration

Supplementary_Methods

Justification for sampling the time-prior from a fixed consensus-tree topology and details of all divergence-time analyses performed

TipandNode_Post_Full

Majority-rule consensus tree obtained from a posterior sample of trees in the combined tip and node calibration analysis. The position of all fossil taxa are presented in this topology

TED_Post_Full

Majority-rule consensus tree obtained from a sample from the posterior distribution in the total-evidence, tip-calibrated, divergence time analysis.The position of all fossil taxa are presented in this topology

suppFigureS1

Supplementary Figure S1. Bayesian, Maximum Likelihood, and Parsimony topologies of the data from Hilton and Bateman (2006). The optimal tree with node support is shown for each method (a-c) as well as the topologies that are produced after nodes with <0.5 support are collapsed to polytomies (d-f), and when nodes with <0.8 support are collapsed (g-i)

suppFigureS2

Supplementary Figure S2. Bayesian, Maximum Likelihood, and Parsimony topologies of the data from Luo et al. (2015). The optimal tree with node support is shown for each method (a-c) as well as the topologies that are produced after nodes with <0.5 support are collapsed to polytomies (d-f), and when nodes with <0.8 support are collapsed (g-i)

MrBayesBlock

Commands used for Bayesian Analyse

Literature reviewed from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history: a response to Brown <i>et al.</i>

ES

Electronic supplementary material from Parsimony and maximum-likelihood phylogenetic analyses of morphology do not generally integrate uncertainty in inferring evolutionary history. A response to Brown <i>et al.</i>

Literature reviewe