Fig. 3

Uncertainty of trees reconstructed from phylogenies simulated under three models with different relationships between molecular evolution and speciation, in width as a percentage of reconstructed node age. Precision is measured by averaging the width of 95% highest posterior density intervals as a proportion of reconstructed node height across each tree, with a larger score indicating less precise estimates (HPD width). The three simulation models are Unlinked (instantaneous covariance of molecular rates and speciation rates = 0), Continuous (instantaneous covariance = 0.0044), and Punctuated (instantaneous covariance = 0, bursts of substitutions added at speciation events). Topologies and node times were reconstructed using three different analytical methods, the uncorrelated lognormal ‘relaxed clock’ (UCLN) rate prior in BEAST 2, the autocorrelated lognormal rate (ACLN) prior in PAML, and the UCLN in PAML