Fig. 2

Topological error of trees reconstructed from data sets simulated under three simulation types with different relationships between molecular evolution and speciation (see Table 1). Topological error is given by the Robinson-Foulds distance (number of non-shared bipartitions). 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 the uncorrelated lognormal ‘relaxed clock’ rate prior in BEAST 2 (UCLN). No results are available for PAML because the topology was fixed for these analyses