Table 2.

Bayesian phylogenetic estimates of substitution rates and root ages from data simulated under various conditions, with all values calculated from 1000 independent replicates.

structure of sequence ages	model used in simulation	model used in analysis	substitution rate estimate			root age estimate
			mean (substitution per site yr−1)	accuracya (%)	precisionb	accuracya (%)
uniform	constant size	constant size	4.95×10−7	94.4	2.52×10−7	94.9
uniform	constant size	exponential growth	5.03×10−7	94.2	2.52×10−7	94.5
uniform	constant size	Bayesian skyline plot	5.03×10−7	94.0	2.51×10−7	94.6
uniform	exponential growth	constant size	5.00×10−7	94.3	2.44×10−7	95.6
uniform	exponential growth	exponential growth	5.08×10−7	94.2	2.46×10−7	93.5
uniform	exponential growth	Bayesian skyline plot	5.10×10−7	94.0	2.47×10−7	94.8
layered	constant size	constant size	4.95×10−7	95.0	2.65×10−7	95.6
layered	constant size	exponential growth	5.03×10−7	95.4	2.66×10−7	95.1
layered	constant size	Bayesian skyline plot	5.04×10−7	94.8	2.66×10−7	95.3
layered	exponential growth	constant size	5.00×10−7	94.7	2.59×10−7	94.6
layered	exponential growth	exponential growth	5.09×10−7	93.8	2.61×10−7	92.6
layered	exponential growth	Bayesian skyline plot	5.11×10−7	95.4	2.63×10−7	93.8

^aAccuracy refers to the percentage of datasets for which the true (simulation) value was contained in the 95% highest posterior density (HPD) of the estimated rate.

^bPrecision refers to the average size of the 95% HPD on rate estimates.