Figure 3

Underestimate of Bayesian branch lengths for 8-taxon trees. Percentage that branch lengths were underestimated for 1 kb datasets simulated on 8-taxon trees with equal branch lengths (inset) using the HKY model with a transition/transversion ratio of 2 and equal base frequencies, and analyzed using MrBayes with an HKY model, estimated model parameters, and the default exponential prior (mean = 1/10) on branch lengths. Branches with depth = 1 and depth = 2 (see inset) were evaluated separately (white and gray boxes, respectively).