Figure 2

Underestimate of Bayesian branch lengths for 4-taxon trees. Percentage that branch lengths were underestimated for 1 and 10 kb datasets simulated on 4-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 = 0.1) on branch lengths. The box plot shows the range of misestimation across all branches and simulations; results were identical for single branches and total tree length.