Figure 4

Underestimate of Bayesian branch lengths on unequal branch length trees. Effects of unequal branch lengths on branch length estimation. Gray boxes are the percent underestimation of depth 2 branch lengths for 4-taxon trees with the depth 2 branch length = half the depth 1 branch length (left inset). White boxes are the percent underestimation of depth 2 branch lengths for 4-taxon trees with the depth 2 branch length = double the depth 1 branch length (right inset). Depth 2 branch lengths were expected to be underestimated at the same rate as depth 2 branch lengths of 8-taxon, equal-branch-length datasets (mean underestimation shown as filled circles). Half-length depth 2 branches (gray boxes) were underestimated at a significantly higher rate than expected (filled circles). Double-length depth 2 branches (white boxes) were underestimated at a rate significantly lower than expected (filled circles and extrapolating from the trend of underestimation (spline interpolation line)). The range of depth 2 branch lengths examined in this analysis was dictated by the range of depth 1 branch lengths examined in the overall study (0.01-1.4 substitutions/site).