Figure 10

Underestimate of ML branch lengths on unequal branch length trees. Effects of unequal branch lengths on branch length estimation in a maximum likelihood framework. Results are plotted as for Figure 4. 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. 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 (outliers of up to -30000% for branches of 1.4 substitutions/site are not shown for clarity). 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 generally overestimated (negatively underestimated) at a higher rate than expected (filled circles). Double-length depth 2 branches (white boxes) were overestimated at a lower rate than expected (filled circles and extrapolating from the trend of underestimation (spline interpolation line)).