FIGURE S4. Estimates of gene trees for individual UCEs are poorly resolved. Box plot showing the number of resolved branches when those branches with <50% support in ML bootstrap analyses (using the indicated programs) or posterior probabilities <0.5 (using MrBayes). Similar data are shown for the optimal tree identified using GARLI with very short branches collapsed to form a polytomy (‘GARLI-opt’). Numbers of parsimony informative sites per UCE are used to define the sets of UCEs considered (‘all’ indicates that all UCEs with at least one parsimony informative site were included)
