Fig. 3

Accuracy verification. Absolute error for dwelling times and number of transitions. Errors were computed by comparing the differences between simulated (observed) and estimated dwelling times and absolute numbers of transitions across trees obtained using SFREEMAP and make.simmap. The latter were obtained for a range of replicates, from 100 to 2500. Boxes correspond to standard deviations, dashes to means, whiskers to the min-max ranges and dots to outliers. a) Dwelling times, i.e. the fraction of the tree expected to have been “spent” on a given state, represented as percentages of tree length. b) Absolute numbers of transitions summed across tree branches