The basis of phylogenetic uncertainty
We evaluated whether phylogenetic uncertainty arises from phylogeny structure or stochastic character mapping. To do so we used a randomization procedure, repeated 1,000 times. In each step of this procedure, we took 10 estimates of each tip-based metric produced by simulations within one phylogeny, and 10 estimates of each tip-based metric produced by one simulation of 10 different phylogenies. We then calculated the standard deviation of pooled estimates, and counted the number of randomizations that the standard deviation was lower within than between phylogenies.