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.