  Huelsenbeck and Rannala (2004, Systematic Biology 53, 904-913) presented a
series of simulations in order to assess the extent to which the bayesian
posterior probabilities associated with phylogenetic trees represent the
standard frequentist statistical interpretation. They concluded that when the
analysis model matches the generating model then the bayesian posterior
probabilities are correct, but that the probabilities are much too large when
the model is under-specified and slightly too small when the model is
over-specified. Here, I take issue with the first conclusion, and instead
contend that their simulation data show that the posterior probabilities are
still slightly too large even when the models match. Furthermore, I suggest
that the data show that the degree of this over-estimation increases as the
sequence length increases, and that it might increase as model complexity
increases. I also provide some comments on the authors' conclusions concerning
whether bootstrap proportions over- or under-estimate the true probabilities.
