title: Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics.
abstract: Many empirical studies have revealed considerable differences between nonparametric bootstrapping and Bayesian posterior probabilities in terms of the support values for branches, despite claimed predictions about their approximate equivalence. We investigated this problem by simulating data, which were then analyzed by maximum likelihood bootstrapping and Bayesian phylogenetic analysis using identical models and reoptimization of parameter values. We show that Bayesian posterior probabilities are significantly higher than corresponding nonparametric bootstrap frequencies for true clades, but also that erroneous conclusions will be made more often. These errors are strongly accentuated when the models used for analyses are underparameterized. When data are analyzed under the correct model, nonparametric bootstrapping is conservative. Bayesian posterior probabilities are also conservative in this respect, but less so.
authors.affiliation: Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-75236 Uppsala, Sweden. per.erixon@ebc.uu.se
authors.forename: Per
authors.initials: P
authors.lastname: Erixon
authors.forename: Bodil
authors.initials: B
authors.lastname: Svennblad
authors.forename: Tom
authors.initials: T
authors.lastname: Britton
authors.forename: Bengt
authors.initials: B
authors.lastname: Oxelman
mesh_terms: D001499:Bayes Theorem; D003198:Computer Simulation; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D015203:Reproducibility of Results