Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Syst Biol. 2003 Oct;52(5):665-73.

Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics.

Author information

  • 1Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-75236 Uppsala, Sweden. per.erixon@ebc.uu.se

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.

PMID:
14530133
[PubMed - indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire
    Loading ...
    Write to the Help Desk