Journal of Molecular Evolution

, Volume 57, Supplement 1, pp S290–S296

Reanalysis of Murphy et al.’s Data Gives Various Mammalian Phylogenies and Suggests Overcredibility of Bayesian Trees

Article

DOI: 10.1007/s00239-003-0039-7

Cite this article as:
Misawa, K. & Nei, M. J Mol Evol (2003) 57(Suppl 1): S290. doi:10.1007/s00239-003-0039-7

Abstract

Murphy and colleagues reported that the mammalian phylogeny was resolved by Bayesian phylogenetics. However, the DNA sequences they used had many alignment gaps and undetermined nucleotide sites. We therefore reanalyzed their data by minimizing unshared nucleotide sites and retaining as many species as possible (13 species). In constructing phylogenetic trees, we used the Bayesian, maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ) methods with different substitution models. These trees were constructed by using both protein and DNA sequences. The results showed that the posterior probabilities for Bayesian trees were generally much higher than the bootstrap values for ML, MP, and NJ trees. Two different Bayesian topologies for the same set of species were sometimes supported by high posterior probabilities, implying that two different topologies can be judged to be correct by Bayesian phylogenetics. This suggests that the posterior probability in Bayesian analysis can be excessively high as an indication of statistical confidence and therefore Murphy et al.’s tree, which largely depends on Bayesian posterior probability, may not be correct.

Keywords

Mammalian phylogenyBayesian methodCredibility value

Copyright information

© Springer-Verlag New York LLC 2003

Authors and Affiliations

  1. 1.Institute of Molecular Evolutionary Genetics, Department of BiologyThe Pennsylvania State University, 328 Mueller Laboratory, University Park, PA 16802USA