Skip Navigation

Systematic Biology 2004 53(6):904-913; doi:10.1080/10635150490522629
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (136)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Huelsenbeck, J. P.
Right arrow Articles by Rannala, B.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Huelsenbeck, J. P.
Right arrow Articles by Rannala, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2004 Society of Systematic Biologists

Frequentist Properties of Bayesian Posterior Probabilities of Phylogenetic Trees Under Simple and Complex Substitution Models

John P. Huelsenbeck1 and Bruce Rannala2

1 Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego La Jolla, California 92093–0116, USA E-mail: johnh{at}biomail.ucsd.edu
2 Genome Center & Section of Evolution and Ecology, University of California Davis, One Shields Avenue Davis California 95616, USA

Edited by Thomas Buckley: Associate Editor


  Abstract

What does the posterior probability of a phylogenetic tree mean? This simulation study shows that Bayesian posterior probabilities have the meaning that is typically ascribed to them; the posterior probability of a tree is the probability that the tree is correct, assuming that the model is correct. At the same time, the Bayesian method can be sensitive to model misspecification, and the sensitivity of the Bayesian method appears to be greater than the sensitivity of the nonparametric bootstrap method (using maximum likelihood to estimate trees). Although the estimates of phylogeny obtained by use of the method of maximum likelihood or the Bayesian method are likely to be similar, the assessment of the uncertainty of inferred trees via either bootstrapping (for maximum likelihood estimates) or posterior probabilities (for Bayesian estimates) is not likely to be the same. We suggest that the Bayesian method be implemented with the most complex models of those currently available, as this should reduce the chance that the method will concentrate too much probability on too few trees.

Keywords: Bayesian estimation; Markov chain Monte Carlo; posterior probability; prior probability

Received July 22, 2003; Revised November 18, 2003; Accepted July 18, 2004
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
D. M. Simon, S. A. Kelchner, and S. Zimmerly
A Broadscale Phylogenetic Analysis of Group II Intron RNAs and Intron-Encoded Reverse Transcriptases
Mol. Biol. Evol., December 1, 2009; 26(12): 2795 - 2808.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
K. A. Cranston, B. Hurwitz, D. Ware, L. Stein, and R. A. Wing
Species Trees from Highly Incongruent Gene Trees in Rice
Syst Biol, October 1, 2009; 58(5): 489 - 500.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
M. C. Brandley, D. L. Warren, A. D. Leache, and J. A. McGuire
Homoplasy and Clade Support
Syst Biol, June 29, 2009; (2009) syp019v1.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
P. Q. Spinks and H. B. Shaffer
Conflicting Mitochondrial and Nuclear Phylogenies for the Widely Disjunct Emys (Testudines: Emydidae) Species Complex, and What They Tell Us about Biogeography and Hybridization
Syst Biol, May 28, 2009; (2009) syp005v1.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc BHome page
K. Munch, W. Boomsma, E. Willerslev, and R. Nielsen
Fast phylogenetic DNA barcoding
Phil Trans R Soc B, December 27, 2008; 363(1512): 3997 - 4002.
[Abstract] [Full Text] [PDF]

Home page
 Phil Trans R Soc BHome page
Z. Yang
Empirical evaluation of a prior for Bayesian phylogenetic inference
Phil Trans R Soc B, December 27, 2008; 363(1512): 4031 - 4039.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
C. R. Linnen and B. D. Farrell
Comparison of Methods for Species-Tree Inference in the Sawfly Genus Neodiprion (Hymenoptera: Diprionidae)
Syst Biol, December 1, 2008; 57(6): 876 - 890.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
A. Dornburg, F. Santini, and M. E. Alfaro
The Influence of Model Averaging on Clade Posteriors: An Example Using the Triggerfishes (Family Balistidae)
Syst Biol, December 1, 2008; 57(6): 905 - 919.
[Abstract] [Full Text] [PDF]

Home page
 J MOLLUS STUDHome page
P. J. Krug, M. S. Morley, J. Asif, L. L. Hellyar, and W. M. Blom
Molecular confirmation of species status for the rare cephalaspidean Melanochlamys lorrainae (Rudman, 1968), and comparison with its sister species M. cylindrica Cheeseman, 1881
J. Mollus. Stud., August 1, 2008; 74(3): 267 - 276.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
E. Susko
On the Distributions of Bootstrap Support and Posterior Distributions for a Star Tree
Syst Biol, August 1, 2008; 57(4): 602 - 612.
[Abstract] [Full Text] [PDF]

Home page
 J. Exp. Biol.Home page
J. C. Spagna, A. I. Vakis, C. A. Schmidt, S. N. Patek, X. Zhang, N. D. Tsutsui, and A. V. Suarez
Phylogeny, scaling, and the generation of extreme forces in trap-jaw ants
J. Exp. Biol., July 15, 2008; 211(14): 2358 - 2368.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
J. P. Huelsenbeck, C. Ane, B. Larget, and F. Ronquist
A Bayesian Perspective on a Non-parsimonious Parsimony Model
Syst Biol, June 1, 2008; 57(3): 406 - 419.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
N. M. Belfiore, L. Liu, and C. Moritz
Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae)
Syst Biol, April 1, 2008; 57(2): 294 - 310.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
J. A. McGuire, C. C. Witt, D. L. Altshuler, and J. V. Remsen
Phylogenetic Systematics and Biogeography of Hummingbirds: Bayesian and Maximum Likelihood Analyses of Partitioned Data and Selection of an Appropriate Partitioning Strategy
Syst Biol, October 1, 2007; 56(5): 837 - 856.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
B. Kolaczkowski and J. W. Thornton
Effects of Branch Length Uncertainty on Bayesian Posterior Probabilities for Phylogenetic Hypotheses
Mol. Biol. Evol., September 1, 2007; 24(9): 2108 - 2118.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
J. M. Brown and A. R. Lemmon
The Importance of Data Partitioning and the Utility of Bayes Factors in Bayesian Phylogenetics
Syst Biol, August 1, 2007; 56(4): 643 - 655.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
Z. Yang
Fair-Balance Paradox, Star-tree Paradox, and Bayesian Phylogenetics
Mol. Biol. Evol., August 1, 2007; 24(8): 1639 - 1655.
[Abstract] [Full Text] [PDF]

Home page
 Biol LettHome page
B. Ujvari, M. Dowton, and T. Madsen
Mitochondrial DNA recombination in a free-ranging Australian lizard
Biol Lett, April 22, 2007; 3(2): 189 - 192.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
T. H. Ogden and M. S. Rosenberg
Alignment and Topological Accuracy of the Direct Optimization approach via POY and Traditional Phylogenetics via ClustalW + PAUP
Syst Biol, April 1, 2007; 56(2): 182 - 193.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
R. A. B. Leschen and T. R. Buckley
Multistate Characters and Diet Shifts: Evolution of Erotylidae (Coleoptera)
Syst Biol, February 1, 2007; 56(1): 97 - 112.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
C. Bonnard, V. Berry, and N. Lartillot
Multipolar Consensus for Phylogenetic Trees
Syst Biol, October 1, 2006; 55(5): 837 - 843.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
M. Anisimova and O. Gascuel
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative
Syst Biol, August 1, 2006; 55(4): 539 - 552.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
T. R. Buckley, M. Cordeiro, D. C. Marshall, and C. Simon
Differentiating between Hypotheses of Lineage Sorting and Introgression in New Zealand Alpine Cicadas (Maoricicada Dugdale)
Syst Biol, June 1, 2006; 55(3): 411 - 425.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
L. Mateiu and B. Rannala
Inferring Complex DNA Substitution Processes on Phylogenies Using Uniformization and Data Augmentation
Syst Biol, April 1, 2006; 55(2): 259 - 269.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
T. H. Ogden and M. S. Rosenberg
Multiple Sequence Alignment Accuracy and Phylogenetic Inference
Syst Biol, April 1, 2006; 55(2): 314 - 328.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
M. E. Alfaro and J. P. Huelsenbeck
Comparative Performance of Bayesian and AIC-Based Measures of Phylogenetic Model Uncertainty
Syst Biol, February 1, 2006; 55(1): 89 - 96.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
M. C. Brandley, A. D. Leache, D. L. Warren, and J. A. McGuire
Are Unequal Clade Priors Problematic for Bayesian Phylogenetics?
Syst Biol, February 1, 2006; 55(1): 138 - 146.
[Full Text] [PDF]

Home page
 SIMHome page
M.-N. Cortinas, P. W. Crous, B. D. Wingfield, and M. J. Wingfield
Multi-gene phylogenies and phenotypic characters distinguish two species within the Colletogloeopsis zuluensis complex associated with Eucalyptus stem cankers.
Stud Mycol, January 1, 2006; 55: 133 - 146.
[Abstract] [Full Text] [PDF]

Home page
 SIMHome page
W. Maier, T. Khoza, N. Harmse, B. D. Wingfield, and M. J. Wingfield
A disease epidemic on Zizyphus mucronata in the Kruger National Park caused by Coniodictyum chevalieri.
Stud Mycol, January 1, 2006; 55: 279 - 288.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
C. Poux, O. Madsen, E. Marquard, D. R. Vieites, W. W. de Jong, and M. Vences
Asynchronous Colonization of Madagascar by the Four Endemic Clades of Primates, Tenrecs, Carnivores, and Rodents as Inferred from Nuclear Genes
Syst Biol, October 1, 2005; 54(5): 719 - 730.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.