© 2005 Society of Systematic Biologists
Branch-Length Prior Influences Bayesian Posterior Probability of Phylogeny
1 Department of Biology, University College London Darwin Building, Gower Street London WC1E 6BT United Kingdom E-mail: z.yang{at}ucl.ac.uk
2 Genome Center and Section of Evolution and Ecology, University of California Davis One Shields Avenue, Davis, California 95616, U.S.A
Edited by Paul Lewis: Associate Editor
 |
Abstract |
|---|
The Bayesian method for estimating species phylogenies from molecular sequence data provides an attractive alternative to maximum likelihood with nonparametric bootstrap due to the easy interpretation of posterior probabilities for trees and to availability of efficient computational algorithms. However, for many data sets it produces extremely high posterior probabilities, sometimes for apparently incorrect clades. Here we use both computer simulation and empirical data analysis to examine the effect of the prior model for internal branch lengths. We found that posterior probabilities for trees and clades are sensitive to the prior for internal branch lengths, and priors assuming long internal branches cause high posterior probabilities for trees. In particular, uniform priors with high upper bounds bias Bayesian clade probabilities in favor of extreme values. We discuss possible remedies to the problem, including empirical and full Bayesian methods and subjective procedures suggested in Bayesian hypothesis testing. Our results also suggest that the bootstrap proportion and Bayesian posterior probability are different measures of accuracy, and that the bootstrap proportion, if interpreted as the probability that the clade is true, can be either too liberal or too conservative.
Keywords: Fair-balance paradox; Lindley's paradox; model selection; molecular phylogenetics; posterior probabilities; prior; star tree paradox
Received May 17, 2004; Revised October 2, 2004; Accepted January 21, 2005
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  D. C. Marshall Cryptic Failure of Partitioned Bayesian Phylogenetic Analyses: Lost in the Land of Long Trees Syst Biol, November 17, 2009; (2009) syp080v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L.-J. Liang, R. E. Weiss, B. Redelings, and M. A. Suchard Improving phylogenetic analyses by incorporating additional information from genetic sequence databases Bioinformatics, October 1, 2009; 25(19): 2530 - 2536. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Liu and S. V. Edwards Phylogenetic Analysis in the Anomaly Zone Syst Biol, August 1, 2009; 58(4): 452 - 460. [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
A. R. Lemmon, J. M. Brown, K. Stanger-Hall, and E. M. Lemmon The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference Syst Biol, May 22, 2009; (2009) syp017v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
J. C. Regier, J. W. Shultz, A. R. D. Ganley, A. Hussey, D. Shi, B. Ball, A. Zwick, J. E. Stajich, M. P. Cummings, J. W. Martin, et al. Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence Syst Biol, December 1, 2008; 57(6): 920 - 938. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Kim and M. J. Sanderson Penalized Likelihood Phylogenetic Inference: Bridging the Parsimony-Likelihood Gap Syst Biol, October 1, 2008; 57(5): 665 - 674. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Baele, Y. Van de Peer, and S. Vansteelandt A Model-Based Approach to Study Nearest-Neighbor Influences Reveals Complex Substitution Patterns in Non-coding Sequences Syst Biol, October 1, 2008; 57(5): 675 - 692. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Dohrmann, D. Janussen, J. Reitner, A. G. Collins, and G. Worheide Phylogeny and Evolution of Glass Sponges (Porifera, Hexactinellida) Syst Biol, June 1, 2008; 57(3): 388 - 405. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Britton, C. L. Anderson, D. Jacquet, S. Lundqvist, and K. Bremer Estimating Divergence Times in Large Phylogenetic Trees Syst Biol, October 1, 2007; 56(5): 741 - 752. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. A. Henk and R. Vilgalys Molecular phylogeny suggests a single origin of insect symbiosis in the Pucciniomycetes with support for some relationships within the genus Septobasidium Am. J. Botany, September 1, 2007; 94(9): 1515 - 1526. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 K. L Sanders and M. S.Y Lee Evaluating molecular clock calibrations using Bayesian analyses with soft and hard bounds Biol Lett, June 22, 2007; 3(3): 275 - 279. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. V. Edwards, L. Liu, and D. K. Pearl High-resolution species trees without concatenation PNAS, April 3, 2007; 104(14): 5936 - 5941. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Steel and F. A. Matsen The Bayesian "Star Paradox" Persists for Long Finite Sequences Mol. Biol. Evol., April 1, 2007; 24(4): 1075 - 1079. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
J. Muller and R. R. Reisz The Phylogeny of Early Eureptiles: Comparing Parsimony and Bayesian Approaches in the Investigation of a Basal Fossil Clade Syst Biol, June 1, 2006; 55(3): 503 - 511. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. P. Randle and K. M. Pickett Are Nonuniform Clade Priors Important in Bayesian Phylogenetic Analysis? A Response to Brandley et al. Syst Biol, February 1, 2006; 55(1): 147 - 151. [Full Text] [PDF]
|
|