Skip Navigation

Systematic Biology 2006 55(1):138-146; doi:10.1080/10635150500431155
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 (9)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Brandley, M. C.
Right arrow Articles by McGuire, J. A.
Right arrow Search for Related Content
PubMed
Right arrow Articles by Brandley, M. C.
Right arrow Articles by McGuire, J. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2006 Society of Systematic Biologists

Are Unequal Clade Priors Problematic for Bayesian Phylogenetics?

Edited by Paul Lewis: Associate Editor

Matthew C. Brandley1, Adam D. Leaché1, Dan L. Warren2 and Jimmy A. McGuire1

1 Museum of Vertebrate Zoology and Department of Integrative Biology, University of California Berkeley, California, 94720–3160, USA; E-mail: brandley@berkeley.edu
2 Center for Population Biology, Section of Evolution and Ecology, University of California Davis,, California, 95616–5270, USA

Received January 27, 2005; Revised May 31, 2005; Accepted August 15, 2005
The first 150 words of the full text of this article appear below.

Although Bayesian phylogenetic methodologies were first developed in the 1960s (Felsenstein, 1968, 2004), the approach remained relatively obscure until the initial release of the software application MrBayes (Huelsenbeck and Ronquist, 2001). Since that time, the popularity of Bayesian phylogenetics has increased tremendously, and it now must be considered a primary method of analysis on par with maximum likelihood, parsimony, and distance methods. The popularity of Bayesian analysis can be attributed to computational efficiencies that allow for explicit model-based analyses of large data sets in real time with simultaneous estimation of nodal support in the form of posterior probability values. Despite the initial enthusiasm generated by the availability of a fast likelihood-based approach, Bayesian phylogenetic analysis remains somewhat controversial. Much of the controversy is focused on two related issues: (1) the relationship between posterior probability values and nonparametric bootstrap proportions with the nagging suspicion that posterior probabilities are . . . [Full Text of this Article]


   Contrived Data Analyses
 
Reanalysis of the PR Contrived Data Set
The Effect of Adding Characters

   Simulated Data Analyses
 

   Biased Support Values in Empirical Studies
 

   Should We be Concerned by The Effect of Unequal Clade Priors?
 

   Modifying the Posteriors to Accommodate Bias
 

   Conclusion
 

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
 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
 Mol Biol EvolHome page
J. Sukumaran and C. W. Linkem
Choice of Topology Estimators in Bayesian Phylogenetic Analysis
Mol. Biol. Evol., January 1, 2009; 26(1): 1 - 3.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
J. A. Clarke and K. M. Middleton
Mosaicism, Modules, and the Evolution of Birds: Results from a Bayesian Approach to the Study of Morphological Evolution Using Discrete Character Data
Syst Biol, April 1, 2008; 57(2): 185 - 201.
[Abstract] [Full Text] [PDF]