Skip Navigation


MBE Advance Access originally published online on May 12, 2004
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow An erratum has been published
Right arrow All Versions of this Article:
21/8/1534    most recent
msh156v1
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 Similar articles in PubMed
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 (43)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Taylor, D. J.
Right arrow Articles by Piel, W. H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Taylor, D. J.
Right arrow Articles by Piel, W. H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Mol. Biol. Evol. 21(8):1534-1537. 2004
DOI: 10.1093/molbev/msh156
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

An Assessment of Accuracy, Error, and Conflict with Support Values from Genome-Scale Phylogenetic Data

Derek J. Taylor and William H. Piel

Department of Biological Sciences, University at Buffalo, The State University of New York, Buffalo, New York

E-mail: djtaylor{at}buffalo.edu.

Despite the importance of molecular phylogenetics, few of its assumptions have been tested with real data. It is commonly assumed that nonparametric bootstrap values are an underestimate of the actual support, Bayesian posterior probabilities are an overestimate of the actual support, and among-gene phylogenetic conflict is low. We directly tested these assumptions by using a well-supported yeast reference tree. We found that bootstrap values were not significantly different from accuracy. Bayesian support values were, however, significant overestimates of accuracy but still had low false-positive error rates (0% to 2.8%) at the highest values (>99%). Although we found evidence for a branch-length bias contributing to conflict, there was little evidence for widespread, strongly supported among-gene conflict from bootstraps. The results demonstrate that caution is warranted concerning conclusions of conflict based on the assumption of underestimation for support values in real data.

Key Words: Bootstrap • incongruence • Bayesian phylogenetic inference • yeast genome


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
Y. Liu, J. W. Leigh, H. Brinkmann, M. T. Cushion, N. Rodriguez-Ezpeleta, H. Philippe, and B. F. Lang
Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts
Mol. Biol. Evol., January 1, 2009; 26(1): 27 - 34.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
C.-H. Kuo, J. P. Wares, and J. C. Kissinger
The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees
Mol. Biol. Evol., December 1, 2008; 25(12): 2689 - 2698.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
R. A. Scherson, R. Vidal, and M. J. Sanderson
Phylogeny, biogeography, and rates of diversification of New World Astragalus (Leguminosae) with an emphasis on South American radiations
Am. J. Botany, August 1, 2008; 95(8): 1030 - 1039.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
B. R. Holland, A. C. Clarke, and H. M. Meudt
Optimizing Automated AFLP Scoring Parameters to Improve Phylogenetic Resolution
Syst Biol, June 1, 2008; 57(3): 347 - 366.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
J. J. Wiens, C. A. Kuczynski, S. A. Smith, D. G. Mulcahy, J. W. Sites Jr., T. M. Townsend, and T. W. Reeder
Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes
Syst Biol, June 1, 2008; 57(3): 420 - 431.
[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. Gatesy, R. DeSalle, and N. Wahlberg
How Many Genes Should a Systematist Sample? Conflicting Insights from a Phylogenomic Matrix Characterized by Replicated Incongruence
Syst Biol, April 1, 2007; 56(2): 355 - 363.
[Full Text] [PDF]

Home page
 J PLANKTON RESHome page
A. A. Kotov, S. Ishida, and D. J. Taylor
A new species in the Daphnia curvirostris (Crustacea: Cladocera) complex from the eastern Palearctic with molecular phylogenetic evidence for the independent origin of neckteeth
J. Plankton Res., November 1, 2006; 28(11): 1067 - 1079.
[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
 Am. J. Bot.Home page
A. K Monro
The revision of species-rich genera: a phylogenetic framework for the strategic revision of Pilea (Urticaceae) based on cpDNA, nrDNA, and morphology
Am. J. Botany, March 1, 2006; 93(3): 426 - 441.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
F. Ren, H. Tanaka, and Z. Yang
An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction
Syst Biol, October 1, 2005; 54(5): 808 - 818.
[Abstract] [Full Text] [PDF]

Home page
 Syst BiolHome page
T. M. Collins, O. Fedrigo, and G. J. P. Naylor
Choosing the Best Genes for the Job: The Case for Stationary Genes in Genome-Scale Phylogenetics
Syst Biol, June 1, 2005; 54(3): 493 - 500.
[Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Gibson, V. Gowri-Shankar, P. G. Higgs, and M. Rattray
A Comprehensive Analysis of Mammalian Mitochondrial Genome Base Composition and Improved Phylogenetic Methods
Mol. Biol. Evol., February 1, 2005; 22(2): 251 - 264.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. Berlin and H. Ellegren
Chicken W: A genetically uniform chromosome in a highly variable genome
PNAS, November 9, 2004; 101(45): 15967 - 15969.
[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.