Skip Navigation


MBE Advance Access originally published online on February 4, 2003
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (PDF) Freely available
Right arrow All Versions of this Article:
20/2/248    most recent
msg042v1
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 (172)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Douady, C. J.
Right arrow Articles by Douzery, E. J. P.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Douady, C. J.
Right arrow Articles by Douzery, E. J. P.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Mol. Biol. Evol. 20(2):248-254. 2003
DOI: 10.1093/molbev/msg042
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability

Christophe J. Douady*,, Frédéric Delsuc{dagger}, Yan Boucher*, W. Ford Doolittle* and Emmanuel J. P. Douzery{dagger}

* Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
{dagger} Laboratoire de Paléontologie, Paléobiologie et Phylogénie, Institut des Sciences de l'Evolution, Université Montpellier II, Montpellier, France

Owing to the exponential growth of genome databases, phylogenetic trees are now widely used to test a variety of evolutionary hypotheses. Nevertheless, computation time burden limits the application of methods such as maximum likelihood nonparametric bootstrap to assess reliability of evolutionary trees. As an alternative, the much faster Bayesian inference of phylogeny, which expresses branch support as posterior probabilities, has been introduced. However, marked discrepancies exist between nonparametric bootstrap proportions and Bayesian posterior probabilities, leading to difficulties in the interpretation of sometimes strongly conflicting results. As an attempt to reconcile these two indices of node reliability, we apply the nonparametric bootstrap resampling procedure to the Bayesian approach. The correlation between posterior probabilities, bootstrap maximum likelihood percentages, and bootstrapped posterior probabilities was studied for eight highly diverse empirical data sets and were also investigated using experimental simulation. Our results show that the relation between posterior probabilities and bootstrapped maximum likelihood percentages is highly variable but that very strong correlations always exist when Bayesian node support is estimated on bootstrapped character matrices. Moreover, simulations corroborate empirical observations in suggesting that, being more conservative, the bootstrap approach might be less prone to strongly supporting a false phylogenetic hypothesis. Thus, apparent conflicts in topology recovered by the Bayesian approach were reduced after bootstrapping. Both posterior probabilities and bootstrap supports are of great interest to phylogeny as potential upper and lower bounds of node reliability, but they are surely not interchangeable and cannot be directly compared.

Key Words: Bayesian • bootstrap • Markov chain Monte Carlo • maximum likelihood • phylogeny • posterior probability


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
A. B. Prasad, M. W. Allard, NISC Comparative Sequencing Program, and E. D. Green
Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Data Sets
Mol. Biol. Evol., September 1, 2008; 25(9): 1795 - 1808.
[Abstract] [Full Text] [PDF]

Home page
 J. Clin. Microbiol.Home page
K. O'Donnell, D. A. Sutton, A. Fothergill, D. McCarthy, M. G. Rinaldi, M. E. Brandt, N. Zhang, and D. M. Geiser
Molecular Phylogenetic Diversity, Multilocus Haplotype Nomenclature, and In Vitro Antifungal Resistance within the Fusarium solani Species Complex
J. Clin. Microbiol., August 1, 2008; 46(8): 2477 - 2490.
[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
 J. Virol.Home page
B. Ehlers, G. Dural, N. Yasmum, T. Lembo, B. de Thoisy, M.-P. Ryser-Degiorgis, R. G. Ulrich, and D. J. McGeoch
Novel Mammalian Herpesviruses and Lineages within the Gammaherpesvirinae: Cospeciation and Interspecies Transfer
J. Virol., April 1, 2008; 82(7): 3509 - 3516.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
K. K. M. Kulju, S. E. C. Sierra, S. G. A. Draisma, R. Samuel, and P. C. v. Welzen
Molecular phylogeny of Macaranga, Mallotus, and related genera (Euphorbiaceae s.s.): insights from plastid and nuclear DNA sequence data
Am. J. Botany, October 1, 2007; 94(10): 1726 - 1743.
[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
 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
 SIMHome page
G.-H. Sung, N. L. Hywel-Jones, J.-M. Sung, J. J. Luangsa-ard, B. Shrestha, and J. W. Spatafora
Phylogenetic classification of Cordyceps and the clavicipitaceous fungi
Stud Mycol, January 1, 2007; 57(1): 5 - 59.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. J. Salipante and M. S. Horwitz
Phylogenetic fate mapping
PNAS, April 4, 2006; 103(14): 5448 - 5453.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. G. B. Simpson, Y. Inagaki, and A. J. Roger
Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of "Primitive" Eukaryotes
Mol. Biol. Evol., March 1, 2006; 23(3): 615 - 625.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
D. A. Robinson, A. B. Monk, J. E. Cooper, E. J. Feil, and M. C. Enright
Evolutionary Genetics of the Accessory Gene Regulator (agr) Locus in Staphylococcus aureus
J. Bacteriol., December 15, 2005; 187(24): 8312 - 8321.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
K. K. Kojima and H. Fujiwara
An extraordinary retrotransposon family encoding dual endonucleases
Genome Res., August 1, 2005; 15(8): 1106 - 1117.
[Abstract] [Full Text] [PDF]

Home page
 J. Gen. Virol.Home page
D. J. McGeoch, D. Gatherer, and A. Dolan
On phylogenetic relationships among major lineages of the Gammaherpesvirinae
J. Gen. Virol., February 1, 2005; 86(2): 307 - 316.
[Abstract] [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
 Am. J. Bot.Home page
F. Lutzoni, F. Kauff, C. J. Cox, D. McLaughlin, G. Celio, B. Dentinger, M. Padamsee, D. Hibbett, T. Y. James, E. Baloch, et al.
Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits
Am. J. Botany, October 1, 2004; 91(10): 1446 - 1480.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. M. Krishnan, H. Seligmann, C.-B. Stewart, A. P. J. de Koning, and D. D. Pollock
Ancestral Sequence Reconstruction in Primate Mitochondrial DNA: Compositional Bias and Effect on Functional Inference
Mol. Biol. Evol., October 1, 2004; 21(10): 1871 - 1883.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
D. Moreira, P. Lopez-Garcia, and K. Vickerman
An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea
Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1861 - 1875.
[Abstract] [Full Text] [PDF]

Home page
 Am. J. Bot.Home page
R. E. Miller, J. A. McDonald, and P. S. Manos
Systematics of Ipomoea subgenus Quamoclit (Convolvulaceae) based on ITS sequence data and a Bayesian phylogenetic analysis
Am. J. Botany, August 1, 2004; 91(8): 1208 - 1218.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
N. Takezaki, F. Figueroa, Z. Zaleska-Rutczynska, N. Takahata, and J. Klein
The Phylogenetic Relationship of Tetrapod, Coelacanth, and Lungfish Revealed by the Sequences of Forty-Four Nuclear Genes
Mol. Biol. Evol., August 1, 2004; 21(8): 1512 - 1524.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. J. Taylor and W. H. Piel
An Assessment of Accuracy, Error, and Conflict with Support Values from Genome-Scale Phylogenetic Data
Mol. Biol. Evol., August 1, 2004; 21(8): 1534 - 1537.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
I. Oksanen, K. Lohtander, K. Sivonen, and J. Rikkinen
Repeat-type distribution in trnL intron does not correspond with species phylogeny: comparison of the genetic markers 16S rRNA and trnL intron in heterocystous cyanobacteria
Int J Syst Evol Microbiol, May 1, 2004; 54(3): 765 - 772.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
G. M. Stellari, M. A. Jaramillo, and E. M. Kramer
Evolution of the APETALA3 and PISTILLATA Lineages of MADS-Box-Containing Genes in the Basal Angiosperms
Mol. Biol. Evol., March 1, 2004; 21(3): 506 - 519.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. A. Gontcharov, B. Marin, and M. Melkonian
Are Combined Analyses Better Than Single Gene Phylogenies? A Case Study Using SSU rDNA and rbcL Sequence Comparisons in the Zygnematophyceae (Streptophyta)
Mol. Biol. Evol., March 1, 2004; 21(3): 612 - 624.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
E. M. Kramer, M. A. Jaramillo, and V. S. Di Stilio
Patterns of Gene Duplication and Functional Evolution During the Diversification of the AGAMOUS Subfamily of MADS Box Genes in Angiosperms
Genetics, February 1, 2004; 166(2): 1011 - 1023.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Reyes, C. Gissi, F. Catzeflis, E. Nevo, G. Pesole, and C. Saccone
Congruent Mammalian Trees from Mitochondrial and Nuclear Genes Using Bayesian Methods
Mol. Biol. Evol., February 1, 2004; 21(2): 397 - 403.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T. J. Barkman, S.-H. Lim, K. M. Salleh, and J. Nais
From the Cover: Mitochondrial DNA sequences reveal the photosynthetic relatives of Rafflesia, the world's largest flower
PNAS, January 20, 2004; 101(3): 787 - 792.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. P. Simmons, K. M. Pickett, and M. Miya
How Meaningful Are Bayesian Support Values?
Mol. Biol. Evol., January 1, 2004; 21(1): 188 - 199.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C. J. Douady, F. Catzeflis, J. Raman, M. S. Springer, and M. J. Stanhope
The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews)
PNAS, July 8, 2003; 100(14): 8325 - 8330.
[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.