Mol. Biol. Evol. 13(7):999-1011. 1996
DOI:
© 1996 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
On the Interpretation of Bootstrap Trees: Appropriate Threshold of Clade Selection and Induced Gain
LIRMM, UMR 9928 Universite Montpellier II/CNRS, 161, Rue Ada, 34392 Montpellier cedex 5, France
E-mail: gascuel{at}lirmm.fr.
In this study we address the problem of interpreting a bootstrap tree. The main issue is choosing the threshold of clade selection in order to separate reliable clades from unreliable ones, depending on their bootstrap proportion. This threshold depends on the chosen error measure. We investigate error measures that stem from a generalization of Robinson and Foulds' (1981) distance, used to quantify the divergence between the true phylogeny and the estimated trees. We propose two analytical approximations of the optimum threshold of clade selection to interpret (i.e., reduce) the bootstrap tree. We performed extensive simulations along the lines of Kuhner and Felsenstein (1994) using the neighbor-joining and the maximum-parsimony methods. These simulations show that our approximations cause only small losses in quality when compared to the optimum threshold resulting from empirical observation. Next, we measured the error reduction achieved when estimating the true phylogeny by the properly reduced bootstrap tree rather than by the complete original tree, obtained with a classical tree-building method. Our simulations on short sequences show than an error reduction of 39% is achieved with the parsimony method and an error reduction of 33% is achieved with the distance method when the error is measured with the standard Robinson and Foulds distance. The observed error reduction is shown to originate from an important decrease in Type I error (wrong inferences), while Type II error (omitted correct clades) is only slightly increased. Greater error reduction is achieved when shorter sequences are used, and when more importance is given to Type I error than to Type II error. To investigate the causes of error from another point of view, we propose a general decomposition of the error expectation in two terms of bias, and one of variance. Results for these terms show that no fundamental bias is introduced by the bootstrap process, the only source of bias being structural (lack of resolution). Moreover, the variance in the estimations is greatly reduced, providing another explanation for the better results of the reduced bootstrap tree compared with the original tree estimate.
Key Words: bootstrap method • threshold of clade selection • topological distance • Type I and Type II error • bias/variance compromise • maximum parsimony • neighbor joining • computer simulations
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. T Holder, D. J Zwickl, and C. Dessimoz Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes Phil Trans R Soc B, December 27, 2008; 363(1512): 4013 - 4021. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T. Holder, J. Sukumaran, and P. O. Lewis A Justification for Reporting the Majority-Rule Consensus Tree in Bayesian Phylogenetics Syst Biol, October 1, 2008; 57(5): 814 - 821. [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]
|
|
|
|
|
|
A. Criscuolo, V. Berry, E. J. P. Douzery, and O. Gascuel SDM: A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics Syst Biol, October 1, 2006; 55(5): 740 - 755. [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]
|
|
|
|
|
|
V. Berry and C. Semple Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa Syst Biol, April 1, 2006; 55(2): 270 - 288. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Yang and B. Rannala Branch-Length Prior Influences Bayesian Posterior Probability of Phylogeny Syst Biol, June 1, 2005; 54(3): 455 - 470. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Sanjuan and B. Wrobel Weighted Least-Squares Likelihood Ratio Test for Branch Testing in Phylogenies Reconstructed from Distance Measures Syst Biol, April 1, 2005; 54(2): 218 - 229. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. P. Ivanova, O. M. Onyshchenko, R. Christen, A. M. Lysenko, N. V. Zhukova, L. S. Shevchenko, and E. A. Kiprianova Marinomonas pontica sp. nov., isolated from the Black Sea Int J Syst Evol Microbiol, January 1, 2005; 55(1): 275 - 279. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. P. Ivanova, S. Flavier, and R. Christen Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov. Int J Syst Evol Microbiol, September 1, 2004; 54(5): 1773 - 1788. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. P. Ivanova, Y. V. Alexeeva, S. Flavier, J. P. Wright, N. V. Zhukova, N. M. Gorshkova, V. V. Mikhailov, D. V. Nicolau, and R. Christen Formosa algae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae Int J Syst Evol Microbiol, May 1, 2004; 54(3): 705 - 711. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. P. Ivanova, N. M. Gorshkova, T. Sawabe, N. V. Zhukova, K. Hayashi, V. V. Kurilenko, Y. Alexeeva, V. Buljan, D. V. Nicolau, V. V. Mikhailov, et al. Sulfitobacter delicatus sp. nov. and Sulfitobacter dubius sp. nov., respectively from a starfish (Stellaster equestris) and sea grass (Zostera marina) Int J Syst Evol Microbiol, March 1, 2004; 54(2): 475 - 480. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Galtier Sampling Properties of the Bootstrap Support in Molecular Phylogeny: Influence of Nonindependence Among Sites Syst Biol, February 1, 2004; 53(1): 38 - 46. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Gardan, R. Christen, W. Achouak, and P. Prior Erwinia papayae sp. nov., a pathogen of papaya (Carica papaya) Int J Syst Evol Microbiol, January 1, 2004; 54(1): 107 - 113. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
K. Hayashi, J. Moriwaki, T. Sawabe, F. L. Thompson, J. Swings, N. Gudkovs, R. Christen, and Y. Ezura Vibrio superstes sp. nov., isolated from the gut of Australian abalones Haliotis laevigata and Haliotis rubra Int J Syst Evol Microbiol, November 1, 2003; 53(6): 1813 - 1817. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. P. Ivanova, O. I. Nedashkovskaya, N. V. Zhukova, D. V. Nicolau, R. Christen, and V. V. Mikhailov Shewanella waksmanii sp. nov., isolated from a sipuncula (Phascolosoma japonicum) Int J Syst Evol Microbiol, September 1, 2003; 53(5): 1471 - 1477. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Gardan, C. Gouy, R. Christen, and R. Samson Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov. Int J Syst Evol Microbiol, March 1, 2003; 53(2): 381 - 391. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Brettar, R. Christen, and M. G. Hofle Idiomarina baltica sp. nov., a marine bacterium with a high optimum growth temperature isolated from surface water of the central Baltic Sea Int J Syst Evol Microbiol, March 1, 2003; 53(2): 407 - 413. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. E. Alfaro, S. Zoller, and F. Lutzoni Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence Mol. Biol. Evol., February 1, 2003; 20(2): 255 - 266. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Sanchis, J. M. Michelena, A. Latorre, D. L. J. Quicke, U. Gärdenfors, and R. Belshaw The Phylogenetic Analysis of Variable-Length Sequence Data: Elongation Factor-1{{alpha}} Introns in European Populations of the Parasitoid Wasp Genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) Mol. Biol. Evol., June 1, 2001; 18(6): 1117 - 1131. [Abstract] [Full Text]
|
|