MBE Advance Access originally published online on February 4, 2003
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Mol. Biol. Evol. 20(2):255-266. 2003
DOI: 10.1093/molbev/msg028
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Bayes or Bootstrap? A Simulation Study Comparing the Performance of Bayesian Markov Chain Monte Carlo Sampling and Bootstrapping in Assessing Phylogenetic Confidence
* Evolution and Ecology, University of California, Davis
Department of Biology, Duke University
Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.
Key Words: Bayesian Markov chain Monte Carlo • bootstrap • maximum parsimony • maximum likelihood • posterior probability • phylogenetic confidence • simulation
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  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]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
M. Escudero, P. Vargas, V. Valcarcel, and M. Luceno Strait of Gibraltar: an effective gene-flow barrier for wind-pollinated Carex helodes (Cyperaceae) as revealed by DNA sequences, AFLP, and cytogenetic variation Am. J. Botany, June 1, 2008; 95(6): 745 - 755. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
W. J. M. Koopman, V. Wissemann, K. De Cock, J. Van Huylenbroeck, J. De Riek, G. J. H. Sabatino, D. Visser, B. Vosman, C. M. Ritz, B. Maes, et al. AFLP markers as a tool to reconstruct complex relationships: A case study in Rosa (Rosaceae) Am. J. Botany, March 1, 2008; 95(3): 353 - 366. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. L. Moody and D. H. Les Phylogenetic systematics and character evolution in the angiosperm family Haloragaceae Am. J. Botany, December 1, 2007; 94(12): 2005 - 2025. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 I. M. Chelo, L. Ze-Ze, and R. Tenreiro Congruence of evolutionary relationships inside the Leuconostoc-Oenococcus-Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK Int J Syst Evol Microbiol, February 1, 2007; 57(2): 276 - 286. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. K. Kuhner and L. P. Smith Comparing Likelihood and Bayesian Coalescent Estimation of Population Parameters Genetics, January 1, 2007; 175(1): 155 - 165. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Holterman, A. van der Wurff, S. van den Elsen, H. van Megen, T. Bongers, O. Holovachov, J. Bakker, and J. Helder Phylum-Wide Analysis of SSU rDNA Reveals Deep Phylogenetic Relationships among Nematodes and Accelerated Evolution toward Crown Clades Mol. Biol. Evol., September 1, 2006; 23(9): 1792 - 1800. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. van den Berg, D. H. Goldman, J. V. Freudenstein, A. M. Pridgeon, K. M. Cameron, and M. W. Chase An overview of the phylogenetic relationships within Epidendroideae inferred from multiple DNA regions and recircumscription of Epidendreae and Arethuseae (Orchidaceae) Am. J. Botany, April 1, 2005; 92(4): 613 - 624. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
M. F. Wojciechowski, M. Lavin, and M. J. Sanderson A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well-supported subclades within the family Am. J. Botany, November 1, 2004; 91(11): 1846 - 1862. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
 |
|
 A. N. Miller and S. M. Huhndorf Using phylogenetic species recognition to delimit species boundaries within Lasiosphaeria Mycologia, September 1, 2004; 96(5): 1106 - 1127. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
X. Gu and H. Zhang Genome Phylogenetic Analysis Based on Extended Gene Contents Mol. Biol. Evol., July 1, 2004; 21(7): 1401 - 1408. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
M. Lutz, R. Bauer, D. Begerow, F. Oberwinkler, and D. Triebel Tuberculina: rust relatives attack rusts Mycologia, May 1, 2004; 96(3): 614 - 626. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. M. Huhndorf, A. N. Miller, and F. A. Fernandez Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined Mycologia, March 1, 2004; 96(2): 368 - 387. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
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]
|
|
|
|
|
|
J. Miadlikowska, F. Lutzoni, T. Goward, S. Zoller, and D. Posada New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex Mycologia, November 1, 2003; 95(6): 1181 - 1203. [Abstract] [Full Text] [PDF]
|
|