Molecular Biology and Evolution, Vol 14, 717-724, Copyright © 1997 by Society for Molecular Biology and Evolution
Z Yang and B Rannala
An improved Bayesian method is presented for estimating phylogenetic trees
using DNA sequence data. The birth-death process with species sampling is
used to specify the prior distribution of phylogenies and ancestral
speciation times, and the posterior probabilities of phylogenies are used
to estimate the maximum posterior probability (MAP) tree. Monte Carlo
integration is used to integrate over the ancestral speciation times for
particular trees. A Markov Chain Monte Carlo method is used to generate the
set of trees with the highest posterior probabilities. Methods are
described for an empirical Bayesian analysis, in which estimates of the
speciation and extinction rates are used in calculating the posterior
probabilities, and a hierarchical Bayesian analysis, in which these
parameters are removed from the model by an additional integration. The
Markov Chain Monte Carlo method avoids the requirement of our earlier
method for calculating MAP trees to sum over all possible topologies (which
limited the number of taxa in an analysis to about five). The methods are
applied to analyze DNA sequences for nine species of primates, and the MAP
tree, which is identical to a maximum-likelihood estimate of topology, has
a probability of approximately 95%.
ORIGINAL ARTICLE
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method
Department of Integrative Biology, University of California, Berkeley 94720-3140, USA.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. A. Beilstein, I. A. Al-Shehbaz, S. Mathews, and E. A. Kellogg Brassicaceae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited Am. J. Botany, October 1, 2008; 95(10): 1307 - 1327. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. A. McDade, T. F. Daniel, and C. A. Kiel Toward a comprehensive understanding of phylogenetic relationships among lineages of Acanthaceae s.l. (Lamiales) Am. J. Botany, September 1, 2008; 95(9): 1136 - 1152. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. I. Cabrera, G. A. Salazar, M. W. Chase, S. J. Mayo, J. Bogner, and P. Davila Phylogenetic relationships of aroids and duckweeds (Araceae) inferred from coding and noncoding plastid DNA Am. J. Botany, September 1, 2008; 95(9): 1153 - 1165. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 W. M. Jaklitsch, C. P. Kubicek, and I. S. Druzhinina Three European species of Hypocrea with reddish brown stromata and green ascospores Mycologia, September 1, 2008; 100(5): 796 - 815. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. R. Duvall, J. W. Robinson, J. G. Mattson, and A. Moore Phylogenetic analyses of two mitochondrial metabolic genes sampled in parallel from angiosperms find fundamental interlocus incongruence Am. J. Botany, July 1, 2008; 95(7): 871 - 884. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. M. Mateiu and B. H. Rannala Bayesian Inference of Errors in Ancient DNA Caused by Postmortem Degradation Mol. Biol. Evol., July 1, 2008; 25(7): 1503 - 1511. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Shaw, S. Boles, and B. Shaw A phylogenetic delimitation of the "Sphagnum subsecundum complex" (Sphagnaceae, Bryophyta) Am. J. Botany, June 1, 2008; 95(6): 731 - 744. [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]
|
|
|
|
 |
|
 V. Nagy, V. Seidl, G. Szakacs, M. Komon-Zelazowska, C. P. Kubicek, and I. S. Druzhinina Application of DNA Bar Codes for Screening of Industrially Important Fungi: the Haplotype of Trichoderma harzianum Sensu Stricto Indicates Superior Chitinase Formation Appl. Envir. Microbiol., November 1, 2007; 73(21): 7048 - 7058. [Abstract] [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]
|
|
|
|
|
|
L. V. Wain, E. Bailes, F. Bibollet-Ruche, J. M. Decker, B. F. Keele, F. Van Heuverswyn, Y. Li, J. Takehisa, E. M. Ngole, G. M. Shaw, et al. Adaptation of HIV-1 to Its Human Host Mol. Biol. Evol., August 1, 2007; 24(8): 1853 - 1860. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Takehisa, M. H. Kraus, J. M. Decker, Y. Li, B. F. Keele, F. Bibollet-Ruche, K. P. Zammit, Z. Weng, M. L. Santiago, S. Kamenya, et al. Generation of Infectious Molecular Clones of Simian Immunodeficiency Virus from Fecal Consensus Sequences of Wild Chimpanzees J. Virol., July 15, 2007; 81(14): 7463 - 7475. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. N. Minin, K. S. Dorman, F. Fang, and M. A. Suchard Phylogenetic Mapping of Recombination Hotspots in Human Immunodeficiency Virus via Spatially Smoothed Change-Point Processes Genetics, April 1, 2007; 175(4): 1773 - 1785. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Hey and R. Nielsen Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics PNAS, February 20, 2007; 104(8): 2785 - 2790. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Savard, D. Tautz, S. Richards, G. M. Weinstock, R. A. Gibbs, J. H. Werren, H. Tettelin, and M. J. Lercher Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects Genome Res., November 1, 2006; 16(11): 1334 - 1338. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. D. Bailey, M. A. Koch, M. Mayer, K. Mummenhoff, S. L. O'Kane Jr, S. I. Warwick, M. D. Windham, and I. A. Al-Shehbaz Toward a Global Phylogeny of the Brassicaceae Mol. Biol. Evol., November 1, 2006; 23(11): 2142 - 2160. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. J. McKenzie, E. M. Muller, A. K. W. Skinner, P. O. Karis, and N. P. Barker Phylogenetic relationships and generic delimitation in subtribe Arctotidinae (Asteraceae: Arctotideae) inferred by DNA sequence data from ITS and five chloroplast regions Am. J. Botany, August 1, 2006; 93(8): 1222 - 1235. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. M. Jaklitsch, M. Komon, C. P. Kubicek, and I. S. Druzhinina Hypocrea crystalligena sp. nov., a common European species with a white-spored Trichoderma anamorph. Mycologia, May 1, 2006; 98(3): 499 - 513. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Y. Tseng and J. Liang Estimation of Amino Acid Residue Substitution Rates at Local Spatial Regions and Application in Protein Function Inference: A Bayesian Monte Carlo Approach Mol. Biol. Evol., February 1, 2006; 23(2): 421 - 436. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Shapiro, A. Rambaut, and A. J. Drummond Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences Mol. Biol. Evol., January 1, 2006; 23(1): 7 - 9. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Yang and B. Rannala Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds Mol. Biol. Evol., January 1, 2006; 23(1): 212 - 226. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
W. M. Jaklitsch, M. Komon, C. P. Kubicek, and I. S. Druzhinina Hypocrea voglmayrii sp. nov. from the Austrian Alps represents a new phylogenetic clade in Hypocrea/Trichoderma. Mycologia, November 1, 2005; 97(6): 1365 - 1378. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. L. Santiago, F. Range, B. F. Keele, Y. Li, E. Bailes, F. Bibollet-Ruche, C. Fruteau, R. Noe, M. Peeters, J. F. Y. Brookfield, et al. Simian Immunodeficiency Virus Infection in Free-Ranging Sooty Mangabeys (Cercocebus atys atys) from the Tai Forest, Cote d'Ivoire: Implications for the Origin of Epidemic Human Immunodeficiency Virus Type 2 J. Virol., October 1, 2005; 79(19): 12515 - 12527. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Mossel and E. Vigoda Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees Science, September 30, 2005; 309(5744): 2207 - 2209. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. M. Kim, Y.-G. Yoon, and H. S. Jung Evaluation of the monophyly of Fomitopsis using parsimony and MCMC methods Mycologia, July 1, 2005; 97(4): 812 - 822. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 V. N. Minin, K. S. Dorman, F. Fang, and M. A. Suchard Dual multiple change-point model leads to more accurate recombination detection Bioinformatics, July 1, 2005; 21(13): 3034 - 3042. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. E. Abdel-Ghany, I. S. Day, M. P. Simmons, P. Kugrens, and A. S.N. Reddy Origin and Evolution of Kinesin-Like Calmodulin-Binding Protein Plant Physiology, July 1, 2005; 138(3): 1711 - 1722. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Suchard Stochastic Models for Horizontal Gene Transfer: Taking a Random Walk Through Tree Space Genetics, May 1, 2005; 170(1): 419 - 431. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Y. W. Ho, M. J. Phillips, A. J. Drummond, and A. Cooper Accuracy of Rate Estimation Using Relaxed-Clock Models with a Critical Focus on the Early Metazoan Radiation Mol. Biol. Evol., May 1, 2005; 22(5): 1355 - 1363. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Larget, D. L. Simon, J. B. Kadane, and D. Sweet A Bayesian Analysis of Metazoan Mitochondrial Genome Arrangements Mol. Biol. Evol., March 1, 2005; 22(3): 486 - 495. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. H. Oakley, Z. Gu, E. Abouheif, N. H. Patel, and W.-H. Li Comparative Methods for the Analysis of Gene-Expression Evolution: An Example Using Yeast Functional Genomic Data Mol. Biol. Evol., January 1, 2005; 22(1): 40 - 50. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. Sanderson, J. L. Thorne, N. Wikstrom, and K. Bremer Molecular evidence on plant divergence times Am. J. Botany, October 1, 2004; 91(10): 1656 - 1665. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Peintner, J.-M. Moncalvo, and R. Vilgalys Toward a better understanding of the infrageneric relationships in Cortinarius (Agaricales, Basidiomycota) Mycologia, September 1, 2004; 96(5): 1042 - 1058. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Lartillot and H. Philippe A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process Mol. Biol. Evol., June 1, 2004; 21(6): 1095 - 1109. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. D. Smith, T. W. H. Lui, and E. R. M. Tillier Empirical Models for Substitution in Ribosomal RNA Mol. Biol. Evol., March 1, 2004; 21(3): 419 - 427. [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]
|
|
|
|
|
|
S. Aris-Brosou and Z. Yang Bayesian Models of Episodic Evolution Support a Late Precambrian Explosive Diversification of the Metazoa Mol. Biol. Evol., December 1, 2003; 20(12): 1947 - 1954. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. S. Rest and D. P. Mindell Retroids in Archaea: Phylogeny and Lateral Origins Mol. Biol. Evol., July 1, 2003; 20(7): 1134 - 1142. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Husmeier and G. McGuire Detecting Recombination in 4-Taxa DNA Sequence Alignments with Bayesian Hidden Markov Models and Markov Chain Monte Carlo Mol. Biol. Evol., March 1, 2003; 20(3): 315 - 337. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. J. Douady, F. Delsuc, Y. Boucher, W. F. Doolittle, and E. J. P. Douzery Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability Mol. Biol. Evol., February 1, 2003; 20(2): 248 - 254. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Delsuc, M. Scally, O. Madsen, M. J. Stanhope, W. W. de Jong, F. M. Catzeflis, M. S. Springer, and E. J. P. Douzery Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting Mol. Biol. Evol., October 1, 2002; 19(10): 1656 - 1671. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Jow, C. Hudelot, M. Rattray, and P. G. Higgs Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution Mol. Biol. Evol., September 1, 2002; 19(9): 1591 - 1601. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. J. Drummond, G. K. Nicholls, A. G. Rodrigo, and W. Solomon Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data Genetics, July 1, 2002; 161(3): 1307 - 1320. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. Bollback Bayesian Model Adequacy and Choice in Phylogenetics Mol. Biol. Evol., July 1, 2002; 19(7): 1171 - 1180. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 GASTROPOD PHYLOGENETICS: PROGRESS, PROBLEMS, AND IMPLICATIONS Journal of Paleontology, November 1, 2001; 75(6): 1128 - 1140.
|
|
|
|
|
|
R. Nielsen Mutations as Missing Data: Inferences on the Ages and Distributions of Nonsynonymous and Synonymous Mutations Genetics, September 1, 2001; 159(1): 401 - 411. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Nieselt-Struwe and A. von Haeseler Quartet-Mapping, a Generalization of the Likelihood-Mapping Procedure Mol. Biol. Evol., July 1, 2001; 18(7): 1204 - 1219. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Suchard, R. E. Weiss, and J. S. Sinsheimer Bayesian Selection of Continuous-Time Markov Chain Evolutionary Models Mol. Biol. Evol., June 1, 2001; 18(6): 1001 - 1013. [Abstract] [Full Text]
|
|
|
|
|
|
H. Kishino, J. L. Thorne, and W. J. Bruno Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution Mol. Biol. Evol., March 1, 2001; 18(3): 352 - 361. [Abstract] [Full Text]
|
|
|
|
|
|
L. Markovtsova, P. Marjoram, and S. Tavaré The Effects of Rate Variation on Ancestral Inference in the Coalescent Genetics, November 1, 2000; 156(3): 1427 - 1436. [Abstract] [Full Text]
|
|
|
|
|
|
S. C. Thomas and W. G. Hill Estimating Quantitative Genetic Parameters Using Sibships Reconstructed From Marker Data Genetics, August 1, 2000; 155(4): 1961 - 1972. [Abstract] [Full Text]
|
|
|
|
|
|
M. Steel and D. Penny Parsimony, Likelihood, and the Role of Models in Molecular Phylogenetics Mol. Biol. Evol., June 1, 2000; 17(6): 839 - 850. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. A. Beaumont Detecting Population Expansion and Decline Using Microsatellites Genetics, December 1, 1999; 153(4): 2013 - 2029. [Abstract] [Full Text]
|
|
|
|
|
|
G. Cooper, N. J. Burroughs, D. A. Rand, D. C. Rubinsztein, and W. Amos Markov Chain Monte Carlo analysis of human Y-chromosome microsatellites provides evidence of biased mutation PNAS, October 12, 1999; 96(21): 11916 - 11921. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. W. Diaconis and S. P. Holmes Matchings and phylogenetic trees PNAS, December 8, 1998; 95(25): 14600 - 14602. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Liò and N. Goldman Models of Molecular Evolution and Phylogeny Genome Res., December 1, 1998; 8(12): 1233 - 1244. [Abstract] [Full Text]
|
|
|
|
|
|
J. Shoemaker, I. Painter, and B. S. Weir A Bayesian Characterization of Hardy-Weinberg Disequilibrium Genetics, August 1, 1998; 149(4): 2079 - 2088. [Abstract] [Full Text] [PDF]
|
|