Access provided by Autonomous University of Puebla. Download to read the full chapter text
Chapter PDF
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
References
J. Adachi and M. Hasegawa. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Computer Science Monographs of Institute of Statistical Mathematics, 28:1–150, 1996.
J. Adachi, P. Waddell, W. Martin, and M. Hasegawa. Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. Journal of Molecular Evolution, 50:348–358, 2000.
H. Akaike. Information theory as an extension of the maximum likelihood principle. In B. N. Petrov and F. Csaki, editors, Second International Symposium on Information Theory, pages 267–281. Akademiai Kiado, Budapest, 1973.
U. Arnason, A. Gullberg, and A. Janke. Phylogenetic analyses of mitochondrial DNA suggest a sister group relationship between Xenartha (Edentata) and Ferungulates. Molecular Biology and Evolution, 14:762–768, 1997.
E. T. Bell. Exponential numbers. American Mathematical Monthly, 41:411–419, 1934.
J. O. Berger, B. Liseo, and R. L. Wolpert. Integrated likelihood methods for eliminating nuisance parameters. Statistical Science, 14:1–28, 1999.
M. J. Bishop and A. E. Friday. Tetrapod relationships: The molecular evidence. In C. Patterson, editor, Molecules and Morphology in Evolution, pages 123–139. Cambridge University Press, Cambridge, England, 1987.
Y. Cao, A. Janke, P. J. Waddell, M. Westerman, O. Takenaka, S. Murata, N. Okada, S. Paabo, and M. Hasegawa. Conflict amongst individual mitochondrial proteins in resolving the phylogeny of eutherian orders. Journal of Molecular Evolution, 47:307–322, 1998.
J. T. Chang. Full reconstruction of Markov models on evolutionary tree: Identifiability and consistency. Mathematical Bioscience, 137:51–73, 1996.
D. R. Cox. Further results on tests of families of alternate hypotheses. Journal of the Royal Statistical Society B, 24:406–424, 1962.
M. O. Dayhoff, R. M. Schwartz, and B. C. Orcutt. A model of evolutionary change in proteins. In Atlas of Protein Sequence and Structure, volume 5, pages 345–352. National Biomedical Research Foundation, Washington, DC, 1978. Suppl. 3.
M. W. Dimmic, J. S. Rest, D. P. Mindell, and D. Goldstein. rtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. Journal of Molecular Evolution, 55:65–73, 2002.
J. Felsenstein. Statistical inference and the estimation of phylogenies. PhD thesis, University of Chicago, 1968.
J. Felsenstein. Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17:368–376, 1981.
J. Felsenstein. Distance methods for inferring phylogenies: A justification. Evolution, 38:16–24, 1984.
J. Felsenstein. Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39:783–791, 1985.
P. G. Foster. Modeling compositional heterogeneity. Systematic Biology, 53:485–495, 2004.
N. Galtier and M. Gouy. Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Molecular Biology Evolution, 15:871–879, 1998.
N. Galtier, N. Tourasse, and M. Gouy. A nonhyperthermophilic common ancestor to extant life forms. Science, 283:220–221, 1999.
N. Goldman. Maximum likelihood inference of phylogenetic trees with special reference to a Poisson process model of DNA substitution and to parsimony analyses. Systematic Zoology, 39:345–361, 1990.
N. Goldman and Z. Yang. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution, 11:725–736, 1994.
P. J. Green. Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika, 82:711–732, 1995.
M. Hasegawa, H. Kishino, and T. Yano. Dating the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22:160–174, 1985.
M. Hasegawa, T. Yano, and H. Kishino. A new molecular clock of mitochondrial DNA and the evolution of Hominoids. Proceedings of the Japan Academy Series B, 60:95–98, 1984.
W. K. Hastings. Monte Carlo sampling methods using Markov chains and their applications. Biometrika, 57:97–109, 1970.
S. Henikoff and J. G. Henikoff. Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences, USA, 89:10915–10919, 1992.
D. M. Hillis and J. J. Bull. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology, 42:182–192, 1993.
S. Holmes. Bootstrapping phylogenetic trees: Theory and methods. Statistical Science, 18:241–255, 2003.
J. P. Huelsenbeck. Performance of phylogenetic methods in simulation. Systematic Biology, 44:17–48, 1995.
J. P. Huelsenbeck. The robustness of two phylogenetic methods: Four taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Molecular Biology and Evolution, 12:843–849, 1995.
J. P. Huelsenbeck and K. A. Dyer. Bayesian estimation of positively selected sites. Journal of Molecular Evolution, 58:661–672, 2004.
J. P. Huelsenbeck, B. Larget, and M. E. Alfaro. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Mol. Biol. Evol, 21:1123–1133, 2004.
J. P. Huelsenbeck, B. Larget, and D. Swofford. A compound Poisson process for relaxing the molecular clock. Genetics, 154:1879–1892, 2000.
J. P. Huelsenbeck and B. Rannala. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Systematic Biology. In press.
J. P. Huelsenbeck and F. Ronquist. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics, 17:754–755, 2001.
H. Jeffreys. Theory of Probability. Oxford University Press, Oxford, 1961.
D. T. Jones, W. R. Taylor, and J. M. Thornton. The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences, 8:275–282, 1992.
T. H. Jukes and C. R. Cantor. Evolution of protein molecules. In H. N. Munro, editor, Mammalian Protein Metabolism, pages 21–123. Academic Press, New York, 1969.
S. Kim, K. M. Kjer, and C. N. Duckett. Comparison between molecular and morphological-based phylogenies of galerucine/alticine leaf beetles (Coleoptera: Chrysomelidae). Insect Systematic Evolution, 34:53–64, 2003.
M. Kimura. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16:111–120, 1980.
B. Larget and D. Simon. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution, 16:750–759, 1999.
M. S. Y. Lee. Molecular clock calibrations and metazoan divergence dates. Journal of Molecular Evolution, 49:385–391, 1999.
P. O. Lewis. A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology, 50:913–925, 2001.
S. Li. Phylogenetic tree construction using Markov chain Monte Carlo. PhD thesis, Ohio State University, Columbus, 1996.
B. Mau. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. PhD thesis, University of Wisconsin, Madison, 1996.
B. Mau and M. Newton. Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. Journal of Computational and Graphical Statistics, 6:122–131, 1997.
B. Mau, M. Newton, and B. Larget. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics, 55:1–12, 1999.
N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. W. Teller, and E. Teller. Equations of state calculations by fast computing machines. Journal of Chemical Physics, 21:1087–1091, 1953.
T. Muller and M. Vingron. Modeling amino acid replacement. Journal of Computational Biology, 7:761–776, 2000.
S. V. Muse and B. S. Gaut. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates with application to the chloroplast genome. Molecular Biology and Evolution, 11:715–724, 1994.
M. Nei, P. Xu, and G. Glazko. Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms. Proceedings of the National Academy of Sciences, USA, 98:2497–2502, 2001.
M. Newton, B. Mau, and B. Larget. Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences. In F. Seillier-Moseiwitch, T. P. Speed, and M. Waterman, editors, Statistics in Molecular Biology. Monograph Series of the Institute of Mathematical Statistics, 1999.
R. Nielsen. Mapping mutations on phylogenies. Systematic Biology, 51:729–739, 2002.
R. Nielsen and Z. Yang. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148:929–936, 1998.
J. A. A. Nylander, F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldrey. Bayesian phylogenetic analysis of combined data. Systematic Biology, 53:47–67, 2004.
D. Posada and K. A. Crandall. Modeltest: Testing the model of DNA substitution. Bioinformatics, 14:817–818, 1998.
B. Rannala and Z. Yang. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. Journal of Molecular Evolution, 43:304–311, 1996.
J. S. Rogers. On the consistency of maximum likelihood estimation of phylogenetic trees from nucleotide sequences. Systematic Biology, 46:354–357, 1997.
F. Ronquist and J. P. Huelsenbeck. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19:1572–1574, 2003.
M. Schöniger and A. von Haeseler. A stochastic model and the evolution of autocorrelated DNA sequences. Mol. Phyl. Evol., 3:240–247, 1994.
E. Schröder. Vier combinatorische probleme. Z. Math. Phys., 15:361–376, 1870.
M. A. Suchard, R. E. Weiss, and J. S. Sinsheimer. Bayesian selection of continuous-time Markov chain evolutionary models. Molecular Biology and Evolution, 18:1001–1013, 2001.
Y. Suzuki, G. V. Glazko, and M. Nei. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proceedings of the National Academy of Sciences, USA, 99:15138–16143, 2002.
D. L. Swofford. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, MA, 2002.
N. Takezaki, A. Rzhetsky, and M. Nei. Phylogenetic test of molecular clock and linearized trees. Molecular Biology and Evolution, 12:823–833, 1995.
K. Tamura and M. Nei. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10:512–526, 1993.
S. Tavaré. Some probabilistic and statistical problems on the analysis of DNA sequences. Lectures in Mathematics in the Life Sciences, 17:57–86, 1986.
J. L. Thorne, H. Kishino, and I. S. Painter. Estimating the rate of evolution of the rate of molecular evolution. Molecular Biology and Evolution, 15:1647–1657, 1998.
L. Tierney. Markov chains for exploring posterior distributions. Annals of Statistics, 22:1701–1762, 1994.
C. Tuffey and M. Steel. Modeling the covarion hypothesis of nucleotide substitution. Mathematical Biosciences, 147:63–91, 1998.
S. Whelan and N. Goldman. A general empirical model of protein evolution derived from multiple protein families using a maximum likelihood approach. Molecular Biology and Evolution, 18:691–699, 2001.
Z. Yang. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution, 10:1396–1401, 1993.
Z. Yang. PAML: A program package for phylogenetic analysis by maximum likelihood. Comptuer Applications in Bioscience, 15:555–556, 1997.
Z. Yang and B. Rannala. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Molecular Biology and Evolution, 14:717–724, 1997.
E. Zuckerkandl and L. Pauling. Molecular disease, evolution, and genetic heterogeneity. In M. Kasha and B. Pullman, editors, Horizons in Biochemistry, pages 189–225. Academic Press, New York, 1962.
E. Zuckerkandl and L. Pauling. Evolutionary divergence and convergence in proteins. In V. Bryson and H. J. Vogel, editors, Evolving Genes and Proteins, pages 97–166. Academic Press, New York, 1965.
Author information
Authors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer Science+Business Media, Inc.
About this chapter
Cite this chapter
Huelsenbeck, J.P., Ronquist, F. (2005). Bayesian Analysis of Molecular Evolution Using MrBayes. In: Statistical Methods in Molecular Evolution. Statistics for Biology and Health. Springer, New York, NY. https://doi.org/10.1007/0-387-27733-1_7
Download citation
DOI: https://doi.org/10.1007/0-387-27733-1_7
Publisher Name: Springer, New York, NY
Print ISBN: 978-0-387-22333-9
Online ISBN: 978-0-387-27733-2
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)