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References (46)
-
L. Tierney (1994)
Markov Chains for Exploring Posterior DistributionsAnnals of Statistics, 22
-
M. Hasegawa, H. Kishino (1989)
CONFIDENCE LIMITS ON THE MAXIMUM‐LIKELIHOOD ESTIMATE OF THE HOMINOID TREE FROM MITOCHONDRIAL‐DNA SEQUENCESEvolution, 43
-
(1992)
Practical Markov chain Monte Carlo ( with discussion ) -
J. Felsenstein (1978)
The number of evolutionary treesSystematic Biology, 27
-
Tierney Tierney
Markov chains for exploring posterior distributions (with discussion)Annals of Statistics, 22
-
B. Mau, M. Newton (1997)
Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte CarloJournal of Computational and Graphical Statistics, 6
-
M. Newton (1996)
Bootstrapping phylogenies: Large deviations and dispersion effectsBiometrika, 83
-
Simon Tavar, Y. Feng (1995)
Reconstructing phylogenetic trees when sites are dependent -
K. Sytsma, L. Gottlieb (1986)
CHLOROPLAST DNA EVOLUTION AND PHYLOGENETIC RELATIONSHIPS IN CLARKIA SECT. PERIPETASMA (ONAGRACEAE)Evolution, 40
-
J. Besag, P. Green (1993)
Spatial Statistics and Bayesian ComputationJournal of the royal statistical society series b-methodological, 55
-
Shuying Li, D. Pearl, Hani Doss (2000)
Phylogenetic Tree Construction Using Markov Chain Monte CarloJournal of the American Statistical Association, 95
-
J. Felsenstein (1985)
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAPEvolution, 39
-
P. Sneath, ROBERT Sokal (1962)
Numerical TaxonomyNature, 193
-
J. Felsenstein (1992)
PHYLOGENIES FROM RESTRICTION SITES: A MAXIMUM‐LIKELIHOOD APPROACHEvolution, 46
-
M. Cowles, B. Carlin (1996)
Markov Chain Monte Carlo conver-gence diagnostics: a comparative review -
F. Lapointe, P. Legendre (1991)
The generation of random ultrametric matrices representing dendrogramsJournal of Classification, 8
-
P. Smouse, Wen-Hsiung Li (1987)
LIKELIHOOD ANALYSIS OF MITOCHONDRIAL RESTRICTION‐CLEAVAGE PATTERNS FOR THE HUMAN‐CHIMPANZEE‐GORILLA TRICHOTOMYEvolution, 41
-
J. Felsenstein (1983)
Statistical inference of phylogeniesJournal of the Royal Statistical Society, 146
-
J. Camin, R. Sokal (1965)
A METHOD FOR DEDUCING BRANCHING SEQUENCES IN PHYLOGENYEvolution, 19
-
W. Navidi, G. Churchill, A. Haeseler (1993)
Phylogenetic inference: linear invariants and maximum likelihood.Biometrics, 49 2
-
J. Felsenstein (1985)
Phylogenies and the Comparative MethodThe American Naturalist, 125
-
Goldman Goldman
Statistical tests of models of DNA substitutionJournal of Molecular Evolution, 36
-
Ziheng Yang, B. Rannala (1997)
Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method.Molecular biology and evolution, 14 7
-
Thomas Kocher, Janet Conroy, K. McKaye, Jay Stauffer, Samuel Lockwood (1995)
Evolution of NADH dehydrogenase subunit 2 in east African cichlid fish.Molecular phylogenetics and evolution, 4 4
-
M. Schöniger, A. Haeseler (1994)
A stochastic model for the evolution of autocorrelated DNA sequences.Molecular phylogenetics and evolution, 3 3
-
Felsenstein Felsenstein
Evolutionary trees from DNA sequences: A maximum likelihood approachJournal of Molecular Evolution, 17
-
Hasegawa Hasegawa, Kishino Kishino, Yano Yano
Dating the human‐ape splitting by a molecular clock of mitochondrial DNAJournal of Molecular Evolution, 22
-
W. Fitch, E. Margoliash (1967)
Construction of phylogenetic trees.Science, 155 3760
-
C.
Simulating Probability Distributions in the Coalescent * -
S. Evans, T. Speed (1993)
Invariants of Some Probability Models Used in Phylogenetic InferenceAnnals of Statistics, 21
-
(1985)
Dating the Human-Ape Splitting -
M. Newton, B. Mau, B. Larget (1999)
Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences -
M. Kuhner, Jon Yamato, J. Felsenstein (1997)
Applications of Metropolis-Hastings Genealogy Sampling -
Shuying Li, F. Hutchinson, Hani Doss (1996)
Phylogenetic Tree Construction using Markov Chain -
O. Correspondent (1967)
Chloroplast DNANature, 216
-
A. Rambaut, N. Grassly (1997)
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic treesComputer applications in the biosciences : CABIOS, 13 3
-
Ziheng Yang (1996)
Among-site rate variation and its impact on phylogenetic analyses.Trends in ecology & evolution, 11 9
-
J. Huelsenbeck, B. Rannala (1997)
Phylogenetic methods come of age: testing hypotheses in an evolutionary context.Science, 276 5310
-
F. Lapointe, P. Legendre (1992)
A STATISTICAL FRAMEWORK TO TEST THE CONSENSUS AMONG ADDITIVE TREES (CLADOGRAMS)Systematic Biology, 41
-
R. Griffiths, S. Tavaré (1994)
Ancestral Inference in Population GeneticsStatistical Science, 9
-
J. Besag, P. Green (1993)
Spatial statistics and Bayesian computation (with discussion), 55
-
J. Sinsheimer, J. Lake, R. Little (1996)
Bayesian hypothesis testing of four-taxon topologies using molecular sequence data.Biometrics, 52 1
-
F. Lapointe, P. Legendre (1990)
A statistical framework to test the consensus of two nested classificationsSystematic Biology, 39
-
N. Goldman (1990)
MAXIMUM LIKELIHOOD INFERENCE OF PHYLOGENETIC TREES, WITH SPECIAL REFERENCE TO A POISSON PROCESS MODEL OF DNA SUBSTITUTION AND TO PARSIMONY ANALYSESSystematic Biology, 39
-
J. Felsenstein (1988)
Phylogenies from molecular sequences: inference and reliability.Annual review of genetics, 22
-
Patricia Zambryski (1988)
Basic processes underlying Agrobacterium-mediated DNA transfer to plant cells.Annual review of genetics, 22
- Publisher
- Oxford University Press
- Copyright
- Copyright © 1999 Wiley Subscription Services, Inc., A Wiley Company
- ISSN
- 0006-341X
- eISSN
- 1541-0420
- DOI
- 10.1111/j.0006-341x.1999.00001.x
- Publisher site
- See Article on Publisher Site
Abstract
Summary. We derive a Markov chain to sample from the posterior distribution for a phylogenetic tree given sequence information from the corresponding set of organisms, a stochastic model for these data, and a prior distribution on the space of trees. A transformation of the tree into a canonical cophenetic matrix form suggests a simple and effective proposal distribution for selecting candidate trees close to the current tree in the chain. We illustrate the algorithm with restriction site data on 9 plant species, then extend to DNA sequences from 32 species of fish. The algorithm mixes well in both examples from random starting trees, generating reproducible estimates and credible sets for the path of evolution.
Journal
Biometrics – Oxford University Press
Published: Mar 1, 1999