Inferring the root of a phylogenetic tree.

Phylogenetic trees can be rooted by a number of criteria. Here, we introduce a Bayesian method for inferring the root of a phylogenetic tree by using one of several criteria: the outgroup, molecular clock, and nonreversible model of DNA substitution. We perform simulation analyses to examine the relative ability of these three criteria to correctly identify the root of the tree. The outgroup and molecular clock criteria were best able to identify the root of the tree, whereas the nonreversible model was able to identify the root only when the substitution process was highly nonreversible. We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results.

[1]  Ziheng Yang.  Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

[2]  Ziheng Yang.  Estimating the pattern of nucleotide substitution , 1994, Journal of Molecular Evolution.

[3]  Hani Doss,et al.  Phylogenetic Tree Construction Using Markov Chain Monte Carlo , 2000 .

[4]  J. Huelsenbeck,et al.  A compound poisson process for relaxing the molecular clock. , 2000, Genetics.

[5]  M. P. Cummings,et al.  PAUP* Phylogenetic analysis using parsimony (*and other methods) Version 4 , 2000 .

[6]  M. Donoghue,et al.  The root of angiosperm phylogeny inferred from duplicate phytochrome genes. , 1999, Science.

[7]  Gary A. Churchill,et al.  THE ROLE OF SUBJECTIVITY IN RECONSTRUCTING ANCESTRAL CHARACTER STATES : A BAYESIAN APPROACH TO UNKNOWN RATES, STATES, AND TRANSFORMATION ASYMMETRIES , 1999 .

[8]  M A Newton,et al.  Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods , 1999, Biometrics.

[9]  B. Larget,et al.  Markov Chain Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees , 2000 .

[10]  Bob Mau,et al.  Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences , 1999 .

[11]  B. Rannala,et al.  Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method. , 1997, Molecular biology and evolution.

[12]  M. Newton,et al.  Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo , 1997 .

[13]  P. Green.  Reversible jump Markov chain Monte Carlo computation and Bayesian model determination , 1995 .

[14]  Z. Yang,et al.  On the use of nucleic acid sequences to infer early branchings in the tree of life. , 1995, Molecular biology and evolution.

[15]  Z. Yang,et al.  Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. , 1993, Molecular biology and evolution.

[16]  Ward C. Wheeler,et al.  NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS , 1990, Cladistics : the international journal of the Willi Hennig Society.

[17]  W. Wheeler.  COMBINATORIAL WEIGHTS IN PHYLOGENETIC ANALYSIS: A STATISTICAL PARSIMONY PROCEDURE , 1990 .

[18]  Patrick L. Williams,et al.  Finding the Minimal Change in a Given Tree , 1990 .

[19]  S. Osawa,et al.  Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[20]  S. Tavaré.  Some probabilistic and statistical problems in the analysis of DNA sequences , 1986 .

[21]  Wayne P. Maddison,et al.  Outgroup Analysis and Parsimony , 1984 .

[22]  H. Kishino,et al.  A New Molecular Clock of Mitochondrial DNA and the Evolution of Hominoids , 1984 .

[23]  S. Jeffery.  Evolution of Protein Molecules , 1979 .

[24]  D. Sankoff.  Minimal Mutation Trees of Sequences , 1975 .

[25]  D. Sankoff,et al.  Locating the vertices of a Steiner tree in arbitrary space , 1975 .

[26]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[27]  T. Jukes.  CHAPTER 24 – Evolution of Protein Molecules , 1969 .

[28]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.