Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference

@article{Rannala2006ProbabilityDO,
  title={Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference},
  author={Bruce Rannala and Ziheng Yang},
  journal={Journal of Molecular Evolution},
  year={2006},
  volume={43},
  pages={304-311}
}
A new method is presented for inferring evolutionary trees using nucleotide sequence data. The birth-death process is used as a model of speciation and extinction to specify the prior distribution of phylogenies and branching times. Nucleotide substitution is modeled by a continuous-time Markov process. Parameters of the branching model and the substitution model are estimated by maximum likelihood. The posterior probabilities of different phylogenies are calculated and the phylogeny with the… 
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References

SHOWING 1-10 OF 54 REFERENCES
Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock.
TLDR
Bootstrapping is a conservative approach for estimating the reliability of an inferred phylogeny for four taxa by using model trees of three taxa with an outgroup and by assuming a constant rate of nucleotide substitution.
Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites
TLDR
Several maximum likelihood and distance matrix methods for estimating phylogenetic trees from homologous DNA sequences were compared when substitution rates at sites were assumed to follow a gamma distribution and suggested that the joint likelihood analysis is found to be more robust when rate variation over sites is present but ignored and an assumption is thus violated.
Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters
TLDR
The application of maximum likelihood methods to discrete characters is examined, and it is shown that parsimony methods are notmaximum likelihood methods under the assumptions made by Farris, and an algorithm which enables rapid calculation of the likelihood of a phylogeny is described.
Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea
TLDR
A new method for estimating the variance of the difference between log likelihood of different tree topologies is developed by expressing it explicitly in order to evaluate the maximum likelihood branching order among Hominoidea.
MAXIMUM LIKELIHOOD TREES FROM DNA SEQUENCES: A PECULIAR STATISTICAL ESTIMATION PROBLEM
The parameter space of the phylogenetic tree estimation problem consists of three com? ponents, T, t, and 8. The tree topology T is a discrete entity that is not a proper statistical parameter but
Phylogenetic analysis using parsimony and likelihood methods
  • Ziheng Yang
  • Biology, Medicine
    Journal of Molecular Evolution
  • 2005
TLDR
Evidence was presented showing that the Felsenstein approach does not share the asymptotic efficiency of the maximum likelihood estimator of a statistical parameter, and its performance relative to that of the likelihood method was especially noted.
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
  • Ziheng Yang
  • Biology, Medicine
    Journal of Molecular Evolution
  • 2004
TLDR
Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites, and one of them uses several categories of rates to approximate the gamma distribution, with equal probability for each category.
Robustness of maximum likelihood tree estimation against different patterns of base substitutions
TLDR
The results are in accordance with those from the simulation study, showing that Jukes and Cantor's model is as useful as a more complicated one for making inferences about molecular phylogeny of the viruses.
Molecular Evolutionary Genetics
TLDR
Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
MAXIMUM LIKELIHOOD INFERENCE OF PHYLOGENETIC TREES, WITH SPECIAL REFERENCE TO A POISSON PROCESS MODEL OF DNA SUBSTITUTION AND TO PARSIMONY ANALYSES
Maximum likelihood inference is discussed, and some of its advantages and dis- advantages are noted. The application of maximum likelihood inference to phylogenetics is examined, and a simple Poisson
...
1
2
3
4
5
...