Evolutionary trees from DNA sequences: A maximum likelihood approach

@article{Felsenstein2005EvolutionaryTF,
  title={Evolutionary trees from DNA sequences: A maximum likelihood approach},
  author={Joseph Felsenstein},
  journal={Journal of Molecular Evolution},
  year={2005},
  volume={17},
  pages={368-376}
}
  • J. Felsenstein
  • Published 2005
  • Biology, Computer Science
  • Journal of Molecular Evolution
SummaryThe application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of… 
Constructing Phylogenetic Trees Using Maximum Likelihood
TLDR
This paper explores the method of finding an estimate for the maximum likelihood phylogenetic tree using base substitution probabilities and conditional likelihoods using continuous-time Markov chains.
Constructing Phylogenetic Trees Using Maximum Likelihood
TLDR
This paper explores the method of finding an estimate for the maximum likelihood phylogenetic tree using base substitution probabilities and conditional likelihoods using continuous-time Markov chains.
On the maximum likelihood method in molecular phylogenetics
TLDR
It was shown that the maximum likelihood method is superior to distance methods in the efficiency particularly when the evolutionary rate differs among lineages.
An evolutionary model for maximum likelihood alignment of DNA sequences
TLDR
A parameter-estimation approach which takes into account all possible alignments between two sequences is introduced; the danger of estimating evolutionary parameters from a single alignment is discussed.
Maximum Likelihood in Molecular Phylogenetics
TLDR
The calculation of likelihood, given a topology and a substitution model, is illustrated with both a brute-force approach and the pruning algorithm which is the most fundamental algorithm in likelihood calculation.
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.
Phylogeny estimation: traditional and Bayesian approaches
TLDR
The ability of the new approaches to address previously intractable questions is making phylogenetic analysis an essential tool in an increasing number of areas of genetic research.
The maximum likelihood approach for phylogenetic prediction.
TLDR
The ML method is similar to the maximum parsimony method in that the analysis is performed on each column of an msa, and the observed data are the observed sequence variations found within the columns of a msa.
Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites
  • Ziheng Yang
  • Environmental Science
    Journal of Molecular Evolution
  • 2004
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.
Inferring Phylogenies Using Evolutionary Algorithms: A maximum likelihood approach for constructing phylogenetic trees from molecular data
TLDR
The computationally expensive maximum-likelihood method coupled with an evolutionary algorithm (EA) for the problem of inferring evolutionary relationships among species (phylogenies) from molecular data shows promising results and is able to utilize processors of a massively parallel system in a transparent manner.
...
...

References

SHOWING 1-10 OF 43 REFERENCES
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.
Estimation of time of divergence from phylogenetic studies.
  • R. Chakraborty
  • Biology
    Canadian journal of genetics and cytology. Journal canadien de genetique et de cytologie
  • 1977
TLDR
It is shown in this paper that the least squares theory may be applied to obtain simple estimates of the relative time lengths for each segment of the tree under the assumption of uniform random substitutions in each segment.
A new estimate of sequence divergence of mitochondrial DNA using restriction endonuclease mappings
TLDR
A new estimate of the sequence divergence of mitochondrial DNA in related species using restriction enzyme maps is constructed assuming a simple Posisson-like model for the evolutionary process and is chosen to maximize an expression which is a reasonable approximation to the true likelihood of the restriction map data.
Alternative Methods of Phylogenetic Inference and their Interrelationship
TLDR
A probabilistic model of evolution in a character, which explains parallelism and convergence by persistence of character-state polymorphism after a unique orgin of the derived character state, and attempts to find that evolutionary tree which requires the least extent of polymorphism.
Statistical estimation of parameters in a phylogenetic tree using a dynamic model of the substitutional process.
An examination of the constancy of the rate of molecular evolution
TLDR
The overall rate of nucleotide substitution within the primates is again found to be less than the rest of the mammals and the procedure employed provides estimates of the relative time of divergence which correlate well with paleontological dates.
A SIMPLE TEST FOR THE POSSIBLE SIMULTANEOUS EVOLUTIONARY DIVERGENCE OF TWO AMINO ACID POSITIONS
TLDR
A simple test to determine when it is not possible for two amino acid (or nucleotide) positions to be divergent at the same time is described.
Are evolutionary rates really variable?
TLDR
It is pointed out in this note that a process which is temporally homogeneous but not a Poisson process is compatible with the data if the coefficient of variation of the time between substitutions is around 1.63.
Cases in which Parsimony or Compatibility Methods will be Positively Misleading
TLDR
Parsimony or minimum evolution methods were first introduced into phylogenetic inference by Camin and Sokal (1965), and a number of other parsimony methods have since appeared in the systematic literature and found widespread use in studies of molecular evolution.
Theoretical foundations for a quantitative approach to paleogenetics
TLDR
It is shown that neglecting the phenomena of multiple hits, back mutation, and chance coincidence can lead to errors larger than 100% in the calculated value of the average number of nucleotide base differences to be expected between two homologous polynucleotides.
...
...