Taking Variation of Evolutionary Rates Between Sites into Account in Inferring Phylogenies

@article{Felsenstein2001TakingVO,
  title={Taking Variation of Evolutionary Rates Between Sites into Account in Inferring Phylogenies},
  author={J. Felsenstein},
  journal={Journal of Molecular Evolution},
  year={2001},
  volume={53},
  pages={447-455}
}
  • J. Felsenstein
  • Published 2001
  • Biology, Medicine
  • Journal of Molecular Evolution
Abstract. As methods of molecular phylogeny have become more explicit and more biologically realistic following the pioneering work of Thomas Jukes, they have had to relax their initial assumption that rates of evolution were equal at all sites. Distance matrix and likelihood methods of inferring phylogenies make this assumption; parsimony, when valid, is less limited by it. Nucleotide sequences, including RNA sequences, can show substantial rate variation; protein sequences show rates that… Expand
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References

SHOWING 1-10 OF 33 REFERENCES
A likelihood approach to character weighting and what it tells us about parsimony and compatibility
TLDR
The statistical framework of maximum likelihood estimation is used to examine character weighting in inferring phylogenies and provides a spectrum of intermediates between these methods that may be of use in analysing real data. Expand
A Hidden Markov Model approach to variation among sites in rate of evolution.
TLDR
The method of Hidden Markov Models is used to allow for unequal and unknown evolutionary rates at different sites in molecular sequences and it is shown how to use the Newton-Raphson method to estimate branch lengths of a phylogeny and to infer from a phylogenies what assignment of rates to sites has the largest posterior probability. Expand
Estimating divergence times in the presence of an overdispersed molecular clock.
  • D. Cutler
  • Biology, Medicine
  • Molecular biology and evolution
  • 2000
TLDR
A method was developed to estimate divergence times using loci that may be overdispersed, and a model consistent with a Cambrian origination of the animal phyla, although significantly less likely than a much older divergence, fitted the data well. Expand
A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy
A new method for estimating divergence times when evolutionary rates are variable across lineages is proposed. The method, called nonparametric rate smoothing (NPRS), relies on minimization ofExpand
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods.
TLDR
This chapter discusses the development of maximum likelihood methods for inferring phylogenies from protein data, which used the highly oversimplified model of symmetric change among amino acids but could not handle more than three or four sequences in the tree in a reasonably exact way. Expand
A compound poisson process for relaxing the molecular clock.
TLDR
This work introduces a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process and uses Markov chain Monte Carlo integration to evaluate the posterior probability distribution. Expand
Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.
  • Z. Yang
  • Biology, Medicine
  • Molecular biology and evolution
  • 1993
TLDR
Felsenstein's maximum-likelihood approach for inferring phylogeny from DNA sequences is extended to the case where substitution rates over sites are described by the gamma distribution and a numerical example is presented to show that the method fits the data better than do previous models. Expand
Limitations of the evolutionary parsimony method of phylogenetic analysis.
  • L. Jin, M. Nei
  • Biology, Medicine
  • Molecular biology and evolution
  • 1990
TLDR
The theoretical basis of Lake's evolutionary parsimony method of constructing a phylogenetic tree, which is primarily applied to four DNA sequences, is examined and it is found that when the rates of two transversional changes from a nucleotide are unequal, his invariance property breaks down. Expand
General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites.
TLDR
This work illustrates graphically ways to interpret the reliability of distance-based transformations, using the corrected transition to transversion ratio returned for pairs of sequences which are successively more diverged. Expand
A space-time process model for the evolution of DNA sequences.
  • Z. Yang
  • Biology, Medicine
  • Genetics
  • 1995
TLDR
Tremendous variation of rates among sites in the sequence is revealed by the analyses, and when rate differences for different codon positions are appropriately accounted for in the models, substitution rates at adjacent sites are found to be strongly (positively) correlated. Expand
...
1
2
3
4
...