Relative-Rate Test for Nucleotide Substitutions between Two Lineages

@article{Li1992RelativeRateTF,
  title={Relative-Rate Test for Nucleotide Substitutions between Two Lineages},
  author={Peng Li and Jean Bousquet},
  journal={Molecular Biology and Evolution},
  year={1992},
  volume={9},
  pages={1185-1185}
}
  • P. Li, J. Bousquet
  • Published 1 November 1992
  • Biology
  • Molecular Biology and Evolution
The molecular-clock hypothesis, i.e., the rate constancy of molecular evolution (Zuckerkandl and Pauling 1965), has been a cornerstone for several issues in molecular evolution, such as the neutral mutation hypothesis (Kimura 1983) and the estimation of phylogenies (Nei 1987, pp. 309-3 13 ) and divergence times (Li and Graur 199 1, pp. 117-l 18). For the purpose of assessing the constancy of molecular evolution, a relative-rate test was developed to determine whether protein replacements are… 

Figures and Tables from this paper

Estimating Rate and Time in Molecular Phylogenies: Beyond the Molecular Clock?
TLDR
The study of rates of character evolution has been a cornerstone of evolutionary biology since the pioneering work of Simpson (1944) and molecular rate constancy continues to be viewed as a reasonable model even across vast reaches of the tree of life (Wray et al., 1996).
RATES OF MOLECULAR EVOLUTION: Phylogenetic Issues and Applications
TLDR
Methods for assessing rate variability are reviewed, and comparative absolute rates of change for five sets of mitochondrial DNAs in 12 vertebrates for application in phylogenetic analyses are estimated.
Performance of the relative-rate test under nonstationary models of nucleotide substitution.
TLDR
Simulations to assess the performance of the relative-rate tests when the molecular-clock (MC) hypothesis is true, but the stationarity and uniformity assumptions are violated found that the test using Kimura's distances performs better than the LogDet test.
Phylogenetic test of the molecular clock and linearized trees.
TLDR
To estimate approximate divergence times of species or species groups with molecular data, a method of constructing a linearized tree under the assumption of a molecular clock is developed and used to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.
Evolution of genes and taxa: a primer
TLDR
The Neutral Theory of Molecular Evolution serves as the null model of molecular evolution and plays a central role in data analysis, three areas in which the Neutral Theory plays a vital role are: interpreting ratios of nonsynonymous to synonymous nucleotide substitutions, assessing the reliability of molecular clocks, and providing a foundation for molecular population genetics.
Molecular Clocks and Nucleotide Substitution Rates in Higher Plants
TLDR
An important corollary prediction of the molecular clock hypothesis is that rates of molecular evolution are equal among diverse evolutionary lineages.
Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects.
TLDR
It is proposed that increased rates of nucleotide substitution may lead to increase rates of gene rearrangement in the mt genomes of insects.
Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution.
  • X. Gu, W. Li
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
This paper reviews recent studies on correcting the estimation bias of evolutionary distances, the estimation of the pattern of nucleotide substitution, andThe estimation of rate variation among the sites in a sequence.
Relative-rate tests versus paleontological divergence data for diatoms and vertebrates
TLDR
It is concluded that each of these two approaches suffers from weaknesses of its own and that the absolute divergence rates are more reliable than those derived from the relative-rate test.
Testing relative evolutionary rates and estimating divergence times among six genera of Rhizophoraceae using cpDNA and nrDNA sequences
The molecular phylogenetic trees of 10 species representing 6 genera of the family Rhizophoraceae have been constructed using the sequences of chloroplast genesmatK andrbcL as well as the ITS regions
...
...

References

SHOWING 1-10 OF 16 REFERENCES
The molecular clock runs more slowly in man than in apes and monkeys
TLDR
The results suggest that the variation in rate among mammals is primarily due to differences in generation time8 rather than changes in DNA repair mechanisms9, and propose a method for estimating the divergence times between species when the rate constancy assumption is violated.
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
  • M. Kimura
  • Biology
    Journal of Molecular Evolution
  • 2005
TLDR
Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes.
TLDR
The implication of the results for the mechanisms of DNA evolution and that of the relative likelihood of codon interchanges in parsimonious phylogenetic reconstruction are discussed.
Evidence for higher rates of nucleotide substitution in rodents than in man.
  • C. Wu, W. Li
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1985
TLDR
It is found that rodents evolve significantly faster than man when the coding regions of 11 genes from rodents (mouse or rat) and man are compared with those from another mammalian species (usually bovine).
Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs.
TLDR
The rate of cpDNA evolution appears to have slowed in some dicot lineages following the monocot/dicot split, and the slowdown is more conspicuous at nonsynonymous sites than at synonymous sites.
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.
Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes.
TLDR
The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species, which is in agreement with that for the tree obtained from chromosomal studies and DNA-hybridization experiments.
Complete congruence between morphological and rbcL-based molecular phylogenies in birches and related species (Betulaceae).
TLDR
The topologies obtained by the different methods were completely congruent, and bootstrapping strongly supported the division of the family Betulaceae into two major clades, Betuleae (Alnus and Betula) and Coryleae (other members).
Apes and monkeys
The apes and monkeys that we provide for you will be ultimate to give preference. This reading book is your chosen book to accompany you when in your free time, in your lonely. This kind of book can
...
...