Estimation of evolutionary distances between homologous nucleotide sequences.

@article{Kimura1981EstimationOE,
  title={Estimation of evolutionary distances between homologous nucleotide sequences.},
  author={Motoo Kimura},
  journal={Proceedings of the National Academy of Sciences of the United States of America},
  year={1981},
  volume={78 1},
  pages={
          454-8
        }
}
  • M. Kimura
  • Published 1981
  • Biology
  • Proceedings of the National Academy of Sciences of the United States of America
By using two models of evolutionary base substitutions--"three-substitution-type" and "two-frequency-class" models--some formulae are derived which permit a simple estimation of the evolutionary distances (and also the evolutionary rates when the divergence times are known) through comparative studies of DNA (and RNA) sequences. These formulae are applied to estimate the base substitution rates at the first, second, and third positions of codons in genes for presomatotropins, preproinsulins… 

Figures and Tables from this paper

Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated.
TLDR
Most data sets are so heterogeneous in their number of transition and transversion differences that none of the current models of nucleotide substitution seem to fit them even after (a) segregation of coding from noncoding sequences and (b) splitting of the codon into three subsets by codon position.
Estimation of evolutionary distance between nucleotide sequences.
TLDR
Application of this method to globin gene data indicates that the number of nucleotide changes per site increases with evolutionary time but the pattern of the increase is quite irregular, and the frequency of cases to which the formula is inapplicable is much lower than that for other similar methods recently proposed.
The estimate of total nucleotide substitutions from pairwise differences is biased.
  • W. Fitch
  • Biology
    Philosophical transactions of the Royal Society of London. Series B, Biological sciences
  • 1986
A nomographic method is presented that estimates the number of nucleotide substitutions since the common ancestor of two nucleotide sequences with no assumption about the proportion of transition and
Estimates of DNA and protein sequence divergence: an examination of some assumptions.
TLDR
Some of the assumptions underlying estimates of DNA and protein sequence divergence are examined and it is shown that these conditions do not strongly affect estimates of divergence, and the binomial variance that is usually assumed for these estimates is safely conservative.
Estimating the pattern of nucleotide substitution
TLDR
It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation.
Patterns of nucleotide substitution in pseudogenes and functional genes
TLDR
The pattern obtained suggests that transition mutations occur somewhat more frequently than transversion mutations and that mutations result more often in A or T than in G or C.
Transitions and transversions in evolutionary descent: An approach to understanding
TLDR
Three methods—direct count, regression, and informational entropy maximization—are described by which these probabilities can be estimated from experimental data are used to study the ratio of transversions to transitions during gene divergence.
Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat
TLDR
Several factors suggest that synonymous codon usage in rodent genes is not subject to selection, and rates of synonymous and nonsynonymous substitution are correlated, apparently because of an excess of substitutions involving adjacent pairs of nucleotides.
A method of estimating from two aligned present-day DNA sequences their ancestral composition and subsequent rates of substitution, possibly different in the two lineages, corrected for multiple and parallel substitutions at the same site
TLDR
It was shown how to resolve an ambiguity in the assignment of two different substitution rates to the two descendant lineages when four or more similar sequences are available, and it was proved that all elements of the equilibrium divergence matrix equal 1/16.
...
...

References

Mammalian Protein Metabolism, III, ed
  • Nati Acad. Sci. USA
  • 1979