Evolutionary Distance: Estimation

Abstract

Evolutionary distance refers to the number of nucleotide substitutions per site between two homologous DNA sequences or the number of amino acid substitutions per site between two homologous protein sequences.

Keywords: nucleotide substitution; synonymous distance; nonsynonymous distance; protein evolution

References

Dayhoff MO, Schwartz RM and Hung LT (1978) A model of evolutionary change in proteins. In: Dayhoff MO (ed.) Atlas of Protein Sequence and Structure, pp. 345–352. Silver Spring, MD: National Biomedical Research Foundation

Goldman N and Yang Z (1994) A codon‐based model of nucleotide substitution for protein‐coding DNA sequences. Molecular Biology and Evolution 11: 725–736.

Gu X and Zhang J (1997) A simple method for estimating the parameter of substitution rate variation among sites. Molecular Biology and Evolution 14: 1106–1113.

Hughes AL, Ota T and Nei M (1990) Positive Darwinian selection promotes charge profile diversity in the antigen‐binding cleft of class I major‐histocompatibility‐complex molecules. Molecular Biology and Evolution 7: 515–524.

Ina Y (1995) New methods for estimating the numbers of synonymous and nonsynonymous substitutions. Journal of Molecular Evolution 40: 190–226.

Jones DT, Taylor WR and Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275–282.

Jukes TH and Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed.) Mammalian Protein Metabolism, pp. 21–123. New York: Academic Press

Lake JA (1994) Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proceedings of the National Academy of Sciences of the United States of America 91: 1455–1459.

Lockhart PJ, Steel MA, Hendy MD and Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence. Molecular Biology and Evolution 11: 605–612.

Nei M and Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution 3: 418–426.

Nei M and Kumar S (2000) Molecular Evolution and Phylogenetics. New York: Oxford University Press.

Tajima F and Nei M (1984) Estimation of evolutionary distance between nucleotide sequences. Molecular Biology and Evolution 1: 269–285.

Tamura K and Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution 10: 512–526.

Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Computer Applications in the Biosciences 13: 555–556.

Zhang J (2000) Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. Journal of Molecular Evolution 50: 56–68.

Further Reading

Comeron JM (1995) A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. Journal of Molecular Evolution 41: 1152–1159.

Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111–120.

Li WH (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. Journal of Molecular Evolution 36: 96–99.

Zhang J, Rosenberg HF and Nei M (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proceedings of the National Academy of Sciences of the United States of America 95: 3708–3713.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Nei, Masatoshi, and Zhang, Jianzhi(Jul 2006) Evolutionary Distance: Estimation. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005108]