Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide

Takashi Gojobori, Kazushige Ishii, Masatoshi Nei*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

230 Scopus citations

Abstract

A formal mathematical analysis of Kimura's (1981) six-parameter model of nucleotide substitution for the case of unequal substitution rates among different pairs of nucleotides is conducted, and new formulae for estimating the number of nucleotide substitutions and its standard error are obtained. By using computer simulation, the validities and utilities of Jukes and Cantor's (1969) one-parameter formula, Takahata and Kimura's (1981) four-parameter formula, and our sixparameter formula for estimating the number of nucleotide substitutions are examined under three different schemes of nucleotide substitution. It is shown that the one-parameter and four-parameter formulae often give underestimates when the number of nucleotide substitutions is large, whereas the six-parameter formula generally gives a good estimate for all the three substitution schemes examined. However, when the number of nucleotide substitutions is large, the six-parameter and four-parameter formulae are often inapplicable unless the number of nucleotides compared is extremely large. It is also shown that as long as the mean number of nucleotide substitutions is smaller than one per nucleotide site the three formulae give more or less the same estimate regardless of the substitution scheme used.

Original languageEnglish (US)
Pages (from-to)414-422
Number of pages9
JournalJournal of Molecular Evolution
Volume18
Issue number6
DOIs
StatePublished - Nov 1 1982

Keywords

  • Evolutionary distance
  • Molecular evolution
  • Nucleotide substitution

ASJC Scopus subject areas

  • Genetics(clinical)
  • Molecular Biology
  • Genetics
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Ecology, Evolution, Behavior and Systematics
  • Agricultural and Biological Sciences (miscellaneous)
  • Agricultural and Biological Sciences(all)

Fingerprint Dive into the research topics of 'Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide'. Together they form a unique fingerprint.

Cite this