Journal of Molecular Evolution

, Volume 24, Issue 1, pp 28–38

An evolutionary perspective on synonymous codon usage in unicellular organisms

  • Paul M. Sharp
  • Wen-Hsiung Li

DOI: 10.1007/BF02099948

Cite this article as:
Sharp, P.M. & Li, WH. J Mol Evol (1986) 24: 28. doi:10.1007/BF02099948


Observed patterns of synonymous codon usage are explained in terms of the joint effects of mutation, selection, and random drift. Examination of the codon usage in 165Escherichia coli genes reveals a consistent trend of increasing bias with increasing gene expression level. Selection on codon usage appears to be unidirectional, so that the pattern seen in lowly expressed genes is best explained in terms of an absence of strong selection. A measure of directional synonymous-codon usage bias, the Codon Adaptation Index, has been developed. In enterobacteria, rates of synonymous substitution are seen to vary greatly among genes, and genes with a high codon bias evolve more slowly. A theoretical study shows that the patterns of extreme codon bias observed for someE. coli (and yeast) genes can be generated by rather small selective differences. The relative plausibilities of various theoretical models for explaining nonrandom codon usage are discussed.

Key words

Codon usageSynonymous substitution rateCodon Adaptation IndexEnterobacterial genesG+C contentTheoretical models

Copyright information

© Springer-Verlag New York Inc. 1986

Authors and Affiliations

  • Paul M. Sharp
    • 1
    • 2
  • Wen-Hsiung Li
    • 1
  1. 1.Center for Demographic and Population GeneticsUniversity of TexasHoustonUSA
  2. 2.Department of GeneticsTrinity CollegeDublin 2Ireland