Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Brief Communications Arising
  • Published:

Evolutionary genomics

Codon bias and selection on single genomes


Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature 428, 942–945 (2004); see also communication from Nielsen et al.; Chen et al.; Plotkin et al. reply The idea that natural selection on genes might be detected using only a single genome has been put forward by Plotkin and colleagues1, who present a method that they claim can detect selection without the need for comparative data and which, if correct, would confer greater power of analysis with less information. Here we argue that their method depends on assumptions that confound their conclusions and that, even if these assumptions were valid, the authors' inferences about adaptive natural selection are unjustified.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Codon bias explains volatility.

Similar content being viewed by others


  1. Plotkin, J. B., Dushoff, J. & Fraser, H. B. Nature 428, 942–945 (2004).

    Article  ADS  CAS  Google Scholar 

  2. Akashi, H. Genetics 136, 927–935 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Chiapello, H. et al. Gene 209, GC1–GC38 (1998).

    Article  CAS  Google Scholar 

  4. Coghlan, A. & Wolfe, K. H. Yeast 16, 1131–1145 (2000).

    Article  CAS  Google Scholar 

  5. Marais, G., Mouchiroud, D. & Duret, L. Proc. Natl Acad. Sci. USA 98, 5688–5692 (2001).

    Article  ADS  CAS  Google Scholar 

  6. Ikemura, T. Mol. Biol. Evol. 2, 13–34 (1985).

    CAS  PubMed  Google Scholar 

  7. Sharp, P. M. J. Mol. Evol. 33, 23–33 (1991).

    Article  ADS  CAS  Google Scholar 

  8. Akashi, H. Curr. Opin. Gen. Dev. 11, 660–666 (2001).

    Article  CAS  Google Scholar 

  9. Goldman, N. & Yang, Z. Mol. Biol. Evol. 11, 725–736 (1994).

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations


Corresponding author

Correspondence to Matthew W. Hahn.

Additional information

Reply: J. B. Plotkin, J. Dushoff and H. B. Fraser reply to this communication (doi:10.1038/nature03224).

Rights and permissions

Reprints and permissions

About this article

Cite this article

Hahn, M., Mezey, J., Begun, D. et al. Codon bias and selection on single genomes. Nature 433, E5–E6 (2005).

Download citation

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing