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 volatility does not detect selection


Arising from: J. B. Plotkin, J. Dushoff & H. B. Fraser Nature 428, 942–945 (2004); see also communication from Hahn et al.; Nielsen et al.; Plotkin et al. reply Plotkin et al.1 introduce a method to detect selection that is based on an index called codon volatility and that uses only the sequence of a single genome, claiming that this method is applicable to a large range of sequenced organisms1. Volatility for a given codon is the ratio of non-synonymous codons to all sense codons accessible by one point mutation. The significance of each gene's volatility is assessed by comparison with a simulated distribution of 106 synonymous versions of each gene, with synonymous codons drawn randomly from average genome frequencies. Here we re-examine their method and data and find that codon volatility does not detect selection, and that, even if it did, the genomes of Mycobacterium tuberculosis and Plasmodium falciparum, as well as those of most sequenced organisms, do not meet the assumptions necessary for application of their method.

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: Volatility P value plotted against volatility deviation.

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. van Nimwegen, E., Crutchfield, J. P. & Huynen, M. Proc. Natl Acad. Sci. USA 96, 9716–9720 (1999).

    Article  ADS  CAS  Google Scholar 

  3. Akashi, H. Curr. Opin. Genet. Dev. 11, 660–666 (2001).

    Article  CAS  Google Scholar 

  4. Lynch, M. & Conery, J. S. Science 302, 1401–1404 (2003).

    Article  ADS  CAS  Google Scholar 

  5. Hughes, A. L. & Verra, F. Proc. R. Soc. Lond. 268, 1855–1860 (2001).

    Article  CAS  Google Scholar 

  6. Sreevatsan, S. et al. Proc. Natl Acad. Sci. USA 94, 9869–9874 (1997).

    Article  ADS  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations


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

Chen, Y., Emerson, J. & Martin, T. Codon volatility does not detect selection. Nature 433, E6–E7 (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