Skip to main content

Thank you for visiting nature.com. 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 (reply)

Abstract

Plotkin et al. reply - The criticisms of our results1 by Hahn et al.2, Nielsen and Hubisz3, and Chen, Emerson and Martin4 fall into three categories: the formal justification for our method, the potential for confounding factors, and the interpretation of our empirical results.

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

Similar content being viewed by others

References

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

    Article  ADS  CAS  Google Scholar 

  2. Hahn, M. W. et al. Nature doi:10.1038/nature03221 (2004).

  3. Nielsen, R. & Hubisz, M. J. Nature doi:10.1038/nature03222 (2004).

  4. Chen, Y., Emerson, J. J. & Martin, T. M. Nature doi:10.1038/nature03223 (2004).

  5. Haldane, J. B. S. Proc. Camb. Phil. Soc. 23, 838–844 (1927).

    Article  ADS  Google Scholar 

  6. Plotkin, J. B. et al. Preprint at http://arxiv.org/abs/q-bio/0410013 (2004).

  7. Wright, S. Genetics 16, 97–159 (1931).

    CAS  PubMed  PubMed Central  Google Scholar 

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

    CAS  Google Scholar 

  9. Dagan, T. & Graur, D. Mol. Biol. Evol. doi:10.1093/molbev/msi033 (2004).

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

    Article  ADS  CAS  Google Scholar 

  11. Berg, O. Genetics 142, 1379–1382 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Tajima, F. Genetics 143, 1457–1465 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Fleischmann, R. D. et al. J. Bacteriol. 184, 5479–5490 (2002).

    Article  CAS  Google Scholar 

  14. Clark, A. G. et al. Science 302, 1960–1963 (2004).

    Article  ADS  Google Scholar 

  15. Katz, L. A. et al. Mol. Biol. Evol. 21, 555–562 (2004).

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to J. B. Plotkin.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Plotkin, J., Dushoff, J. & Fraser, H. Codon volatility does not detect selection (reply). Nature 433, E7–E8 (2005). https://doi.org/10.1038/nature03224

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature03224

This article is cited by

Comments

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.

Search

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