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MBE Advance Access published online on June 5, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl021
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted April 28, 2006

Letter

Estimating Selection Pressures from Limited Comparative Data

Joshua B. Plotkin 1 *, Jonathan Dushoff 2, Michael M. Desai 3, and Hunter B. Fraser 4

1 Harvard Society of Fellows and Bauer Center for Genomics Research, Harvard University, Cambridge MA, USA
2 Department of Ecology and Evolutionary Biology, Princeton University, Princeton NJ, USA
3 Department of Molecular and Cellular Biology and Dept of Physics, Harvard University, Cambridge MA, USA
4 Broad Institute of Harvard and the Massachusetts Institute of Technology, Cambridge, MA, USA

* To whom correspondence should be addressed.
Joshua B. Plotkin, E-mail: jplotkin{at}fas.harvard.edu


  Abstract

We recently introduced a novel method for estimating selection pressures on proteins, termed "volatility," which requires only a single genome sequence. Some criticisms that have been levied against this approach are valid, but many others are based on misconceptions of volatility, or they apply equally to comparative methods of estimating selection. Here, we introduce a simple regression technique for estimating selection pressures on all proteins in a genome, on the basis of limited comparative data. The regression technique does not depend on an underlying population-genetic mechanism. This new approach to estimating selection across a genome should be more powerful and more widely applicable than volatility itself.


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