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MBE Advance Access published online on March 7, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm044
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© The Author 2007. 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

Research Article

Assessing the Determinants of Evolutionary Rates in the Presence of Noise

Joshua B. Plotkin*,1 and Hunter B. Fraser{dagger}

* Department of Biology, The University of Pennsylvania, Philadephia, PA, USA
{dagger} The Broad Institute of Harvard University and MIT, Cambridge, MA, USA

1 Corresponding author, email: jplotkin{at}sas.upenn.edu

Received for publication December 4, 2006. Revision received January 26, 2007. Accepted for publication February 8, 2007.

Although protein sequences are known to evolve at vastly different rates, little is known about what determines their rate of evolution. However, a recent study using principal component regression has concluded that evolutionary rates in yeast are primarily governed by a single determinant, related to translation frequency (Drummond et al. 2006). Here, we demonstrate that noise in biological data can confound principal component regressions, leading to spurious conclusions. When equalizing noise levels across seven predictor variables used in previous studies, we find no evidence that protein evolution is dominated by a single determinant. Our results indicate that a variety of factors – including expression level, gene dispensability, and protein-protein interactions – may independently affect evolutionary rates in yeast. More accurate measurements or more sophisticated statistical techniques will be required to determine which one, if any, of these factors dominates protein evolution.


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