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MBE Advance Access published online on May 11, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl010
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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 May 8, 2006

Research Article

Observations of Amino Acid Gain and Loss During Protein Evolution are Explained by Statistical Bias

Richard A. Goldstein 1 * and David D. Pollock 2

1 Mathematical Biology, National Institute of Medical Research, Mill Hill, London, NW7 1AA, UK
2 Department of Biological Sciences, Biological Computation and Visualisation Center, Louisiana State University, Baton Rouge, LA 70803, USA

* To whom correspondence should be addressed.
Richard A. Goldstein, E-mail: richard.goldstein{at}nimr.mrc.ac.uk


  Abstract

The authors of a recent manuscript in Nature claim to have discovered ‘universal trends’ of amino acid gain and loss in protein evolution. Here, we show that this ‘universal trend’ can be simply explained by a bias that is unavoidable with the three-taxon trees used in the original analysis. We demonstrate that a rigorously reversible equilibrium model, when analyzed with the same methods as the Nature manuscript, yields identical (and in this case, clearly erroneous) conclusions. A main source of the bias is the division of the sequence data into ‘informative’ and ‘non-informative’ sites, which favors the observation of certain transitions.

Keywords: amino acid bias; ancestral reconstruction; molecular evolution; parsimony.
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