Observations of amino acid gain and loss during protein evolution are explained by statistical bias

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 3-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 "noninformative" sites, which favors the observation of certain transitions. © The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved.