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

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.