Journal
MOLECULAR BIOLOGY AND EVOLUTION
Volume 23, Issue 7, Pages 1444-1449Publisher
OXFORD UNIV PRESS
DOI: 10.1093/molbev/msl010
Keywords
amino acid bias; ancestral reconstruction; molecular evolution; parsimony
Funding
- MRC [MC_U117573805] Funding Source: UKRI
- Medical Research Council [MC_U117573805] Funding Source: researchfish
- Medical Research Council [MC_U117573805] Funding Source: Medline
- NIGMS NIH HHS [R21 GM065612, GM065612-01, R24 GM065580, GM065580-01, R33 GM065612, R33 GM065612-03] Funding Source: Medline
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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.
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