Goldstein Richard A, Pollock David D
Division of Mathematical Biology, National Institute of Medical Research, Mill Hill, London, United Kingdom.
Mol Biol Evol. 2006 Jul;23(7):1444-9. doi: 10.1093/molbev/msl010. Epub 2006 May 11.
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.
最近发表在《自然》杂志上的一篇论文的作者声称，他们在蛋白质进化过程中发现了氨基酸增减的“普遍趋势”。在此，我们表明，这种普遍趋势可以简单地用原始分析中使用的三分类树所不可避免的偏差来解释。我们证明，当用与《自然》杂志论文相同的方法分析一个严格可逆的平衡模型时，会得出相同（且在这种情况下明显错误）的结论。偏差的一个主要来源是将序列数据分为“信息性”和“非信息性”位点，这有利于观察某些转变。
