Suzuki Yoshiyuki, Nei Masatoshi
Institute of Molecular Evolutionary Genetics, Department of Biology, The Pennsylvania State University, University Park, 16802, USA.
Mol Biol Evol. 2002 Nov;19(11):1865-9. doi: 10.1093/oxfordjournals.molbev.a004010.
Inferring positive selection at single amino acid sites is of biological and medical importance. Parsimony-based and likelihood-based methods have been developed for this purpose, but the reliabilities of these methods are not well understood. Because the evolutionary models assumed in these methods are only rough approximations to reality, it is desirable that the methods are not very sensitive to violation of the assumptions made. In this study we show by computer simulation that the likelihood-based method is sensitive to violation of the assumptions and produces many false-positive results under certain conditions, whereas the parsimony-based method tends to be conservative. These observations, together with those from previous studies, suggest that the positively selected sites inferred by the parsimony-based method are more reliable than those inferred by the likelihood-based method.
推断单个氨基酸位点的正选择具有生物学和医学重要性。为此已开发了基于简约法和基于似然法的方法，但这些方法的可靠性尚未得到充分理解。由于这些方法中假设的进化模型只是对现实的粗略近似，所以希望这些方法对违反所做假设不太敏感。在本研究中，我们通过计算机模拟表明，基于似然法的方法对违反假设很敏感，并且在某些条件下会产生许多假阳性结果，而基于简约法的方法则趋于保守。这些观察结果与先前研究的结果一起表明，基于简约法推断出的正选择位点比基于似然法推断出的更可靠。
