Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites
Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites
复制标题
DOI：
10.1093/oxfordjournals.molbev.a003764
复制
发表时间：
2001-12-01
影响因子：
10.7
通讯作者：
Nei, M
中科院分区：
文献类型：
--
作者：
Suzuki, Y;Nei, M
利用人类白细胞抗原(人类白细胞抗原)基因的核苷酸序列，研究了基于简约和基于似然的方法在单个氨基酸位点推断正选择的可靠性，其中正选择是在抗原识别位置进行的。结果表明，基于简约的方法的推理对不同进化模型的使用是稳健的，并且总体上比基于似然的方法更可靠。相反，基于似然的方法得到的结果取决于模型和使用的初始参数值。对于给定的模型，有时很难获得参数的最大似然估计，并且根据初始参数值的不同，所获得的结果可能是假阴性或假阳性。因此，只要序列的数量相对较大，而系统发育树的分支长度相对较小，则最好使用基于简约的方法。
The reliabilities of parsimony-based and likelihood-based methods for inferring positive selection at single amino acid sites were studied using the nucleotide sequences of human leukocyte antigen (HLA) genes, in which positive selection is known to be operating at the antigen recognition site. The results indicate that the inference by parsimony-based methods is robust to the use of different evolutionary models and generally more reliable than that by likelihood-based methods. In contrast, the results obtained by likelihood-based methods depend on the models and on the initial parameter values used. It is sometimes difficult to obtain the maximum likelihood estimates of parameters for a given model, and the results obtained may be false negatives or false positives depending on the initial parameter-values. It is therefore preferable to use parsimony-based methods as long as the number of sequences is relatively large and the branch lengths: of the phylogenetic tree are relatively small.