Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods
Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods
复制标题
DOI：
10.1016/j.ympev.2006.07.015
复制
发表时间：
2007-02-01
影响因子：
4.1
通讯作者：
Hughes, Austin L.
中科院分区：
文献类型：
--
作者：
Friedman, Robert;Hughes, Austin L.
两种常用的方法的基础上的似然比测试（LRTs）检测积极的达尔文选择在分子水平上被施加到一个数据集的604个基因家族，其中包含两个成员在人类基因组和两个成员在小鼠基因组。这些方法在很高比例的家庭中检测到正选择;在超过50%的家庭中，有一种或两种方法都有正选择的显著证据。然而，不到三分之一的家庭显示的证据，积极选择的至少一种方法显示的证据，积极选择的两种方法。这些测试的结果是预测更好的序列长度，G + C含量在第三密码子的位置，和水平的同义取代比水平的非同义取代或非同义取代的比率。这些结果表明，基于LRT的阳性选择测试可能对某些因素敏感，这些因素使得难以重建核苷酸取代的真实模式。(c)2006年爱思唯尔公司All rights reserved.
Two commonly used methods based on likelihood-ratio tests (LRTs) for detecting positive Darwinian selection at the molecular level were applied to a data set of 604 gene families containing two members in the human genome and two members in the mouse genome. These methods detected positive selection in a very high proportion of families; in over 50% of families, there was significant evidence of positive selection by one or both methods. However, less than a third of families showing evidence for positive selection by at least one of the methods showed evidence of positive selection by both methods. The outcome of these tests was predicted better by sequence length, G + C content at third-codon positions, and the level of synonymous substitution than by the level of nonsynonymous substitution or the ratio of nonsynonymous to synonymous substitution. These results suggested that LRT-based tests for positive selection may be sensitive to certain factors that make it difficult to reconstruct the true pattern of nucleotide substitution. (c) 2006 Elsevier Inc. All rights reserved.