A likelihood method for the detection of selection and recombination using nucleotide sequences
A likelihood method for the detection of selection and recombination using nucleotide sequences
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DOI：
10.1093/oxfordjournals.molbev.a025760
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发表时间：
1997-03-01
影响因子：
10.7
通讯作者：
Holmes, EC
中科院分区：
文献类型：
--
作者：
Grassly, NC;Holmes, EC
沿着核苷酸序列的不同区域沿着核苷酸序列通常受到不同的进化力量的影响。进化会导致不同区域有不同的进化历史，而选择会导致不同区域以不同的速度进化。本文提出了一种基于似然的统计方法，通过识别不符合单一系统发育拓扑结构的区域和整个序列沿着的核苷酸替换过程来检测这种过程。随后对这些异常区域的重新分析可能是可能的。该方法进行了测试，使用模拟，并证明其应用程序使用灵长类动物psi β-珠蛋白假基因，HIV-1的包膜基因的V3区，和从奈瑟氏菌的argF序列。异常区域的重新分析表明，可能的免疫选择在HIV-1和重组奈瑟菌。实现该方法的计算机程序是可用的。
Different regions along nucleotide sequences are often subject to different evolutionary forces. Recombination will result in regions having different evolutionary histories, while selection can cause regions to evolve at different rates. This paper presents a statistical method based on likelihood for detecting such processes by identifying the regions which do not fit with a single phylogenetic topology and nucleotide substitution process along the entire sequence. Subsequent reanalysis of these anomalous regions may then be possible. The method is tested using simulations, and its application is demonstrated using the primate psi eta-globin pseudogene, the V3 region of the envelope gene of HIV-1, and argF sequences from Neisseria bacteria. Reanalysis of anomalous regions is shown to reveal possible immune selection in HIV-1 and recombination in Neisseria. A computer program which implements the method is available.