Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny
Reconstruction of ancestral nucleotide sequences and estimation of substitution frequencies in a star phylogeny
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DOI：
10.1016/j.gene.2006.11.022
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发表时间：
2007-04-01
期刊：
影响因子：
3.5
通讯作者：
Arndt, Peter F.
中科院分区：
文献类型：
--
作者：
Arndt, Peter F.
最大似然演化重建方法被广泛应用于揭示和评估自然系统的演化历史和相互关系。然而，本分析中常见的几个简化假设限制了所得结果的解释力。我们提出了一种算法，进行系统发育分析，而不作出共同的假设，序列数据从至少三个叶节点在星星的系统发育。特别是，潜在的核苷酸取代模型不一定是可逆的，并且可以包括邻居依赖性过程，如CpG甲基化脱氨基过程（CpG效应）。在外部节点处的序列的碱基组成和祖先序列的碱基组成可以彼此不同，并且它们不必是相应替代模型的稳态分布。该算法能够重建祖先的碱基组成，并准确地估计替代频率的分支的星星的基因。大量的模拟数据测试验证了该算法的良好性能。作为一个应用程序，我们提出了从人类，小鼠和狗的比对基因组序列的分析。在三个谱系中可以观察到不同的替代模式。(c)2006 Elsevier B.V.保留所有权利。
Maximum likelihood phylogeny reconstruction methods are widely used in uncovering and assessing the evolutionary history and relationships of natural systems. However, several simplifying assumptions commonly made in this analysis limit the explanatory power of the results obtained. We present an algorithm that performs the phylogenetic analysis without making the common assumptions for sequence data from at least three leaf nodes in a star phylogeny. In particular, the underlying nucleotide substitution model does not have to be reversible and may include neighbor-dependent processes like the CpG methylation deamination process (CpG-effect). The base composition of the sequences at the external nodes and the one of the ancestral sequence may be different from each other and they do not have to be stationary state distributions of the corresponding substitution model. The algorithm is able to reconstruct the ancestral base composition and accurately estimate substitution frequencies in the branches of the star phylogeny. Extensive tests on simulated data validate the very favorable performance of the algorithm. As an application we present the analysis of aligned genomic sequences from human, mouse, and dog. Different substitution pattern can be observed in the three lineages. (c) 2006 Elsevier B.V. All rights reserved.