Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis
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DOI：
10.1093/oxfordjournals.molbev.a025991
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发表时间：
1998-07-01
影响因子：
10.7
通讯作者：
Gouy, M
中科院分区：
文献类型：
--
作者：
Galtier, N;Gouy, M
为了处理碱基组成不等的序列，设计了一个非均匀的，非平稳的随机模型的DNA序列进化允许不同的平衡G + C含量的谱系。一个最大似然实现该模型的系统发育分析允许处理一个合理数量的序列。模型的相关性和参数估计的准确性进行了理论和经验评估，使用真实的或模拟的数据集。总的来说，可以从DNA序列中提取大量关于过去进化模式的信息，这表明可以同时推断过程（不同种类核苷酸取代的速率）和模式（进化树）。在祖先节点的G + C含量是相当准确的估计。新的方法似乎是有用的系统发育重建时，比较序列之间的碱基组成不同。它也可能适用于分子进化研究。
A nonhomogeneous, nonstationary stochastic model of DNA sequence evolution allowing varying equilibrium G + C contents among lineages is devised in order to deal with sequences of unequal base compositions. A maximum-likelihood implementation of this model for phylogenetic analyses allows handling of a reasonable number of sequences. The relevance of the model and the accuracy of parameter estimates are theoretically and empirically assessed, using real or simulated data sets. Overall, a significant amount of information about past evolutionary modes can be extracted from DNA sequences, suggesting that process (rates of distinct kinds of nucleotide substitutions) and pattern (the evolutionary tree) can be simultaneously inferred. G + C contents at ancestral nodes are quite accurately estimated. The new method appears to be useful for phylogenetic reconstruction when base composition varies among compared sequences. It may also be suitable for molecular evolution studies.