Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data.
Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data.
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DOI：
10.1073/pnas.0408313102
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发表时间：
2005-03
影响因子：
11.1
通讯作者：
Tae-Kun Seo;H. Kishino;J. Thorne
中科院分区：
文献类型：
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作者：
Tae-Kun Seo;H. Kishino;J. Thorne
由于基因组数据的增加，多个基因往往可用于推断系统发育关系。组合来自同一分类单元的多个基因的简单方法是将序列连接起来，然后忽略连接序列中不同位置来自不同基因的事实。在这里，我们讨论了两个标准推断的最佳树拓扑结构的数据集与多个基因。这些标准是为多基因数据集而设计的，其中基因特异性进化特征太重要而不能忽视。一个标准是常规的，并且通过在所有基因上取对数似然的总和来获得。另一个标准是通过将基因的对数似然除以其序列长度，然后取这些比率的基因的算术平均值来获得的。对于简约分数，可以采用类似的策略。最优树然后被宣布为一个总和或算术平均值最大化。这些标准是合理的两个阶段的层次框架内。层次结构的第一级代表基因特异性进化特征，第二级代表给定基因的位点特异性特征。为了测试最佳拓扑结构的意义，我们建议一个两阶段的bootstrap程序，涉及重新定位基因，然后重新定位重新采样的基因内的对齐列。这个过程的优点是，它可以有效地解释基因特异性的进化特征。讨论了两阶段自举方法对Kishino-Hasegawa检验和Shimodaira-Hasegawa检验的适用性。
Because of the increase of genomic data, multiple genes are often available for the inference of phylogenetic relationships. The simple approach for combining multiple genes from the same taxon is to concatenate the sequences and then ignore the fact that different positions in the concatenated sequence came from different genes. Here, we discuss two criteria for inferring the optimal tree topology from data sets with multiple genes. These criteria are designed for multigene data sets where gene-specific evolutionary features are too important to ignore. One criterion is conventional and is obtained by taking the sum of log-likelihoods over all genes. The other criterion is obtained by dividing the log-likelihood for a gene by its sequence length and then taking the arithmetic mean over genes of these ratios. A similar strategy could be adopted with parsimony scores. The optimal tree is then declared to be the one for which the sum or the arithmetic mean is maximized. These criteria are justified within a two-stage hierarchical framework. The first level of the hierarchy represents gene-specific evolutionary features, and the second represents site-specific features for given genes. For testing significance of the optimal topology, we suggest a two-stage bootstrap procedure that involves resampling genes and then resampling alignment columns within resampled genes. An advantage of this procedure over concatenation is that it can effectively account for gene-specific evolutionary features. We discuss the applicability of the two-stage bootstrap idea to the Kishino-Hasegawa test and the Shimodaira-Hasegawa test.