Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies
Assessing the Performance of Single-Copy Genes for Recovering Robust Phylogenies
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DOI：
10.1080/10635150802306527
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发表时间：
2008-01-01
影响因子：
6.5
通讯作者：
Giraud, T.
中科院分区：
文献类型：
--
作者：
Aguileta, G.;Marthey, S.;Giraud, T.
涉及非模型物种的系统发育基于一些基因，主要根据历史或实际标准选择。由于基因树有时与物种树不一致，因此产生的系统发育可能无法准确反映物种之间的进化关系。现在，基因组序列的可用性增加提供了可用于构建系统发育的大量基因。但是，出于实际原因，只能为广泛的物种测序一些基因。在这里，我们询问我们是否可以在大多数真菌基因组共有的单拷贝基因中识别一些基因，这些基因足以恢复准确且支持良好的系统发育。真菌代表系统基因组学的模型组，因为许多完整的真菌基因组可用。开发了一种自动化程序，以使用马尔可夫聚类算法（Tribe-MCL）从完整的真菌基因组中提取单拷贝直系同源基因。使用具有可靠蛋白质预测的21个完整的，公开可用的真菌基因组，鉴定了246个单拷贝直系同源基因簇。我们使用各个直系同源序列推断出最大似然树，并通过串联蛋白比对构建了参考树。使用三种不同的方法将单个基因树的拓扑与参考树的拓扑进行了比较。单个基因在恢复参考树时的性能是高度可变的。基因大小和可变位点的数量高度相关，并显着影响基因的性能，但平均取代率没有。两个基因恢复了与参考树完全相同的拓扑结构，并且在串联时提供了高的引导值。通常用于真菌系统发育的基因表现不佳，这表明基于这些基因的当前真菌系统发育可能无法准确反映物种之间的进化关系。对物种子集的分析表明，系统发育性能似乎并不强烈取决于样品。我们预计，至少在大型分类尺度上，这里确定的表现最佳的基因对于真菌的系统发育研究将非常有用。此外，我们比较了这里开发的用于寻找用于构建鲁棒系统发育基因的方法与以前的基因，我们主张我们的方法可以在有更多完整的基因组时应用于其他生物群。
Phylogenies involving nonmodel species are based on a few genes, mostly chosen following historical or practical criteria. Because gene trees are sometimes incongruent with species trees, the resulting phylogenies may not accurately reflect the evolutionary relationships among species. The increase in availability of genome sequences now provides large numbers of genes that could be used for building phylogenies. However, for practical reasons only a few genes can be sequenced for a wide range of species. Here we asked whether we can identify a few genes, among the single-copy genes common to most fungal genomes, that are sufficient for recovering accurate and well-supported phylogenies. Fungi represent a model group for phylogenomics because many complete fungal genomes are available. An automated procedure was developed to extract single-copy orthologous genes from complete fungal genomes using a Markov Clustering Algorithm (Tribe-MCL). Using 21 complete, publicly available fungal genomes with reliable protein predictions, 246 single-copy orthologous gene clusters were identified. We inferred the maximum likelihood trees using the individual orthologous sequences and constructed a reference tree from concatenated protein alignments. The topologies of the individual gene trees were compared to that of the reference tree using three different methods. The performance of individual genes in recovering the reference tree was highly variable. Gene size and the number of variable sites were highly correlated and significantly affected the performance of the genes, but the average substitution rate did not. Two genes recovered exactly the same topology as the reference tree, and when concatenated provided high bootstrap values. The genes typically used for fungal phylogenies did not perform well, which suggests that current fungal phylogenies based on these genes may not accurately reflect the evolutionary relationships among species. Analyses on subsets of species showed that the phylogenetic performance did not seem to depend strongly on the sample. We expect that the best-performing genes identified here will be very useful for phylogenetic studies of fungi, at least at a large taxonomic scale. Furthermore, we compare the method developed here for finding genes for building robust phylogenies with previous ones and we advocate that our method could be applied to other groups of organisms when more complete genomes are available.