Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.
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DOI：
10.1186/1745-6150-5-4
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发表时间：
2010-01-15
期刊：
影响因子：
5.5
通讯作者：
Wolf M
中科院分区：
文献类型：
--
作者：
Keller A;Förster F;Müller T;Dandekar T;Schultz J;Wolf M
在一些研究中，核糖体基因的二级结构已被用于提高系统发育重建的质量。然而，对二级结构的益处还缺乏广泛的评价。这是第一个针对这一缺陷的研究。我们通过模拟实验对多达18个分类群的人工树拓扑结构和典型系统发育研究范围内的差异水平进行了系统发育的准确性和鲁棒性检验。我们选择核糖体反流子的内部转录间隔2作为示例标记区域。模拟整合了序列与二级结构的协同进化过程。此外，研究了标记大小重复的系统发育能力，并与序列和序列结构重建方法进行了比较。结果清楚地表明，与仅序列数据相比，结构信息大大提高了邻居连接树的准确性和鲁棒性，而加倍的标记大小仅说明鲁棒性。核糖体RNA序列的单个二级结构为系统发育提供了有用的信息内容。因此，推荐使用ITS2序列和二级结构进行分类推断。其他重建方法，如最大似然、贝叶斯推理或最大简约，同样可以从二级结构包含中获益。本文由Shamil Sunyaev， Andrea Tanzer（由Frank Eisenhaber提名）和Eugene V. Koonin审阅。由沙米尔·苏尼亚耶夫、安德里亚·坦泽（由弗兰克·艾森哈伯提名）和尤金·v·库宁评审。对于完整的评论，请转到评论者的评论部分。
In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers' comments section.
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