Structural partitioning, paired-sites models and evolution of the ITS transcript in Syzygium and Myrtaceae
Structural partitioning, paired-sites models and evolution of the ITS transcript in Syzygium and Myrtaceae
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DOI：
10.1016/j.ympev.2006.08.013
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发表时间：
2007-04-01
影响因子：
4.1
通讯作者：
Gadek, P. A.
中科院分区：
文献类型：
--
作者：
Biffin, E.;Harrington, M. G.;Gadek, P. A.
核核糖体 DNA 的内部转录间隔区 (ITS) 广泛用于系统发育推断。一些特征，包括 RNA 二级结构对 ITS 突变动力学的影响，可能会影响从这些区域估计的系统发育的准确性。在这里，我们开发了被子植物科桃金娘科代表的 RNA 二级结构预测。在此基础上，我们评估了结构（茎与环）划分和 RNA 特异性（配对位点）模型对于 76 个分类单元 Syzygium 比对以及更广泛的全科桃金娘科 ITS 数据集的实用性。我们使用排列方法来证明结构分区显着提高了数据的可能性。同样，解释 RNA 结构中茎对非独立性的模型比不解释的模型更有可能。 ITS 的最佳拟合 RNA 模型是那些排除茎对中同时双替换的模型，这表明在高比例的茎配对位点上缺乏针对非规范 (G.U/U.G) 碱基对的强选择。我们将 RNA 特异性模型应用于丁香属和桃金娘科的系统发育，并将这些模型与使用标准 4 状态模型得出的假设进行对比。尽管对于桃金娘科而言，存在一些差异，但对于丁香属推断的关系之间几乎没有实际差异。与 4 态模型相比，RNA 特异性方法发现的拓扑结构解析度较低，但与桃金娘关系的传统观点更一致。 (c) 2006 Elsevier Inc. 保留所有权利。
The internal transcribed spacers (ITS) of nuclear ribosomal DNA are widely used for phylogenetic inference. Several characteristics, including the influence of RNA secondary structure on the mutational dynamics of ITS, may impact on the accuracy of phylogenies estimated from these regions. Here, we develop RNA secondary structure predictions for representatives of the angiosperm family Myrtaceae. On this basis, we assess the utility of structural (stem vs. loop) partitioning, and RNA-specific (paired-sites) models for a 76 taxon Syzygium alignment, and for a broader, family-wide Myrtaceae ITS data set. We use a permutation approach to demonstrate that structural partitioning significantly improves the likelihood of the data. Similarly, models that account for the non-independence of stem-pairs in RNA structure have a higher likelihood than those that do not. The best-fit RNA models for ITS are those that exclude simultaneous double substitutions in stem-pairs, which suggests an absence of strong selection against non-canonical (G.U/U.G) base-pairs at a high proportion of stem-paired sites. We apply the RNA-specific models to the phylogeny of Syzygium and Myrtaceae and contrast these with hypotheses derived using standard 4-state models. There is little practical difference amongst relationships inferred for Syzygium although for Myrtaceae, there are several differences. The RNA-specific approach finds topologies that are less resolved but are more consistent with conventional views of myrtaceous relationships, compared with the 4-state models. (c) 2006 Elsevier Inc. All rights reserved.