Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches:: Case studies with diploblast LSU
Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches:: Case studies with diploblast LSU
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DOI：
10.1007/s00239-006-0146-3
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发表时间：
2007-05-01
影响因子：
3.9
通讯作者：
Woerheide, Gert
中科院分区：
文献类型：
--
作者：
Erpenbeck, Dirk;Nichols, Scott A.;Woerheide, Gert
许多rDNA分子系统发育研究的结果是树不符合替代基因树的重建和/或形态假设。这一结果的一个原因可能是应用了次优的系统发育替代模型。虽然最常用的模型很好地描述了独立进化的特征的进化，但它们没有考虑到特征的相关性，例如在核糖体中形成螺旋的rRNA链。这种非独立的位点需要使用考虑到完整核苷酸对(二重体)的共同进化的模型。我们使用配对位点(rRNA-螺旋)模型分析了28S rDNA(LSU)去共振系统发育，并将我们的发现与使用贝叶斯因子的“标准”方法的结果进行了比较。我们证明，同一基因的配对和未配对的位置会导致不同的重构，并且使用二元组模型会产生更可靠的去响应树。我们展示了更复杂的模型对早期分枝的后生动物的系统发育重建的影响，以及去共振目的系统发育关系。
Many rDNA molecular phylogenetic studies result in trees that are incongruent to either alternative gene tree reconstructions and/or morphological assumptions. One reason for this outcome might be the application of suboptimal phylogenetic substitution models. While the most commonly implemented models describe the evolution of independently evolving characters fairly well, they do not account for character dependencies such as rRNA strands that form a helix in the ribosome. Such non-independent sites require the use of models that take into account the coevolution of the complete nucleotide pair (doublet). We analyzed 28S rDNA (LSU) demosponge phylogenies using a '' doublet '' model for pairing sites (rRNA-helices) and compared our findings with the results of '' standard '' approaches using Bayes factors. We demonstrate that paired and unpaired sites of the same gene result in different reconstructions and that usage of a doublet model leads to more reliable demosponge trees. We show the influence of more sophisticated models on phylogenetic reconstructions of early-branching metazoans and the phylogenetic relationships of demosponge orders.