RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences
RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences
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DOI：
10.1016/s1055-7903(03)00061-7
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发表时间：
2003-08-01
影响因子：
4.1
通讯作者：
Higgs, PG
中科院分区：
文献类型：
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作者：
Hudelot, C;Gowri-Shankar, V;Higgs, PG
PHASE软件包允许构建系统发育树，其中许多进化模型专门设计用于具有保守二级结构的RNA序列。RNA的成对区域的进化通过补偿性取代发生，因此一对RNA任一侧的变化是相关的。考虑这种相关性对于系统发育推断是重要的，因为它影响可能性计算。在本研究中，我们使用了69个完整的哺乳动物线粒体基因组的tRNA和rRNA序列的完整集合。似然计算同时使用两个进化模型的不同部分的序列：配对的网站和一个单一的网站模型的配对网站模型的配对网站。我们使用贝叶斯系统发育的方法和马尔可夫链蒙特卡罗算法是用来获得最可能的树和后验概率的分支。结果很好地解决了几乎所有的重要分支的哺乳动物树。他们支持的安排哺乳动物的订单内的四个超序数的分支，已确定了更大的数据集，主要包括核基因的研究。像刺猬和鼠科啮齿动物这样的群体，在以前的线粒体蛋白质研究中一直存在问题，出现在他们与其他成员的预期位置。我们对基因和进化模型的选择似乎比以前对线粒体基因组的研究更可靠，并且更少受到碱基组成变化引起的偏差的影响。(C)2003 Elsevier Science（美国）。All rights reserved.
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs via compensatory substitutions, hence changes on either side of a pair are correlated. Accounting for this correlation is important for phylogenetic inference because it affects the likelihood calculation. In the present study we use the complete set of tRNA and rRNA sequences from 69 complete mammalian mitochondrial genomes. The likelihood calculation uses two evolutionary models simultaneously for different parts of the sequence: a paired-site model for the paired sites and a single-site model for the unpaired sites. We use Bayesian phylogenetic methods and a Markov chain Monte Carlo algorithm is used to obtain the most probable trees and posterior probabilities of clades. The results are well resolved for almost all the important branches on the mammalian tree. They support the arrangement of mammalian orders within the four supra-ordinal clades that have been identified by studies of much larger data sets mainly comprising nuclear genes. Groups such as the hedgehogs and the murid rodents, which have been problematic in previous studies with mitochondrial proteins, appear in their expected position with the other members of their order. Our choice of genes and evolutionary model appears to be more reliable and less subject to biases caused by variation in base composition than previous studies with mitochondrial genomes. (C) 2003 Elsevier Science (USA). All rights reserved.