Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
复制标题
DOI：
10.1128/jb.184.8.2072-2080.2002
复制
发表时间：
2002-04-01
影响因子：
3.2
通讯作者：
Charlebois, RL
中科院分区：
文献类型：
--
作者：
Clarke, GDP;Beiko, RG;Charlebois, RL
达尔文的范式认为，现代生物体的多样性是通过一个带有修改的遗传过程而产生的，就像在一棵分叉的树上一样。越来越多的证据表明，基因有时不是沿着沿着谱系转移，而是跨谱系转移。在这种程度上，达尔文的范式只能不完美地应用于基因组，可能会使重建基因组之间历史关系的尝试复杂化，甚至破坏这种尝试（即，基因组树）。如果使用足够完整的基因组序列，就可以检验基因组中的大多数基因是通过树状（垂直）遗传还是通过跨谱系的横向转移产生的。我们将遗传学不一致序列（PDS）定义为开放阅读框架（ORF），其显示出与同一基因组中大多数其他ORF在统计学上可区分的相似性关系模式。PDSs在28种细菌、8种古细菌和1种真核生物（酿酒酵母）的基因组中占可分析ORF的6.0%至16.8%（平均10.8%）。在这项研究中，我们开发和评估了基于距离的方法，平均成对序列相似性的基础上，生成基因组树。排除PDS提高了引导支持的基础节点，但改变了一些拓扑特征，这表明PDS之间几乎没有系统性的偏见。排除PDS的基因组树的许多但不是所有特征与16S rRNA树一致。
Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.