Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer K H
Lehrstuhl für Mikrobiologie, Technische Universität München, Germany.
Electrophoresis. 1998 Apr;19(4):554-68. doi: 10.1002/elps.1150190416.
Comparative sequence analysis of small subunit rRNA is currently one of the most important methods for the elucidation of bacterial phylogeny as well as bacterial identification. Phylogenetic investigations targeting alternative phylogenetic markers such as large subunit rRNA, elongation factors, and ATPases have shown that 16S rRNA-based trees reflect the history of the corresponding organisms globally. However, in comparison with three to four billion years of evolution the phylogenetic information content of these markers is limited. Consequently, the limited resolution power of the marker molecules allows only a spot check of the evolutionary history of microorganisms. This is often indicated by locally different topologies of trees based on different markers, data sets or the application of different treeing approaches. Sequence peculiarities as well as methods and parameters for data analysis were studied with respect to their effects on the results of phylogenetic investigations. It is shown that only careful data analysis starting with a proper alignment, followed by the analysis of positional variability, rates and character of change, testing various data selections, applying alternative treeing methods and, finally, performing confidence tests, allows reasonable utilization of the limited phylogenetic information.
小亚基核糖体RNA的比较序列分析是目前阐明细菌系统发育以及细菌鉴定的最重要方法之一。针对大型亚基核糖体RNA、延伸因子和ATP酶等替代系统发育标记的系统发育研究表明，基于16S rRNA的树状图在全球范围内反映了相应生物的进化史。然而，与三四十亿年的进化相比，这些标记的系统发育信息含量有限。因此，标记分子有限的分辨能力仅允许对微生物的进化史进行抽样检查。这通常表现为基于不同标记、数据集或不同建树方法的树状图在局部具有不同的拓扑结构。研究了序列特性以及数据分析的方法和参数对系统发育研究结果的影响。结果表明，只有从正确的比对开始进行仔细的数据分析，随后分析位置变异性、变化速率和特征，测试各种数据选择，应用替代建树方法，最后进行置信度检验，才能合理利用有限的系统发育信息。
