Van de Peer Y, Baldauf S L, Doolittle W F, Meyer A
Department of Biology, University of Konstanz, D-78457 Konstanz, Germany.
J Mol Evol. 2000 Dec;51(6):565-76. doi: 10.1007/s002390010120.
Recent experience with molecular phylogeny has shown that all molecular markers have strengths and weaknesses. Nonetheless, despite several notable discrepancies with phylogenies obtained from protein data, the merits of the small subunit ribosomal RNA (SSU rRNA) as a molecular phylogenetic marker remain indisputable. Over the last 10 to 15 years a massive SSU rRNA database has been gathered, including more then 3000 complete sequences from eukaryotes. This creates a huge computational challenge, which is exacerbated by phenomena such as extensive rate variation among sites in the molecule. A few years ago, a fast phylogenetic method was developed that takes into account among-site rate variation in the estimation of evolutionary distances. This "substitution rate calibration" (SRC) method not only corrects for a major source of artifacts in phylogeny reconstruction but, because it is based on a distance approach, allows comprehensive trees including thousands of sequences to be constructed in a reasonable amount of time. In this study, a nucleotide variability map and a phylogenetic tree were constructed, using the SRC method, based on all available (January 2000) complete SSU rRNA sequences (2551) for species belonging to the so-called eukaryotic crown. The resulting phylogeny constitutes the most complete description of overall eukaryote diversity and relationships to date. Furthermore, branch lengths estimated with the SRC method better reflect the huge differences in evolutionary rates among and within eukaryotic lineages. The ribosomal RNA tree is compared with a recent protein phylogeny obtained from concatenated actin, alpha-tubulin, beta-tubulin, and elongation factor 1-alpha amino acid sequences. A consensus phylogeny of the eukaryotic crown based on currently available molecular data is discussed, as well as specific problems encountered in analyzing sequences when large differences in substitution rate are present, either between different sequences (rate variation among lineages) or between different positions within the same sequence (among-site rate variation).
近期分子系统发育学的研究经验表明，所有分子标记都各有优缺点。尽管如此，尽管与从蛋白质数据获得的系统发育存在一些显著差异，但小亚基核糖体RNA（SSU rRNA）作为分子系统发育标记的优点仍然无可争议。在过去10到15年里，已经收集了大量的SSU rRNA数据库，其中包括来自真核生物的3000多个完整序列。这带来了巨大的计算挑战，而分子中位点间广泛的速率变化等现象则加剧了这一挑战。几年前，开发了一种快速系统发育方法，该方法在估计进化距离时考虑了位点间的速率变化。这种“替代率校准”（SRC）方法不仅纠正了系统发育重建中主要的人为误差来源，而且由于它基于距离方法，能够在合理的时间内构建包含数千个序列的综合树。在本研究中，使用SRC方法，基于所有可用的（2000年1月）属于所谓真核生物冠群物种的完整SSU rRNA序列（2551个）构建了核苷酸变异性图谱和系统发育树。所得的系统发育构成了迄今为止对真核生物整体多样性和关系的最完整描述。此外，用SRC方法估计的分支长度能更好地反映真核生物谱系间和谱系内进化速率的巨大差异。将核糖体RNA树与最近从串联的肌动蛋白、α-微管蛋白、β-微管蛋白和延伸因子1-α氨基酸序列获得的蛋白质系统发育进行了比较。讨论了基于当前可用分子数据的真核生物冠群的一致系统发育，以及在分析序列时遇到的特定问题，即不同序列之间（谱系间速率变化）或同一序列内不同位置之间（位点间速率变化）存在替代率的巨大差异。
