An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances
An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances
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DOI：
10.1007/s002390010120
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发表时间：
2000-12-01
影响因子：
3.9
通讯作者：
Meyer, A
中科院分区：
文献类型：
--
作者：
Van de Peer, Y;Baldauf, SL;Meyer, A
最近的分子系统发育经验表明，所有分子标记都有优点和缺点。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着差异，小亚基核糖体 RNA (SSU rRNA) 作为分子系统发育标记的优点仍然是无可争议的。在过去的 10 到 15 年里，我们收集了一个庞大的 SSU rRNA 数据库，其中包括超过 3000 个来自真核生物的完整序列。这带来了巨大的计算挑战，而分子位点之间广泛的速率变化等现象加剧了这一挑战。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）方法不仅可以纠正系统发育重建中伪影的主要来源，而且由于它基于距离方法，因此可以在合理的时间内构建包括数千个序列的综合树。在这项研究中，基于属于所谓真核皇冠的物种的所有可用（2000 年 1 月）完整的 SSU rRNA 序列（2551），使用 SRC 方法构建了核苷酸变异图和系统发育树。由此产生的系统发育构成了迄今为止对整体真核生物多样性和关系的最完整的描述。此外，用SRC方法估计的分支长度更好地反映了真核谱系之间和内部进化速率的巨大差异。将核糖体 RNA 树与从串联肌动蛋白、α-微管蛋白、β-微管蛋白和延伸因子 1-α 氨基酸序列获得的最新蛋白质系统发育进行比较。讨论了基于当前可用分子数据的真核冠的共有系统发育，以及当替换率存在较大差异时分析序列时遇到的具体问题，无论是在不同序列之间（谱系之间的速率变化）还是在同一序列内的不同位置之间（位点之间的速率变化）。
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).