Bioinformatics and Genomics Program, Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Spain.
Mol Biol Evol. 2012 Apr;29(4):1277-89. doi: 10.1093/molbev/msr295. Epub 2011 Dec 1.
By exploiting the large body of genome data and the considerable progress in phylogenetic methodology, recent phylogenomic studies have provided new insights into the relationships among major eukaryotic groups. However, confident placement of the eukaryotic root remains a major challenge. This is due to the large evolutionary distance separating eukaryotes from their closest relatives, the Archaea, implying a weak phylogenetic signal and strong long-branch attraction artifacts. Here, we apply a new approach to the rooting of the eukaryotic tree by using a subset of genomic information with more recent evolutionary origin-mitochondrial sequences, whose closest relatives are α-Proteobacteria. For this, we identified and assembled a data set of 42 mitochondrial proteins (mainly encoded by the nuclear genome) and performed Bayesian and maximum likelihood analyses. Taxon sampling includes the recently sequenced Thecamonas trahens, a member of the phylogenetically elusive Apusozoa. This data set confirms the relationships of several eukaryotic supergroups seen before and places the eukaryotic root between the monophyletic "unikonts" and "bikonts." We further show that T. trahens branches sister to Opisthokonta with significant statistical support and question the bikont/excavate affiliation of Malawimonas species. The mitochondrial data set developed here (to be expanded in the future) constitutes a unique alternative means in resolving deep eukaryotic relationships.
利用大量的基因组数据和系统发育方法学的显著进展，最近的系统基因组学研究为主要真核生物类群之间的关系提供了新的见解。然而，真核生物的系统发生位置仍然是一个主要挑战。这是由于真核生物与其最近的亲缘生物古菌之间存在巨大的进化距离，这意味着系统发育信号较弱，而长枝吸引artifact 较强。在这里，我们应用一种新的方法来确定真核生物树的根，方法是使用具有更近的进化起源的基因组信息的子集——线粒体序列，其最近的亲缘生物是α变形菌。为此，我们鉴定并组装了一个包含 42 种线粒体蛋白（主要由核基因组编码）的数据集，并进行了贝叶斯和最大似然分析。分类群采样包括最近测序的 Thecamonas trahens，它是进化上难以捉摸的 Apusozoa 的成员。这个数据集证实了以前看到的几个真核超群的关系，并将真核生物的根放在单系的“单系生物”和“双系生物”之间。我们进一步表明，T. trahens 与后生动物的分支具有显著的统计支持，并对 Malawimonas 物种的双系/挖掘联系提出了质疑。这里开发的线粒体数据集（将来会扩展）是解决深层真核生物关系的独特替代方法。
