Phylogenetic place of archaebacteria and the origin of eukaryotes

从对复制基因的复合树的最大似然分析中，本已经证实了古细菌更接近于真核生物，而不是真细菌。关于古细菌主要类群之间的关系，有两种可能性：1)古细菌是单系的，2)卵母细胞与真核生物更接近，但其他考古细菌如产甲烷菌和盐生细菌与这些类群关系较远。没有线粒体的原生动物的系统发育位置对于理解真核细胞的早期进化至关重要。以往关于这一问题的研究大多是利用小亚基核糖体RNA(SrRNA)序列。我们已经指出了sRNA分析中固有的一个严重问题；即，当G+C压力作用于任何被研究生物的基因组时，基于sRNA的分子系统发育有时是误导的。我们进一步证明，即使在这种情况下，保守蛋白质的氨基酸序列数据，如伸长因子和RNA聚合酶，也没有这个问题，并给出了比sRNA更可靠的树。我们从一个非线粒体原生动物蓝氏贾第鞭毛虫中测序了伸长因子EF-1α基因。从数据的最大似然性分析，我们已经表明，这种有机体可能代表了真核生物进化的早期分支。

From maximum likelihood analyses of composite trees of duplicated genes, it has ben confirmed that archaebacteria are closer to eukaryotes rather than to eubacteria. Concerning the relationship among the tree major groups of archaebacteria, there remains two possibilities; 1) the archaebacteria are monophyletic, and 2) eocyte is closer to eukaryotes, but other archaebacteria such as methanogens and halobacteria are distantly related to these groups.Phylogenetic placings of protozoa without mitochondria are crucial in understanding the early evolution of eukaryotic cells. Previous studies relevant to this problem have been done mostly by using small-subunit ribosomal RNA (SrRNA) sequences. We have pointed out a serious problem inherent in the analyses of SrRNAs; that is, when G+C pressure is operating to the genome of any of the organisms under study, the molecular phylogeny based on the SrRNA is sometimes misleading. We have further shown that, even in such a situation, amino acid sequence data of conservative proteins, such as, elongation factor and RNA polymerase, are free from the problem, and give more reliable trees than SrRNA.We sequenced elongation factor EF-1alpha gene from an amitochondrial protozoan, Giardia lamblia. From a maximum likelihood analysis of the data, we have shown that this organism may represent an early offshoot in the evolution of eukaryotes.