Phylogenetic place of archaebacteria and the origin of eukaryotes

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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.