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tion factors, the alignment between EF1-α/Tu types and EF-2/G species, on the correctness of which the accuracy of the rooting absolutely depends, is highly problematic. More data for precenancestral gene duplications are sorely needed.
Along with the ATPase and elongation factor gene duplication analyses, it has become common to stress the similarity in sequence of archaebacterial and eukaryotic RNA polymerase subunits or (certain) ribosomal proteins. These indeed have shown a close archaebacterial/eukaryotic relationship by a variety of measures (Zillig et al., 1993). A broader survey of homologous genes for which readily alignable sequences are available for at least one species of each of the three domains is presented as Figure 7. (Eukaryotic nuclear genes suspected of being more recent acquisitions from bacterial endosymbiosis and extensively polyphyletic gene data sets are not shown.) In this figure, mean interdomain distances were used to construct midpoint rooted trees. The Iwabe tree is the most frequent among them, but not significantly so, and of course midpoint rootings can be correct only with constant molecular clocks.
So we must continue to remain open. If the currently accepted rooting were wrong, then an archaebacterial/eubacterial sisterhood seems the next most likely possibility, given the remarkable similarity in genetic organization between these two prokaryotic domains. The cenancestor could (again) be seen as a more primitive cell. Although it would have to possess all of those biochemical features known to be homologous in archaebacteria, eubacteria, and eukaryotes now (DNA genome, DNA polymerases, RNA polymerases, two-subunit ribosomes, the "universal code," most of metabolism, and many features of cell-cycle and growth regulation), we are free to see its genome as eubacteria-like, eukaryote-like, or something altogether different still (Woese, 1982; Woese, 1987). The fluid exchange of genes between lineages imagined by Woese in his early descriptions of the progenote remains possible.
The root of the universal tree is still "up in the air," and we don't know as much about the cenancestor as we had hoped. Why is this? One possibility is that we are pushing molecular phylogenetic methods to their limits: although we have reasonable ways of assessing how well any given tree is supported by the data on which it is based, methods for determining the likelihood that this is the "true tree" are poorly developed. Another is hidden paralogy—gene duplication events (of which there are only scattered detected survivors, different in different lineages) are fatal to the enterprise of phylogenetic reconstruction.