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disorganized (or reorganized) since its divergence from its more immediate archaebacterial ancestor. As well, other characteristic features of eukaryotic nuclear molecular biology, such as multiple RNA polymerases and complex mRNA processing and intron splicing, must have appeared since this divergence.
We simply do not know how soon after the nuclear divergence these changes were wrought. The eukaryotes whose molecular biology we understand well—animals and fungi—are part of what has been called ''the crown" (Sogin, 1991) of the eukaryotic subtree (Figure 6). Very few genes have been cloned from protists diverging below the trypanosomes, and virtually nothing is known about their expression. It would not be foolish, if the Iwabe rooting holds, to anticipate that some diplomonads or microsporidia, which are thought to have diverged from the rest of the eukaryotes before the mitochondrial invasion, will turn out to have operons. Hopes of finding out just how archaebacteria-like such archezoal eukaryotic genomes are have now captured the interests and energies of several laboratories.
But Is the Rooting Right?
In a sense this new direction is an old one. Once again, we are examining the prokaryote -> eukaryote transition. Once again, as in Figure 2, we see the eukaryotic nuclear genome as the highly modified descendant of an already well-formed prokaryotic genome. The difference is that the immediate prokaryotic ancestors of the eukaryotic nuclear-cytoplasmic component are cells of a type we did not know when we first adopted the view shown in Figure 2. How we feel about the importance and novelty of this Hegelian outcome may depend on the side we take in the clade versus grade (Woese versus Mayr and Cavalier-Smith) debate discussed above. More to the point, however, is the possibility that we have accepted the Iwabe rooting, and consequently its implications for the modernity of the cenancestor and the radical remaking of the nuclear genome, too quickly and too uncritically. Iwabe and colleagues' data set included only one archaebacterial ATPase subunit pair (from Sulfolobus), only one elongation factor pair (Methanococcus), and a very limited representation of eubacterial sequences. As Gogarten (Hilario and Gogarten, 1993), and Forterre and his coworkers have recently and persuasively argued, both data sets can be questioned (Forterre et al., 1993). There is increasing evidence for multiple gene duplication events in the history of the ATPase genes, and it is difficult to distinguish orthologues (descendant from the same cenancestral α or β subunit gene) from paralogs (descendants of more distant homologs produced by gene duplication before the cenancestor). For the elonga-