cations concerning the nature of the cenancestor and the possibility of learning about the period of progressive Darwinian evolution.
For instance, a specific lesson can be drawn from work in our laboratory (Cohen et al., 1992; Lam et al., 1990). The halophilic archaebacterium Haloferax volcanii was shown, by a variety of physical and genetic techniques, to have a genome made up of a large circular DNA of 2.92 million base pairs (Mbp) and several smaller but still sizeable molecules at 690, 442, 86, and 6 kbp. Of 60 or 70 genes known from cloned and sequenced fragments or through mutants, all but a doubtful 1 mapped to the 2.9 Mbp circle, which we thus called the chromosome, considering it similar to eubacterial chromosomes. There may of course be only so many ways to assemble a small genome: more telling is the fact that genes on this chromosome, and in thermophilic and methanogenic archaebacteria as well, are often organized into operons—cotranscribed and coordinately regulated clusters of overlapping genes controlling biochemically related functions. This too might be dismissed as a convergent or coincidental "eubacterial" feature (operons being unknown in eukaryotes), but the finding of tryptophan operons in Haloferax and in a methanogen and in the thermophile Sulfolobus (Meile et al., 1991; Tutino et al., 1993) seems more than coincidental, since clustering of tryptophan biosynthetic genes is almost universal among eubacteria. Most compelling of all are ribosomal protein gene clusters. In the L11-L10 clusters and the spectinomycin, S10, and streptomycin operons, 4 of 4, 11 of 11, 8 of 8, and 3 of 3 ribosomal protein genes are linked in the very same order (Ramirez et al., 1993) in E. coli and in the archaebacteria that have been looked at (often including a halophile, a methanogen, and a thermophile). These remarkable organizational similarities cannot be mere coincidence and are most unlikely to reflect convergence, since there is no clear reason why the genes must be linked in these precise orders. In fact, gene order is conserved even when positions of promoters (and hence units of coordinate regulation) are not. The last common archaebacterial/eubacterial ancestral genome must have had operons just like this and likely was very much like the present E. coli or Haloferax genomes in other specific and general respects (including origins and mechanism of replication, and so forth). If the Iwabe rooting is right, the last common archaebacterial/eubacterial ancestor is the last common ancestor of all Life. The genome of this cell, the cenancestor, would have been—as far as its organization is concerned—remarkably like that of a modern eubacterium, and we would have no hope of recreating the period of progressive Darwinian evolution by the comparative method.
There is a consolation, however, if this is true. We can then more surely say that the eukaryotic nuclear genome has become drastically