ribonuclease. Comparing catalogs from different bacteria (scoring for presence or absence of identical oligonucleotides) by methods of numerical taxonomy allowed the construction of dendrograms showing relationships between them (Woese and Fox, 1977). Methods have been updated, cataloging giving way to reverse-transcriptase sequencing of rRNA, and this in turn to cloning (and now PCR cloning) of DNAs encoding rRNA (rDNAs). The data bases presently contain partial or complete sequences for some 1500 small-subunit rRNAs from prokaryotes and a rapidly growing collection of eukaryotic cytoplasmic small-subunit sequences, which track the evolutionary history of the nucleus (Olsen et al., 1994).
The rRNA data support the consensual picture represented in Figure 2 in many important ways. Such data not only confirm that chloroplasts and mitochondria descend from free-living prokaryotes but also show that the former belong close to (perhaps within) the cyanobacteria, while the latter derive from the alpha subdivision of the purple bacteria (proteobacteria). These data also establish relationships within the bacteria that are sensible in terms of advancing knowledge of prokaryotic biochemical and ecological diversity and often congruent with more traditional classification schemes, at least at lower taxonomic rank. However, there were two major surprises, both announced by Woese and colleagues in 1977 (Woese and Fox, 1977; Fox et al., 1977).
The first was that the eukaryotic nuclear lineage, as tracked by (18S) cytoplasmic small-subunit rRNA, was not demonstrably related to any specific, previously characterized prokaryotic lineage (Figure 3). This was not expected: the endosymbiont hypothesis saw the endosymbiotic host arising within the bacteria, the descendant of some otherwise typical prokaryote that had lost its cell wall and acquired the ability to engulf other cells. Differences in primary sequence between eukaryotic and prokaryotic small-subunit rRNAs also bespoke differences in secondary structure, consonant with the known differences in size (80S versus 70S), ribosomal protein content (75–90 polypeptides rather than 50–60), and function (initiation through ''scanning" rather than base-pairing via the Shine-Dalgarno sequence, unformylated rather than formylated initiator tRNA).
Because of these differences, Woese argued that the ribosome of the last common ancestor of bacteria and eukaryotes (their nuclear-cytoplasmic part, that is) was itself a primitive ribosome, a structure still experiencing progressive Darwinian evolution. He ventured (Woese, 1982) that the same might be said for other components of this cenancestral information processing system and that:
… in such a progenote, molecular functions would not be of the complex, refined nature we associate with functions today. Thus subsequent evolution would alter functions mainly in the sense of refining them. In this way, the