I've just finished catching up on all the posts in this discussion and, although it probably would have been more appropriate earlier, I have a couple of points to add regarding the monoplyetic nature of the Archaea and relationship to (eu)bacteria.
There is a system that is identical functionally and very similar structurally in the eubacteria and archaea - the flagellar system. However at the molecular level - there is no genetic similarity and in fact the molecular mechanisms are quite different.
All bacterial flagellins (the protein that make up flagella) are homologous. The mechanism of flagellar assembly in bacteria is quite unique and appears to be the same in all bacteria.
In the archaea flagella perform the same function and look the same but the flagellins are quite distinct - definetly no homology. The flagellins from the genera Halobacterium, Sulfolobus and most of the methanogens all of homologous N-termini.
Rather than being 'just another protein' that is different between Archaea and bacteria this is an entire system (a system described in some reviews as comprising 2% of the genome) which supports the distinct and monphyletic nature of the archaea (ie the Woese-Kandler-Wheeler paradigm). If anyone is interested (and has bothered to read this far) I can supply references, etc.
I'd like to hear people's thoughts on this, especially the idea of looking at systems rather than gene sequences (this is not meant to be an argument for morphology vs sequence in phylogeny).
Dept. of Microbiology