[Taxacom] Parabacteria (incl. viruses) came before Eubacteria

[Kenneth Kinman]

Hi Curtis, 
        Since the Eubacteria are a paraphyletic
grouping, it would have been clearer if I had said that two or more
clades of eubacteria split off before the neomuran clade (Phylum
Metabacteria + eukaryotes). However, before eubacteria arose, there was
the RNA world and then various extinct progenotes (protocells or
Cavalier-Smith's obcells) which bridge the gap between ancient viruses
and the first eubacterium (LUCA).
       Therefore, at the base of my prokaryotic Kingdom
(Bacteria or Monera or Prokaryota), I recognize a Phylum Parabacteria
containing two classes: (1) the paraphyletic Class Progenotea (for the
ancient viruses and progenotes); and (2) the polyphyletic Class Viralea
(for viruses, viroids, and virusoids which we have today). I don't
really like having a polyphyletic class, but I think that viruses are in
a sense "living", and that they therefore should have a place in
biological classifications.  Some of our modern viruses are probably the
descendants of ancient viruses (popping in and out of genomes and
mutating for over three billion years).  Other viruses seem to be merely
escaped genes of more recent origin.  Genomics may someday allow us to
broadly map out viral evolution and produce real viral classifications
(but they will be extremely complex).
            ----------Cheers,            
                       Ken
Kinman             
P.S.  Instead of having progenotes as immediate ancestors of just the
eubacteria (as Cavalier-Smith and I believe), Woese believed that
progenotes independently gave rise to his Three Urkingdoms. However,
when the Three Urkingdom hypothesis was discredited, he morphed it into
the Three Domains (with eubacterial progenotes splitting off first, and
archaeal and eukaryotic progenotes being more closely related to one
another).  Woese would have you believe that progenotes crossed his
"Darwinian Threshold" three separate times to produce three domains
independently.  This idea has also been criticized, and it seems much
more parsimonious to assume that crossing his complex "Darwinian
Threshold" happened only once (at or near the base of the Eubacteria).
Metabacteria have too much in common with Eubacteria on the one hand,
and with eukaryotes on the other, to have arisen directly and
independently from a progenote.