In article <1994Feb26.184229.21317 at dal1> aroger at ac.dal.ca writes:
>The attempts to root the tree by Gogarten and Iwabe (using genes duplicated
>prior to the divergence of all extant groups) have been promising.
>However, they will only allow us to determine a root if all the
>RELEVANT taxa are included. In Iwabe's paper only two representative
>eubacteria are used. How are we to know whether the root of the
>tree falls within or outside of most known eubacterial groups
> if they do not appear on the tree?
>aroger at ac.dal.ca
In case of the elongation factor and ATPase subunit phylogenies meanwhile
many more sequences have been incorporated. With a few interesting
exceptions (see Hilario E, Gogarten JP: Horizontal Transfer of ATPase
Genes -The Tree of Life becomes a Net of Life, BioSystems 31,
111-119, 1993) the topology within the domains is very similar to the 16S
rRNA data. The deepest branching eubacterium for which the ATPase
catalytic subunit sequence is known is Thermotoga maritima. This sequence
groups in significant distance to the root placed by the noncatalytic
subunits (it is closer to E.coli than to the root). The known
archaebacterial type ATPases subunits (Halobacterium, Methanococci,
Methanosarcina, Sulfolobus and Thermoplasma) group either as a mono or a
paraphyletic group (depending on the algorithms used, but in either case
all of the archaebacteria group far away from the root given by the
non-catalytic subunits. The same is true for the elongation
factor data (Karl Heinz Schleifer, Tech. Univ. Munich, pers.
communication). The root placed by the ancient gene duplications of ATPase
subunits and elongation factors is well outside the known
groups of eubacteria.
(I'm posting his email to me...A. Roger)