There are two major questions involved with the
rooting and structure of the universal tree. First, what
is the level of support for the revelation of rRNA based
phylogenetic analysis that the universal tree of life can
be subdivided into archaebacterial, eubacterial and
eukaryotic domains? Second, what is the true order of
descent of archaebacteria, eubacteria and eukaryotes
from the last common ancestral cell? rRNA
phylogenies do show the presence of three domains but
do not support the notion that archaebacteria and
eukaryotes are sister groups. The only reliable way to
root the universal tree is using ancient duplicated genes
such as ATPase and Ef genes. However, recent
findings of archaebacterial-like V-type ATPase in
eubacteria and F1-type ATPase in archaebacteria
suggest that the full extent of the ATPase gene family
has yet to be determined. Furthermore, the elongation
factor data set should be re-examined in the light of
many more sequences being available since Iwabe's
1989 analysis. Finally, phylogenies based on other
duplicated gene families need to be developed. Garcfa-
Meza et al. (1994) have listed several candidate genes
including lactate/malate dehydrogenases, LepA
protein/initiation factor 2, superoxide dismutases,
pyruvate oxidase/acetohydroxy acid synthetase,
HisA/HisF, initiator/elongator met-tRNA and
aminoacyl-tRNA synthetases. In fact, we are obtaining
new sequences and developing phylogenies for the
latter.
I have made an earnest, but likely incomplete attempt,
to collate all gene sequences which are readily alignable
for all three domains. Presently, I have found about 40
types of genes which are represented by at least one
species from each domain. Based on this aggregate
data, there is no statistical basis for saying that a
majority of genes or the majority of genes in a
particular metabolic or synthesis pathway support one
tree topology over another. (At this point, I digress to
say that I would be interested in hearing about any
findings about new, unpublished genes not previously
detected in a particular domain). Many gene trees
support the concept of three separate domains but there
are a number of important exceptions such as glutamine
synthetase, GDH, etc. In summary, the rooting of the
universal tree and the sanctity of the three domains are
still open questions. That's my two cents worth.
References:
Garcfa-Meza, V., Gonzalez-Rodriguez, A., Lazcano.
1994. Ancient paralogous duplications and the search
of archean cells. in G.R. Fleischaker, S. Colonna and
P.L. Luisi (ed) Self-reproduction of supramolecular
structures: From synthetic structures to models of
minimal living systems. Kluwer, Amsterdam.
James R. Brown
Program in Evolutionary Biology
Canadian Institute for Advanced Research
Dept. of Biochemistry
Dalhousie University
Halifax, Nova Scotia
Canada B3H 4H7
(902) 494-3569
Internet: JRBROWN at ac.dal.ca
