Archaebacteria and the Three Kingdoms

Paul Lepp lepppaul at studentl.msu.edu
Tue Apr 12 16:19:17 EST 1994

First off let me thank L. Moran for generating some very interesting
discussion on this group.  This discussion has certainly casued me to
reanalyze my position  on the position of Archea.

  There do seem to be several problems with the Gupta and Golding paper
(1993).  I could be persuaded that the Archea are more closely related to
the Eubacteria than to the Eukarya, as long as the Archea remain
monophyletic.  What I find most disturbing is the polyphyletic origins of
Archea that Gupta and Golding propose.  If this were the case There would
have to be a hell of a lot of horizontal transfer to explain cell wall
constituents.  More importantly it would require at least 3 instances of
convergent evolution to produce the ether linked lipids of the CM.

	 An analogous situtation of conflicting phylogenies occurred when
examining the phylogeny of chloroplasts.   Morden and Golden (1989)
examined the phylogeny of chloroplasts using the psbA genes and found them
most closely related to prochlorophytes.  This conclusion was at odds with
the 16S data (Turner, et al; 1989) and the psbA phylogeny generated by
Kishino, et al (1990).  It turns out Morden and Golden's analysis included
a seven amino acid domain that was missing in Prochlorothrix, much like the
Gupta and Golding paper.  The original analysis treated each of missing
seven a.a. as individual evolutionary events, resulting in chloroplasts
being grouped with the Prochlorophytes.  Reanalysis treating the missing
domain as a single event or excluding it entirely produced a tree
concurring with those of Turner and Kishino (Morden and Golden; 1989).  So,
the treatment of a seven a.a. domain, much smaller than signature in HSP70,
resulted in a substantially different phylogeny.  To their credit Gupta and
Golding did exclude shared G+/Archea domain upon reanalysis and got the
same phylogeny.  But was excluding the sequence enough?  It is unclear from
the paper if the deleted domain was treated as a single event or multiple
events in the analysis.  Perhaps they should try treating it as a single

		Finally, for those haven't seen it the February issue of Systematic and
Applied Microbiology is dedicated to "the Molecular Biology of Archea".  It
is well worth the time hunting this issue down.
Paul Lepp

 Gupta, R.H., and Golding, G.B. (1993) Evolution of HSP70 gene and its 
 implications regarding relationships between archaebacteria, eubacteria
 eukaryotes. J. Mol. Evol. 37, 573-582.

	Kishino, H., Miyata, T., Hasegawa, M. (1990)  Maximum Likelihood Inference
of Protein Phylogeny and the Origin of Chloroplasts.  J. Mol. Evol. 31:

	Morden, C.W., and Golden, S.S. (1989) psbA genes indicate common ancestry
of prochlorophytes and chloroplasts. Nature 337: 382-384

	Morden, C.W., and Golden, S.S. (1989) Corrigendum: psbA genes indicate
common ancestry of prochlorophytes and chloroplasts. Nature 339: 400

	Turner, S., Burger-Wiersma, T., Giovannoni, S.J., Mur, L.R., Pace, N.R.
(1989).  The relationship of a prochlorophyte Prochlorothrix hollandica to
green chloroplasts. Nature 337:380-382

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