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Morphological similarity amongst organisms in the domain of known Archae does not correlate to a species level of differentiation. They relate more to the phylum level. And for the oldest Kingdom Archae, considered to be the closest known thing to this common ancestor it is currently impossible to even test its morphology.
This is not a settled issue. Indeed, recent arguments are disputing that that Archea evolved from eukaryotic root due to high genetic similarities inferred from complete genome analysis between Archaebacteria and Eubacteria inferred from complete genome analysis. . See:Herv Philippe, Patrick Forterre. The Rooting of the Universal Tree of Life Is Not Reliable. Journal Of Molecular Evolution. 49, 509 (1999). They argue for a eukaryotic ancestor and provide several reasons why. They specifically take issue with previous attempts to create a tree of life
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Furthermore, the addition of new sequences to data sets has often turned apparently reasonable phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria-Eukaryota sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to root the universal tree of life could be biased by the phenomenon of long branch attraction.
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You may access some of the work done in the area at a conference that addresses many of these issues at:
LesTreilles_e.
The essential reasons for inferring a single common ancestor whether several of one species one organism comes from the observations:
http://www.mines.unr.edu/able/GEOL100-11/tsld010.htmTaken from a lower level course, but a nice summary is there.
Could the inference be wrong? Sure, but given the uncertainty of the actual tree of life and those 5 factors, it is still a quite viable hypothesis. At most, even if it is wrong, evolution still holds back a couple billion years.
[This message has been edited by Percipient (edited 03-19-2001).]