Ribosomal RNA and the major lines of evolution: a perspective

Does the "universal tree" based on small-subunit ribosomal RNA sequences show the phylogenetic relationship of all modern organisms? The answer is "yes" only if all these rRNAs are orthologous. Herein I argue that the major rRNA lineages (e.g. eubacterial, one or more archaebacterial and eukaryotic nucleocytoplasmic) probably arose from a divergent population of rRNAs in the progenote, antedating the universal common ancestral organism. Thus the major lineages of rRNA are probably not orthologous, but paralogous. The extrapolated date for the origin of the common ancestral small-subunit rRNA (3.6-4.7 x 10(9) years ago) is consistent with major rRNA lineages being paralogous. This perspective on the early evolution of genes and organisms rationalizes the presence of unexpected ribosomal characters in microsporidia, and bears on xenogenous and endogenous theories of the origin of the organelles in eukaryotes.