Eukaryotes
HUMAN – Homo sapiens, ORYSA – Oriza sativa, ARATH – Arabidopsis thaliana, ICTPU – Ictalurus punctatus, DROME – Drosophila Melanogaster, CAEEL – Caenorhabditis elegans, SCHPO – Schizosaccharomyces pombe, ENCCU – Encephalitozoon Cuniculi, GUITH – Guillardia Theta, PLAFA – Plasmodium Falciparum, DICDI – Dictyostelium discoideum

Archaea
AERPE – Aeropyrum pernix, ARCFU – Archaeoglobus fulgidus, HALMA – Haloarcula marismortui, METJA – Methanococcus jannischii, METKA – Methanopyrus kandleri, METMA – Methanosarcina mazei, METTH – Methanobacterium thermoautotrophicum, PYRAB – Pyrococcus abyssi, PYRAE – Pyrobaculum aerophilum,
SULSO – Sulfolobolus solfataricus, THEAC – Thermoplasma acidophilum.

Bacteria
BACSU – Bacillus subtilis, CAUCR – Caulobacter crescentus, CHLTR – Chlamydia trachomatis, CHLTE – Chlorobium tepidum, ECOLI – Escherichia coli, HELPY – Helicobacter pylori, FUSNN – Fusobacterium nucleatum, STRCO – Streptomyces coelicolor, SYNY3 – Synechocystis sp. (strain PCC 6803), THEMA – Thermotoga maritima, THETH – Thermus thermophilus, TREPA – Treponema pallidum.

Venn diagrams representing the frequency distribution (‰) of absolutely conserved amino acid residue positions in representative alignments of homologous ribosomal proteins from all three phylodomains. (a) Concatenated SSU proteins. (b) Concatenated LSU proteins. In both cases, the three-circle diagram reports the number of absolutely conserved residues per 1000 residues in each category for positions in aligned universal (3-domain) blocks, the single circle reports on the bacterial-specific blocks, and the double circle reports on the blocks specific to Archaea and eukaryotes.

E - positions absolutely conserved only within the eukaryotic sequences
A - positions absolutely conserved only within the archaeal sequences
B - positions absolutely conserved only within the bacterial sequences
EA - positions absolutely conserved within eukaryotic and archaeal, but not bacterial sequences
EB - positions absolutely conserved within eukaryotic and bacterial, but not archaeal sequences
AB - positions absolutely conserved within archaeal and bacterial, but not eukaryotic sequences
AEB - positions absolutely conserved within archaeal, eukaryotic and bacterial sequences

Frequency of Absolutely Conserved Positions in Aligned Blocks of Universal Proteins

Frequency (per thousand) of absolutely conserved amino acid positions in aligned blocks of universally conserved riboproteins.
E - eukaryotic specific block
A -archaeal specific block
B - bacterial specific block
EA -eukaryotic and archaeal, but not bacterial, specific block
EB - eukaryotic and bacterial, but not archaeal, specific block
AB - archaeal and bacterial, but not eukaryotic, specific block
AEB - universal block

Phylogenetic trees were constructed from the concatenated multialignments of all universal blocks using TREE-PUZZLE with the following parameters:

Tree search procedure:	Quartet puzzling
Approximate quartet likelihood:	No
Parameter estimation:	Exact by Quartet sampling + NJ tree
Model of amino acid substitution:	JTT (Jones et al. 1992)
Amino acid frequencies:	estimated from data set
Model of rate heterogeneity:	Mixed (1 invariable + 8 gamma rates)