Maximum-likelihood unrooted trees constructed from the positional
variation among aligned sets of ribosomal proteins. (a) Tree
constructed from the concatenated set of alignment blocks common
in the 34 universal ribosomal proteins from the three
phylodomains: Bacteria, Archaea and Eukarya, labeled by orange
bars in Figure 3. (b) Tree
constructed from the concatenated set of alignment blocks common
to both the eukaryotic and archaeal representatives and labeled by
purple bars in Figures 1 and
2. The trees were constructed
by the maximum likelihood approach with the TREE-PUZZLE procedure,
Quartet Puzzling, 1000 steps and the JTT model of substitution.
Abbreviations are Swiss-Prot codes: Eukarya (top set): ARATH =
Arabidopsis thaliana, CAEEL =
Caenorhabditis elegans, DROME =
Drosophila melanogaster, GUITH =
Guillardia theta, HUMAN = Homo
sapiens, ICTPU = Ictalurus punctatus,
ORYSA = Oryza sativa, SCHPO =
Schizosaccharomyces pombe, TETHY =
Tetrahymena thermophila and YEAST =
Saccharomyces cerevisiae; Archaea (middle set):
AERPE = Aeropyrum pernix, ARCFU =
Archaeoglobus fulgidus, HALMA =
Haloarcula marismortui, METJA =
Methanococcus jannischii, METKA =
Methanopyrus kandleri, METTH =
Methanobacterium thermoautotrophicum, NANEQ =
Nanoarchaeum equitans, PYRAB = Pyrococcus
abyssi, PYRAE = Pyrobaculum aerophilum,
SULSO = Sulfolobolus solfataricus and THEAC =
Thermoplasma acidophilum; Bacteria (bottom set):
AQUAE = Aquifex aeolicus, BACSU =
Bacillus subtilis, CAUCR = Caulobacter
crescentus, CHLTR = Chlamydia
trachomatis, CHLTE = Chlorobium tepidum,
ECOLI = Escherichia coli, HELPY =
Helicobacter pylori, STRCO = Streptomyces
coelicolor, SYNY3 = Synechocystis sp.
(strain PCC 6803), THEMA = Thermotoga maritima
and TREPA = Treponema pallidum.