Universal trees based on large combined protein sequence data sets

Universal trees of life based on small-subunit (SSU) ribosomal RNA (rRNA) s upport the separate mono/holophyly of the domains Archaea (archaebacteria), Bacteria (eubacteria) and Eucarya (eukaryotes) and the placement of extrem e thermophiles at the base of the Bacteria(1-4). The concept of universal t ree reconstruction recently has been upset by protein trees that show inter mixing of species from different domains(5,6). Such tree topologies have be en attributed to either extensive horizontal gene transfer(7) or degradatio n of phylogenetic signals because of saturation for amino acid substitution s(8). Here we use large combined alignments of 23 orthologous proteins cons erved across 45 species from all domains to construct highly robust univers al trees. Although individual protein trees are variable in their support o f domain integrity, trees based on combined protein data sets strongly supp ort separate monophyletic domains. Within the Bacteria, we placed spirochae tes as the earliest derived bacterial group. However, elimination from the combined protein alignment of nine protein data sets, which were likely can didates for horizontal gene transfer, resulted in trees showing thermophile s as the earliest evolved bacterial lineage. Thus, combined protein univers al trees are highly congruent with SSU rRNA trees in their strong support f or the separate monophyly of domains as well as the early evolution of ther mophilic Bacteria.