Phylogenetic Depth of the Bacterial Genera Aquifex and Thermotoga Inferred from Analysis of Ribosomal Protein, Elongation Factor, and RNA Polymerase Subunit Sequences

摘要: The phylogenetic placement of the Aquifex and Thermotoga lineages has been inferred from (i) concatenated ribosomal proteins S10, L3, L4, L23, L2, S19, L22, S3 encoded in S10 operon (833 aa positions); (ii) joint sequences elongation factors Tu(1α) G(2) coded by str tuf fus genes (733 (iii) RNA polymerase β- β′-type subunits rpoBC (1130 positions). Phylogenies r-protein EF support with moderate (r-proteins) to high statistical confidence (EFs) two hyperthermophiles at base bacterial clade agreement phylogenies rRNA sequences. In more robust EF-based phylogenies, branching below successive is given bootstrap proportions 82% (maximum likelihood; ML) 85% parsimony; MP), contrast trees separate EF-Tu(1α) EF-G(2) data sets, which lack both resolution robustness. analysis MP outperforms ML discriminating (at 0.05 level) having A. pyrophilus T. maritima as most basal competing alternatives that have mesophiles, or Thermus genus, deepest radiation a monophyletic pyrophilus–T. cluster situated clade. RNAP-based are equivocal respect placements. fall all other phyla when potential artifacts contributed compositionally biased fast-evolving Mycoplasma genitalium pneumoniae eschewed. However, order tenuously supported exhaustive search method unresolved quartet puzzling algorithm. A rooting polymerase-subunit tree mycoplasma level seen reconstructed suboptimal amino acid substitution models not robustly affiliate mycoplasmas low-G+C gram-positives and, probably, reflects ``long branch attraction'' artifact.