Ancient horizontal gene transfer (original) (raw)

• Bushman, F. Lateral DNA Transfer (Cold Spring Harbor Laboratory Press, New York, 2002).
  Google Scholar
• Woese, C. R., Kandler, O. & Wheelis, M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc. Natl Acad. Sci. USA 87, 4576–4579 (1990). Proposal for a new classification of all living organisms based on the three domains of life and the universal tree.
  CAS PubMed PubMed Central Google Scholar
• Doolittle, R. F., Feng, D. F., Anderson, K. L. & Alberro, M. R. A naturally occurring horizontal gene transfer from a eukaryote to prokaryote. J. Mol. Evol. 31, 383–388 (1990).
  CAS PubMed Google Scholar
• Smith, M. W., Feng, D. -F. & Doolittle, R. F. Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem. Sci. 17, 489–493 (1992).
  CAS PubMed Google Scholar
• Golding, G. B. & Gupta, R. S. Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Mol. Evol. Biol. 12, 1–6 (1995).
  CAS Google Scholar
• Brown, J. R. & Doolittle, W. F. Archaea and the prokaryote to eukaryotes transition. Microbiol. Mol. Biol. Rev. 61, 456–502 (1997).
  CAS PubMed PubMed Central Google Scholar
• Doolittle, W. F. Phylogenetic classification and the universal tree. Science 284, 2124–2128 (1999). An important view on the issues that surround the phylogenetic reconstruction of the universal tree.
  CAS PubMed Google Scholar
• Felmingham, D. & Washington, J. Trends in the antimicrobial susceptibility of bacterial respiratory tract pathogens — findings of the Alexander Project 1992–1996. J. Chemother. 11, 5–21 (1999).
  CAS PubMed Google Scholar
• Brown, J. R., Zhang, J. & Hodgson, J. E. A bacterial antibiotic resistance gene with eukaryotic origins. Curr. Biol. 8, R365–R367 (1998).
  CAS PubMed Google Scholar
• Dröge, M., Pühler, A. & Selbitschka, W. Horizontal gene transfer as a biosafety issue: a natural phenomenon of public concern. J. Biotechnol. 64, 75–90 (1998). Reviews the studies on HGT and genetically modified (GM) organisms and finds little evidence for horizontal gene transfer from GM bacteria to eukaryotes in the field.
  PubMed Google Scholar
• International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).
• Salzberg, S. L., White, O., Peterson, J. & Eisen, J. A. Microbial genes in the human genome: lateral transfer or gene loss? Science 292, 1903–1906 (2001).
  CAS PubMed Google Scholar
• Roelofs, J. & Van Haastert, P. J. Genes lost during evolution. Nature 411, 1013–1014 (2001).
  CAS PubMed Google Scholar
• Stanhope, M. J. et al. Phylogenetic analyses of genomic and EST sequences do not support horizontal gene transfers between bacteria and vertebrates. Nature 411, 940–944 (2001).
  CAS PubMed Google Scholar
• Fox, G. E. et al. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proc. Natl Acad. Sci. USA 74, 4537–4541 (1977).
  CAS PubMed PubMed Central Google Scholar
• Woese, C. R. & Fox, G. E. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl Acad. Sci. USA 51, 221–271 (1977).
  Google Scholar
• Fleischmann, R. D. et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269, 496–512 (1995).
  CAS PubMed Google Scholar
• Gupta, R. S. & Golding, G. B. The origin of the eukaryotic cell. Trends Biochem. Sci. 21, 166–171 (1996).
  CAS PubMed Google Scholar
• Feng, D. -F., Cho, G. & Doolittle, W. F. Determining divergence times with a protein clock: update and reevaluation. Proc. Natl Acad. Sci. USA 94, 13028–13033 (1997).
  CAS PubMed PubMed Central Google Scholar
• Roger, A. J. & Brown, J. R. A chimeric origin for eukaryotes re-examined. Trends Biochem. Sci. 21, 370–371 (1996).
  CAS PubMed Google Scholar
• Pennisi, E. Genome data shake tree of life. Science 280, 672–674 (1998).
  CAS PubMed Google Scholar
• Pennisi, E. Is it time to uproot the tree of life? Science 284, 1305–1307 (1999).
  CAS PubMed Google Scholar
• Lawrence, J. G. & Ochman, H. Molecular archaeology of the Escherichia coli genome. Proc. Natl Acad. Sci. USA 95, 9413–9417 (1998).
  CAS PubMed PubMed Central Google Scholar
• Garcia-Vallvé, S., Romeu, A. & Palau, J. Horizontal gene transfer in bacterial and archaea complete genomes. Genome Res. 10, 1719–1725 (2000).
  PubMed PubMed Central Google Scholar
• Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000).
  CAS PubMed Google Scholar
• Lawrence, J. G. & Ochman, H. Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10, 1–3 (2002). A defence of the methods that detect HGT by using differences in nucleotide composition, in light of critiques by Ragan (references 23 and 24).
  CAS PubMed Google Scholar
• Ragan, M. Reconciling the many faces of lateral gene transfer: response. Trends Microbiol. 10, 3 (2002).
  Google Scholar
• Ragan, M. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201, 187–191 (2001).
  CAS PubMed Google Scholar
• Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
  CAS PubMed PubMed Central Google Scholar
• Nelson, K. E. et al. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–329 (1999).
  CAS PubMed Google Scholar
• Koonin, E. V., Makarova, K. S. & Aravind, L. Horizontal gene transfer in prokaryotes: quantification and classification. Annu. Rev. Microbiol. 55, 709–742 (2001).
  CAS PubMed PubMed Central Google Scholar
• Koski, L. B. & Golding, B. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52, 540–542 (2001).
  CAS PubMed Google Scholar
• Kyrpides, N. C. & Olsen, G. J. Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry? Trends Genet. 15, 298–299 (1999).
  CAS PubMed Google Scholar
• Logsdon, J. M. Jr & Faguy, D. M. Evolutionary genomics: Thermotoga heats up lateral gene transfer. Curr. Biol. 9, R747–R751 (1999).
  CAS PubMed Google Scholar
• Grauer, D. & Li, W. H. Fundamentals of Molecular Evolution 2nd edn (Sinauer Associates, Sunderland, Massachusetts, 2000). A good introductory volume to molecular evolution.
  Google Scholar
• Huynen, M., Snel, B. & Bork, P. Lateral gene transfer, genome surveys and the phylogeny of prokaryotes. Technical comments. Science 286, 1443a (1999).
  Google Scholar
• Snel, B., Bork, P. & Huynen, M. A. Genome phylogeny based on gene content. Nature Genet. 21, 108–110 (1999).
  CAS PubMed Google Scholar
• Fitz-Gibbon, S. T. & House, C. H. Whole genome-based phylogenetic analysis of free-living organisms. Nucleic Acids Res. 27, 4218–4222 (1999).
  CAS PubMed PubMed Central Google Scholar
• Doolittle, W. F. Lateral gene transfer, genome surveys and the phylogeny of prokaryotes. Technical comments. Science 286, 1443a (1999).
  Google Scholar
• Xiong, J., Inoue, K. & Bauer, C. E. Tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from Heliobacillus mobilis. Proc. Natl Acad. Sci. USA 95, 14851–14856 (1998).
  CAS PubMed PubMed Central Google Scholar
• Baldauf, S. L., Roger, A. J., Wenk-Siefert, I. & Doolittle, W. F. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290, 972–977 (2000).
  CAS PubMed Google Scholar
• Hansmann, S. & Martin, W. Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis. Int. J. Syst. Evol. Microbiol. 50, 1655–1663 (2000).
  CAS PubMed Google Scholar
• Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E. & Stanhope, M. J. Universal trees based on large combined protein sequence datasets. Nature Genet. 28, 281–285 (2001).
  CAS PubMed Google Scholar
• Koonin, E. V., Aravind, L. & Kondrashov, A. S. The impact of comparative genomics on our understanding of evolution. Cell 101, 573–576 (2000).
  CAS PubMed Google Scholar
• Gribaldo, S. et al. Discontinuous occurrence of the hsp70 (dnaK) gene among Archaea and sequence features of HSP70 suggest a novel outlook on phylogenies inferred from this protein. J. Bacteriol. 181, 434–443 (1999).
  CAS PubMed PubMed Central Google Scholar
• Zambryski, P., Tempe, J. & Schell, J. Transfer and function of T-DNA genes from Agrobacterium Ti and Ri plasmids. Cell 56, 193–201 (1989).
  CAS PubMed Google Scholar
• Kondo, N., Nikoh, N., Ijichi, N., Shimada, M. & Fukatsu, T. Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect. Proc. Natl Acad. Sci. USA. 99, 14280–14285 (2002).
  CAS PubMed PubMed Central Google Scholar
• Tourmen, Y. et al. Structure and chromosomal distribution of human mitochondrial pseudogenes. Genomics 80, 71–77 (2002).
  CAS PubMed Google Scholar
• Courvalin, P., Goussard, S. & Grillot-Courvalin, C. Gene transfer from bacteria to mammalian cells. C. R. Acad. Sci. Paris Life Sci. 318, 1207–1212 (1995).
  CAS Google Scholar
• Kunik, T. et al. Genetic transformation of HeLa cells by Agrobacterium. Proc. Natl Acad. Sci. USA 98, 1871–1876 (2001).
  CAS PubMed PubMed Central Google Scholar
• Kurland, C. G. Something for everyone: horizontal gene transfer in evolution. EMBO Rep. 1, 92–95 (2000). Argues that HGT is used too frequently to explain evolutionary patterns.
  CAS PubMed PubMed Central Google Scholar
• Martin, W. & Müller, M. The hydrogen hypothesis for the first eukaryote. Nature 392, 37–41 (1998). Describes the hypothesis that eukaryotes evolved from a symbiosis of an archaeon and a hydrogen-producing bacterium.
  CAS PubMed Google Scholar
• Moreira, D. & López-García, P. Symbiosis between methanogenic Archaea and δ-Proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J. Mol. Evol. 47, 517–530 (1998).
  CAS PubMed Google Scholar
• Horiike, T., Hamada, K., Kanaya, S. & Shinozawa, T. Origin of eukaryotic cell nuclei by symbiosis of Archaea in Bacteria is revealed by homology-hit analysis. Nature Cell Biol. 3, 210–214 (2002).
  Google Scholar
• Poole, A. & Penny, D. Does endosymbiosis explain the origin of the nucleus? Nature Cell Biol. 3, E173 (2001).
  CAS PubMed Google Scholar
• Rotte, C. & Martin, W. Does endosymbiosis explain the origin of the nucleus? Nature Cell Biol. 3, E173 (2001).
  CAS PubMed Google Scholar
• von Dohlen, C. D., Kohler, S., Alsop, S. T. & McManus, W. R. Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts. Nature 412, 433–436 (2001).
  CAS PubMed Google Scholar
• Huber, H. et al. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417, 63–67 (2002).
  CAS PubMed Google Scholar
• Hartman, H. & Fedorov, A. The origin of the eukaryotic cell: a genomic investigation. Proc. Natl Acad. Sci. USA 99, 1420–1425 (2002). Identifies a core set of proteins that are specific to eukaryotes.
  CAS PubMed PubMed Central Google Scholar
• Doolittle, W. F. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet. 14, 307–311 (1998). Proposes an influential explanation of how eukaryotic genomes would accumulate bacterial genes through interdomain HGT.
  CAS PubMed Google Scholar
• Woese, C. R. On the evolution of cells. Proc. Natl Acad. Sci. USA 99, 8742–8747 (2002).
  CAS PubMed PubMed Central Google Scholar
• Forterre, P. & Philippe, H. Where is the root of the universal tree of life? BioEssays 21, 871–879 (1999).
  CAS PubMed Google Scholar
• Gupta, R. H. Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiol. Mol. Biol. Rev. 62, 1435–1491 (1998).
  CAS PubMed PubMed Central Google Scholar
• Olsen, G. J. & Woese, C. R. Archaeal genomics — an overview. Cell 89, 991–994 (1997).
  CAS PubMed Google Scholar
• Rivera, M. C., Jain, R., Moore, J. E. & Lake, J. A. Genomic evidence for two functionally distinct gene classes. Proc. Natl Acad. Sci. USA 95, 6239–6244 (1998).
  CAS PubMed PubMed Central Google Scholar
• Jain, R., Rivera, M. C. & Lake, J. A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA 96, 3801–3806 (1999).
  CAS PubMed PubMed Central Google Scholar
• Lathe, W. C., Snel, B. & Bork, P. Gene context conservation of a higher order than operons. Trends Biochem. Sci. 25, 474–479 (2000).
  CAS PubMed Google Scholar
• Brochier, C., Philippe, H. & Moreira, D. The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet. 16, 529–533 (2000).
  CAS PubMed Google Scholar
• Brinkman, H. & Philippe, H. Archaea sister group of bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol. Biol. Evol. 16, 817–825 (1999).
  Google Scholar
• Horner, D. S., Heil, B., Happe, T. & Embley, T. M. Iron hydrogenases — ancient enzymes in modern eukaryotes. Trends Biochem. Sci. 27, 148–153 (2002).
  CAS PubMed Google Scholar
• Horner, D. S., Hirt, R. P. & Embley, T. M. A single eubacterial origin of eukaryotic pyruvate:ferredoxin oxidoreductase genes: implications for the evolution of anaerobic eukaryotes. Mol. Biol. Evol. 16, 1280–1291 (1999).
  CAS PubMed Google Scholar
• Chihade, J., Brown, J. R., Schimmel, P. & Ribas de Pouplana, L. Origin of mitochondria in relation to evolutionary history of eukaryotic alanyl-tRNA synthetase. Proc. Natl Acad. Sci. USA 97, 12153–12157 (2000).
  CAS PubMed PubMed Central Google Scholar
• Brown, J. R., Masuchi, Y., Robb, F. T. & Doolittle, W. F. Evolutionary relationships of bacterial and archaeal glutamine synthetase genes. J. Mol. Evol. 38, 566–576 (1994).
  CAS PubMed Google Scholar
• Benachenhou-Lahfa, N., Forterre, P. & Labedan, B. Evolution of glutamate dehydrogenase genes: evidence for paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life. J. Mol. Evol. 36, 335–346 (1993).
  CAS PubMed Google Scholar
• Forterre, P., Bouthier de la Tour, C., Philippe, H. & Duguet, M. Reverse gyrase from thermophiles: probable transfer of a thermoadaptation trait from Archaea to Bacteria. Trends Genet. 16, 152–154 (2000).
  CAS PubMed Google Scholar
• Faguy, D. M. & Doolittle, W. F. Horizontal transfer of catalase-peroxidase genes between Archaea and pathogenic bacteria. Trends Genet. 16, 196–197 (2000).
  CAS PubMed Google Scholar
• Koretke, K. K., Lupas, A. N., Warren, P. V., Rosenberg, M. & Brown, J. R. Evolution of two-component signal transduction. Mol. Biol. Evol. 17, 1956–1970 (2000).
  CAS PubMed Google Scholar
• Lamour, V. et al. Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case for horizontal gene transfer. Proc. Natl Acad. Sci. USA 91, 8670–8674 (1994).
  CAS PubMed PubMed Central Google Scholar
• Brown, J. R. & Doolittle, W. F. Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases. J. Mol. Evol. 49, 485–495 (1999).
  CAS PubMed Google Scholar
• Margulis, L. Origin of Eukaryotic Cells (Yale University Press, New Haven, Connecticut, 1970).
  Google Scholar
• Kurland, C. & Andersson, S. G. E. Origin and evolution of the mitochondrial proteome. Mol. Biol. Rev. 64, 786–820 (2000). A detailed perspective on proteobacterial genomes and the evolution of mitochondria.
  CAS Google Scholar
• Cavalier-Smith, T. Kingdom protozoa and its 18 phyla. Microbiol. Rev. 57, 953–994 (1993).
  CAS PubMed PubMed Central Google Scholar
• Clark, C. G. & Roger, A. J. Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proc. Natl Acad. Sci. USA 92, 6518–6521 (1995).
  CAS PubMed PubMed Central Google Scholar
• Germot, A., Philippe, H. & Le Guyader, H. Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes. Proc. Natl Acad. Sci. USA 93, 14614–14617 (1996).
  CAS PubMed PubMed Central Google Scholar
• Henze, K. A., Badr, A., Wettern, M., Cerff, R. & Martin, W. A nuclear gene of eubacterial origin in Euglena gracilis reflects cryptic endosymbioses during protist evolution. Proc. Natl Acad. Sci. USA 92, 9122–9126 (1995).
  CAS PubMed PubMed Central Google Scholar
• Keeling, P. J. & Doolittle, W. F. Evidence that eukaryotic triosephosphate isomerase is of α-proteobacterial origin. Proc. Natl Acad. Sci. USA 94, 1270–1275 (1997).
  CAS PubMed PubMed Central Google Scholar
• Keeling, P. J. & McFadden, G. I. Origins of microsporidia. Trends Microbiol. 6, 19–23 (1998).
  CAS PubMed Google Scholar
• Roger, A. J., Clark, C. G. & Doolittle, W. F. A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis. Proc. Natl Acad. Sci. USA 93, 14618–14622 (1996).
  CAS PubMed PubMed Central Google Scholar
• van der Giezen, M. et al. Conserved properties of hydrogenosomal and mitochondrial ADP/ATP carriers: a common origin for both organelles. EMBO J. 21, 572–579 (2002).
  CAS PubMed Google Scholar
• Tielens, A. G. M., Rotte, C., van Hellemond, J. J. & Martin, W. Mitochondria as we don't know them. Trends Biochem. Sci. 27, 564–572 (2002). Describes the broad range of mitochondrial metabolic diversity.
  CAS PubMed Google Scholar
• Andersson, S. G. et al. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396, 133–140 (1998).
  CAS PubMed Google Scholar
• Karlberg, O., Canbäck, B., Kurland, C. G. & Andersson, S. G. E. The dual origin of the yeast mitochondrial proteome. Yeast Comp. Funct. Genomics 17, 170–187 (2000). An evolutionary analysis of the archaeal and bacterial contributions to the mitochondrial proteome.
  CAS Google Scholar
• Thorsness, P. E. & Fox, T. D. Escape of DNA from mitochondria to nucleus in Saccharomyces cerevisiae. Nature 346, 376–379 (1990).
  CAS PubMed Google Scholar
• Thorsness, P. E. & Fox, T. D. Nuclear mutations in Saccharomyces cerevisiae that affect the escape of DNA from mitochondria to the nucleus. Genetics 134, 21–28 (1993).
  CAS PubMed PubMed Central Google Scholar
• Rujan, T. & Martin, W. How many genes in Arabidopsis come from cyanobacteria? An estimate from 386 protein phylogenies. Trends Genet. 17, 113–119 (2001).
  CAS PubMed Google Scholar
• Martin, W. et al. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl Acad. Sci. USA 99, 12246–12251 (2002). An assessment of the potential contribution of the plastid symbiont to the plant nuclear genome.
  CAS PubMed PubMed Central Google Scholar
• Palenik, B. The genomics of symbiosis: host keep the baby and the bath water. Proc. Natl Acad. Sci. USA 99, 11996–11997 (2002).
  CAS PubMed PubMed Central Google Scholar
• Brinkman, F. S. L. et al. Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, Cyanobacteria, and the chloroplast. Genome Res. 12, 1159–1167 (2002).
  CAS PubMed PubMed Central Google Scholar
• Martin, W. Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays 21, 99–104 (1999). Discusses the possible impacts on genome evolution of mixing bacterial lineages.
  CAS PubMed Google Scholar
• Berg, O. G. & Kurland, C. G. Why mitochondrial genes are most often found in nuclei. Mol. Biol. Evol. 17, 951–961 (2000).
  CAS PubMed Google Scholar
• Blanchard, J. L. & Lynch, M. Organellar genes: why do they end up in the nucleus? Trends Genet. 16, 315–320 (2000).
  CAS PubMed Google Scholar
• Canback, B., Andersson, S. G. E. & Kurland, C. G. The global phylogeny of glycolytic enzymes. Proc. Natl Acad. Sci. USA 99, 6097–6102 (2002).
  CAS PubMed PubMed Central Google Scholar
• Brown, J. R. & Doolittle, W. F. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl Acad. Sci. USA 92, 2441–2445 (1995).
  CAS PubMed PubMed Central Google Scholar
• Hashimoto, T., Sánchez, L. B., Shirakura, T., Müller, M. & Hasegawa, M. Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc. Natl Acad. Sci. USA 95, 6860–6865 (1998).
  CAS PubMed PubMed Central Google Scholar
• Deppenmeier, U. et al. The genome of Methanosacrina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4, 453–461 (2002).
  CAS PubMed Google Scholar
• Wren, B. W. Microbial genome analysis: insight into virulence, host adaptation and evolution. Nature Rev. Genet. 1, 30–39 (2000).
  CAS PubMed Google Scholar
• Huang, P. & Oliff, A. Signaling pathways in apoptosis as potential targets for cancer therapy. Trends Cell Biol. 11, 343–348 (2001).
  CAS PubMed Google Scholar
• Koonin, E. V. & Aravind, L. Origin and evolution of eukaryotic apoptosis: the bacterial connection. Cell Death Differ. 9, 394–404 (2002).
  CAS PubMed Google Scholar
• Dehal, P. et. al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298, 2157–2167 (2002).
  CAS PubMed Google Scholar
• Graham, D. E., Overbeek, R., Olsen, G. J. & Woese, C. R. An archaeal genomic signature. Proc. Natl Acad. Sci. USA 97, 3304–3308 (2000).
  CAS PubMed PubMed Central Google Scholar
• Iwabe, N., Kuma, K. -I., Hasegawa, M., Osawa, S. & Miyata, T. Evolutionary relationship of Archaea, Bacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc. Natl Acad. Sci. USA 86, 9355–9359 (1989).
  CAS PubMed PubMed Central Google Scholar
• Gogarten, J. P. et al. Evolution of the vacuolar H+-ATPase: implications for the origin of eukaryotes. Proc. Natl Acad. Sci. USA 86, 6661–6665 (1989).
  CAS PubMed PubMed Central Google Scholar
• Olsen, G. J., Woses, C. R. & Overbeek, R. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176, 1–6 (1994). Contains a comprehensive ribosomal RNA phylogeny of the Bacteria and Archaea.
  CAS PubMed PubMed Central Google Scholar
• Hilario, E. & Gogarten, J. P. Horizontal transfer of ATPase genes — the tree of life becomes the net of life. BioSystems 31, 111–119 (1993).
  CAS PubMed Google Scholar
• Woese, C. R., Olsen, G. J., Ibba, M. & Söll, D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64, 202–236 (2000).
  CAS PubMed PubMed Central Google Scholar
• Lopez, P., Forterre, P. & Philippe, H. The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49, 496–508 (1999).
  CAS PubMed Google Scholar
• Baldauf, S. L., Palmer, J. D. & Doolittle, W. F. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc. Natl Acad. Sci. USA 93, 7749–7754 (1996).
  CAS PubMed PubMed Central Google Scholar
• Wolf, Y. I., Aravind, L., Grishin, N. V. & Koonin, E. V. Evolution of aminoacyl-tRNA synthetases — analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9, 689–710 (1999).
  CAS PubMed Google Scholar
• Teichmann, S. A. & Mitchison, G. Is there a phylogenetic signal in prokaryote proteins? J. Mol. Evol. 49, 98–107 (1999).
  CAS PubMed Google Scholar
• Brown, J. R. Genomic and phylogenetic perspectives on the evolution of prokaryotes. Syst. Biol. 50, 497–512 (2001).
  CAS PubMed Google Scholar
• Boucher, Y. & Doolittle, W. F. The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways. Mol. Microbiol. 37, 703–716 (2000).
  CAS PubMed Google Scholar
• Aravind, L., Tatusov, R. L., Wolf, Y. I., Walker, D. R. & Koonin, E. V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 14, 442–444 (1998).
  CAS PubMed Google Scholar
• Eisen, J. A. Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr. Opin. Genet. Dev. 10, 606–611 (2000).
  CAS PubMed Google Scholar
• Martin, W. Is something wrong with the tree of life? Bioessays 18, 523–527 (1996).
  CAS Google Scholar
• Tiboni, O., Cammarano, P. & Sanangelantoni, A. M. Cloning and sequencing the gene encoding glutamine synthetase I from the archaeum Pyrococcus woesei: anomalous phylogenies inferred from analysis of archaeal and bacterial glutamine synthetase I sequences. J. Bacteriol. 175, 2961–2969 (1993).
  CAS PubMed PubMed Central Google Scholar
• Swofford, D. L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods) Ver. 4 (Sinauer Associates, Sunderland, Massachusetts, 1999).
• Felsenstein, J. PHYLIP (Phylogeny Inference Package) Ver. 3, 57c. Distributed by the author: http://evolution.genetics.washington.edu/phylip.html (Department of Genetics, University of Washington, Seattle, 1993).
• Page, R. D. M. TREEVIEW: an application to display phylogenetic trees on personal computers. Comp. Appl. Biosci. 12, 357–358 (1996).
  CAS PubMed Google Scholar
• Gardner, M. J. et al. Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419, 498–511 (2002).
  CAS PubMed Google Scholar
• Carlton, J. M. et al. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 419, 512–519 (2002).
  CAS PubMed Google Scholar
• Baldauf, S. L. & Doolittle, W. F. Origin and evolution of the slime molds (Mycetozoa). Proc. Natl Acad. Sci. USA 94, 12007–12012 (1997).
  CAS PubMed PubMed Central Google Scholar