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The Tree of Life Viewed Through the Contents of Genomes

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Horizontal Gene Transfer

Part of the book series: Methods in Molecular Biology ((MIMB,volume 532))

Abstract

A universal Tree of Life has been a longstanding goal of the biosciences. The most common Tree of Life, based on the small subunit rRNA gene, may or may not represent the phylogenetic history of microorganisms. The horizontal transfer of genes from one taxon to another provides a means by which each gene may tell of an independent history. When complete genomes became available, the extent to which horizontal gene transfer (HGT) has occurred became more evident. When using genomic data to study the Tree of Life, one can use any of the four broad approaches: (i) build lots of individual gene trees (“phylogenomics”), (ii) concatenate genes together for an analysis yielding one “supergene” tree, (iii) form a single tree based on the “gene content” within genomes using either orthologs or homologs, or (iv) investigate the order of genes within genomes to discern some aspects of microbial evolution. The application of whole genome tree building has suggested that there is a core tree, that such a core tree can be investigated using these varied methods, and that the results are largely similar to those of the rRNA universal Tree of Life. Some of the most interesting features of the rRNA tree, such as early diverging hyperthermophilic lineages are still uncertain, but remain a possibility. Genomic trees and geologic evidence together suggest that the vertical descent of genes and the horizontal transfer of genes between genetically similar lineages ultimately results in a core Tree of Life with at least some lineages that have phenotypic characteristics recognizable for billions of years.

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References

  1. aeckel, E. (1874) Anthropogenie. Engelmann, Leipzig.

    Google Scholar 

  2. aeckel, E. (1896) The Evolution of Man: A Popular Exposition of the Principal Points of Human Ontogeny and Phylogeny. Appleton, NewYork.

    Google Scholar 

  3. ayat, B. (2003) The roots of ‘Phylogeny’: how did Haeckel really build his trees? System Biol 52, 515–27.

    Google Scholar 

  4. ohen, H. J. (1872) Untersuchungen über Bacterien. I. Beitr Biol Pfl 1, 127.

    Google Scholar 

  5. neath, P. H. A. (1962) Construction of taxa, in Microbial Classification (Cain, A. J., ed.), Cambridge University Press, London.

    Google Scholar 

  6. rla-Jensen, S. (1909) Die Hauptlinien des natürlichen Bakteriensystems. Zbl Bakt 22, 305.

    Google Scholar 

  7. iller, S. L. (1953) A production of amino acids under possible primitive earth conditions. Science 117, 528–9.

    Article  Google Scholar 

  8. parin, A. I. (1953) The Origin of Life. Dover Publications Inc., New York.

    Google Scholar 

  9. luyver, A. J., van Niel, C. B. (1936) Prospects for a natural system of classification of bacteria. Zbl Bakt  94, 369.

    Google Scholar 

  10. Stanier, R. Y., van Niel, C. B. (1941) The main outlines of bacterial classification. J Bact 42, 437.

    CAS  PubMed  Google Scholar 

  11. Murray, R. G. E. (1962) Fine structure and taxonomy of Bacteria, in Microbial Classification (Cain, A. J., ed.), Cambridge University Press, London.

    Google Scholar 

  12. De Ley, J. (1962) Comparative biochemistry and enzymology in bacterial classification, in Microbial Classification (Cain, A. J., ed.), Cambridge University Press, London.

    Google Scholar 

  13. Sanger, F., Thompson, O. P., Kitai, R. (1955) The amide groups of insulin. Biochem J 59, 509–18.

    CAS  PubMed  Google Scholar 

  14. Pauling, L., Zuckerkandl, E. (1962) Molecular paleontology. Acta Chem Scand 17, S9–S16.

    Article  Google Scholar 

  15. Jukes, T. H., Cantor, C. R. (1969) Evolution of protein molecules, in Mammalian Protein Metabolism, III. (Munro, H. N., ed.) Academic Press, New York.

    Google Scholar 

  16. Dayhoff, M. O. (1978) Observed frequencies of amino acid replacements between closely related proteins, in Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, D.C.

    Google Scholar 

  17. Woese, C. R., Fox, G. E. (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Nat Acad Sci U S A 74, 5088–90.

    Article  CAS  Google Scholar 

  18. Pace, N. R. (1997) A molecular view of microbial diversity and the biosphere. Science 276, 734–40.

    Article  CAS  PubMed  Google Scholar 

  19. Woese, C. R., Kandler, O., Wheelis, M. L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87, 4576–9.

    Article  CAS  PubMed  Google Scholar 

  20. Woese, C. R. (1987) Bacterial evolution. Microbiol Rev 51, 221–71.

    CAS  PubMed  Google Scholar 

  21. Stetter, K. O. (1996) Hyperthermophilic prokaryotes. FEMS Microbiol Rev 18, 149–58.

    Article  CAS  Google Scholar 

  22. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17, 368–76.

    Article  CAS  PubMed  Google Scholar 

  23. Marshall, C. R. (1997) Statistical and computational problems in reconstructing evolutionary histories from DNA data. Comput Sci Statist 29, 218–26.

    Google Scholar 

  24. Gribaldo, S., Philippe, H. (2002) Ancient phylogenetic relationships. Theor Popul Biol 61, 391–408.

    Article  PubMed  Google Scholar 

  25. Hartman P. E., Goodgal, S. H. (1959) Bacterial genetics (with particular reference to genetic transfer). Annu Rev Microbiol 13, 465.

    Article  Google Scholar 

  26. Fraser, C. M., Eisen, J. A., Salzberg, S. L. (2000) Microbial genome sequencing. Nature. 406, 799–803.

    Article  CAS  PubMed  Google Scholar 

  27. House C. H., Fitz-Gibbon, S. T. (2002) Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol 54, 539–47.

    Article  CAS  PubMed  Google Scholar 

  28. House, C. H. (2007) Linking taxonomy with environmental geochemistry and why it matters to the field of geobiology. Geobiology. 5, 1–3.

    Article  Google Scholar 

  29. House, C. H., Runnegar, B. Fitz-Gibbon, S. T. (2003) Geobiological analysis using whole genome-based tree building applied to the bacteria, archaea, and eukarya. Geobiology 1, 15–26.

    Article  CAS  Google Scholar 

  30. Zerkle, A. L., House, C. H., Brantley, S. L. (2005) Biogeochemical signatures through time as inferred from whole microbial genomes. Am J Sci 305, 467–502

    Article  CAS  Google Scholar 

  31. Gogarten, J. P., Senejani, A. G., Zhaxybayeva, O., Olendzenski, L., Hilario, E. (2002) Inteins: structure, function, and evolution. Annu Rev Microbiol 56, 263– 287.

    Article  CAS  PubMed  Google Scholar 

  32. Doolittle, W. F. (2000) Uprooting the tree of life. Sci Am 282, 90–95.

    Article  CAS  PubMed  Google Scholar 

  33. Perry, J. (ed.) (1975) Personal Identity. University of California Press, Berkeley, CA.

    Google Scholar 

  34. Hume, D. (1978) in A Treatise on Human Nature, 2nd Edition (Selby-Bigge, L. A., ed.) Clarendon Press, Oxford.

    Google Scholar 

  35. Clough, A (ed.), Dryden, J., and Plutarch (1992) Plutarch’s Lives, Volume 1. Random House, Inc., New York.

    Google Scholar 

  36. House, C. H. (2003) Gene content based phylogenetic methods. Amer Soc of Microb Annu Meeting. Washington, D.C.

    Google Scholar 

  37. Doolittle, W. F. (2004) Q & A. Curr Biol 14, R176–7.

    Article  PubMed  CAS  Google Scholar 

  38. Zhaxybayeva, O., Lapierre, P., Gogarten, J. P. (2004) Genome mosaicism and organismal lineages. Trends Genet 20, 54–260.

    Google Scholar 

  39. Maddison, W. P. (1997) Gene trees in species trees. System Biol 46, 523–36.

    Article  Google Scholar 

  40. Philippe, H., Douady, C. J. (2003) Horizontal gene transfer and phylogenetics. Curr Opin Microbiol 6, 498–505.

    Article  CAS  PubMed  Google Scholar 

  41. Doolittle, W. F. (1999) Phylogenetic classification and the universal tree. Science 284, 2124.

    Article  CAS  PubMed  Google Scholar 

  42. Moret, B. M. E., Nakhleh, L., Warnow, T., Linder, C. R., Tholse, A., Padolina, A., Sun, J., Timme, R. (2004) “Phylogenetic networks: modeling, reconstructibility, and accuracy,” IEEE/ACM Trans Comput Biol Bioinf 1, 13–23.

    Article  CAS  Google Scholar 

  43. Kunin, V., Goldovsky, L., Darzentas, N., Ouzounis, C. A. (2005) The net of life: reconstructing the microbial phylogenetic network. Genome Res 15, 954–59.

    Article  CAS  PubMed  Google Scholar 

  44. Huson, D. H., Bryant, D. (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23, 254–67.

    Article  CAS  PubMed  Google Scholar 

  45. Rivera, M. C., Lake, J. A. (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431, 134–7.

    Article  CAS  Google Scholar 

  46. Rivera, M. C., Jain, R., Moore, J. E., Lake, J. A. (1998) Genomic evidence for two functionally distinct gene classes. Proc Natl Acad Sci U S A 95, 6239–44.

    Article  CAS  PubMed  Google Scholar 

  47. Jain, R., Rivera, M. C., Lake, J. A. (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A 96, 3801–6.

    Article  CAS  PubMed  Google Scholar 

  48. Daubin, V., Gouy, M., Perri‘ere, G. (2001) Bacterial molecular phylogeny using supertree approach. Genome Inform 12, 155–64.

    CAS  PubMed  Google Scholar 

  49. Sicheritz-Ponten, T., Andersson, S. G. (2001) A phylogenomic approach to microbial evolution. Nucleic Acids Res 29, 545–52.

    Article  CAS  PubMed  Google Scholar 

  50. Bapteste, E., Brinkmann, H., Lee, J. A., Moore, D. V., Sensen, C. W., Gordon, P., Durufl’e, L. Gaasterland, T., Lopez, P., Müller, M., Philippe, H. (2002) The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci U S A 99, 1414–19.

    Article  CAS  PubMed  Google Scholar 

  51. Daubin, V., Gouy, M., Perri‘ere, G. (2002) A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history. Genome Res 12, 1080–90.

    Article  CAS  PubMed  Google Scholar 

  52. Daubin, V., Moran, N. A., Ochman, H. Phylogenetics and the cohesion of bacterial genomes. Science 301, 829–32.

    Google Scholar 

  53. Canbddotack, B., Tamas, I., Andersson, S. G. (2004) A phylogenomic study of endosymbiotic bacteria. Mol Biol Evol 21, 1110–22.

    Article  CAS  Google Scholar 

  54. Calteau, A., Daubin, V., Perri‘ere, G. (2004) Super-tree approach for studying the phylogeny of prokaryotes: new results on completely sequenced genomes. International Conference on Computational Science 3039, 700–708.

    Google Scholar 

  55. Sanderson, M. J., Purvis, A., Henze, C. (1998) Phylogenetic supertrees: assembling the trees of life, Trends Ecol Evol 13, 105–109.

    Article  CAS  PubMed  Google Scholar 

  56. Baum, B. R. (1992) Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41, 3–10.

    Article  Google Scholar 

  57. Bininda-Emonds, O. R. P, Gittleman, J. L., Steel, M. A. (2002) The (super)tree of life: procedures, problems, and prospects. Annu Rev Ecol Syst 33, 265–289.

    Article  Google Scholar 

  58. Galtier, N. (2007) A model of horizontal gene transfer and the bacterial phylogeny problem. Syst Biol 56, 633–42.

    Article  PubMed  Google Scholar 

  59. Dutilh, B. E., van Noort, V., van der Heijden, R. T., Boekhout, T., Snel, B., Huynen, M. A. (2007) Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinformatics 23, 815–24.

    Article  CAS  PubMed  Google Scholar 

  60. Hansmann, S., Martin, W. (2000) 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 4, 1655–63.

    Google Scholar 

  61. Brown, J. R., Douady, C. J., Italia, M. J., Marshall, W. E., Stanhope, M. J. (2001) Universal trees based on large combined protein sequence data sets. Nat Genet 28, 281–5.

    Article  CAS  PubMed  Google Scholar 

  62. Wolf, Y., Rogozin, I. B., Grishin, N. V., Tatusov, R. L., Koonin, E. V. (2001) Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol Biol 1, 8.

    Article  CAS  PubMed  Google Scholar 

  63. Brochier, C., Bapteste, E., Moreira, D., Philippe, H. (2002) Eubacterial phylogeny based on translational apparatus proteins. Trends Genet 18, 1–5.

    Article  CAS  PubMed  Google Scholar 

  64. Matte-Tailliez, O., Brochier, C., Forterre, P., Philippe, H. (2002) Archaeal phylogeny based on ribosomal proteins. Mol Biol Evol 19, 631–9.

    CAS  PubMed  Google Scholar 

  65. Battistuzzi, F. U., Feijao, A, Hedges, S. B. (2004) A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evol Biol 4, 44.

    Article  PubMed  CAS  Google Scholar 

  66. Dagan, T., Martin, W. (2006) The tree of one percent. Genome Biol 7, 118.

    Article  PubMed  CAS  Google Scholar 

  67. Fitz-Gibbon, S. T., House, C. H. (1999) Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res 27, 4218–22.

    Article  CAS  PubMed  Google Scholar 

  68. Snel, B., Bork, P., Huynen, M. A. (1999) Genome phylogeny based on gene content. Nat Genet 21, 108–10.

    Article  CAS  PubMed  Google Scholar 

  69. Tekaia, F., Lazcano, A., Dujon, B. (1999) The genomic tree as revealed from whole proteome comparisons. Genome Res 9, 550–557.

    CAS  PubMed  Google Scholar 

  70. Lin, J., Gerstein, M. (2000) Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res 10, 808–818.

    Article  CAS  PubMed  Google Scholar 

  71. Montague, M. G., Hutchison, C. A. (2000) Gene content phylogeny of herpesviruses. Proc Natl Acad Sci U S A 97, 5334–9.

    Article  CAS  PubMed  Google Scholar 

  72. Bansal, A. K., Meyer, T. E. (2002) Evolutionary analysis by whole-genome comparisons. J Bacteriol 184, 2260–72.

    Article  CAS  PubMed  Google Scholar 

  73. Clarke, G. D., Beiko, R. G., Ragan, M. A., Charlebois, R. L. (2002) Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol 184, 2072–80.

    Article  CAS  PubMed  Google Scholar 

  74. Korbel, J. O., Snel, B., Huynen, M. A., Bork, P. (2002) SHOT: a web server for the construction of genome phylogenies. Trends Genet 18, 158–62.

    Article  CAS  PubMed  Google Scholar 

  75. Li, W., Fang, W., Ling, L., Wang, J., Xuan, Z., Chen, R. (2002) Phylogeny based on whole genome as inferred from complete information set analysis. J Biol Physics 28, 439–47.

    Article  CAS  Google Scholar 

  76. Stuart, G. W., Berry, M. W. (2003) A comprehensive whole genome bacterial phylogeny using correlated peptide motifs defined in a high dimensional vector space. J Bioinform Comput Biol 1, 475–93.

    Article  CAS  PubMed  Google Scholar 

  77. Maruyama, O., Matsuda, A., Kuhara, S. (2005) Reconstructing phylogenetic trees of prokaryote genomes by randomly sampling oligopeptides. Int J Bioinfo Res Applic 1, 429–46.

    Article  CAS  Google Scholar 

  78. Tekaia, F., Yeramian, E. (2005) Genome trees from conservation profiles. PLoS Comput Biol 1, e75.

    Article  PubMed  CAS  Google Scholar 

  79. Yang, S., Doolittle, R. F., Bourne, P. E. (2005) Phylogeny determined by protein domain content. Proc Natl Acad Sci U S A 102, 373–8.

    Article  CAS  PubMed  Google Scholar 

  80. Gophna, U., Doolittle, W. F., Charlebois, R. L. (2005) Weighted genome trees: refinements and applications. J Bacteriol 187, 1305–16.

    Article  CAS  PubMed  Google Scholar 

  81. Eisen, J. A. (2000) Horizontal gene transfer among microbial genomes: new insights from complete genome analysis. Curr Opin Genet Devel 10, 606–11.

    Article  CAS  Google Scholar 

  82. Rohwer, F., Edwards, R. (2002) The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 184, 4529–35.

    Article  CAS  PubMed  Google Scholar 

  83. Watterson, W. A., Ewens, W. J., Hall, T. E., Morgan, A. (1982) The chromosome inversion problem. J Theor Biol 99, 1–7.

    Article  Google Scholar 

  84. Blanchette, M., Kunisawa, T., Sankoff, S. (1999) Gene order breakpoint evidence in animal mitochondrial phylogeny. J Mol Evol 49, 193–203.

    Article  CAS  PubMed  Google Scholar 

  85. Kunisawa, T. (2001) Gene arrangements and phylogeny in the class proteobacteria. J Theor Biol 213, 9–19.

    Article  CAS  PubMed  Google Scholar 

  86. Kunisawa, T. (2003) Gene arrangements and branching orders of gram-positive bacteria. J Theor Biol 222, 495–503.

    CAS  PubMed  Google Scholar 

  87. Moret, B. M. E., Wang, L. S., Warnow, T., Wyman, S. K. (2001) New approaches for reconstructing phylogenies from gene order data. Bioinformatics 17 Suppl 1, S165–73.

    PubMed  Google Scholar 

  88. Belda, E., Moya, A., Silva, F. J. (2005) Genome rearrangement distances and gene order phylogeny in gamma-proteobacteria. Mol Biol Evol 22, 1456–67.

    Article  CAS  PubMed  Google Scholar 

  89. House, C. H., Fitz-Gibbon, S. T. (submitted) Genome-wide gene order distances support a united Gram-positive bacteria. Geobiology.

    Google Scholar 

  90. Di Giulio, M. (2003) The ancestor of the bacteria domain was a hyperthermophile. J Theor Biol 224, 277–83.

    Article  PubMed  CAS  Google Scholar 

  91. Russell, M. J., Hall, A. J. (1988) Submarine hot springs and the origin of life. Nature 336, 117.

    Article  Google Scholar 

  92. Wächtershäuser, G. (1988) Pyrite formation, the first energy source for life: a hypothesis. Syst Appl Microbiol 10, 207.

    Google Scholar 

  93. Russell, M. J., Hall, A. J. (1990) Pyrite and the origin of life. Nature 344, 387.

    Article  Google Scholar 

  94. Shock, E. (1990) Geochemical constraints on the origin of organic compounds in hydrothermal systems. Orig Life Evol Biosph 20, 331–67.

    Article  CAS  Google Scholar 

  95. Pace, N. R. (1991) Origin of life – facing up to the physical setting. Cell 65, 531–33.

    Article  CAS  PubMed  Google Scholar 

  96. Schwartzman, D. W., Lineweaver, C. H. (2004) The hyperthermophilic origin of life revisited. Biochem Soc Trans 32, 168–71.

    Article  CAS  PubMed  Google Scholar 

  97. Wächtershäuser, G. (2006) From volcanic origins of chemoautotrophic life to bacteria, archaea and eukarya. Philos Trans R Soc Lond B Biol Sci 361, 1787–806.

    Article  PubMed  CAS  Google Scholar 

  98. Forterre, P., Philippe, H. (2004) Where is the root of the universal tree of life? Bioessays 21, 871–79.

    Article  Google Scholar 

  99. Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., McDonald, L., Utterback, T. R., Malek, J. A., Linher, K. D., Garrett, M. M., Stewart, A. M., Cotton, M. D., Pratt, M. S., Phillips, C. A., Richardson, D., Heidelberg, J., Sutton, G. G., Fleischmann, R. D., Eisen, J. A., White, O., Salzberg, S. L., Smith, H. O., Venter, J. C., Fraser, C. M. (1999) Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima. Nature 399, 323–9.

    Article  CAS  PubMed  Google Scholar 

  100. Davey, M. E., Wood, W. A., Key, R., Nakamura, K., Stahl, D. A. (1993) Isolation of three species of Geotoga and Petrotoga: Two new genera, representing a new lineage in the bacterial line of descent distantly related to the “Thermotogales”. Syst Appl Microbiol 16, 191–200.

    Google Scholar 

  101. Maher, K. A., Stevenson, D. J. (1988) Impact frustration of the origin of life. Nature 331, 612–4.

    Article  CAS  PubMed  Google Scholar 

  102. Sleep, N. H., Zahnle, K. J., Kasting, J. F., Morowitz, H. J. (1989) Annihilation of ecosystems by large asteroid impacts on the early Earth. Nature 342, 139–42.

    Article  CAS  PubMed  Google Scholar 

  103. Miller, S. L., Lazcano, A. (1995) The origin of life–-did it occur at high temperatures? J Mol Evol 41, 1432.

    Article  Google Scholar 

  104. Gogarten-Boekels, M., Hilario, E., Gogarten, J. P. (1995) The effects of heavy meteorite bombardment on the early evolution – the emergence of the three domains of life. Orig Life Evol Biosph 25, 251–64.

    Article  CAS  PubMed  Google Scholar 

  105. Islas, S., Velasco, A. M., Becerra, A., Delaye, L., Lazcano, A. (2007) Extremophiles and the origin of life, in Physiology and Biochemistry of Extremophiles (Gerday, C., and Glansdorff, N., ed.), ASM Press, Washington, D.C.

    Google Scholar 

  106. Slesarev, A. I., Mezhevaya, K. V., Makarova, K. S., Polushin, N. N., Shcherbinina, O. V., Shakhova, V. V., Belova, G. I., Aravind, L., Natale, D. A., Rogozin, I. B., Tatusov, R. L., Wolf, Y. I., Stetter, K. O., Malykh, A. G., Koonin, E. V., Kozyavkin, S. A. (2002) The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A 99, 4644–9.

    Article  CAS  PubMed  Google Scholar 

  107. Wolf, Y. I., Rogozin, I. B., Grishin, N. V., Koonin, E. V. (2002) Trends Genet 18, 472–9.

    Article  CAS  PubMed  Google Scholar 

  108. Brochier, C., Forterre, P., Gribaldo, S. (2004) Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol 5, R17.

    Article  PubMed  Google Scholar 

  109. Vargas, M., Kashefi, K., Blunt-Harris, E. L., Lovley, D. R. (1998) Microbiological evidence for Fe(III) reduction on early Earth. Nature 395, 65–7.

    Article  CAS  PubMed  Google Scholar 

  110. Farquhar, J., Bao, H., Thiemens, M. (2001) Atmospheric influence of Earth’s earliest sulfur cycle. Science 289, 756–8.

    Article  Google Scholar 

  111. Pavlov, A. A., Kasting, J. F. (2002) Mass-independent fractionation of sulfur isotopes in Archean sediments: strong evidence for an anoxic Archean atmosphere. Astrobiology 2, 27–41.

    Article  CAS  PubMed  Google Scholar 

  112. Ono, S., Eigenbrode, J. L., Pavlov, A. A., Kharecha, P., Rumble, D., Kasting, J. F., Freeman, K. H. (2003) New insights into Archean sulfur cycle from mass-independent sulfur isotope records from the Hamersley Basin, Australia. Earth Planet Sc Lett 213, 15–30.

    Article  CAS  Google Scholar 

  113. Gogarten, J. P., Doolittle, W. F., Lawrence, J. G. (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19, 2226–38.

    CAS  PubMed  Google Scholar 

  114. Ferry, J. G., House, C. H. (2006) The stepwise evolution of early life driven by energy conservation. Mol Biol Evol 23, 1286–92.

    Article  CAS  PubMed  Google Scholar 

  115. Eigenbrode, J. L., Freeman, K. H. (2006) Late Archean rise of aerobic microbial ecosystems. Proc Natl Acad Sci U S A 103, 15759–64.

    Article  CAS  PubMed  Google Scholar 

  116. Hayes, J. M. (1994) Global methanotrophy at the Archean-Proterozoic transition, in Early life on Earth (S. Bengtson, ed.) Columbia University Press, New York, 220–36.

    Google Scholar 

  117. Schopf, J. W. (1994) Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic. Proc Natl Acad Sci U S A 91, 6735–42.

    Article  CAS  PubMed  Google Scholar 

  118. Golubic, S., Hofmann, H. J. (1976) Comparison of Holocene and mid-Precambrian Entophysalidaceae (Cyanophyta) in stromatolitic algal mats; cell division and degradation. J Paleontol 50, 1074–82.

    Google Scholar 

  119. Barghoorn, E. S., Schopf, J. W. (1965) Microorganisms from the late Precambrian of central Australia. Science 150, 337–9.

    Article  CAS  PubMed  Google Scholar 

  120. Summons, R. E., Jahnke, L. L. (1990) Identification of the methylhopanes in sediments and petroleum. Geochim Cosmochim Acta 54, 247–51.

    Article  CAS  PubMed  Google Scholar 

  121. Brocks, J. J., Logan, G. A., Buick, R., Summons, R. E. (1999) Archean molecular fossils and the early rise of eukaryotes. Science 285, 1033–36.

    Article  CAS  PubMed  Google Scholar 

  122. Summons, R. E., Jahnke, L. L., Hope, J. M., Logan, G. A. (1999) 2-Methylhopanoids as biomarkers for cyanobacterial oxygenic photosynthesis. Nature 400, 554–7.

    Article  CAS  PubMed  Google Scholar 

  123. Brocks, J. J., Love, G. D., Summons, R. E., Knoll, A. H., Logan, G. A., Bowden, S. A. (2005) Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeoproterozoic sea. Nature 437, 866–70.

    Article  CAS  PubMed  Google Scholar 

  124. Eigenbrode, J. L., Freeman, K. H., Summons, R. E. (2008) Methylhopane biomarker hydrocarbons in Hamersley Province sediments provide evidence for Neoarchean aerobiosis, Earth Planet Sci Lett 273, 323–31.

    Article  CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. Department of Geosciences and Pennsylvania State Astrobiology Research Center, Pennsylvania State University, University Park, PA, USA

    Christopher H. House

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  1. Christopher H. House
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Editors and Affiliations

  1. University of Connecticut, 968 Warrenville Road, Mansfield Center, CT 06250, USA

    Maria Boekels Gogarten

  2. Dept. Molecular & Cell Biology, University of Connecticut, 91 North Eagleville Rd., Storrs, CT 06269-3125, USA

    Johann Peter Gogarten

  3. Biology Department, St. Lawrence University, 23 Romoda Drive, Canton, NY 13617, USA

    Lorraine C. Olendzenski

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© 2009 Humana Press, a part of Springer Science+Business Media, LLC

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House, C.H. (2009). The Tree of Life Viewed Through the Contents of Genomes. In: Gogarten, M.B., Gogarten, J.P., Olendzenski, L.C. (eds) Horizontal Gene Transfer. Methods in Molecular Biology, vol 532. Humana Press. https://doi.org/10.1007/978-1-60327-853-9_8

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  • DOI: https://doi.org/10.1007/978-1-60327-853-9_8

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60327-852-2

  • Online ISBN: 978-1-60327-853-9

  • eBook Packages: Springer Protocols

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