Epistemological Impacts of Horizontal Gene Transfer on Classification in Microbiology

  • Eric Bapteste
  • Yan Boucher
Part of the Methods in Molecular Biology book series (MIMB, volume 532)


We describe the reasons why the newly recognized process of horizontal gene transfer (HGT) forces evolutionists who study classification and microbiology to go beyond the classical Darwinian framework. We recall the importance of processes in philosophical definitions of species and for taxonomical purposes in general. More precisely, we present a brief description of a possible transition from a thinking inspired by essentialism to eliminative pluralism in the species debate and we insist on a major philosophical lesson: that processes matter and that, consequently, HGT cannot be overlooked in microbial classification. We then expand the conclusions of eliminative pluralism to microbial classification, namely (i) that species are not real and (ii) that overlapping taxonomies are equally legitimate when they are based on real natural processes. We introduce alternatives to the traditional species concept and describe what we call evolutionary units. Two types of units can be described: coherent and composite. The former are sets of co-evolving genes, pathways, or organisms, which share the same phylogenetic origin, while the latter comprise genes, pathways, or organisms with component parts from multiple phylogenetic origins. These evolutionary units are either “mostly flexible” or “mostly rigid” in their genetic composition and we discuss how this dissimilarity could profoundly affect our systematics practice. In this chapter, we illustrate how much there is to learn from the reconstruction of the complex evolutionary histories of all evolutionary units – large or small – by giving up the notion of species for recombining microbes, and suggest replacing a unique nested hierarchy of life with a comprehensive database including overlapping taxonomical groups.


Species concept pluralism systematics horizontal gene transfer evolutionary units nested hierarchy 


  1. 1.
    Panchen, A. L. (1992) Classification, Evolution, and the Nature of Biology, Cambridge University Press, Cambridge.Google Scholar
  2. 2.
    Sober, E. (1991) Reconstructing the Past: Parsimony, Evolution, and Inference, The MIT Press, Cambridge.Google Scholar
  3. 3.
    Woese, C. R. (1987) Bacterial evolution. Microbiol Rev 51, 221–71.PubMedGoogle Scholar
  4. 4.
    Ereshefsky, M. (2006) Species, in The Stanford Encyclopedia of Philosophy (Zalta, E. N., ed.) The Metaphysics Research Lab, Stanford.Google Scholar
  5. 5.
    Hull, D. L. (1965) The effect of essentialism on taxonomy – two thousands years of stasis (I). Br J Philos Sci 15, 314–26.CrossRefGoogle Scholar
  6. 6.
    Rieppel, O. (2005) The philosophy of total evidence and its relevance for phylogenetic inference. Papéis Avulsos Zoologia 45, 1–31.Google Scholar
  7. 7.
    Winsor, M. P. (2003) Non-essentialist methods in pre-Darwinian taxonomy. Biol Phil 18, 387–400.CrossRefGoogle Scholar
  8. 8.
    Muller-Wille, S. (2007) Collection and collation: theory and practice of Linnaean botany. Stud Hist Philos Biol Biomed Sci 38, 541–62.CrossRefPubMedGoogle Scholar
  9. 9.
    reshefsky, M. (1998) Species Pluralism and Anti-Realism. Philos Sci 65, 103–20.CrossRefGoogle Scholar
  10. 10.
    Ghiselin, M. T. (1974) A radical solution to the species problem. Systematic Zoology 23, 491–503.Google Scholar
  11. 11.
    Mishler, B. D., Donoghue, M. J. (1982) Species concepts: A case for pluralism. Syst Zool 31, 491–503.CrossRefGoogle Scholar
  12. 12.
    Dupre, J. (1981) Natural kinds and biological taxa. The Philosophical Review 90, 66–90.CrossRefGoogle Scholar
  13. 13.
    Kitcher, P. (1984) Species. Philos Sci 51, 308–33.CrossRefGoogle Scholar
  14. 14.
    Ereshefsky, M. (1992) Eliminative pluralism. Philos Sci 59, 671–90.CrossRefGoogle Scholar
  15. 15.
    Doolittle, W. F., Papke, R. T. (2006) Genomics and the bacterial species problem. Genome Biol 7, 116.CrossRefPubMedGoogle Scholar
  16. 16.
    Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E., Van De Peer, Y., Vandamme, P., Thompson, F. L., Swings, J. (2005) Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol 3, 733–9.CrossRefPubMedGoogle Scholar
  17. 17.
    Splitter, L. J. (1988) Species and identity. Philos Sci 55, 323–48.CrossRefGoogle Scholar
  18. 18.
    Dagan, T., Martin, W. (2006) The tree of one percent. Genome Biol 7, 118.CrossRefPubMedGoogle Scholar
  19. 19.
    Rescher, N. (2002) Process philosophy, in The Stanford Encyclopedia of Philosophy (Zalta, E. N., ed.) The Metaphysics Research Lab, Stanford.Google Scholar
  20. 20.
    Bedau, M. A. (2003) Downward causation and autonomy in weak emergence. Principia 6, 5–50.Google Scholar
  21. 21.
    Brooks, D. R. (2001) Evolution in the information age: rediscovering the nature of the organism. Semiosis, Evolution, Energy, Development 1, 1–29.Google Scholar
  22. 22.
    Kim, J. (1999) Making sense of emergence. Philosophical Studies 95, 3–36.CrossRefGoogle Scholar
  23. 23.
    Woese, C. R. (2004) A new biology for a new century. Microbiol Mol Biol Rev 68, 173–86.CrossRefPubMedGoogle Scholar
  24. 24.
    Charlebois, R. L., Doolittle, W. F. (2004) Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res 14, 2469–77.CrossRefPubMedGoogle Scholar
  25. 25.
    Staley, J. T., Konopka, A. (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 39, 321–46.CrossRefPubMedGoogle Scholar
  26. 26.
    Nauhaus, K., Albrecht, M., Elvert, M., Boetius, A., Widdel, F. (2007) In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environ Microbiol 9, 187–96.CrossRefPubMedGoogle Scholar
  27. 27.
    Ruepp, A., Graml, W., Santos-Martinez, M. L., Koretke, K. K., Volker, C., Mewes, H. W., Frishman, D., Stocker, S., Lupas, A. N., Baumeister, W. (2000) The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature 407, 508–13.Google Scholar
  28. 28.
    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.Google Scholar
  29. 29.
    Gupta, R. S. (2001) The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. Int Microbiol 4, 187–202.CrossRefPubMedGoogle Scholar
  30. 30.
    Wake, D. B. (2004) A tree grows in Manhattan, in Assembling the Tree of Life (Cracraft, J., ed.) Oxford University Press, New York.Google Scholar
  31. 31.
    Steel, D. (2004) Can a reductionist be a pluralist? Biol Philos 19, 55–73.CrossRefGoogle Scholar
  32. 32.
    Doolittle, W. F. (1999) Lateral genomics. Trends Cell Biol 9, M5–8.CrossRefPubMedGoogle Scholar
  33. 33.
    Medini, D., Donati, C., Tettelin, H., Masignani, V., Rappuoli, R. (2005) The microbial pan-genome. Curr Opin Genet Dev 15, 589–94.CrossRefPubMedGoogle Scholar
  34. 34.
    Gophna, U., Bapteste, E., Doolittle, W. F., Biran, D., Ron, E. Z. (2005) Evolutionary plasticity of methionine biosynthesis. Gene 355, 48–57.CrossRefPubMedGoogle Scholar
  35. 35.
    Bucknam, J., Boucher, Y., Bapteste, E. (2006) Refuting phylogenetic relationships. Biol Direct 1, 26.CrossRefPubMedGoogle Scholar
  36. 36.
    Bapteste, E., Susko, E., Leigh, J., Ruiz-Trillo, I., Bucknam, J., Doolittle, W. F. (2008) Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny. Mol Biol Evol 25, 83–91.CrossRefPubMedGoogle Scholar
  37. 37.
    Leigh, J. W., Susko, E., Baumgartner, M., Roger, A. J. (2008) Testing congruence in phylogenomic analysis. Syst Biol 57, 104–15.CrossRefPubMedGoogle Scholar
  38. 38.
    haxybayeva, O., Gogarten, J. P., Charlebois, R. L., Doolittle, W. F., Papke, R. T. (2006) Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events. Genome Res 16, 1099–108.CrossRefGoogle Scholar
  39. 39.
    Doolittle, W. F., Bapteste, E. (2007) Pattern pluralism and the tree of life hypothesis. Proc Natl Acad Sci U S A 104, 2043–9.CrossRefPubMedGoogle Scholar

Copyright information

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

Authors and Affiliations

  • Eric Bapteste
    • 1
  • Yan Boucher
    • 2
  1. 1.UPMC UMR 7138ParisFrance
  2. 2.Department of Civil and Environmental EngineeringMassachusetts Institute of TechnologyCambridgeUSA

Personalised recommendations