Genome Acquisition in Horizontal Gene Transfer: Symbiogenesis and Macromolecular Sequence Analysis

  • Lynn Margulis
Part of the Methods in Molecular Biology book series (MIMB, volume 532)


Phylogenetic diagrams (“trees of life”) based on computer-generated analyses of nucleic acid (DNA, RNA) or protein (amino acid residues) sequences are purported to reconstruct evolutionary history of the living organisms from which the macromolecules were isolated (1). “Horizontal gene transfer”, an expression that refers to the ad hoc explanation of anomalous distribution of these macromolecular sequences, is an inferred past event to explain evolution that, even in principle, is not documentable. Although the diagrams (“phylogenies”) help establish the details of relationships among important and widely distributed essential components of living systems (e.g., DNA of large and small replicons such as plasmids, viruses, genophores), chromatin, or protein enzymes that have conserved their function throughout the history of the evolutionary lineage (e.g., DNA that codes for polymerases or 16/18S ribosomal RNA), the HGT concept is an Alfred North Whiteheadian fallacy of misplaced concreteness (2). It is deeply flawed because of sets of unstated, unwarranted assumptions accepted as fact by practitioners: genomics and proteomic experts. They tend to be zoocentric and in particular anthropocentric computer scientists. Their relative lack of familiarity with the fossil record, hard-won life histories and transmission-genetics, taxonomy, physiology, metabolism, and ecology of the communities in which the organisms invariably reside, and many other aspects of life have led to codification of systematic errors in analysis of their, often superb, molecular data. Here we point to a prodigious but little-known symbiogenesis literature that contrasts the transfer of sets of genes with HGT taken to mean one or a-very-few-genes at a time.


Elysia karyomastigont symbiogenesis replicons parasexuality fallacy of misplaced concreteness microbial communities as units of selection 


  1. 1.
    Margulis, L., Dolan, M. F., Guerrero, R. (1999) The molecular tangled bank: not seeing the phylogenies for the trees. Bio Bull 196, 413–14.CrossRefGoogle Scholar
  2. 2.
    Cobb, J. B. Jr., Ed. (2008) Back to Darwin: A Richer Account of Evolution. Wm. B. Eerdmans Publihing Co., Grand Rapids, MI, pp. 167–175; 176–184.Google Scholar
  3. 3.
    Margulis, L., Chapman, M., Guerrero, R., Hall. J. (2006) The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic eon. Proc Nat Acad Sci U S A 103, 13080–5.CrossRefGoogle Scholar
  4. 4.
    Dolan, M. F. (2005) The missing piece: the microtubule cytoskeleton and the origin of eukaryotes, in Microbial Phylogeny and Evolution: Concepts and Controversies. (eapp, J., ed.), Oxford University Press, New York, pp. 281–89.Google Scholar
  5. 5.
    Chapman, M. J., Alliegro, M. C. (2007). A symbiogenetic basis for the centrosome? Symbiosis 44, 23–32.Google Scholar
  6. 6.
    Kozo-Polyansky, B.M. (1924) Symbiogenesis: A New Principle of Evolution (in Russian, translated and edited by Victor Fet., Harvard University Press, Cambridge MA, English edition, 2009, in press.)Google Scholar
  7. 7.
    Kluge, M., Mollenhauer, D., Mollenhauer, R., Kape, R. (1992) Geosiphon pyriforme, an endosymbiotic consortium of a fungus and a cyanobacterium (Nostoc), fixes nitrogen. Bot Acta, 105, 343–44.Google Scholar
  8. 8.
    McFall-Ngai, M. J. (2002) The influence of bacteria on animal development. Dev Biol 242, 1–14.CrossRefPubMedGoogle Scholar
  9. 9.
    Rumpho, M. E., Worful, J. M., Lee, J., Kannan, Tyler, M. S, Battacharya, D., Moustafa, A., Manhart, J. R. (2008) Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica. Proc Nat Acad Sci U S A 105, 17867–71.CrossRefGoogle Scholar
  10. 10.
    Sapp, J. (1999) Evolution by Association: History of Symbiosis Research. Cambridge University Press, Cambridge, MA.Google Scholar
  11. 11.
    Sapp, J., (ed). (2005) Molecular Phylogeny and Evolution: Concepts and Controversies. Oxford University Press, New York.Google Scholar
  12. 12.
    Morowitz, H. J., Broyles, D., Lasus, H. (2005) The robustness of intermediary metabolism, in Microbial Phylogeny and Evolution: Concepts and Controversies. (Sapp, J., ed.), Oxford University Press, New York, pp. 154–9.Google Scholar
  13. 13.
    Margulis, L., Sagan, D. (2000) What Is Life? University of California, Berkeley CA.Google Scholar
  14. 14.
    Sonea, S., Matthieu L. G. (2001) Prokaryotology: A Coherent View. Les Presses De L’universit é de Montré al, Montréal, Canada.Google Scholar
  15. 15.
    Margulis, L., Sagan, D. (2002) Acquiring Genomes: A Theory of the Origins of Species. Basic Books, New York.Google Scholar
  16. 16.
    Wallin, I. E. (1926) Symbionticism and the Origin of Species, Williams and Wilkins, Baltimore, MD, p. 8.Google Scholar
  17. 17.
    Williamson, D. I., Vickers, S. E. (2007) The origins of larvae: mismatches between the forms of adult animals and their larvae may reflect fused genomes, expressed in sequence in complex life histories, Am Sci 95, 509–17.Google Scholar
  18. 18.
    LeBlanc, M., Dyer, B. (2007) PERL for Exploring DNA. Oxford University Press, New York.CrossRefGoogle Scholar
  19. 19.
    Hall, J. L. (2009) The spirochete contribution to the eukaryotic lineage: a novel genomic analysis, Proc Natl Acad Sci U S A (in press).Google Scholar
  20. 20.
    Bergey’s Manual of Systematic Bacteriology, 2nd Edition, Volumes 1–5, Springer, New York.Google Scholar
  21. 21.
    Dworkin, M. M., Falkow, S., Rosenberg, E., Schleifer, K.-H. Stackebrandt, E. (eds.) The Prokaryotes: A Handbook on the Biology of Bacteria, 3rd Edition, Volumes 1–7, Springer-Verlag, New York.Google Scholar
  22. 22.
    Margulis, L., Corliss, J. O., Melkonian, M., Chapman, D. J. (eds.) (2010) Handbook of Protoctists, 2nd Edition. Jones and Bartlett Publishers, Sudbury, MA.Google Scholar
  23. 23.
    Kendrick, B. (2005) The Fifth Kingdom, 2nd Edition, Mycologue Press, Waterloo, Ontario, Canada.Google Scholar
  24. 24.
    Margulis, L., Chapman, M. J. (2009) Kingdoms and Domains illustrated: Phyla of Life on Earth, 4th Edition, Acadamic Press-Elsevier, London, UK, New York and San Diego, CA.Google Scholar
  25. 25.
    Okamoto, N., Inouye, I. (2006) Hatena arenicola gen. et sp. nov., a katablepharid undergoing probable plastid acquisition. Protist 157, 401–19.CrossRefPubMedGoogle Scholar
  26. 26.
    Margulis, L. (1993) Symbiosis in Cell Evolution: Life and Its Environment on the Early Earth, 3rd Edition, W. H. Freeman, San Francisco, CA.Google Scholar
  27. 27.
    Kostas, B., Miller, T. A. (2006) Insect Symbiosis, Volume 2 Contemporary Topics in Entomology, CRC Publishers, Boca Raton, FL.Google Scholar
  28. 28.
    Margulis, L., Dolan, M., Whiteside J. (2005) “Imperfections and oddities” in the origin of the nucleus. Paleobiology 31, 175–91.CrossRefGoogle Scholar
  29. 29.
    Margulis, L., Brynes. L. (1990) Hard testimony: teaching past environments with fossil foraminifera. UNESCO Nature & Resources 35, 4–17. (English, French and Spanish).Google Scholar
  30. 30.
    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, 4576–79.CrossRefPubMedGoogle Scholar

Copyright information

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

Authors and Affiliations

  • Lynn Margulis
    • 1
  1. 1.Department of GeosciencesUniversity of MassachusettsAmherstUSA

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