Hostname: page-component-586b7cd67f-t7czq Total loading time: 0 Render date: 2024-11-27T20:26:35.728Z Has data issue: false hasContentIssue false
  • English
  • Français

Bacteria, Sex, and Systematics

Published online by Cambridge University Press:  01 January 2022

L. R. Franklin
Get access Rights & Permissions [Opens in a new window]

Abstract

Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique of phylogenetic bacterial species, arguing that phylogenetic bacterial classification requires a questionable metaphysical commitment to the existence of essential genes. I conclude by considering how microbiologists have dealt with these biological complexities by using more pragmatic and not exclusively evolutionary accounts of species. I argue that this pragmatism is not borne of laziness but rather of the substantial conceptual problems in classifying bacteria based on any evolutionary standard.

Type
Research Article
Information
Philosophy of Science , Volume 74 , Issue 1 , January 2007 , pp. 69 - 95
Copyright
Copyright © The Philosophy of Science Association

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

‡

Four anonymous reviewers at Philosophy of Science were helpful in clarifying the arguments in this article. I would also like to thank Philip Kitcher for his comments and encouragement.

References

Belkum, Alex van, Struelens, Marc, Visser, Arjan de, Verbrugh, Henri, and Tibayrenc, Michel (2001), “Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology,” Clinical Microbiology Review 14:547–560.CrossRefGoogle ScholarPubMed
Cavalier-Smith, Thomas (2000), “Membrane Heredity and Early Chloroplast Evolution,” Trends in Plant Science 5:174–182.CrossRefGoogle ScholarPubMed
Cohan, Frederick (2002), “Sexual Isolation and Speciation in Bacteria,” Genetica 116:359–370.CrossRefGoogle Scholar
Daubin, Vincent, Guy, Manolo, and Perrière, Guy (2002), “A Phylogenetic Approach to Bacterial Phylogeny: Evidence of a Core of Genes Sharing a Common History,” Genome Research 12:1080–1090.CrossRefGoogle ScholarPubMed
de Queiroz, Kevin (1999), “The General Lineage Concept of Species and the Defining Properties of the Species Category,” in Wilson, Robert A. (ed.), Species: New Interdisciplinary Essays. Cambridge, MA: MIT Press, 49–90.Google Scholar
de Queiroz, Kevin (2005), “Different Species Problems and Their Resolution,” BioEssays 27:1263–1269.CrossRefGoogle ScholarPubMed
Dixon, Robert M. W. (1997), The Rise and Fall of Languages. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Doolittle, W. Ford (1999), “Phylogenetic Classification and the Universal Tree,” Science 284:2124–2128.CrossRefGoogle ScholarPubMed
Doolittle, W. Ford, and Bapteste, Eric (2007), “Pattern Pluralism and the Tree of Life Hypothesis,” Proceedings of the National Academy of Sciences 104:2043–2049.CrossRefGoogle ScholarPubMed
Dupré, John (1993), The Disorder of Things: Metaphysical Foundations of the Disunity of Science. Cambridge, MA: Harvard University Press.Google Scholar
Dutta, Chitra, and Pan, Archana (2002), “Horizontal Gene Transfer and Bacterial Diversity,” Journal of Biosciences 27, suppl. 1:27–33.CrossRefGoogle ScholarPubMed
Dykhuizen, Daniel E., and Green, Louis (1991), “Recombination in Escherichia coli and the Definition of Biological Species,” Journal of Bacteriology 173:7257–7268.CrossRefGoogle ScholarPubMed
Ereshefsky, Marc, ed. (1992), The Units of Evolution: Essays on the Nature of Species. Cambridge, MA: MIT Press.Google Scholar
Gevers, Dirk, Cohan, Frederick, Lawrence, Jeffrey, Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E. et al. (2005), “Re-evaluating Prokaryotic Species,” Nature Reviews: Microbiology 3:733–739.Google ScholarPubMed
Gogarten, J. Peter, Doolittle, W. Ford, and Lawrence, Jeffrey G. (2002), “Prokaryotic Evolution in Light of Gene Transfer,” Molecular Biology and Evolution 19:2226–2238.CrossRefGoogle ScholarPubMed
Gogarten, J. Peter, and Townsend, Jeffrey P. (2005), “Horizontal Gene Transfer, Genome Innovation and Evolution,” Nature Reviews Microbiology 3:679–687.CrossRefGoogle ScholarPubMed
Goodfellow, Michael, Manfio, Gilson P., and Chun, J. (1997), “Towards a Practical Species Concept for Cultivatable Bacteria,” in Claridge, Michael, Dawah, H., and Wilson, M. (eds.), Species: The Units of Biodiversity. London: Chapman & Hall, 25–59.Google Scholar
Goodwin, Brian (1994), How the Leopard Changed Its Spots: The Evolution of Complexity. New York: Scribner’s.Google Scholar
Hanage, William, Fraser, Christophe, and Spratt, Brian (2005), “Fuzzy Species among Recombinogenic Bacteria,” BMC Biology 3 (6), http://www.biomedcentral.com/1741-7007/3/6.CrossRefGoogle ScholarPubMed
Hull, David (1997), “The Ideal Species Concept—and Why We Can’t Get It,” in Claridge, Michael, Dawah, H., and Wilson, M. (eds.), Species: The Units of Biodiversity. London: Chapman & Hall, 357–380.Google Scholar
Hull, David (1999), “On the Plurality of Species: Questioning the Party Line,” in Wilson, Robert A. (ed.), Species: New Interdisciplinary Essays. Cambridge, MA: MIT Press, 23–48.Google Scholar
Jain, Ravi, Rivera, Maria C., and Lake, James A. (1999), “Horizontal Gene Transfer among Genomes: The Complexity Hypothesis,” Proceedings of the National Academy of Sciences 96:3801–3806.CrossRefGoogle ScholarPubMed
Judson, Olivia, and Normark, Benjamin B. (1996), “Ancient Asexual Scandals,” Trends in Ecology and Evolution 11:41–46.CrossRefGoogle ScholarPubMed
Kitcher, Philip (1984), “Species,” Philosophy of Science 51:308–333.CrossRefGoogle Scholar
Koehler, Andreas, Karch, Helge, Beikler, Thomas, Flemmig, Thomas F., Suerbaum, Sebastian, and Schmidt, Herbert (2003), “Multilocus Sequence Analysis of Porphyromonas gingivalis Indicates Frequent Recombination,” Microbiology 149:2407–2415.CrossRefGoogle ScholarPubMed
La Cruz, Fernando de, and Davies, Julian (2000), “Horizontal Gene Transfer and the Origin of Species: Lessons from Bacteria,” Trends in Microbiology 8:128–133.CrossRefGoogle Scholar
Lan, Ruiting, and Reeves, Peter (2001), “When Does a Clone Deserve a Name? A Perspective on Bacterial Species Based on Population Genetics,” Trends in Microbiology 9:419–424.CrossRefGoogle Scholar
Lawrence, Jeffrey G. (2002), “Gene Transfer in Bacteria: Speciation without Species?” Theoretical Population Biology 61:449–460.CrossRefGoogle ScholarPubMed
Lederberg, Joshua, and Tatum, E. L. (1946), “Gene Recombination in Escherichia coli,” Nature 158: 558.CrossRefGoogle Scholar
Lerat, Emmanuelle, Daubin, Vincent, and Moran, Nancy A. (2003), “From Gene Trees to Organismal Phylogeny in Prokaryotes: The Case of the γ-Proteobacteria,” PloS Biology 1:101–109.CrossRefGoogle ScholarPubMed
Levin, B. R., and Bergstrom, C. T. (2000), “Bacteria Are Different: Observations, Interpretations Speculations and Opinions about the Mechanisms of Adaptive Evolution in Prokaryotes,” Proceedings of the National Academy of Sciences 97:6981–6985.CrossRefGoogle ScholarPubMed
Margulis, Lynn, and Sagan, Dorion (1995), What Is Life? Berkeley: University of California Press.Google Scholar
Margulis, Lynn, and Sagan, Dorion (2002), Acquiring Genomes: A Theory of the Origin of Species. New York: Basic.Google Scholar
Mayden, R. L. (1997), “A Hierarchy of Species Concepts: The Denoument in the Saga of the Species Problem,” in Claridge, Michael, Dawah, H., and Wilson, M. (eds.), Species: The Units of Biodiversity. London: Chapman & Hall, 381–424.Google Scholar
Maynard Smith, John (1990), “The Evolution of Prokaryotes: Does Sex Matter?” Annual Review of Ecology and Systematics 21:1–12.CrossRefGoogle Scholar
Maynard Smith, John, Feil, Edward J., and Smith, Noel H. (2000), “Population Structure and Evolutionary Dynamics of Pathogenic Bacteria,” BioEssays 22:1115–1122.3.0.CO;2-R>CrossRefGoogle Scholar
Maynard Smith, John, Smith, Noel H., O’Rourke, Maria, and Spratt, Brian G. (1993), “How Clonal Are Bacteria?” Proceedings of the National Academy of Sciences 90:4384–4388.CrossRefGoogle Scholar
Maynard Smith, John, and Szathmáry, Eörs (1995), The Major Transitions in Evolution. Oxford: Oxford University Press.Google Scholar
Mayr, Ernst (1963), Animal Species and Evolution. Cambridge, MA: Harvard University Press.CrossRefGoogle Scholar
Mayr, Ernst (1992), “Species Concepts and Their Application,” in Ereshefsky 1992, 15–25.Google Scholar
Mayr, Ernst ([1981] 1994), “Biological Classification: Towards a Synthesis of Opposing Methodologies,” in Sober, Elliot (ed.), Conceptual Issues in Evolutionary Biology. Cambridge, MA: MIT Press, 277–294.Google Scholar
Mayr, Ernst (2001), What Evolution Is. New York: Basic.Google Scholar
Nanney, David (1999), “When Is a Rose? The Kinds of Tetrahymena,” in Wilson, Robert A. (ed.), Species: New Interdisciplinary Essays. Cambridge, MA: MIT Press, 98–118.Google Scholar
Ochman, Howard, Lawrence, J. G., and Groisman, E. A. (2000), “Lateral Gene Transfer and the Nature of Bacterial Innovation,” Nature 405:299–304.CrossRefGoogle ScholarPubMed
Olsen, G. J., and Woese, C. J. (1993), “Ribosomal RNA: A Key to Phylogeny,” Journal of the Federation of American Societies for Experimental Biology 7:113–123.CrossRefGoogle Scholar
O’Malley, Maureen, and Dupré, John (2007), “Size Doesn’t Matter: Towards a More Inclusive Philosophy of Biology,” Biology and Philosophy 22:155–191.CrossRefGoogle Scholar
Philippe, Hervé, and Douady, Christophe J. (2003), “Horizontal Gene Transfer and Phylogenetics,” Current Opinion in Microbiology 6:498–505.CrossRefGoogle ScholarPubMed
Planet, Paul (2002), “Reexamining Microbial Evolution through the Lens of Horizontal Transfer,” in DeSalle, R., Giribet, G., and Wheeler, W. (eds.), Molecular Systematics and Evolution: Theory and Practice. Basel: Birkhauser.Google Scholar
Ravin, Arnold W. (1963), “Experimental Approaches to the Study of Bacterial Phylogeny,” American Naturalist 47:307–318.CrossRefGoogle Scholar
Redfield, Rosemary (2001), “Do Bacteria Have Sex?” Nature Reviews: Genetics 2:634–639.CrossRefGoogle ScholarPubMed
Rosselló-Moran, Ramon, and Amann, Rudolf (2001), “The Species Concept for Prokaryotes,” FEMS Microbiology Reviews 25:39–67.CrossRefGoogle Scholar
Sneath, Peter H. A. (2000), “Reticulate Evolution in Bacteria and Other Organisms: How Can We Study It?” Journal of Classification 17:159–163.CrossRefGoogle Scholar
Simpson, George Gaylord (1961), Principles of Animal Taxonomy. Edinburgh: Edinburgh University Press.CrossRefGoogle Scholar
Sonea, S., and Panisset, M. (1983), A New Bacteriology. Boston: Jones & Bartlett.Google Scholar
Stackebrandt, Erko (2006), “Defining Taxonomic Ranks,” in Dworkin, Martin, Falkow, Stanley, Rosenberg, Eugene, Schleifer, Karl-Heinz, and Stackebrandt, Erko (eds.), The Prokaryotes. New York: Springer, 25–57.Google Scholar
Stackebrandt, Erko, Frederiksen, Wilhelm, Garrity, George M., Grimont, Patrick A. D., Kämpfer, Peter, Maiden, Martin C. J., Nesme, Xavier et al. (2002), “Report of the Ad Hoc Committee for the Re-evaluation of the Species Definition in Bacteriology,” International Journal of Systematic and Evolutionary Microbiology 52:1043–1047.Google Scholar
Staley, James (1997), “Biodiversity: Are Microbial Species Threatened?” Current Opinion in Biotechnology 8:340–345.CrossRefGoogle ScholarPubMed
Tibayrenc, M. (1996), “Towards a Unified Evolutionary Genetics of Microorganisms,” Annual Review of Microbiology 50:401–429.CrossRefGoogle ScholarPubMed
Vellai, Tibor, Kovacs, Attila L., Kovacs, Gabor, Ortutay, Csaba, and Vida, Gabor (1999), “Genome Economization and a New Approach to the Species Concept in Bacteria,” Proceedings of the Royal Society of London B 266:1953–1958.CrossRefGoogle Scholar
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsy, M. I., Moore, L. H. et al. (1987), “Report of the Ad Hoc Committee on Reconciliation of Approaches to Bacterial Systematics,” International Journal of Systematics and Bacteriology 37:463–464.Google Scholar
Wertz, J. E, Goldstone, C., Gordon, D. M., and Riley, M. A. (2003), “A Molecular Phylogeny of Enteric Bacteria and Implications for a Bacterial Species Concept,” Journal of Evolutionary Biology 16:1236–1248.CrossRefGoogle ScholarPubMed
Young, J. M. (2001), “Implications of Alternative Classifications and Horizontal Gene Transfer for Bacterial Taxonomy,” International Journal of Systematic and Evolutionary Microbiology 51:945–953.CrossRefGoogle ScholarPubMed