Microbiology and the species problem

Marc Ereshefsky1
1Department of Philosophy, University of Calgary, Calgary, Canada

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Achtman M, Wagner M (2008) Microbial diversity and the genetic nature of microbial species. Nature Rev 6:431–440

Bapteste E, Boucher Y (2008) Lateral gene transfer challenges principles of microbial systematics. Trends Microbiol 16:200–2007

Bapteste E, Boucher Y (2009) Some epistemological impacts of horizontal gene transfer on classification and microbiology. Methods Mol Biol 532:55–72

Baum D, Donoghue M (1995) Choosing among alternative “phylogenetic” species concepts. Syst Biol 20:560–573

Beatty J (1992) Speaking of species: Darwin’s strategy. In: Ereshefsky M (ed) The units of evolution. MIT Press, Cambridge, pp 227–246

Boyd R (1999) Homeostasis, species, and higher taxa. In: Wilson R (ed) Species: new interdisciplinary essays. MIT Press, Cambridge, pp 141–186

Brigandt I (2003) Species pluralism does not imply species eliminativism. Philos Sci 70:1305–1316

Cohan F (2002) What are bacterial species? Annu Rev Microbiol 56:457–487

Coyne J, Orr A (2004) Speciation. Sinauer Associates, Sutherland

Darwin C (1859[1964]) On the origin of species: a facsimile of the first edition. Harvard University Press, Cambridge

De Queiroz K (1999) The general lineage concept of species and the defining properties of the species category. In: Wilson R (ed) Species: new interdisciplinary essays. MIT Press, Cambridge, pp 49–90

De Queiroz K (2005) Different species problems and their resolution. BioEssays 27:1263–1269

De Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56:866–879

Doolittle F, Bapteste E (2007) Pattern pluralism and the tree of life hypothesis. Proc Natl Acad Sci 104:2043–2049

Doolittle F, Papke T (2006) Genomics and the bacterial species problem. Genome Biol 7:116.1–116.7

Doolittle F, Zhaxybayeva O (2009) On the origin of prokaryotic species. Genome Res 19:744–756

Dykuizen D, Green L (1991) Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173:7257–7268

Ereshefsky M (ed) (1992a) The units of evolution: essays on the nature of species. MIT Press, Cambridge

Ereshefsky M (1992b) Eliminative pluralism. Philos Sci 59:671–690

Ereshefsky M (1998) Species pluralism and anti-realism. Philos Sci 65:103–120

Ereshefsky M (2001) The poverty of the linnaean hierarchy: a philosophical study of biological taxonomy. Cambridge University Press, Cambridge

Ereshefsky M (2009) Darwin’s solution to the species problem. Synthese. doi: 10.1007/s11229-009-9538-4

Franklin L (2007) Bacteria, sex, and systematics. Philos Sci 74:69–95

Fraser C, Hange B, Spratt B (2007) Recombination and the nature of bacterial speciation. Science 315:476–480

Gevers D et al (2005) Re-evaluating prokaryote species. Nat Rev Microbiol 3:1043–1047

Gogarten J, Townsend J (2005) Horizontal gene transfer, genome innovation and evolution. Nat Rev Microbiol 3:679–687

Griffiths PE (2006) Function, homology and character individuation. Philos Sci 73:1–25

Griffiths PE (2007) The phenomena of homology. Biol Philos 22:643–658

Hanage W, Fraser C, Spratt B (2005) Fuzzy species among recombinogenic bacteria. BMC Biol 3:6

Hull D (1965) The effect of essentialism on taxonomy: two thousand years of stasis. Br J Philos Sci 15:314–326, 16:1–18

Konstantinidis K, Tiedje J (2005) Genomic insights that advance the species definition for prokaryotes. PNAS 102:2567–2572

Lan R, Reeves P (2001) When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol 9:419–424

Lawrence J (2002) Gene transfer in bacteria: speciation without species? Theor Popul Biol 61:449–460

Lawrence JG, Retchless A (2010) The myth of bacterial species and speciation. Biol Phil. doi: 10.1007/s10539-010-9215-5

Maddison W (1997) Gene trees in species trees. Syst Biol 46:523–536

Mayden R (2002) On biological species, species concepts and individuation in the natural world. Fish Fish 3:171–196

Mayr E (1970) Populations, species and evolution. Harvard University Press, Cambridge

Mishler B, Brandon R (1987) Individuality, pluralism, and the phylogenetic species concept. Biol Philos 2:397–414

Morgan G, Pitts W (2008) Evolution without species: the case of mosaic bacteriophages. Br J Philos sci 59:745–765

Nesbø C, Dultek M, Doolittle F (2006) Recombination in thermotoga: implications for species concepts and biogeography. Genetics 172:759–769

Nixon W, Wheeler Q (1990) An amplification of the phylogenetic species concept. Cladistics 6:211–223

O’Malley M, Duprè J (2007) Size doesn’t matter: towards a more inclusive philosophy of biology. Biol Philos 22:155–191

Paul J (1999) Microbial transfer: an ecological perspective. J Mol Microbiol Biotechnol 1:45–50

Pigliucci M (2003) Species as family resemblance concepts: the (dis-)solution of the species problem? BioEssays 25:96–602

Pigliucci M, Kaplan J (2006) Making sense of evolution: conceptual foundations of evolutionary biology. Chicago University Press, Chicago

Rosselló-Mora R, Amann R (2001) The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67

Stackebrandt E (2006) Defining taxonomic ranks. In: Dworkin M (ed) Prokaryotes: a handbook on the biology of bacteria, vol 1. Springer, New York, pp 29–57

Stackebrandt E, Frederiksen W, Garrity G et al (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047

Touhon M, Hoede C, Tenaillon O et al (2009) Organised genome dynamics in the Escherihcia coli species results in highly diverse adaptive paths. PLos Genetics 5:e1000344. doi: 10.1371/journal.pgen.1000344

Van Valen L (1976) Ecological species, multispecies, and oaks. Taxon 25:233–239

Wertz J, Goldstone C, Gordon D, Riley M (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol 16:1236–1248

Wilson R (ed) (1999) Species: new interdisciplinary essays. MIT Press, Cambridge

Wilson R, Barker M, Brigandt I (2009) When traditional essentialism fails: biological natural kinds. Philosophical Topics (in press)

Xu J (2004) The prevalence and evolution of sex in microorganisms. Genome 47:775–780