9
Views
1
CrossRef citations to date
0
Altmetric
Original Articles

Identifying the Fundamental Units of Diversity Among Bacillus Isolates From "Evolution Canyon" III

, , , , , & show all
Pages 543-552 | Published online: 14 Mar 2013

References

  • Acinas, S.G., Klepac-Ceraj, V., Hunt, D.E., Pharino, C., Ceraj, I., Distel, D.L., Polz, M.F. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430: 551-554.
  • Avise, J.C. 2000. Phylogeography: the history and formation of species. Harvard Univ. Press, Cambridge, MA.
  • Avise, J.C., Walker, D. 1999. Species realities and numbers in sexual vertebrates: perspectives from an asexually transmitted genome. Proc. Natl. Acad. Sci. USA 96: 992-995.
  • Barrett, S.J., Sneath, P.H. 1994. A numerical phenotypic taxonomic study of the genus Neisseria. Microbiology 140: 2867-2891.
  • Cianciotto, N.P., Abu Kwaik, Y., Edelstein, P.H., Fields, B.S., Geary, D.F., Harrison, T.G., Joseph, C., Ratcliff, R.M., Stout, J.E., Swanson, M.S., eds. 2006. Legionella: state of the art 30 years after its recognition. American Society for Microbiology Press, Washington, DC, pp. 367-376.
  • Cohan, F.M. 1994. The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am. Nat. 143: 965-986.
  • Cohan, F.M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56: 457-87.
  • Cohan, F.M. 2006. Toward a conceptual and operational union of bacterial systematics, ecology, and evolution. Proc. R. Soc. London Ser. B 361: 1985-1996.
  • Cohan, F.M., Perry, E.B. 2007. A systematics for discovering the fundamental units of bacterial diversity. Curr. Biol. 17: R373-R386.
  • Dykhuizen, D.E. 1998. Santa Rosalia revisited: why are there so many species of bacteria? Antonie Van Leeuwenhoek 73: 25-33.
  • Embley, T.M., Stackebrandt, E. 1997. Species in practice: exploring uncultured prokaryote diversity in natural samples. In: Claridge, M.F., Dawah, H.A., Wilson, M.R., eds. Species: the units of diversity. Chapman & Hall, London, pp. 61-81.
  • Falush, D., Kraft, C., Taylor, N.S., Correa, P., Fox, J.G., Achtman, M., Suerbaum, S. 2001. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc. Natl. Acad. Sci. USA 98: 15056-15061.
  • Gans, J., Wolinsky, M., Dunbar, J. 2005. Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
  • 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: 733-739.
  • Giovannoni, S.J., Stingl, U. 2005. Molecular diversity and ecology of microbial plankton. Nature 437: 343-348.
  • Godreuil, S., Cohan, F., Shah, H., Tibayrenc, M. 2005. Which species concept for pathogenic bacteria? An E-debate. Infect. Genet. Evol. 5: 375-387.
  • Goodfellow, M., Manfio, G.P., Chun, J. 1997. Towards a practical species concept for cultivable bacteria. In: Claridge, M.F., Dawah, H.A., Wilson, M.R., eds. Species: the units of diversity. Chapman & Hall, London, pp. 25-59.
  • Konstantinidis, K.T., Tiedje, J.M. 2005. Genomic insights that advance the species definition for prokaryotes. Proc. Natl. Acad. Sci. USA 102: 2567-2572.
  • Martin, A.P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68: 3673-3682.
  • Palys, T., Nakamura, L.K., Cohan, F.M. 1997. Discovery and classification of ecological diversity in the bacterial world: the role of DNA sequence data. Int. J. Syst. Bacteriol. 47: 1145-1156.
  • Roberts, M.S., Cohan, F.M. 1995. Recombination and migration rates in natural populations of Bacillus subtilis and Bacillus mojavensis. Evolution 49: 1081-1094.
  • Smith, N.H., Kremer, K., Inwald, J., Dale, J., Driscoll, J.R., Gordon, S.V., van Soolingen, D., Hewinson, R.G., Smith, J.M. 2006. Ecotypes of the Mycobacterium tuberculosis complex. J.Theor. Biol. 239: 220-225.
  • Stackebrandt, E., Goebel, B.M. 1994. Taxonomic note: a place for DNA:DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846-849.
  • Staley, J.T. 2003. Speciation and bacterial phylospecies. In: Bull, A.T., ed. Microbial diversity and bioprospecting. American Society for Microbiology Press, Washington, DC.
  • Templeton, A. 1989. The meaning of species and speciation: a genetic perspective. In: Otte, D., Endler, J., eds. Speciation and its consequences. Sinauer Assoc., Sunderland, MA, pp. 3-27.
  • Torsvik, V., Daae, F.L., Sandaa, R.A., Ovreas, L. 1998. Novel techniques for analysing microbial diversity in natural and perturbed environments. J. Biotechnol. 64: 53-62.
  • Ward, D.M., Cohan, F.M. 2005. Microbial diversity in hot spring cyanobacterial mats: pattern and prediction. In: Inskeep, W.P., McDermott, T., eds. Geothermal biology and geochemistry in Yellowstone National Park. Thermal Biology Institute, Bozeman, Montana, pp. 185-202.
  • Ward, D.M., Bateson, M.M., Ferris, M.J., Kühl, M., Wieland, A., Koeppel, A., Cohan, F.M. 2006. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function. Phil. Trans. R. Soc. Ser. B. 361: 1997-2008.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.