Origins of Bacterial Diversity—Biology 337
March 27, 2003
Sequence-based approaches to mapping bacterial biodiversity: how to discover
ecological diversity within the bacterial world even when we are ignorant of the
ecology
REQUIRED READING
(Stackebrandt et al. 2002)
I have assigned this article as a quick overview of the methods used by mainstream
bacterial systematists to identify and classify bacterial species. You will see that
phenotype is an important part of traditional bacterial systematics, but systematics does
not directly take ecology into account. You will see that systematists are very much open
to improving their system. However, I feel that at present they are merely piling on new
molecular techniques as they become available, and calibrating each to yield previously
existing species demarcations (which were originally based on phenotypic clustering).
(Cohan 2002)
I would like you to review the section on sequence-based methods for identifying
ecotypes (pp. 471-480). The theory we have developed shows first that ecotypes are
expected to fall into separate sequence clusters. We next developed a more discerning
method for identifying ecotypes—that the sequence-based phylogeny of an ecotype
should look very much like a star (where all individuals within an ecotype are equally
closely related to one another; see Figure 6). The section I’ve assigned explains the
results of our Star algorithm, which calculates how closely an ecotype’s phylogeny
should resemble a star-shaped phylogeny.
(Cohan and Libsch ms. in prep.)
This paper, in preparation, explains how the Star algorithm works. You needn’t read the
appendices.
REFERENCES
Cohan, F. M. 2002. What are bacterial species? Annu Rev Microbiol 56:457-487.
Cohan, F. M., and J. Libsch. ms. in prep. Sequence-based evidence for numerous
ecologically distinct and irreversibly separate taxa within bacterial species. in.
Stackebrandt, E., W. Frederiksen, G. M. Garrity, P. A. Grimont, P. Kampfer, M. C.
Maiden, X. Nesme, R. Rossello-Mora, J. Swings, H. G. Truper, L. Vauterin, A. C.
Ward, and W. B. Whitman. 2002. Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol Microbiol
52:1043-1047.