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Chapter 5 : Are Species Cohesive?—A View from Bacteriology
Author:
Frederick M. Cohan1
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Affiliations:
1: Department of Biology, Wesleyan University, Middletown, CT 06459-0170
Content Type: Monograph
Publication Year:
2011
Category: Bacterial Pathogenesis
Book DOI:
10.1128/9781555817114
Chapter DOI:
10.1128/9781555817114.ch5
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Abstract:
This chapter briefly summarizes the most important differences in genetic exchange. In bacteria, genetic exchange is unidirectional, where a usually small chromosomal segment transfers from a donor to a recipient. Bacterial recombination can occur across vastly more divergent organisms than is possible in animals and plants. The chapter also talks about the challenge of identifying ecotypes, or bacterial species subjected to intrapopulation cohesion provided by periodic selection and/or drift. The Recurrent Niche Invasion model takes into account the role of mobile genetic elements, such as plasmids or phage, in determining bacterial niches. Recombination does not seem likely to be a cohesive force that quashes speciation in either the macroorganisms or bacteria. Most clearly in bacteria, recombination is not sufficient to prevent adaptive divergence in niche-specifying genes, and sexual isolation is not required for bacterial speciation. Studies of speciation in bacteria have focused on the origins of niche-specifying adaptations that distinguish newly divergent species, by investigating the ecological dimensions of speciation and the roles of horizontal genetic transfer and homologous recombination in bacterial speciation. This emphasis on the origins of ecological divergence was forced on bacteriology because bacteria can acquire niche-transcending genes potentially from any organism; so it would be futile to study the end of sharing niche-transcending adaptations in bacteria. It appears that, fortuitously, bacteriology has produced a paradigm of value for species studies in macroorganisms as well as bacteria—that our focus should be on the origins of ecological diversity and not on barriers to recombination.
Citation:
Cohan F.
2011.
Are Species Cohesive?—A View from Bacteriology,
p 43-65.
In
Walk S, Feng P (ed),
Population Genetics of Bacteria.
ASM Press, Washington, DC.
doi: 10.1128/9781555817114.ch5
Figures
Are Species Cohesive?—A View from Bacteriology
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Citation:
Cohan F.
2011.
Are Species Cohesive?—A View from Bacteriology,
p 43-65.
In
Walk S, Feng P (ed),
Population Genetics of Bacteria.
ASM Press, Washington, DC.
doi: 10.1128/9781555817114.ch5
/content/10.1128/9781555817114.ch05.ch05fig01
Figure 1.
Three classes of mutation and recombination events that determine ecotype diversity in bacteria. The circles and triangles represent individuals within ecotypes 1 and 2, respectively; the asterisks represent adaptive mutations. (A) Niche-invasion mutations. Here a mutation changes the ecological niche of the cell, such that it can now escape periodic selection events in its former ecotype. This founds a new ecotype. (B) Periodic-selection mutations. These improve the fitness of an individual such that the mutant and its descendants outcompete all other cells within the ecotype; periodic selection events precipitated by these mutations generally do not affect the diversity within other ecotypes, owing to the differences in ecological niche. Periodic selection enhances the distinctness of ecotypes by purging the divergence within but not between ecotypes. (C) Speciation-quashing mutations in the Nano-Niche model. Even if two ecotypes have sustained a history of separate periodic selection events, an extraordinarily adaptive genotype may outcompete another ecotype to extinction. Competitive extinction of another ecotype (ecotype 2) is possible only if all of ecotype 2’s resources are also used by ecotype 1. Used with permission from Landes Bioscience (
10
).
10.1128/9781555817114/f0047-01_thmb.gif
10.1128/9781555817114/f0047-01.gif
Figure 1.
Three classes of mutation and recombination events that determine ecotype diversity in bacteria. The circles and triangles represent individuals within ecotypes 1 and 2, respectively; the asterisks represent adaptive mutations. (A) Niche-invasion mutations. Here a mutation changes the ecological niche of the cell, such that it can now escape periodic selection events in its former ecotype. This founds a new ecotype. (B) Periodic-selection mutations. These improve the fitness of an individual such that the mutant and its descendants outcompete all other cells within the ecotype; periodic selection events precipitated by these mutations generally do not affect the diversity within other ecotypes, owing to the differences in ecological niche. Periodic selection enhances the distinctness of ecotypes by purging the divergence within but not between ecotypes. (C) Speciation-quashing mutations in the Nano-Niche model. Even if two ecotypes have sustained a history of separate periodic selection events, an extraordinarily adaptive genotype may outcompete another ecotype to extinction. Competitive extinction of another ecotype (ecotype 2) is possible only if all of ecotype 2’s resources are also used by ecotype 1. Used with permission from Landes Bioscience ( 10 ).
Citation:
Cohan F.
2011.
Are Species Cohesive?—A View from Bacteriology,
p 43-65.
In
Walk S, Feng P (ed),
Population Genetics of Bacteria.
ASM Press, Washington, DC.
doi: 10.1128/9781555817114.ch5
/content/10.1128/9781555817114.ch05.ch05fig02
Figure 2.
The Species-less model of bacterial diversification. In the Species-less model, the diversity within an ecotype is not limited by periodic selection but instead by the short time from the ecotype’s invention as a single mutant until its extinction. Each ecotype is represented in the figure by a unique line style; the origination and extinction of each ecotype i are indicated by si
and ei
, respectively. (A) In the absence of periodic selection, each extant ecotype that has given rise to another ecotype is a paraphyletic group, and each recent ecotype that has not yet given rise to another ecotype is monophyletic. If two closely related ecotypes represent a monophyletic-paraphyletic pair (as in the case of ecotypes D and E, in bold), then we may conclude that a periodic selection event has not occurred in the parental ecotype since the origin of the daughter ecotype. (B) If instead a periodic selection event has occurred in the parental ecotype since the founding of the daughter ecotype, then the parent and daughter ecotypes will be sister monophyletic groups. Observing that pairs of most-closely-related ecotypes usually form monophyletic-paraphyletic pairs would indicate that the origin of new ecotypes is more frequent than periodic selection events in established ecotypes.
10.1128/9781555817114/f0054-01_thmb.gif
10.1128/9781555817114/f0054-01.gif
Figure 2.
The Species-less model of bacterial diversification. In the Species-less model, the diversity within an ecotype is not limited by periodic selection but instead by the short time from the ecotype’s invention as a single mutant until its extinction. Each ecotype is represented in the figure by a unique line style; the origination and extinction of each ecotype i are indicated by si and ei , respectively. (A) In the absence of periodic selection, each extant ecotype that has given rise to another ecotype is a paraphyletic group, and each recent ecotype that has not yet given rise to another ecotype is monophyletic. If two closely related ecotypes represent a monophyletic-paraphyletic pair (as in the case of ecotypes D and E, in bold), then we may conclude that a periodic selection event has not occurred in the parental ecotype since the origin of the daughter ecotype. (B) If instead a periodic selection event has occurred in the parental ecotype since the founding of the daughter ecotype, then the parent and daughter ecotypes will be sister monophyletic groups. Observing that pairs of most-closely-related ecotypes usually form monophyletic-paraphyletic pairs would indicate that the origin of new ecotypes is more frequent than periodic selection events in established ecotypes.
Citation:
Cohan F.
2011.
Are Species Cohesive?—A View from Bacteriology,
p 43-65.
In
Walk S, Feng P (ed),
Population Genetics of Bacteria.
ASM Press, Washington, DC.
doi: 10.1128/9781555817114.ch5
/content/10.1128/9781555817114.ch05.ch05fig03
Figure 3.
Ecological conversion from one plasmid-defined ecotype to another. Each cell is represented by a large circle, and its chromosomal genotype is represented as ABC or abc. Ecotype 1 is determined by a plasmid represented by a small solid-line circle, and ecotype 2 is determined by a plasmid represented by a small dashed circle. (A) A transfer of an ecotype 1-determining plasmid into a recipient member of ecotype 2 (indicated by the bold circle), along with subsequent loss of the ecotype 2-determining plasmid. (B) The recipient is converted to become a member of ecotype 1, so all of its chromosomal genes are effectively transferred into ecotype 1.
10.1128/9781555817114/f0056-01_thmb.gif
10.1128/9781555817114/f0056-01.gif
Figure 3.
Ecological conversion from one plasmid-defined ecotype to another. Each cell is represented by a large circle, and its chromosomal genotype is represented as ABC or abc. Ecotype 1 is determined by a plasmid represented by a small solid-line circle, and ecotype 2 is determined by a plasmid represented by a small dashed circle. (A) A transfer of an ecotype 1-determining plasmid into a recipient member of ecotype 2 (indicated by the bold circle), along with subsequent loss of the ecotype 2-determining plasmid. (B) The recipient is converted to become a member of ecotype 1, so all of its chromosomal genes are effectively transferred into ecotype 1.
Citation:
Cohan F.
2011.
Are Species Cohesive?—A View from Bacteriology,
p 43-65.
In
Walk S, Feng P (ed),
Population Genetics of Bacteria.
ASM Press, Washington, DC.
doi: 10.1128/9781555817114.ch5
References
/content/book/10.1128/9781555817114.ch05
1.
Achtman, M.,, and M. Wagner. 2008. Microbial diversity and the genetic nature of microbial species. Nat. Rev. Microbiol. 6: 431– 440.
2.
Allewalt, J. P.,, M. M. Bateson,, N. P. Revsbech,, K. Slack, and, D. M. Ward. 2006. Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the Octopus Spring microbial mat community of Yellowstone National Park. Appl. Environ. Microbiol. 72: 544– 550.
3.
Anantha, R. P.,, A. L. McVeigh,, L. H. Lee,, M. K. Agnew,, F. J. Cassels,, D. A. Scott,, T. S. Whittam, and, S. J. Savarino. 2004. Evolutionary and functional relationships of colonization factor antigen I and other class 5 adhesive fimbriae of enterotoxigenic Escherichia coli. Infect. Immun. 72: 7190– 7201.
4.
Atwood, K. C.,, L. K. Schneider, and, F. J. Ryan. 1951. Periodic selection in Escherichia coli. Proc. Natl. Acad. Sci. USA 37: 146– 155.
5.
Barraclough, T. G.,, M. Hughes,, N. Ashford-Hodges, and, T. Fujisawa. 2009. Inferring evolutionarily significant units of bacterial diversity from broad environmental surveys of single-locus data. Biol. Lett. 5: 425– 428.
6.
Barrett, E. L.,, R. E. Solanes,, J. S. Tang, and, N. J. Palleroni. 1986. Pseudomonas fluorescens biovar V: its resolution into distinct component groups and the relationship of these groups to other P. fluorescens biovars, to P. putida, and to psychrotrophic pseudomonads associated with food spoilage. J. Gen. Microbiol. 132: 2709– 2721.
7.
Bhaya, D.,, A. R. Grossman,, A. S. Steunou,, N. Khuri,, F. M. Cohan,, N. Hamamura,, M. Melendrez,, M. M. Bateson,, D. M. Ward, and, J. F. Heidelberg. 2007. Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses. ISME J. 1: 703– 713.
8.
Bradshaw, W. E.,, and C. M. Holzapfel. 2008. Genetic response to rapid climate change: it’s seasonal timing that matters. Mol. Ecol. 17: 157– 166.
9.
Cohan, F. M. 1994. The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am. Naturalist 143: 965– 986.
10.
Cohan, F. M. 2005. Periodic selection and ecological diversity in bacteria, p. 78–93. In D. Nurminsky (ed.), Selective Sweep. Landes Bioscience, Georgetown, TX.
11.
Cohan, F. M. 2002. Population structure and clonality of bacteria, p. 161–163. In M. Pagel (ed.), Encyclopedia of Evolution, vol. 1. Oxford University Press, New York, NY.
12.
Cohan, F. M. 1996. The role of genetic exchange in bacterial evolution. ASM News 62: 631– 636.
13.
Cohan, F. M. 2002. Sexual isolation and speciation in bacteria. Genetica 116: 359– 370.
14.
Cohan, F. M. 2002. What are bacterial species? Annu. Rev. Microbiol. 56: 457– 487.
15.
Cohan, F. M.,, A. Koeppel, and, D. Krizanc. 2006. Sequence-based discovery of ecological diversity within Legionella, p. 367–376. In N. P. Cianciotto,, Y. Abu Kwaik,, P. H. Edelstein,, B. S. Fields,, D. F. Geary,, T. G. Harrison,, C. Joseph,, R. M. Ratcliff,, J. E. Stout, and, M. S. Swanson (ed.), Legionella: State of the Art 30 Years after Its Recognition. ASM Press, Washington, DC.
16.
Cohan, F. M.,, and A. F. Koeppel. 2008. The origins of ecological diversity in prokaryotes. Curr. Biol. 18: R1024– R1034.
17.
Cohan, F. M.,, and E. B. Perry. 2007. A systematics for discovering the fundamental units of bacterial diversity. Curr. Biol. 17: R373– R386.
18.
Connor, N.,, J. Sikorski,, A. P. Rooney,, S. Kopac,, A. F. Koeppel,, A. Burger,, S. G. Cole,, E. B. Perry,, D. Krizanc,, N. C. Field,, M. Slaton, and, F. M. Cohan. 2010. The ecology of speciation in Bacillus. Appl. Environ. Microbiol. 76: 1349– 1358.
19.
Corander, J.,, P. Marttinen,, J. Siren, and, J. Tang. 2008. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9: 539.
20.
Coyne, J. A. 2009. Why Evolution Is True, p. 189. Oxford University Press, Oxford, United Kingdom.
21.
Coyne, J. A.,, and H. A. Orr. 2004. Speciation. Sinauer Associates, Sunderland, MA.
22.
Darwin, C. 1859. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London. United Kingdom.
23.
de Queiroz, K. 2005. Ernst Mayr and the modern concept of species. Proc. Natl. Acad. Sci. USA 102 (Suppl. 1): 6600– 6607.
24.
Dieckmann, U.,, M. Doebeli,, J. A. J. Metz, and, D. Tautz (ed.). 2004. Adaptive Speciation. Cambridge University Press, Cambridge, United Kingdom.
25.
Doolittle, W. F. 2009. Eradicating typological thinking in prokaryotic systematics and evolution. Cold Spring Harb. Symp. Quant. Biol. 74: 197– 204.
26.
Dykhuizen, D. E.,, D. Brisson,, S. Sandigursky,, G. P. Wormser,, J. Nowakowski,, R. B. Nadelman, and, I. Schwartz. 2008. The propensity of different Borrelia burgdorferi sensu stricto genotypes to cause disseminated infections in humans. Am. J. Trop. Med. Hyg. 78: 806– 810.
27.
Fraser, C.,, W. P. Hanage, and, B. G. Spratt. 2007. Recombination and the nature of bacterial speciation. Science 315: 476– 480.
28.
Futuyma, D. J. 1987. On the role of species in anagenesis. Am. Naturalist 130: 465– 473.
29.
Gevers, D.,, F. M. Cohan,, J. G. Lawrence,, B. G. Spratt,, T. Coenye,, E. J. Feil,, E. Stackebrandt,, Y. Van de Peer,, P. Vandamme,, F. L. Thompson, and, J. Swings. 2005. Re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3: 733– 739.
30.
Gogarten, J. P.,, W. F. Doolittle, and, J. G. Lawrence. 2002. Prokaryotic evolution in light of gene transfer. Mol. Biol. Evol. 19: 2226– 2238.
31.
Goris, J.,, K. T. Konstantinidis,, J. A. Klappenbach,, T. Coenye,, P. Vandamme, and, J. M. Tiedje. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57: 81– 91.
32.
Guttman, D. S.,, and D. E. Dykhuizen. 1994. Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138: 993– 1003.
33.
Haldane, J. B. S. 1932. The Causes of Evolution. Longmans, Green, and Co., London, United Kingdom.
34.
Hawks, J.,, E. T. Wang,, G. M. Cochran,, H. C. Harpending, and, R. K. Moyzis. 2007. Recent acceleration of human adaptive evolution. Proc. Natl. Acad. Sci. USA 104: 20753– 20758.
35.
Hey, J. 2001. Genes, Categories, and Species: the Evolutionary and Cognitive Cause of the Species Problem. Oxford University Press, Oxford, United Kingdom.
36.
Hunt, D. E.,, L. A. David,, D. Gevers,, S. P. Preheim,, E. J. Alm, and, M. F. Polz. 2008. Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320: 1081– 1085.
37.
Kämpfer, P.,, R. M. Kroppenstedt, and, W. Dott. 1991. A numerical classification of the genera Streptomyces and Streptoverticillium using miniaturized physiological tests. J. Gen. Microbiol. 137: 1831– 1891.
38.
Kanhere, A.,, and M. Vingron. 2009. Horizontal gene transfers in prokaryotes show differential preferences for metabolic and translational genes. BMC Evol. Biol. 9: 9.
39.
Kassen, R.,, and T. Bataillon. 2006. Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria. Nat. Genet. 38: 484– 488.
40.
Koch, A. L. 1974. The pertinence of the periodic selection phenomenon to prokaryote evolution. Genetics 77: 127– 142.
41.
Koeppel, A.,, E. B. Perry,, J. Sikorski,, D. Krizanc,, W. A. Warner,, D. M. Ward,, A. P. Rooney,, E. Brambilla,, N. Connor,, R. M. Ratcliff,, E. Nevo, and, F. M. Cohan. 2008. Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proc. Natl. Acad. Sci. USA 105: 2504– 2509.
42.
Kuo, C. H.,, N. A. Moran, and, H. Ochman. 2009. The consequences of genetic drift for bacterial genome complexity. Genome Res. 19: 1450– 1454.
43.
Levin, B. R. 1981. Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics 99: 1– 23.
44.
Maiden, M. C. J.,, J. A. Bygraves,, E. Feil,, G. Morelli,, J. E. Russell,, R. Urwin,, Q. Zhang,, J. Zhou,, K. Zurth,, D. A. Caugant,, I. M. Feavers,, M. Achtman, and, B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95: 3140– 3145.
45.
Majewski, J. 2001. Sexual isolation in bacteria. FEMS Microbiol. Lett. 199: 161– 169.
46.
Majewski, J.,, and F. M. Cohan. 1999. Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics 152: 1459– 1474.
47.
Majewski, J.,, P. Zawadzki,, P. Pickerill,, F. M. Cohan, and, C. G. Dowson. 2000. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J. Bacteriol. 182: 1016– 1023.
48.
Mallet, J. 2008. Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philos. Trans. R. Soc. Lond. B Biol. Sci. 363: 2971– 2986.
49.
Mallet, J. 2008. Mayr’s view of Darwin: was Darwin wrong about speciation? Biol. J. Linn. Soc. Lond. 95: 3– 16.
50.
Manning, S. D.,, A. S. Motiwala,, A. C. Springman,, W. Qi,, D. W. Lacher,, L. M. Ouellette,, J. M. Mladonicky,, P. Somsel,, J. T. Rudrik,, S. E. Dietrich,, W. Zhang,, B. Swaminathan,, D. Alland, and, T. S. Whittam. 2008. Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks. Proc. Natl. Acad. Sci. USA 105: 4868– 4873.
51.
Mayr, E. 1963. Animal Species and Evolution. Belknap Press of Harvard University Press, Cambridge, MA.
52.
Mayr, E. 1982. The Growth of Biological Thought: Diversity, Evolution, and Inheritance. Harvard University Press, Cambridge, MA.
53.
Mayr, E. 1944. Systematics and the Origin of Species from the Viewpoint of a Zoologist. Columbia University Press, New York, NY.
54.
McVean, G.,, P. Awadalla, and, P. Fearnhead. 2002. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231– 1241.
55.
Meglitsch, P. 1954. On the nature of species. Syst. Zool. 3: 491– 503.
56.
Miller, S. R.,, and R. W. Castenholz. 2000. Evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Appl. Environ. Microbiol. 66: 4222– 4229.
57.
Ochman, H.,, and L. M. Davalos. 2006. The nature and dynamics of bacterial genomes. Science 311: 1730– 1733.
58.
Orsi, R. H.,, M. L. Borowsky,, P. Lauer,, S. K. Young,, C. Nusbaum,, J. E. Galagan,, B. W. Birren,, R. A. Ivy,, Q. Sun,, L. M. Graves,, B. Swaminathan, and, M. Wiedmann. 2008. Short-term genome evolution of Listeria monocytogenes in a non-controlled environment. BMC Genomics 9: 539.
59.
Palenik, B.,, Q. Ren,, V. Tai, and, I. T. Paulsen. 2009. Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity. Environ. Microbiol. 11: 349– 359.
60.
Papke, R. T.,, O. Zhaxybayeva,, E. J. Feil,, K. Sommerfeld,, D. Muise, and, W. F. Doolittle. 2007. Searching for species in haloarchaea. Proc. Natl. Acad. Sci. USA 104: 14092– 14097.
61.
Polz, M. F.,, D. E. Hunt,, S. P. Preheim, and, D. M. Weinreich. 2006. Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361: 2009– 2021.
62.
Ramsing, N. B.,, M. J. Ferris, and, D. M. Ward. 2000. Highly ordered vertical structure of Synechococcus populations within the one-millimeter-thick photic zone of a hot spring cyanobacterial mat. Appl. Environ. Microbiol. 66: 1038– 1049.
63.
Rieseberg, L. H.,, O. Raymond,, D. M. Rosenthal,, Z. Lai,, K. Livingstone,, T. Nakazato,, J. L. Durphy,, A. E. Schwarzbach,, L. A. Donovan, and, C. Lexer. 2003. Major ecological transitions in wild sunflowers facilitated by hybridization. Science 301: 1211– 1216.
64.
Schemske, D. W. 2000. Understanding the origin of species. Evolution 54: 1069– 1073.
65.
Segovia, L.,, D. Piñero,, R. Palacios, and, E. Martínez-Romero. 1991. Genetic structure of a soil population of nonsymbiotic Rhizobium leguminosarum. Appl. Environ. Microbiol. 57: 426– 433.
66.
Sheppard, S. K.,, N. D. McCarthy,, D. Falush, and, M. C. Maiden. 2008. Convergence of Campylobacter species: implications for bacterial evolution. Science 320: 237– 239.
67.
Sikorski, J. 2008. Populations under microevolutionary scrutiny: what will we gain? Arch. Microbiol. 189: 1– 5.
68.
Sikorski, J.,, and E. Nevo. 2007. Patterns of thermal adaptation of Bacillus simplex to the microclimatically contrasting slopes of ‘Evolution Canyons’ I and II, Israel. Environ. Microbiol. 9: 716– 726.
69.
Smith, N. H.,, S. V. Gordon,, R. de la Rua-Domenech,, R. S. Clifton-Hadley, and, R. G. Hewinson. 2006. Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis. Nat. Rev. Microbiol. 4: 670– 681.
70.
Soyer, Y.,, R. H. Orsi,, L. D. Rodriguez-Rivera,, Q. Sun, and, M. Wiedmann. 2009. Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes. BMC Evol. Biol. 9: 264.
71.
Stackebrandt, E. 2002. From species definition to species concept: population genetics is going to influence the systematics of Prokaryotes. WFCC Newsletter 35: 1– 4.
72.
Stackebrandt, E.,, and J. Ebers. 2006. Taxonomic parameters revisited: tarnished gold standards. Microbiol. Today 33: 152– 155.
73.
Stackebrandt, E.,, W. Frederiksen,, G. M. Garrity,, P. A. Grimont,, P. Kämpfer,, 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 re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 1043– 1047.
74.
Staley, J. T. 2006. The bacterial species dilemma and the genomic-phylogenetic species concept. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361: 1899– 1909.
75.
Stamos, D. N. 2007. Darwin and the Nature of Species. State University of New York Press, Albany, NY.
76.
Swiecicka, I.,, and J. Mahillon. 2005. The clonal structure of Bacillus thuringiensis isolates from north-east Poland does not correlate with their cry gene diversity. Environ. Microbiol. 7: 34– 39.
77.
Templeton, A. 1989. The meaning of species and speciation: a genetic perspective, p. 3–27. In D. Otte and, J. Endler (ed.), Speciation and Its Consequences. Sinauer Associates, Sunderland, MA.
78.
Vandamme, P.,, B. Pot,, M. Gillis,, P. de Vos,, K. Kersters, and, J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60: 407– 438.
79.
Vos, M.,, and X. Didelot. 2009. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 3: 199– 208.
80.
Walk, S. T.,, E. W. Alm,, L. M. Calhoun,, J. M. Mladonicky, and, T. S. Whittam. 2007. Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ. Microbiol. 9: 2274– 2288.
81.
Walk, S. T.,, E. W. Alm,, D. M. Gordon,, J. L. Ram,, G. A. Toranzos,, J. M. Tiedje, and, T. S. Whittam. 2009. Cryptic lineages of the genus Escherichia. Appl. Environ. Microbiol. 75: 6534– 6544.
82.
Ward, D. M. 1998. A natural species concept for prokaryotes. Curr. Opin. Microbiol. 1: 271– 277.
83.
Ward, D. M.,, M. M. Bateson,, M. J. Ferris,, M. Kühl,, A. Wieland,, A. Koeppel, and, F. M. Cohan. 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. Philos. Trans. R. Soc. Lond. B Biol Sci. 361: 1997– 2008.
84.
Ward, D. M.,, and F. M. Cohan. 2005. Microbial diversity in hot spring cyanobacterial mats: pattern and prediction, p. 185–202. In W. P. Inskeep and, T. McDermott (ed.), Geothermal Biology and Geochemistry in Yellowstone National Park. Thermal Biology Institute, Bozeman, MT.
85.
Ward, D. M.,, F. M. Cohan,, D. Bhaya,, J. F. Heidelberg,, M. Kühl, and, A. Grossman. 2008. Genomics, environmental genomics and the issue of microbial species. Heredity 100: 207– 219.
86.
Wayne, L. G.,, D. J. Brenner,, R. R. Colwell,, P. A. D. Grimont,, O. Kandler,, M. I. Krichevsky,, W. E. C. Moore,, R. G. E. Murray,, E. Stackebrandt,, M. P. Starr, and, H. G. Trüper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463– 464.
87.
Welch, R. A.,, V. Burland,, G. Plunkett III,, P. Redford,, P. Roesch,, D. Rasko,, E. L. Buckles,, S.-R. Liou,, A. Boutin,, J. Hackett,, D. Stroud,, G. F. Mayhew,, D. J. Rose,, S. Zhou,, D. C. Schwartz,, N. T. Perna,, H. L. T. Mobley,, M. S. Donnenberg, and, F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99: 17020– 17024.
88.
Wernegreen, J. J.,, E. E. Harding, and, M. A. Riley. 1997. Rhizobium gone native: unexpected plasmid stability of indigenous Rhizobium leguminosarum. Proc. Natl. Acad. Sci. USA 94: 5483– 5488.
89.
Whittam, T. S.,, and A. C. Bumbaugh. 2002. Inferences from whole-genome sequences of bacterial pathogens. Curr. Opin. Genet. Dev. 12: 719– 725.
90.
Williamson, S. H.,, M. J. Hubisz,, A. G. Clark,, B. A. Payseur,, C. D. Bustamante, and, R. Nielsen. 2007. Localizing recent adaptive evolution in the human genome. PLoS Genet. 3: e90.
91.
Wu, D.,, P. Hugenholtz,, K. Mavromatis,, R. Pukall,, E. Dalin,, N. N. Ivanova,, V. Kunin,, L. Goodwin,, M. Wu,, B. J. Tindall,, S. D. Hooper,, A. Pati,, A. Lykidis,, S. Spring,, I. J. Anderson,, P. D’haeseleer,, A. Zemla,, M. Singer,, A. Lapidus,, M. Nolan,, A. Copeland,, C. Han,, F. Chen,, J. F. Cheng,, S. Lucas,, C. Kerfeld,, E. Lang,, S. Gronow,, P. Chain,, D. Bruce,, E. M. Rubin,, N. C. Kyrpides,, H. P. Klenk, and, J. A. Eisen. 2009. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056– 1060.
92.
Yoon, C. K. 2009. Naming Nature: the Clash between Instinct and Science. Norton, New York, NY.