References
Achtman M and
Wagner M
(2008)
Microbial diversity and the genetic nature of microbial species.
Nature Reviews Microbiology
6:
431–440.
Achtman M,
Morelli G,
Zhu P et al.
(2004)
Microevolution and history of the plague bacillus, Yersinia pestis.
Proceedings of the National Academy of Sciences of the USA
101:
17837–17842.
Adami C
(2006a)
Digital genetics: unravelling the genetic basis of evolution.
Nature Reviews. Genetics
7:
109–118.
Adami C
(2006b)
Reducible complexity.
Science
312:
61–63.
Bergstrom CT,
Lipsitch M and
Levin BR
(2000)
Natural selection, infectious transfer and the existence conditions for bacterial plasmids.
Genetics
155:
1505–1519.
Brigulla M,
Hoffmann T,
Krisp A et al.
(2003)
Chill induction of the SigB‐dependent general stress response in Bacillus subtilis and its contribution to low‐temperature adaptation.
Journal of Bacteriology
185:
4305–4314.
Buckley M and
Roberts RJ
(2006)
Reconciling Microbial Systematics & Genomics: American Academy of Microbiology.
Washington, DC: ASM.
Choi K‐H,
Heath RJ and
Rock CO
(2000)
β‐ketoacyl‐acyl carrier protein synthase III (FabH) is a determining factor in branched‐chain fatty acid biosynthesis.
Journal of Bacteriology
182:
365–370.
Cohan FM
(1994)
The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes.
American Naturalist
143:
965–986.
Cohan FM and
Perry EB
(2007)
A systematics for discovering the fundamental units of bacterial diversity.
Current Biology
17:
R373–R386.
Dekel E and
Alon U
(2005)
Optimality and evolutionary tuning of the expression level of a protein.
Nature
436:
588–592.
Elena SF and
Lenski RE
(2003)
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation.
Nature Reviews. Genetics
4:
457–469.
Excoffier L and
Heckel G
(2006)
Computer programs for population genetics data analysis: a survival guide.
Nature Reviews. Genetics
7:
745–758.
Falush D,
Kraft C,
Taylor NS et al.
(2001)
Recombination and mutation during long‐term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age.
Proceedings of the National Academy of Sciences of the USA
98:
15056–15061.
Hartl DL and
Clark AG
(2007)
Principles of Population Genetics,
4 edn.
Sunderland, MA: Sinauer Associates.
Herbeck JT,
Funk DJ,
Degnan PH and
Wernegreen JJ
(2003)
A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL.
Genetics
165:
1651–1660.
Jessup CM,
Kassen R,
Forde SE et al.
(2004)
Big questions, small worlds: microbial model systems in ecology.
Trends in Ecology and Evolution
19:
189–197.
Kassen R,
Llewellyn M and
Rainey PB
(2004)
Ecological constraints on diversification in a model adaptive radiation.
Nature
431:
984–988.
Koeppel A,
Perry EB,
Sikorski J et al.
(2008)
Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics.
Proceedings of the National Academy of Sciences of the USA
105:
2504–2509.
Konstantinidis KT and
Tiedje JM
(2005)
Genomic insights that advance the species definition for prokaryotes.
Proceedings of the National Academy of Sciences of the USA
102:
2567–2572.
Lapage SP,
Sneath PHA,
Lessel EF et al.
(1992)
International Code of Nomenclature of Bacteria (1990 Revision). Bacteriological Code.
Washington, DC: American Society for Microbiology.
Lenski RE,
Ofria C,
Collier TC and
Adami C
(1999)
Genome complexity, robustness and genetic interactions in digital organisms.
Nature
400:
661–664.
Lenski RE,
Ofria C,
Pennock RT and
Adami C
(2003)
The evolutionary origin of complex features.
Nature
423:
139–144.
Lynch M
(2007)
The frailty of adaptive hypotheses for the origins of organismal complexity.
Proceedings of the National Academy of Sciences of the USA
104:
8597–8604.
MacLean RC,
Bell G and
Rainey PB
(2004)
The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens.
Proceedings of the National Academy of Sciences of the USA
101:
8072–8077.
Maharjan R,
Seeto S,
Notley‐McRobb L and
Ferenci T
(2006)
Clonal adaptive radiation in a constant environment.
Science
313:
514–517.
Mayr E
(1997)
The objects of selection.
Proceedings of the National Academy of Sciences of the USA
94:
2091–2094.
de Mendoza D,
Schujman GE and
Aguilar PS
(2002)
Biosynthesis and function of membrane lipids.
In: Sonenshein AL,
Hoch JA and
Losick R (eds)
Bacillus Subtilis and Its Closest Relatives: From Genes to Cells,
pp. 43–55.
Washington, DC: ASM Press.
Mutch LA and
Young JPW
(2004)
Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes.
Molecular Ecology
13:
2435–2444.
Nei M
(2007)
The new mutation theory of phenotypic evolution.
Proceedings of the National Academy of Sciences of the USA
104:
12235–12242.
Orr HA
(2005a)
The genetic theory of adaptation: a brief history.
Nature Reviews. Genetics
6:
119–127.
Orr HA
(2005b)
Theories of adaptation: what they do and don't say.
Genetica
123:
3–13.
Papke RT and
Ward DM
(2004)
The importance of physical isolation to microbial diversification.
FEMS Microbiology Ecology
48:
293–303.
Papke RT,
Zhaxybayeva O,
Feil EJ et al.
(2007)
Searching for species in haloarchaea.
Proceedings of the National Academy of Sciences of the USA
104:
14092–14097.
Rainey PB and
Travisano M
(1998)
Adaptive radiation in a heterogeneous environment.
Nature
394:
69–72.
Rasko DA,
Rosovitz MJ,
Okstad OA et al.
(2007)
Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus‐group plasmids, including Bacillus anthracis pXO1.
Journal of Bacteriology
189:
52–64.
Sikorski J
(2008)
Populations under microevolutionary scrutiny: what will we gain?
Archives of Microbiology
189:
1–5.
Sikorski J,
Brambilla E,
Kroppenstedt RM and
Tindall BJ
(2008a)
The temperature adaptive fatty acid content in Bacillus simplex strains from “Evolution Canyon”, Israel.
Microbiology
154:
2416–2426.
Sikorski J and
Nevo E
(2005)
Adaptation and incipient sympatric speciation of Bacillus simplex under microclimatic contrast at “Evolution Canyons” I and II, Israel.
Proceedings of the National Academy of Sciences of the USA
102:
15924–15929.
Sikorski J and
Nevo E
(2007)
Patterns of thermal adaptation of Bacillus simplex to the microclimatically contrasting slopes of “Evolution Canyon” I and II, Israel.
Environmental Microbiology
9:
716–726.
Sikorski J,
Pukall R and
Stackebrandt E
(2008b)
Carbon source utilization patterns of Bacillus simplex ecotypes do not reflect their adaptation to ecologically divergent slopes in “Evolution Canyon”, Israel.
FEMS Microbiology Ecology
66:
38–440.
Smith NH,
Kremer K,
Inwald J et al.
(2006)
Ecotypes of the Mycobacterium tuberculosis complex.
Journal of Theoretical Biology
239:
220–225.
Stackebrandt E
(2002)
From species definition to species concept: population genetics is going to influence the systematics of Prokaryotes.
WFCC Newsletter
35:
1–4.
Stoltzfus A
(2006)
Mutationism and the dual causation of evolutionary change.
Evolution & Development
8:
304–317.
Tanaka MM,
Bergstrom CT and
Levin BR
(2003)
The evolution of mutator genes in bacterial populations: the roles of environmental change and timing.
Genetics
164:
843–854.
Tenaillon O,
Le Nagard H,
Godelle B and
Taddei F
(2000)
Mutators and sex in bacteria: conflict between adaptive strategies.
Proceedings of the National Academy of Sciences of the USA
97:
10465–10470.
Thompson JR,
Pacocha S,
Pharino C et al.
(2005)
Genotypic diversity within a natural coastal bacterioplankton population.
Science
307:
1311–1313.
Vos M and
Velicer GJ
(2008)
Isolation by distance in the spore‐forming soil bacterium Myxococcus xanthus.
Current Biology
18:
386–391.
Ward DM,
Cohan FM,
Bhaya D et al.
(2008)
Genomics, environmental genomics and the issue of microbial species.
Heredity
100:
207–219.
Wiehlmann L,
Wagner G,
Cramer N et al.
(2007)
Population structure of Pseudomonas aeruginosa.
Proceedings of the National Academy of Sciences of the USA
104:
8101–8106.
Wilke CO,
Wang JL,
Ofria C,
Lenski RE and
Adami C
(2001)
Evolution of digital organisms at high mutation rates leads to survival of the flattest.
Nature
412:
331–333.
Further Reading
Kimura M
(1983)
The Neutral Theory of Molecular Evolution.
Cambridge: Cambridge University Press.
Oren A
(2004)
Prokaryote diversity and taxonomy: present status and future challenges.
Philosophical Transactions of the Royal Society. Series B
559:
623–638.
Page RDM and
Holmes EC
(1998)
Molecular Evolution: A Phylogenetic Approach.
Oxford: Blackwell Science.
Stackebrandt E
(2003)
The richness of prokaryotic diversity: there must be a species somewhere.
Food Technology and Biotechnology
41:
17–22.
Tindall BJ,
Kämpfer P,
Euzéby JP and
Oren A
(2006)
Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice.
International Journal of Systematic and Evolutionary Microbiology
56:
2715–2720.
Trüper HG
(1999)
How to name a prokaryote? Etymological considerations, proposals and practical advice in prokaryotic nomenclature.
FEMS Microbiology Reviews
23:
231–249.
