Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Cooper, Tim F ^a   Lenski, Richard E ^b  

^a University of Houston   (United States)

^b Michigan State University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COLIFORM BACTERIUM; DIVERGENCE; ENVIRONMENTAL EFFECT; EVOLUTIONARY BIOLOGY; EXPERIMENTAL STUDY; HETEROGENEITY; POPULATION DISTRIBUTION; RESOURCE AVAILABILITY;

ESCHERICHIA COLI;

ADAPTATION; ANALYSIS OF VARIANCE; ARTICLE; CULTURE MEDIUM; ENVIRONMENT; ESCHERICHIA COLI; GENETIC FITNESS; GENETICS; MOLECULAR EVOLUTION; POPULATION GENETICS;

ADAPTATION, PHYSIOLOGICAL; ANALYSIS OF VARIANCE; CULTURE MEDIA; ENVIRONMENT; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENETIC FITNESS; GENETICS, POPULATION;

EID: 77649133888     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-11     Document Type: Article

References (62)

1. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. ZD Blount CZ Borland RE Lenski, Proc Natl Acad Sci USA 2008 105 7899 7906 10.1073/pnas.0803151105 18524956
2. Can uniform selection retard random genetic divergence between isolated conspecific populations? FM Cohan, Evolution 1984 38 495 504 10.2307/2408699
3. D Schluter, The Ecology of Adaptive Radiation Oxford: Oxford Univ. Press 2000
4. Experimental tests of the roles of adaptation, chance, and history in evolution. M Travisano JA Mongold AF Bennett RE Lenski, Science 1995 267 87 90 10.1126/science.7809610 7809610
5. Surfaces of selective value revisited. S Wright, Am Nat 1988 131 115 123 10.1086/284777
6. PH Harvey MD Pagel, The Comparative Method in Evolutionary Biology Oxford: Oxford Univ. Press 1991
7. GC Simpson, The Major Features of Evolution New York: Columbia Univ. Press 1953
8. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. SF Elena RE Lenski, Nat Rev Genet 2003 4 457 469 10.1038/nrg1088 12776215
9. The Beagle in a bottle. A Buckling RC MacLean MA Brockhurst N Colegrave, Nature 2009 457 824 829 10.1038/nature07892 19212400
10. The population genetics of ecological specialization in evolving Escherichia coli populations. VS Cooper RE Lenski, Nature 2000 407 736 739 10.1038/35037572 11048718
11. Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli. VS Cooper D Schneider M Blot RE Lenski, B J Bacteriol 2001 183 2834 2841 10.1128/JB.183.9.2834-2841.2001 (Pubitemid 32319286)
12. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. TF Cooper DE Rozen RE Rozen, Proc Natl Acad Sci USA 2003 100 1072 1077 10.1073/pnas.0334340100 12538876
13. The effect of population structure on the adaptive radiation of microbial populations evolving in spatially structured environments. MGJL Habets D Rozen RF Hoekstra AGM de Visser, Ecol Lett 2006 9 1041 1048 10.1111/j.1461-0248.2006. 00955.x 16925653
14. Adaptation to structurally different environments. R Korona, Proc R Soc Lond B 1996 263 1665 1669 10.1098/rspb.1996.0243 (Pubitemid 27055559)
15. Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat. R Korona CH Nakatsu LJ Forney RE Lenski, Proc Natl Acad Sci USA 1994 91 9037 9041 10.1073/pnas.91.19.9037 8090765
16. Long term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. RE Lenski MR Rose SC Simpson SC Tadler, Am Nat 1991 138 1315 1341 10.1086/285289
17. Parallel and divergent phenotypic evolution in experimental populations of Ralstonia sp. CH Nakatsu R Korona RE Lenski FJ de Bruijn TL Marsh LJ Forney, J Bacteriol 1994 180 4325 4331
18. Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli. L Pelosi L Kuhn D Guetta J Garin J Geiselmann RE Lenski D Schneider, Genetics 2006 173 1851 1869 10.1534/genetics.105.049619 16702438
19. Adaptive radiation in a heterogeneous environment. PB Rainey M Travisano, Nature 1998 394 69 72 10.1038/27900 9665128
20. Different trajectories of parallel evolution during viral adaptation. HA Wichman MR Badgett LA Scott CM Boulianne JJ Bull, Science 1999 285 422 424 10.1126/science.285.5426.422 10411508
21. Experimental evolution recapitulates natural evolution. HA Wichman LA Scott CD Yarber JJ Bull, Proc R Soc Lond B 2000 355 1677 1684
22. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. R Woods D Schneider CL Winkworth MA Riley RE Lenski, Proc Natl Acad Sci USA 2006 103 9107 9112 10.1073/pnas.0602917103 16751270 (Pubitemid 43902541)
23. The dynamics of diversification in evolving Pseudomonas populations. RDH Barrett G Bell, Evolution 2006 60 484 490 16637494
24. Experimental evolution in Chlamydomonas. II. Genetic variation in strongly contrasted environments. G Bell X Reboud, Heredity 1987 78 498 506 10.1038/hdy.1997.78
25. Evolutionary adaptation to temperature II. Thermal niches of experimental lines of Escherichia coli. AF Bennett RE Lenski, Evolution 1993 47 1 12 10.2307/2410113
26. On the experimental evolution of specialization and diversity in heterogeneous environments. J-N Jasmin R Kassen, Ecol Lett 2007 10 272 281 10.1111/j.1461-0248.2007.01021.x 17355566
27. Experimental evolution in Chlamydomonas. IV. Selection in environments that vary through time at different scales. R Kassen G Bell, Heredity 1988 80 732 741 10.1046/j.1365-2540.1998.00329.x
28. Experimental evolution in Chlamydomonas. III. Evolution of specialist and generalist types in environments that vary in space and time. X Reboud G Bell, Heredity 1997 78 507 514 10.1038/hdy.1997.79
29. Cost of host radiation in an RNA virus. PE Turner SF Elena, Genetics 2000 156 1465 1470 11102349
30. Experimental evolution of Pseudomonas fluorescens in simple and complex environments. RDH Barrett RG MacLean G Bell, Am Nat 2005 166 470 480 10.1086/444440 16224703
31. Unparallel diversification in bacterial microcosms. J Tyerman N Havard G Saxer M Travisano M Doebeli, Proc R Soc Lond B 2005 272 1393 1398 10.1098/rspb.2005.3068 (Pubitemid 41414723)
32. S Wright, Proc Sixth Int Congr Genet 1932 1 356 366
33. Sign epistasis and genetic constraint on evolutionary processes. DM Weinreich RA Watson L Chao, Evolution 2005 59 1165 1174 16050094
34. Multiple fitness peaks and epistasis. MC Whitlock PC Philips FB-G Moore FJ Tonsor, Annu Rev Ecol Syst 1995 26 601 629 10.1146/annurev.es.26.110195. 003125
35. Microbial experiments on adaptive landscapes. N Colegrave A Buckling, BioEssays 2005 27 1167 1173 10.1002/bies.20292 16237671
36. SA Kauffman, The Origins of Order New York: Oxford Univ. Press 1993
37. Experimental studies of pleiotropy and epistasis in Escherichia coli. II. Compensation for maladaptive effects associated with resistance to virus T4. RE Lenski, Evolution 1988 42 433 440 10.2307/2409029
38. Evolution and the Genetics of Populations. S Wright, Experimental Results and Evolutionary Deductions Chicago: Univ. Chicago Press 1977 3
39. Divergent evolution during an experimental adaptive radiation. RC MacLean G Bell, Proc R Soc Lond B 2003 270 1645 1650 10.1098/rspb.2003.2408 (Pubitemid 36960297)
40. Pleiotropic effects of beneficial mutations in Escherichia coli. EA Ostrowski DE Rozen RE Lenski, Evolution 2005 59 2343 2352 16396175
41. Long-term experimental evolution in Escherichia coli III. Variation among replicate populations in correlated responses to novel environments. M Travisano F Vasi RE Lenski, Evolution 1995 49 189 200 10.2307/2410304
42. Long-term experimental evolution in Escherichia coli. IV. Targets of selection and the specificity of adaptation. M Travisano RE Lenski, Genetics 1996 143 15 26 8722758
43. Theoretical analysis of divergence in mean fitness between initially identical populations. PA Johnson RE Lenski FC Hoppensteadt, Proc R Soc Lond B 1995 259 125 130 10.1098/rspb.1995.0019
44. The dynamics of adaptation on correlated fitness landscapes. S Kryazhimskiy G Tkaik JB Plotkin, Proc Natl Acad Sci USA 2009 106 18638 18643 10.1073/pnas.0905497106 19858497
45. Evolutionary traction: the cost of adaptation and the evolution of sex. L Hadany MW Feldman, J Evol Biol 2005 18 309 314 10.1111/j.1420-9101.2004.00858.x 15715837
46. Sexual selection and the power of natural selection. WL Rice AK Chippindale, Science 2001 294 555 559 10.1126/science.1061380 11641490
47. Genome evolution and adaptation in a long-term experiment with Escherichia coli. JE Barrick DS Yu SH Yoon H Jeong TK Oh D Schneider RE Lenski JF Kim, Nature 2009 461 1243 1247 10.1038/nature08480 19838166
48. Genome-wide mutational diversity in an evolving population of Escherichia coli. JE Barrick RE Lenski, Cold Spring Harb Symp Quant Biol 2009 19776167
49. Empirical fitness landscapes reveal accessible evolution paths. FJ Poelwijk DJ Kiviet DM Weinreich SJ Tans, Nature 2007 445 383 386 10.1038/nature05451 17251971
50. Mutational order: a major stochastic process in evolution. GS Mani BC Clarke, Proc R Soc Lond B 1990 240 29 37 10.1098/rspb.1990.0025 1972992
51. The Red Queen beats the Jack-of-all-trades: the limitations on the evolution of phenotypic plasticity and niche breadth. MC Whitlock, Am Nat 1996 148 65 77 10.1086/285902 (Pubitemid 27050108)
52. Effects of environment on compensatory mutations to ameliorate costs of antibiotic resistance. J Bjorkman I Nagaev OG Berg D Hughes DI Anderson, Science 2000 287 1479 1482 10.1126/science.287.5457.1479 10688795
53. Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. BRL Levin V Perrot N Walker, Genetics 2000 154 985 997 10757748
54. Pervasive compensatory adaptation in Escherichia coli. FB-G Moore DE Rozen RE Lenski, Proc R Soc Lond B 2000 267 515 522 10.1098/rspb.2000.1030
55. Understanding the fate of finite populations: The dynamics of mutational effects. OK Silander O Tenaillon L Chao, PLoS 2007 S4 e94
56. Kinetic models for the growth of Escherichia coli with mixtures of sugars under carbon-limiting conditions. U Lendenmann T Egli, Biotech Bioeng 1998 59 99 107 10.1002/(SICI)1097-0290(19980705)59:1<99::AID-BIT133.0.CO;2-Y
57. Kinetics of the simultaneous utilization of sugar mixtures by Escherichia coli in continuous culture. U Lendenmann M Snozzi T Egli, Appl Environ Microbiol 1996 62 1493 1499 8633848 (Pubitemid 26143413)
58. Regulation of carbon utilization. MH Saier TM Ramsier J Reizer, Escherichia coli and Salmonella typhimurium: cellular and molecular biology ASM Press, Washington, DC, Neidhart FC, 1996 1325 1329
59. Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli. M Novak T Pfeiffer RE Lenski U Sauer S Bonhoeffer, Am Nat 2006 168 242 251 10.1086/506527 16874633
60. Long-term experimental evolution in Escherichia coli. II. Changes in life-history traits during adaptation to growth in a seasonal environment. F Vasi M Travisano RE Lenski, Am Nat 1994 144 432 456 10.1086/285685 (Pubitemid 2139148)
61. Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli. ML Friesen G Saxer M Travisano M Doebeli, Evolution 2004 58 245 260 15068343
62. Analyzing tables of statistical tests. WR Rice, Evolution 1988 43 223 225 10.2307/2409177.