Next-generation sequencing as a tool to study microbial evolution

Molecular Ecology

Volumn 20, Issue 5, 2011, Pages 972-980

  Brockhurst, Michael A ^a   Colegrave, Nick ^b   Rozen, Daniel E ^c  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

evolutionary genomics; experimental evolution; microbes; whole genome sequencing

Indexed keywords

BACTEREMIA; DNA SEQUENCE; GENETIC SELECTION; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; MUTATION; REVIEW; YEAST;

BACTEREMIA; EVOLUTION, MOLECULAR; GENOMICS; MUTATION; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; YEASTS;

EID: 79951808135     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2010.04835.x     Document Type: Review

References (74)

1. Araya CL, Payen C, Dunham MJ, Fields S, (2010) Whole-genome sequencing of a laboratory-evolved yeast strain. BMC Genomics, 11, 88.
2. Barrett RDH, MacLean RC, Bell G, (2006) Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations. Biology Letters, 2, 236-238. (Pubitemid 43938642)
3. Barrick JE, Lenski RE, (2009) Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harbor Symposia on Quantitative Biology. doi:.
4. Barrick JE, Yu DS, Yoon SH, et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature, 461, 1243-1274.
5. Beaumont HJE, Gallie J, Kost C, Ferguson GC, Rainey PB, (2009) Experimental evolution of bet hedging. Nature, 462, 90-93.
6. Betancourt AJ, (2009) Genomewide patterns of substitution in adaptively evolving populations of the RNA Bacteriophage MS2. Genetics, 181, 1535-1544.
7. Brunet E, Rouzine IM, Wilke CO, (2008) The stochastic edge in adaptive evolution. Genetics, 179, 603-620.
8. Buckling A, Wills MA, Colegrave N, (2003) Adaptation limits diversification of experimental bacterial populations. Science, 302, 2107-2109. (Pubitemid 38017939)
9. Buckling A, Maclean RC, Brockhurst MA, Colegrave N, (2009) The Beagle in a bottle. Nature, 457, 824-829.
10. Burch CL, Chao L, (1999) Evolution by small steps and rugged landscapes in the RNA virus phi6. Genetics, 151, 921-927. (Pubitemid 29118104)
11. Chao L, (1990) Fitness of RNA Virus decreased by Muller Ratchet. Nature, 348, 454-455. (Pubitemid 120015089)
12. Colegrave N, Buckling A, (2005) Microbial experiments on adaptive landscapes. Bioessays, 27, 1167-1173. (Pubitemid 43076142)
13. Conrad TM, Joyce AR, Applebee MK, et al. (2009) Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biology, 10, R118.
14. Cooper VS, Lenski RE, (2000) The population genetics of ecological specialization in evolving Escherichia coli populations. Nature, 407, 736-739.
15. Cooper VS, Schneider D, Blot M, Lenski RE, (2001) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. Journal of Bacteriology, 183, 2834-2841. (Pubitemid 32319286)
16. Cooper TF, Rozen DE, Lenski RE, (2003) Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 100, 1072-1077. (Pubitemid 36183957)
17. Cowperthwaite MC, Bull JJ, Meyers LA, (2005) Distributions of beneficial fitness effects in RNA. Genetics, 170, 1449-1457. (Pubitemid 41362805)
18. Crozat E, Philippe N, Lenski RE, Geiselmann J, Schneider D, (2005) Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection. Genetics, 169, 523-532. (Pubitemid 40404290)
19. Cuevas JM, Elena SF, Moya A, (2002) Molecular basis of adaptive convergence in experimental populations of RNA viruses. Genetics, 162, 533-542. (Pubitemid 35365021)
20. De Visser JAGM, (2002) The fate of microbial mutators. Microbiology, 148, 1247-1252.
21. Denver DR, Morris K, Lynch M, Thomas WK, (2004) High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature, 430, 679-682. (Pubitemid 39061683)
22. Denver DR, Dolan PC, Wilhelm LJ, et al. (2009) A genome-wide view of Caenorhabditis elegans base-substitution mutation processes. Proceedings of the National Academy of Sciences of the United States of America, 106, 16310-16314.
23. Desai MM, Fisher DS, Murray AW, (2007) The speed of evolution and maintenance of variation in asexual populations. Current Biology, 17, 385-394.
24. Drake JW, (1991) A constant rate of spontaneous mutation in DNA-based microbes. Proceedings of the National Academy of Sciences of the United States of America, 88, 7160-7164. (Pubitemid 21915109)
25. Elena SF, Lenski RE, (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Review. Genetics, 4, 457-469. (Pubitemid 36648145)
26. Elena SF, Sanjuan R, (2007) Virus evolution: insights from an experimental approach. Annual Review of Ecology Evolution and Systematics, 38, 27-52.
27. Ellis CN, Cooper VS, (2010) Experimental adaptation of Burkholderia cenocepacia to onion medium reduces host range. Applied and Environmental Microbiology, 76, 2387-2396.
28. Fiegna F, Yu YTN, Kadam SV, Velicer GJ, (2006) Evolution of an obligate social cheater to a superior cooperator. Nature, 441, 310-314. (Pubitemid 44050190)
29. Gerrish PJ, Lenski RE, (1998) The fate of competing beneficial mutations in an asexual population. Genetica, 102-3, 127-144. (Pubitemid 28371714)
30. Gresham D, Desai MM, Tucker CM, et al. (2008) The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. Plos Genetics, 4, e1000303.
31. Haag-Liautard C, Dorris M, Maside X, et al. (2007) Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila. Nature, 445, 82-85. (Pubitemid 46067305)
32. Hall AR, Griffiths VF, MacLean RC, Colegrave N, (2010) Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa. Proceedings of the Royal Society B-Biological Sciences, 277, 643-650.
33. Halligan DL, Keightley PD, (2009) Spontaneous mutation accumulation studies in evolutionary genetics. Annual Review of Ecology Evolution and Systematics, 40, 151-172.
34. Harris SR, Feil EJ, Holden MTG, et al. (2010) Evolution of MRSA during hospital transmission and intercontinental spread. Science, 327, 469-474.
35. Hegreness M, Shoresh N, Hartl D, Kishony R, (2006) An equivalence principle for the incorporation of favorable mutations in asexual populations. Science, 311, 1615-1617.
36. Herring CD, Raghunathan A, Honisch C, et al. (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nature Genetics, 38, 1406-1412. (Pubitemid 44837562)
37. Jain K, Krug J, (2007) Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes. Genetics, 175, 1275-1288. (Pubitemid 46798230)
38. Joseph SB, Hall DW, (2004) Spontaneous mutations in diploid Saccharomyces cerevisiae: more beneficial than expected. Genetics, 168, 1817-1825. (Pubitemid 40066324)
39. Kadam SV, Wegener-Feldbrugge S, Sogaard-Andersen L, Velicer GJ, (2008) Novel transcriptome patterns accompany evolutionary restoration of defective social development in the bacterium Myxococcus xanthus. Molecular Biology and Evolution, 25, 1274-1281. (Pubitemid 351882006)
40. Kassen R, Bataillon T, (2006) Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria. Nature Genetics, 38, 484-488.
41. Keightley PD, (1994) The distribution of mutation effects on viability in Drosophila-Melanogaster. Genetics, 138, 1315-1322. (Pubitemid 24375274)
42. Keightley PD, Caballero A, (1997) Genomic mutation rates for lifetime reproductive output and lifespan in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America, 94, 3823-3827. (Pubitemid 27180456)
43. Keightley PD, Trivedi U, Thomson M, et al. (2009) Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines. Genome Research, 19, 1195-1201.
44. Kibota TT, Lynch M, (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E-coli. Nature, 381, 694-696. (Pubitemid 26196567)
45. Kopp M, Hermisson J, (2009) The genetic basis of phenotypic adaptation I: fixation of beneficial mutations in the moving optimum model. Genetics, 182, 233-249.
46. Lenski RE, Travisano M, (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proceedings of the National Academy of Sciences of the United States of America, 91, 6808-6814. (Pubitemid 24226751)
47. Lenski RE, Rose MR, Simpson SC, Tadler SC, (1991) Long term experimental evolution in Escherichia coli. 1. Adaptation and divergence during 2000 generations. The American Naturalist, 138, 1315-1341.
48. Lind PA, Andersson DI, (2008) Whole-genome mutational biases in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 105, 17878-17883.
49. Lynch M, Sung W, Morris K, et al. (2008) A genome-wide view of the spectrum of spontaneous mutations in yeast. Proceedings of the National Academy of Sciences of the United States of America, 105, 9272-9277.
50. Mukai T, (1964) Genetic structure of natural populations of Drosophila Melanogaster.1. Spontaneous mutation rate of polygenes controlling viability. Genetics, 50, 1-19.
51. Notley-McRobb L, Ferenci T, (1999) The generation of multiple co-existing mal-regulatory mutations through polygenic evolution in glucose limited populations of Escherichia coli. Environmental Microbiology, 1, 45-52. (Pubitemid 129640027)
52. Novella IS, Ebendick-Corpus BE, (2004) Molecular basis of fitness loss and fitness recovery in vesicular stomatitis virus. Journal of Molecular Biology, 342, 1423-1430. (Pubitemid 39208669)
53. Ossowski S, Schneeberger K, Lucas-Lledo JI, et al. (2010) The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science, 327, 92-94.
54. Ostrowski EA, Woods RJ, Lenski RE, (2008) The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli. Proceedings of the Royal Society B-Biological Sciences, 275, 277-284. (Pubitemid 350295709)
55. Park SC, Krug J, (2007) Clonal interference in large populations. Proceedings of the National Academy of Sciences of the United States of America, 104, 18135-18140. (Pubitemid 350210833)
56. Paterson S, Vogwill T, Buckling A, et al. (2010) Antagonistic coevolution accelerates molecular evolution. Nature, 464, 275-278.
57. Pelosi L, Kuhn L, Guetta D, et al. (2006) Parallel changes in global protein profiles during long-term experimental evolution in Escherichia coli. Genetics, 173, 1851-1869. (Pubitemid 44285668)
58. Perfeito L, Fernandes L, Mota C, Gordo I, (2007) Adaptive mutations in bacteria: high rate and small effects. Science, 317, 813-815. (Pubitemid 47257920)
59. Racey D, Inglis RF, Harrison F, Oliver A, Buckling A, (2010) The effect of elevated mutation rates on the evolution of cooperation and virulence of Pseudomonas Aeruginosa. Evolution, 64, 515-521.
60. Rokyta DR, Beisel CJ, Joyce P, et al. (2008) Beneficial fitness effects are not exponential for two viruses. Journal of Molecular Evolution, 67, 368-376.
61. Rozen DE, de Visser JA, Gerrish PJ, (2002) Fitness effects of fixed beneficial mutations in microbial populations. Current Biology, 12, 1040-1045. (Pubitemid 34703337)
62. Rozen DE, Habets MG, Handel A, de Visser JA, (2008) Heterogeneous adaptive trajectories of small populations on complex fitness landscapes. PLoS ONE, 3, e1715.
63. Sanjuan R, Moya A, Elena SF, (2004) The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proceedings of the National Academy of Sciences of the United States of America, 101, 8396-8401. (Pubitemid 38736586)
64. Schoustra SE, Bataillon T, Gifford DR, Kassen R, (2009) The properties of adaptive walks in evolving populations of fungus. Plos Biology, 7, e1000250.
65. Shaw RG, Byers DL, Darmo E, (2000) Spontaneous mutational effects on reproductive traits of Arabidopsis thaliana. Genetics, 155, 369-378. (Pubitemid 30257136)
66. Silander OK, Tenaillon O, Chao L, (2007) Understanding the evolutionary fate of finite populations: the dynamics of mutational effects. Plos Biology, 5, 922-931. (Pubitemid 46631867)
67. Smith EE, Buckley DG, Wu ZN, et al. (2006) Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proceedings of the National Academy of Sciences of the United States of America, 103, 8487-8492. (Pubitemid 43838482)
68. Sniegowski PD, Gerrish PJ, (2010) Beneficial mutations and the dynamics of adaptation in asexual populations. Philosophical Transactions of the Royal Society B-Biological Sciences, 365, 1255-1263.
69. Stenseth NC, Maynard Smith J, (1984) Coevolution in ecosystems-Red Queen Evolution or Stasis. Evolution, 38, 870-880. (Pubitemid 16277736)
70. Treves DS, Manning S, Adams J, (1998) Repeated evolution of an acetate-crossfeeding polymorphism in long-term popula-tions of Escherichia coli. Molecular Biology and Evolution, 15, 789-797. (Pubitemid 28321878)
71. Van Valen L, (1973) A new evolutionary law. Evolutionary Theory, 1, 1-30.
72. Wichman HA, Badgett MR, Scott LA, Boulianne CM, Bull JJ, (1999) Different trajectories of parallel evolution during viral adaptation. Science, 285, 422-424. (Pubitemid 29343967)
73. Woods R, Schneider D, Winkworth CL, Riley MA, Lenski RE, (2006) Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, 103, 9107-9112. (Pubitemid 43902541)
74. Zeyl C, DeVisser JAGM, (2001) Estimates of the rate and distribution of fitness effects of spontaneous mutation in Saccharomyces cerevisiae. Genetics, 157, 53-61. (Pubitemid 32066296)