Adaptive landscapes in evolving populations of pseudomonas fluorescens

Evolution

Volumn 65, Issue 11, 2011, Pages 3048-3059

  Melnyk, Anita H ^a   Kassen, Rees ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

Author keywords

Adaptation; Experimental selection; Fitness; Pseudomonas

Indexed keywords

GLUCOSE; XYLOSE;

ADAPTIVE RADIATION; BACTERIUM; CARBON CYCLE; FITNESS; FLUORESCENCE; GLUCOSE; LANDSCAPE; METABOLISM; PHENOTYPE; POPULATION STRUCTURE; SELECTION;

ADAPTATION; ANALYSIS OF VARIANCE; ARTICLE; CULTURE TECHNIQUE; ENVIRONMENT; EVOLUTION; GENETIC SELECTION; GENETICS; GENOTYPE; METABOLISM; PHENOTYPE; PHYSIOLOGY; PSEUDOMONAS FLUORESCENS; REPRODUCTIVE FITNESS;

ADAPTATION, BIOLOGICAL; ANALYSIS OF VARIANCE; BIOLOGICAL EVOLUTION; CELL CULTURE TECHNIQUES; ENVIRONMENT; GENETIC FITNESS; GENOTYPE; GLUCOSE; PHENOTYPE; PSEUDOMONAS FLUORESCENS; SELECTION, GENETIC; XYLOSE;

PSEUDOMONAS; PSEUDOMONAS FLUORESCENS;

EID: 80054924877     PISSN: 00143820     EISSN: 15585646     Source Type: Journal    
DOI: 10.1111/j.1558-5646.2011.01333.x     Document Type: Article

References (55)

1. Barrett, R. D. H., R. C. MacLean, and G. Bell 2005. Experimental evolution of Pseudomonas fluorescens in simple and complex environments. Am. Nat. 166:470-480.
2. Barrick, J. E., M. R. Kauth, C. C. Strelioff, and R. E. Lenski 2010. Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol. Biol. Evol. 27:1338-1347.
3. Bell, G. 2008. Selection the mechanism of evolution. Oxford Univ. press. Oxford, UK
4. Betancourt, A. J. 2009. Genomewide patterns of substitution in adaptively evolving populations of the RNA bacteriophage MS2. Genetics 181:1535-1544.
5. Bollback, J. P. and J. P. Huelsenbeck 2009. Parallel genetic evolution within and between bacteriophage species with varying degrees of divergence. Genetics 181:225-234.
6. Burch, C. and L. Chao 1999. Evolution by small steps and rugged landscapes in the RNA virus φ6. Genetics 151:921-927.
7. Burch, C. and L. Chao 2000. Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature 406:625-628.
8. Colegrave, N., and A. Buckling 2005. Microbial experiments on adaptive landscapes. Bioessays 27: 1167-1173.
9. Colosimo, P. F., K. E. Hosemann, S. Balabhadra, G. Villarreal, Jr., M. Dickson, J. Grimwood, J. Schmutz, R. M. Myers, D. Schluter, and D. M. Kingsley 2005. Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307:1928-1933.
10. Cooper, T. F., D. E. Rozen, and R. E. Lenski 2003. Parallel changes in gene expression after 20, 000 generations of evolved Escherichia coli. Proc. Natl. Acad. Sci. USA 100:1072-1077.
11. Desai, M. M., D. S. Fisher and A. W. Murray 2007. The speed of evolution and maintenance of variation in asexual populations. Curr. Biol. 17:385-394.
12. Elena, S. F., and R. E. Lenski 1997. Long-term experimental evolution in Escherichia coli VII: mechanisms maintaining genetic variability within populations. Evolution 51:1058-1067.
13. Fuhrer, T., E. Fischer, and U. Sauer 2005. Experimental identification and quantification of glucose metabolism in seven bacterial species. J. Bacteriol. 187:1581-1590.
14. Gould, S. J. 1989. Wonderful life: the burgess shale and the nature of history. W. W. Norton, New York
15. Hall, A. R., V. F. Griffiths, R. C. Maclean, and N. Colegrave 2010. Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa. Proc. R. Soc. Lond. B 277:643-650.
16. Hegreness, M., N. Shoresh, D. Hartl and R. Kishony 2006. An equivalence principle for the incorporation of favorable mutations in asexual populations. Science 311:1615-1617.
17. Jacoby, G. A. 2005. Mechanisms of resistance to quinolones. Clin. Infect. Dis. 41:S120-126.
18. Jasmin, J.-N. and R. Kassen 2007. Evolution of a single niche specialist in variable environments. Proc. R. Soc. Lond. B. 274:2761- 2767.
19. Kassen, R., and T. Bataillon 2006. Distribution of fitness effects among beneficial mutations prior to selection in experimental populations of bacteria. Nat. Genet. 38:484-488.
20. Korona, R., C. H. Nakatsu, L. J. Forney, and R. E. Lenski 1994. Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat. Proc. Natl. Acad. Sci. USA 91:9037-9041.
21. Lenski, R. E., M. R. Rose, S. C. Simpson, and S. C Tadler 1991. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2, 000 generations. Am. Nat. 138:1315-1341.
22. Lenski, R. E., and M. Travisano 1994. Dynamics of adaptation and diversification: a 10, 000-generation experiment with bacterial populations. Proc. Natl. Acad. Sci. USA 91:6808-14.
23. Levin B. R., V. Perrot, and N. Walker 2000. Compensatory mutations, antibiotic resistance and the population genetics of adaptive evolution in bacteria. Genetics 154:985-997.
24. Losos, J. B. 1992. The evolution of convergent structure in Caribbean Anolis communities. Syst. Biol. 41:403-420.
25. Maclean, R. C., and G. Bell 2003. Divergent evolution during an experimental adaptive radiation. Proc. R. Soc. Lond. B. 270:1645-1650.
26. Maclean, R. C., G. Bell, and P. B. Rainey 2004. The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens. Proc. Natl. Acad. Sci. USA 101:8072-8077.
27. Maisnier-Patin, S., O. G. Berg, L. Liljas, and D. I. Andersson Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium. Mol. Microbiol. 46:355-366.
28. Martin, G. and T. Lenormand 2008. The distribution of beneficial and fixed mutation fitness effects close to an optimum. Genetics 179: 907-916.
29. Meyer, J. R., S. E. Schoustra, J. Lachapelle, and R. Kassen 2010. Overshooting dynamics in a model adaptive radiation. Proc. R. Soc. Lond. B 278: 392-398.
30. Moore, F. B.-G. and R. Woods 2006. Tempo and constraint of adaptive evolution in Escherichia coli (Enterobacteriaceae, Enterobacteriales). Biol. J. Linn. Soc. 88:403-411.
31. Moore, F. B.-G., D. E. Rozen and R. E. Lenski 2000. Pervasive compensatory adaptation in Escherichia coli. Proc. R. Soc. Lond. B 267:515-522.
32. Nakatsu, C. H., R. Korona, R. E. Lenski, F. J. de Bruijn, T. L. Marsh, and L. J. Forney 1998. Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp. J. Bacteriol. 180:4325-4331.
33. Orr, H. A. 2006. The population genetics of adaptation on correlated fitness landscapes: the block model. Evolution 60:1113-1124.
34. Orr, H. A. 2006. The distribution of fitness effects among beneficial mutations in Fisher's geometric model of adaptation. J. Theor. Biol. 238:279-285.
35. Otto, S. P. and T. Day 2005. A biologist's guide to mathematical modeling in ecology and evolution. Princeton Univ. press. Princeton, NJ
36. Piddock, L. J. V. 1999. Mechanisms of fluoroquinolone resistance: an update 1994-1998. Drugs 58:11-18.
37. Poelwijk F. J., D. J. Kiviet, and S. J. Tans 2007. Evolutionary potential of a duplicated repressor-operator pair: simulating pathways using mutational data. PLoS Comput. Biol. 2:467-75.
38. R Development Core Team. 2009. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria ISBN 3-900051-07-0.
39. Rakhimova, E., A. Munder, L. Wiehlmann, F. Bredenbruch, and B. Tümmler 2008. Fitness of isogenic colony morphology variants of Pseudomonas aeruginosa in murine airway infection. PLoS ONE 3:e1685. doi:.
40. Rainey, P. B. 1999. Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ. Microbiol. 1:243-257.
41. Rainey, P. B., and M. Travisano 1998. Adaptive radiation in a heterogeneous environment. Nature 394:69-72.
42. Rokyta, D. R., Z. Abdo, and H. A. Wichman 2009. The genetics of adaptation for eight Microvirid bacteriophages. J. Mol. Evol. 69:229-239.
43. Rozen, D. E., and R. E. Lenski 2000. Long-term experimental evolution in Escherichia coli VIII. Dynamics of a balanced polymorphism. Am. Nat. 155:24-35.
44. Schoustra, S. E., T. Bataillon, D. R. Gifford, and R. Kassen 2009. The properties of adaptive walks in evolving populations of fungus. PLoS Biol. 7:e1000250.
45. Schrag S. J., V. Perrot, and B. R. Levin 1997. Adaptation to the fitness costs of antibiotic resistance in Escherichia coli. Proc. Biol. Sci. 264:1287-1291.
46. Spencer, C. C., J. Tyerman, M. Bertrand, and M. Doebeli 2008. Adaptation increases the likelihood of diversification in an experimental bacterial lineage. Proc. Natl. Acad. Sci. USA 105:1585-1589.
47. Travisano, M., F. Vasi, and R. E. Lenski 1995a. Long-term experimental evolution in Escherichia coli. III. Variation among replicate populations in correlated responses to novel environments. Evolution 49:189-200.
48. Travisano, M., J. Mongold, A. Bennett, and R. E. Lenski 1995b. Experimental tests of the roles of adaptation, chance and history in evolution. Science 267:87-90.
49. Treves, D. S., S. Manning, and J. Adams 1998. Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 15:789-797.
50. Whitlock, M. C., P. C. Phillips, F. B.-G. Moore, and S. J. Tonsor 1995. Multiple fitness peaks and epistasis. Annu. Rev. Ecol. Syst. 26:601-629.
51. Wichman, H. A., J. Millstein, and J. J. Bull 2005. Adaptive molecular evolution for 13, 000 phage generations: a possible arms race. Genetics 170:19-31.
52. Wong, A. and R. Kassen 2011. Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa. Microbiology 157:937-944.
53. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Pp. 356-366 in Proceedings of the Sixth International Congress of Genetics. University of Chicago, Chicago, Illinois.
54. Wu, T. J., J. P. Burke, and D. B. Davison 1997. A measure of DNA sequence dissimilarity based on Mahalanobis distance between frequencies of words. Biometrics 53:1431-1439.
55. Zhang, X. X., and P. B. Rainey 2007. Construction and validation of a neutrally-marked strain of Pseudomonas fluorescens SBW25. J. Microbiol. Meth. 71:78-81.