Long-term experimental evolution and adaptive radiation

Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments

Volumn , Issue , 2009, Pages 111-133

  Travisano, Michael ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84985878078     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (69)

1. Atwood, K., L. Schneider, and F. Ryan. 1951. Periodic selection in Escherichia coli. Proceedings of the National Academy of Sciences of the USA 37:146-155.
2. Bantinaki, E., R. Kassen, C. Knight, Z. Robinson, A. Spiers, and P. Rainey. 2007. Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176:441-453.
3. Cairns, J., J. Overbaugh, and S. Miller. 1988. The origin of mutants. Nature 335:142-145.
4. Chippindale, A. K., J. A. Alipaz, and M. R. Rose. 2004. Experimental evolution of accelerated development in Drosophila. 2. Adult fitness and the fast development syndrome. Pages 165-192 in M. R. Rose, H. B. Passananti, and M. Matos, eds. Methuselah Flies: A Case Study in the Evolution of Aging. Singapore: World Scientific.
5. Chippindale, A., A. L. Ngo, and M. Rose. 2003. The devil in the details of life-history evolution: Instability and reversal of genetic correlations during selection on Drosophila development. Journal of Genetics 82:133-145.
6. Chopra, I., and M. Roberts. 2001. Tetracycline antibiotics: Mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiology and Molecular Biology Reviews 65:232-260.
7. 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.
8. Cooper, V., and R. Lenski. 2000. The population genetics of ecological specialization in evolving Escherichia coli populations. Nature 407:736-739.
9. Cooper, V., D. Schneider, M. Blot, and R. Lenski. 2001. Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. Journal of Bacteriology 183:2834-2841.
10. de Visser, J. A., and D. E. Rozen. 2006. Clonal interference and the periodic selection of new beneficial mutations in Escherichia coli. Genetics 172:2093-2100.
11. Dean, A., D. Dykhuizen, and D. Hartl. 1988. Fitness effects of amino acid replacements in the beta-galactosidase of Escherichia coli. Molecular Biology and Evolution 5:469-485.
12. Dean, A., and J. Thornton. 2007. Mechanistic approaches to the study of evolution: The functional synthesis. Nature Reviews Genetics 8:675-688.
13. Dobzhansky, T. 1955. A review of some fundamental concepts and problems of population genetics. Cold Spring Harbor Symposium Quantitative Biology 20:1-15.
14. Dykhuizen, D., A. M. Dean, and D. Hartl. 1986. Fitness as a function of b-galactosidase activity in Escherichia coli. Genetical Research 48:1-8.
15. Dykhuizen, D., and D. Hartl. 1983. Selection in chemostats. Microbiological Reviews 47:150-168.
16. Friesen, M., G. Saxer, M. Travisano, and M. Doebeli. 2004. Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli. Evolution 58:245-260.
17. Garland, T., Jr., A. F. Bennett, and E. L. Rezende. 2005. Phylogenetic approaches in comparative physiology. Journal of Experimental Biology 208:3015-3035.
18. Gerrish, P. J., and R. E. Lenski. 1998. The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127-144.
19. Gould, S. J. 2002. The Structure of Evolutionary Theory. Cambridge, MA: Harvard University Press.
20. Gould, S. J., and R. Lewontin. 1979. The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proceedings of the Royal Society of London B, Biological Sciences 205:581-598.
21. Goymer, P., S. Kahn, J. Malone, S. Gehrig, A. Spiers, and P. Rainey. 2006. Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. The role of the GGDEF regulator WspR in evolution and development of the wrinkly spreader phenotype. Genetics 173:515-526.
22. Grant, P. R. 1999. Ecology and Evolution of Darwin's Finches. Princeton, NJ: Princeton University Press.
23. Hall, B. 1988. Adaptive evolution that requires multiple spontaneous mutation. I. Mutations involving an insertion sequence. Genetics 120:887-897.
24. Helling, R., C. Vargas, and J. Adams. 1987. Evolution of Escherichia coli during growth in a constant environment. Genetics 116:349-358.
25. Hill, W. G., and A. Robertson. 1966. The effect of linkage on limits to artificial selection. Genetical Research 8:269-294.
26. Hubbell, S. P. 2001. The Unified Neutral Theory of Biodiversity and Biogeography. Princeton, NJ: Princeton University Press.
27. Imhof, M., and C. Schlötterer. 2001. Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proceedings of the National Academy of Sciences of the USA 98:1113-1117.
28. Laurie, C., S. Chasalow, J. Ledeaux, R. McCarroll, D. Bush, B. Hauge, C. Lai, D. Clark, T. Rocheford, and J. Dudley. 2004. The genetic architecture of response to long-term artificial selection for oil concentration in the maize kernel. Genetics 168:2141-2155.
29. Lenski, R., M. R. Rose, S. Simpson, and S. Tadler. 1991. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2,000 generations. American Naturalist 138:1315-1341.
30. Lenski, R., and M. Travisano. 1994. Dynamics of adaptation and diversification: A 10,000-generation experiment with bacterial populations. Proceedings of the National Academy of Sciences of the USA 91:6808-6814.
31. Leroi, A. M., A. K. Chippindale, and M. R. Rose. 1994. Long-term laboratory evolution of a genetic trade-off in Drosophila melanogaster. I. The role of genotype _ environment interaction. Evolution 48:1244-1257.
32. Levin, B. R. 1972. Coexistence of two asexual strains on a single resource. Science 175:1272-1274.
33. Lewontin, R. C. 1974. The Genetic Basis of Evolutionary Change. New York: Columbia University Press.
34. Luria, S., and M. Delbrück. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491-511.
35. Maderson, P. F. A., and D. G. Homberger. 2000. The evolutionary origin of feathers: A problem demanding interdisciplinary communication. American Zoologist 40:455-460.
36. Maharjan, R., S. Seeto, and T. Ferenci. 2007. Divergence and redundancy of transport and metabolic rate-yield strategies in a single Escherichia coli population. Journal of Bacteriology 189:2350-2358.
37. Medrano-Soto, A., G. Moreno-Hagelsieb, P. Vinuesa, J. Christen, and J. Collado-Vides. 2004. Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes. Molecular Biology and Evolution 21:1884-1894.
38. Miralles, R., P. Gerrish, A. Moya, and S. Elena. 1999. Clonal interference and the evolution of RNA viruses. Science 285:1745-1747.
39. Mittler, J., and R. Lenski. 1992. Experimental evidence for an alternative to directed mutation in the bgl operon. Nature 356:446-448.
40. Ostrowski, E., D. Rozen, and R. Lenski. 2005. Pleiotropic effects of beneficial mutations in Escherichia coli. Evolution 59:2343-2352.
41. Ostrowski, E., R. Woods, and R. Lenski. 2008. The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli. Proceedings Biological Sciences 275:277-284.
42. Park, S.-C., and J. Krug. 2007. Clonal interference in large populations. Proceedings of the National Academy of Sciences of the USA 104:18135-18140.
43. Perrichot, V., L. Marion, D. Néraudeau, R. Vullo, and P. Tafforeau. 2008. The early evolution of feathers: Fossil evidence from Cretaceous amber of France. Proceedings Biological Sciences 275:1197-1202.
44. Petren, K., B. R. Grant, and P. R. Grant. 1999. A phylogeny of Darwin's finches based on microsatellite DNA length variation. Proceedings of the Royal Society of London B, Biological Sciences 266:321-329.
45. Phelan, J. P., M. A. Archer, K. A. Beckman, A. K. Chippindale, T. J. Nusbaum, and M. R. Rose. 2003. Breakdown in correlations during laboratory evolution. I. Comparative analyses of Drosophilia populations. Evolution 57:527-535.
46. Prum, R. O., and A. H. Brush. 2002. The evolutionary origin and diversification of feathers. Quarterly Review of Biology 77:261-295.
47. Rainey, P., and M. Travisano. 1998. Adaptive radiation in a heterogeneous environment. Nature 394:69-72.
48. Reed, D., and E. Bryant. 2000. The evolution of senescence under curtailed life span in laboratory populations of Musca domestica (the housefly). Heredity 85:115-121.
49. Rosenzweig, R., D. Treves, R. Sharp, and J. Adams. 1994. Microbial evolution in a simple unstructured environment: Genetic differentiation in Escherichia coli. Genetics 137:903-917.
50. Rozen, D., J. A. De Visser, and P. Gerrish. 2002. Fitness effects of fixed beneficial mutations in microbial populations. Current Biology 12:1040-1045.
51. Rozen, D., and R. Lenski. 2000. Long-term experimental evolution in Escherichia coli. VIII. Dynamics of a balanced polymorphism. American Naturalist 155:24-35.
52. Saier, M. H., Jr. 1989. Protein phosphorylation and allosteric control of inducer exclusion and catabolite repression by the bacterial phosphoenolpyruvate:sugar phosphotransferase system. Microbiological Reviews 53:109-120.
53. Schluter, D. 2000. The Ecology of Adaptive Radiation. Oxford: Oxford University Press.
54. Schneider, D., E. Duperchy, E. Coursange, R. E. Lenski, M. Blot. 2000. Long-term experimental evolution in Escherchia coli. IX. Characterization of IS-mediated mutations and rearrangements. Genetics 156:477-488.
55. Seehausen, O. 2006. African cichlid fish: A model system in adaptive radiation research. Proceedings Biological Sciences 273:1987-1998.
56. Selander, R. K., and T. S. Whittam. 1983. Protein polymorphism and the genetic structure of populations. Pages 89-114 in M. Nei and R. K Koehn, eds. Evolution of Genes and Proteins. Sunderland, MA: Sinauer.
57. Sokurenko, E., M. Feldgarden, E. Trintchina, S. Weissman, S. Avagyan, S. Chattopadhyay, J. Johnson, and D. Dykhuizen. 2004. Selection footprint in the FimH adhesin shows pathoadaptive niche differentiation in Escherichia coli. Molecular Biology and Evolution 21:1373-1383.
58. Souza, V., P. E. Turner, and R. E. Lenski. 1997. Long-term experimental evolution in Escherichia coli. V. Effects of recombination with immigrant genotypes on the rate of bacterial evolution. Journal of Evolutionary Biology 10:743-769.
59. Spencer, C., M. Bertrand, M. Travisano, and M. Doebeli. 2007. Adaptive diversification in genes that regulate resource use in Escherichia coli. PLoS Genetics 3:e15.
60. Spiers, A., J. Bohannon, S. Gehrig, and P. Rainey. 2003. Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Molecular Microbiology 50:15-27.
61. Stahl, F. 1988. Bacterial genetics: A unicorn in the garden. Nature 335:112-113.
62. Travisano, M. 1997. Long-term experimental evolution in Escherichia coli. VI. Environmental constraints on adaptation and divergence. Genetics 146:471-479.
63. Travisano, M. 2001. Evolution: Towards a genetical theory of adaptation. Current Biology 11:R440-442.
64. Travisano, M., and R. Lenski. 1996. Long-term experimental evolution in Escherichia coli. IV. Targets of selection and the specificity of adaptation. Genetics 143:15-26.
65. Travisano, M., J. A. Mongold, A. F. Bennett, and R. E. Lenski. 1995a. Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267:87-90.
66. Travisano, M., and P. Rainey. 2000. Studies of adaptive radiation using model microbial systems. American Naturalist 156:S35-S44.
67. Travisano, M., F. Vasi, and R. Lenski. 1995b. Long-term experimental evolution in Escherichia coli. III. Variation among replicate populations in correlated responses to novel environments. Evolution 49:189-200.
68. Wilke, C. 2004. The speed of adaptation in large asexual populations. Genetics 167: 2045-2053.
69. Woods, R., D. Schneider, C. Winkworth, M. Riley, and R. Lenski. 2006. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proceedings of the National Academy of Sciences of the USA 103:9107-9112.