A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies

American Naturalist

Volumn 178, Issue 4, 2011, Pages 538-552

  Korolev, Kirill S ^a   Xavier, João B ^b   Nelson, David R ^c   Foster, Kevin R ^d,e  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^c HARVARD UNIVERSITY   (United States)

^d HARVARD UNIVERSITY   (United States)

^e UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Bacterial colonies; Biofilms; Genetic drift; Neutral evolution; Range expansion; Spatial population genetics

Indexed keywords

BACTERIUM; BIOFILM; EFFECTIVE POPULATION SIZE; EMPIRICAL ANALYSIS; GENETIC DRIFT; ONE-DIMENSIONAL MODELING; QUANTITATIVE ANALYSIS; RANGE EXPANSION;

ARTICLE; BIOFILM; BIOLOGICAL MODEL; COMPUTER SIMULATION; ESCHERICHIA COLI; EVALUATION; EVOLUTION; GENETIC VARIABILITY; GENETICS; GROWTH, DEVELOPMENT AND AGING; POPULATION DENSITY; POPULATION DYNAMICS; POPULATION GENETICS; PSEUDOMONAS AERUGINOSA;

BIOFILMS; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; ESCHERICHIA COLI; GENETIC VARIATION; GENETICS, POPULATION; MODELS, BIOLOGICAL; POPULATION DENSITY; POPULATION DYNAMICS; PSEUDOMONAS AERUGINOSA;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PSEUDOMONAS AERUGINOSA;

EID: 80053273724     PISSN: 00030147     EISSN: None     Source Type: Journal    
DOI: 10.1086/661897     Document Type: Article

References (71)

1. Barrett, R. D. H., R. C. MacLean, and G. Bell. 2005. Experimental evolution of Pseudomonas fluorescens in simple and complex environments. American Naturalist 166:470-480.
2. Bartlett, R., M. Mazens, and M. Testa. 1985. Differentiation of Pseudomonas aeruginosa and Enterobacteriaceae in direct smears based on measurements by scanning electron microscopy. Diagnostic Microbiology and Infectious Disease 3:143-147.
3. Barton, N. H., F. Depaulis, and A. M. Etheridge. 2002. Neutral evolution in spatially continuous populations. Theoretical Population Biology 61:31-48.
4. Beloin, C., and J. Ghigo. 2005. Finding gene-expression patterns in bacterial biofilms. Trends in Microbiology 13:16-19.
5. Bramson, M., and J. L. Lebowitz. 1991. Asymptotic behavior of densities for two-particle annihilating random walks. Journal of Statistical Physics 62:297-372.
6. Charlesworth, B., D. Charlesworth, and N. H. Barton. 2003. The effects of genetic and geographic structure on neutral variation. Annual Review of Ecology, Evolution, and Systematics 34:99-125.
7. Cox, J. T., and D. Griffeath. 1986. Diffusive clustering in the two dimensional voter model. Annals of Probability 14:347-370.
8. Crow, J. F., and M. Kimura. 1970. An introduction to population genetics theory. Harper & Row, New York.
9. Dobzhansky, T. 1937. Genetics and the origin of species. Columbia University Press, New York. Dockery, J., and I. Klapper. 2001. Finger formation in biofilm layer. SIAM Journal on Applied Mathematics 62:853-869.
10. Doering, C. R., C. Mueller, and P. Smereka. 2003. Interacting particles, the stochastic Fisher-Kolmogorov-Petrovsky-Piscounov equation, and duality. Physica A 325:243-259.
11. Elena, S. F., and R. E. Lenski. 2003. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Reviews Genetics 4:457-469.
12. Ewens, W. 1982. On the concept of the effective population size. Theoretical Population Biology 21:373-378.
13. Excoffier, L., M. Foll, and R. J. Petit. 2009. Genetic consequences of range expansions. Annual Review of Ecology, Evolution, and Systematics 40:481-501.
14. Felsenstein, J. 1976. The theoretical population genetics of variable selection and migration. Annual Review of Genetics 10:253-280.
15. Fisher, R. A. 1930. The genetical theory of natural selection. Clarendon, Oxford.
16. Fisher, R. A. 1937. The wave of advance of advantageous genes. Annals of Eugenics 7:355-369.
17. Gardiner, C. 1985. Handbook of stochastic methods. Springer, New York.
18. Hallatschek, O., and K. S. Korolev. 2009. Fisher waves in the strong noise limit. Physical Review Letters 103:108103-108106.
19. Hallatschek, O., and D. R. Nelson. 2008. Gene surfing in expanding populations. Theoretical Population Biology 73:158-170.
20. Hallatschek, O., and D. R. Nelson. 2010. Life at the front of an expanding population. Evolution 64:193-206.
21. Hallatschek, O., P. Hersen, S. Ramanathan, and D. R. Nelson. 2007. Genetic drift at expanding frontiers promotes gene segregation. Proceedings of the National Academy of Sciences of the USA 104: 19926-19930.
22. Hamilton, W. D. 1964. The genetical evolution of social behaviour. I. Theoretical Population Biology 7:1-16.
23. Hammer, B., and B. Bassler. 2003. Quorum sensing controls biofilm formation in Vibrio cholerae. Molecular Microbiology 50:101-104.
24. Hauert, C., and M. Doebeli. 2004. Spatial structure often inhibits the evolution of cooperation in the snowdrift game. Nature 428: 643-646.
25. Houchmandzadeh, B., and M. Vallade. 2003. Clustering in neutral ecology. Physical Review E 68:61912-61918.
26. Hubbell, S. P. 2001. The unified neutral theory of biodiversity and biogeography. Princeton University Press, Princeton, NJ.
27. Huntley, H. E. 1970. The divine proportion: a study in mathematical beauty. Dover, New York.
28. Kardar, M., G. Parisi, and Y. Zhang. 1986. Dynamic scaling of growing interfaces. Physical Review Letters 56:889-892.
29. Kerr, B., C. Neuhauser, B. Bohannan, and A. Dean. 2006. Local migration promotes competitive restraint in a host-pathogen "tragedy of the commons. Nature 442:75-78.
30. Kimura, M., and G. H. Weiss. 1964. The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49:561-576.
31. Kingman, J. F. C. 1982. On the genealogy of large populations. Journal of Applied Probability 19A:27-43.
32. Klausen, M., A. Heydorn, P. Ragas, L. Lambertsen, A. Aaes-Jorgensen, S. Molin, and T. Tolker-Nielsen. 2003. Biofilm formation by Pseudomonas aeruginosa wild type, flagella and type IV pili mutants. Molecular Microbiology 48:1511-1524.
33. Kolmogorov, A. N., N. Petrovsky, and N. S. Piscounov. 1937. A study of the equation of diffusion with increase in the quantity of matter, and its application to a biological problem. Moscow State University Bulletin Series International A 1:1-25.
34. Kolter, R., and E. Greenberg. 2006. Microbial sciences: the superficial life of microbes. Nature 441:300-302.
35. Korolev, K. S. 2010. Statistical physics of topological emulsions and expanding populations. PhD thesis. Harvard University, Cambridge, MA.
36. Korolev, K. S., M. Avlund, O. Hallatschek, and D. R. Nelson. 2010. Genetic demixing and evolution in linear stepping stone models. Reviews of Modern Physics 82:1691-1718.
37. Loewe, L., and W. G. Hill. 2010. The population genetics of mutations: good, bad and indifferent. Philosophical Transactions of the Royal Society B: Biological Sciences 365:1153-1167.
38. Lynch, M. 2002. Intron evolution as a population-genetic process. Proceedings of the National Academy of Sciences of the USA 99: 6118-6123.
39. Malécot, G. 1955. The decrease of relationship with distance. Cold Spring Harbor Symposia on Quantitative Biology 20:52-53.
40. Malécot, G. 1975. Heterozygosity and relationship in regularly subdivided populations. Theoretical Population Biology 8:212-241.
41. Maruyama, T. 1970. On the fixation probability of mutant genes in a subdivided population. Genetics Research 15:221-225.
42. Masser, T., and D. ben Avraham. 2000. Kinetics of coalescence, annihilation, and the q-state Potts model in one dimension. Physics Letters A 275:382-385.
43. Mayr, E. 1959. Where are we? Cold Spring Harbor Symposia on Quantitative Biology 24:1-14.
44. Michor, F., S. A. Frank, R. M. May, Y. Iwasa, and M. A. Nowak. 2003. Somatic selection for and against cancer. Journal of Theoretical Biology 225:377-382.
45. Murray, J. D. 2003. Mathematical biology. Springer, Berlin.
46. Nadell, C., J. Xavier, S. Levin, and K. Foster. 2008. The evolution of quorum sensing in bacterial biofilms. PLoS Biology 6:e14.
47. Nadell, C. D., J. Xavier, and K. R. Foster. 2009. The sociobiology of biofilms. FEMS Microbiology Reviews 33:206-224.
48. Nadell, C. D., K. R. Foster, and J. Xavier. 2010. Emergence of spatial structure in cell groups and the evolution of cooperation. PLoS Computational Biology 6:e1000716.
49. Nagylaki, T. 1974. The decay of genetic variability in geographically structured populations. Proceedings of the National Academy of Sciences of the USA 74:2523-2525.
50. Nagylaki, T. 1998. The expected number of heterozygous sites in a subdivided population. Genetics 149:1599-1604.
51. Nagylaki, T., and Y. Lou. 2008. The dynamics of migration-selection models. Tutorials in Mathematical Biosciences IV 1922:117-170.
52. Nowak, M. A., and R. M. May. 1992. Evolutionary games and spatial chaos. Nature 359:826-829.
53. O ́ dor, G. 2004. Universality classes in nonequilibrium lattice systems. Reviews of Modern Physics 76:663-724.
54. Parsek, M., and E. Greenberg. 1999. Quorum sensing signals in development of Pseudomonas aeruginosa biofilms. Methods in Enzymology 310:43-55.
55. Pratt, V. 1987. Direct least-squares fitting of algebraic surfaces. Computer Graphics 21:145-152.
56. Rainey, P., and K. Rainey. 2003. Evolution of cooperation and conflict in experimental bacterial populations. Nature 425:72-74.
57. Rainey, P., and M. Travisano. 1977. Adaptive radiation in a heterogeneous environment. Philosophical Transactions of the Royal Society B: Biological Sciences 280:29-101.
58. Rani, S., B. Pitts, H. Beyenal, R. Veluchamy, Z. Lewandowski, W. Davison, K. Buckingham-Meyer, and P. Stewart. 2007. Spatial patterns of DNA replication, protein synthesis, and oxygen concentration within bacterial biofilms reveal diverse physiological states. Journal of Bacteriology 189:4223-4233.
59. Risken, H. 1989. The Fokker-Planck equation: methods of solution and applications. Springer, Berlin.
60. Rousset, F. 2004. Genetic structure and selection in subdivided populations. Princeton University Press, Princeton, NJ.
61. Stewart, P. 2003. Diffusion in biofilms. Journal of Bacteriology 185: 1485-1491.
62. Vulic, M., and R. Kolter. 2001. Evolutionary cheating in Escherichia coli stationary phase cultures. Genetics 158:519-526.
63. Wakeley, J. 2008. Coalescent theory: an introduction. Roberts, Greenwood Village, CO.
64. Wakita, J., K. Komatsu, A. Nakahara, T. Matsuyama, and M. Matsushita. 1994. Experimental investigation on the validity of population dynamics approach to bacterial colony formation. Journal of the Physical Society of Japan 63:1205-1211.
65. West, S. A., S. P. Diggle, A. Buckling, A. Gardner, and A. S. Griffin. 2007. The social lives of microbes. Annual Review of Ecology, Evolution, and Systematics 38:53-77.
66. Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress of Genetics 1:356-366.
67. Wright, S. 1943. Isolation by distance. Genetics 28:114-138.
68. Xavier, J. B., C. Picioreanu, and M. C. van Loosdrecht. 2005. A framework for multidimensional modelling of activity and structure of multispecies biofilms. Environmental Microbiology 7:1085-1103.
69. Xavier, J. B., E. Martinez-Garcia, and K. R. Foster. 2009. Social evolution of spatial patterns in bacterial biofilms: when conflict drives disorder. American Naturalist 174:1-12.
70. Xavier, J., W. Kim, and K. Foster. 2011. A molecular mechanism that stabilizes cooperative secretions in Pseudomonas aeruginosa. Molecular Microbiology 79:166-179.
71. Yang, L., J. Haagensen, L. Jelsbak, H. Johansen, C. Sternberg, N. Hoiby, and M. Soren. 2008. In situ growth rates and biofilm development of Pseudomonas aeruginosa populations in chronic lung infections. Journal of Bacteriology 190:2767-2776