The impact of host-cell dynamics on the fixation probability for lytic viruses

Journal of Theoretical Biology

Volumn 259, Issue 4, 2009, Pages 799-810

  Patwa, Z ^a   Wahl, L M ^a  

^a UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

Experimental evolution; Host dynamics; Life history; Population bottlenecks

Indexed keywords

HOST; LIFE HISTORY; LYSIS; NUMERICAL MODEL; POPULATION BOTTLENECK; VIRUS;

ALLELE; ARTICLE; CELL DENSITY; CELL POPULATION; DYNAMICS; EVOLUTION; HOST CELL; LYSIS; LYTIC VIRUS; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; PROBABILITY; VIRUS; VIRUS MUTANT; VIRUS MUTATION;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BIOLOGICAL EVOLUTION; CELL DEATH; HOST-PATHOGEN INTERACTIONS; MODELS, GENETIC; MUTATION; POPULATION DYNAMICS; SELECTION, GENETIC; VIRION; VIRUS PHYSIOLOGICAL PROCESSES; VIRUSES;

EID: 67650744273     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.05.008     Document Type: Article

References (46)

1. Abedon S.T., Herschler T.D., and Stopar D. Bacteriophage latent-period evolution as a response to resource availability. Appl. Environ. Microbiol. 67 (2001) 4233-4241
2. Alexander H.K., and Wahl L.M. Fixation probabilities depend on life history: fecundity, generation time and survival in a burst-death model. Evolution 62 (2008) 1600-1609
3. Andre J.B., and Day T. The effect of disease life history on the evolutionary emergence of novel pathogens. Proc. R. Soc. London Ser. B 272 (2005) 1949-1956
4. Bergstrom C.T., McElhany P., and Real L.A. Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens. Proc. Natl. Acad. Sci. USA 96 (1999) 5095-5100
5. Bonhoeffer S., and Nowak M.A. Pre-existence and emergence of drug resistance in HIV-1 infection. Proc. R. Soc. London B 264 (1997) 631-637
6. Bull J.J. Optimality models of phage life history and parallels in disease evolution. J. Theor. Biol. 241 (2006) 928-938
7. Bull J.J., Badgett M.R., and Wichman H.A. Big-benefit mutations in a bacteriophage inhibited with heat. Mol. Biol. Evol. 17 (2000) 942-950
8. Bull J.J., Badgett M.R., Wichman H.A., Huelsenbeck J.P., Hillis D.M., Gulati A., Ho C., and Molineux I.J. Exceptional convergent evolution in a virus. Genetics 147 (1997) 1497-1507
9. Bull J.J., Pfennig D.W., and Wang I.N. Genetic details, optimization and phage life histories. Trends Ecol. Evol. 19 (2004) 76-82
10. Burch C.L., and Chao L. Evolution by small steps and rugged landscapes in the RNA virus φ 6. Genetics 151 (1999) 921-927
11. Burch C.L., and Chao L. Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature 406 (2000) 625-628
12. Coombs D., Gilchrist M.A., and Ball C.L. Evaluating the importance of within- and between-host selection pressures on the evolution of chronic pathogens. Theor. Popul. Biol. 72 (2007) 576-591
13. Desai M.M., and Fisher D.S. Beneficial mutation-selection balance and the effect of linkage on positive selection. Genetics 176 (2007) 1759-1798
14. Ewens W.J. The probability of survival of a new mutant in a fluctuating environment. Heredity 22 (1967) 438-443
15. Fisher R.A. On the dominance ratio. Proc. R. Soc. Edinburgh 50 (1922) 204-219
16. Gerrish P.J., and Lenski R.E. The fate of competing beneficial mutations in an asexual population. Genetica 102/103 (1998) 127-144
17. Grimmett G.R., and Stirzaker D.R. Probability and Random Processes (2001), Oxford University Press, Oxford
18. Haldane J.B.S. The mathematical theory of natural and artificial selection. Proc. Cambridge Philos. Soc. 23 (1927) 838-844
19. Handel A., and Bennett M.R. Surviving the bottleneck: transmission mutants and the evolution of microbial populations. Genetics 180 (2008) 2193-2200
20. Heffernan J.M., and Corless R.M. Solving some delay differential equations with computer algebra. The Mathematical Scientist 31 (2006) 21-34
21. Hubbarde J.E., Wild G., and Wahl L.M. Fixation probabilities when generation times are variable: the burst-death model. Genetics 176 (2007) 1703-1712
22. Joseph S.B., and Kirkpatrick M. Effects of the [PSI +] prion on rates of adaptation in yeast. J. Evol. Biol. 21 (2008) 773-780
23. Kimura M. Some problems of stochastic processes in genetics. Ann. Math. Stat. 28 (1957) 882-901
24. Kimura M. On the probability of fixation of mutant genes in a population. Genetics 47 (1962) 713-719
25. Kimura, M., 1970. Stochastic processes in population genetics, with special reference to distribution of gene frequencies and probability of gene fixation. In: Mathematical Topics in Population Genetics, Springer, New York, pp. 178-209.
26. Krakauer D.C., and Komarova N.L. Levels of selection in positive-strand virus dynamics. J. Evol. Biol. 16 (2003) 64-73
27. Lambert A. Probability of fixation under weak selection: a branching process unifying approach. Theor. Popul. Biol. 69 (2006) 419-441
28. Levin B.R., Stewart F.M., and Chao L. Resource-limited growth, competition and predation-a model and experimental studies with bacteria and bacteriophage. Am. Nat. 111 (1977) 3-24
29. Manrubia S.C., Escarmís C., Domingo E., and Lázaro E. High mutation rates, bottlenecks, and robustness of RNA viral quasispecies. Gene 347 (2005) 273-282
30. Moya A., Holmes E.C., and González-Candelas F. The population genetics and evolutionary epidemiology of RNA viruses. Microbiology 2 (2004) 279-288
31. Otto S.P., and Whitlock M.C. The probability of fixation in populations of changing size. Genetics 146 (1997) 723-733
32. Parsons T.L., and Quince C. Fixation in haploid populations exhibiting density dependence I: the non-neutral case. Theor. Popul. Biol. 72 (2007) 121-135
33. Patwa Z., and Wahl L.M. Fixation probability for lytic viruses: the attachment-lysis model. Genetics 180 (2008) 459-470
34. Patwa Z., and Wahl L.M. The fixation probability of beneficial mutations. J. R. Soc. Interface 5 (2008) 1279-1289
35. Perron G.G., Gonzalez A., and Buckling A. The rate of environmental change drives adaptation to an antibiotic sink. J. Evol. Biol. 21 (2008) 1724-1731
36. Pollak E. Fixation probabilities when the population size undergoes cyclic fluctuations. Theor. Popul. Biol. 57 (2000) 51-58
37. Sanjuán R., Cuevas J.M., Moya A., and Elena S.F. Epistasis and the adaptability of an RNA virus. Genetics 170 (2005) 1001-1008
38. Schoustra S.E., Slakhorst M., Debets A.J.M., and Hoekstra R.F. Comparing artificial and natural selection in rate of adaptation to genetic stress in Aspergillus nidulans. J. Evol. Biol. 18 (2005) 771-778
39. Stilianakis N.I., Perelson A.S., and Hayden F.G. Emergence of drug resistance during an influenza epidemic: insights from a mathematical model. J. Infect. Dis. 177 (1997) 863-873
40. Wahl L.M., and DeHaan C.S. Fixation probability favors increased fecundity over reduced generation time. Genetics 168 (2004) 1009-1018
41. Wang I.N., Dykhuizen D.E., and Slobodkin L.B. The evolution of phage lysis timing. Evol. Ecol. 10 (1996) 545-558
42. Wichman H.A., Badgett M.R., Scott L.A., Boulianne C.M., and Bull J.J. Different trajectories of parallel evolution during viral adaptation. Science 285 (1999) 422-424
43. Wilke C.O. Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics 163 (2003) 467-474
44. Williamson S. Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Mol. Biol. Evol. 20 (2003) 1318-1325
45. Wright S. Evolution in Mendelian populations. Genetics 16 (1931) 97-159
46. Zhan J., Mundt C.C., Hoffer M.E., and McDonald B.A. Local adaptation and effect of host genotype on the rate of pathogen evolution: an experimental test in plant pathosystem. J. Evol. Biol. 15 (2002) 634-647