The pace of evolution across fitness valleys

Journal of Theoretical Biology

Volumn 259, Issue 3, 2009, Pages 613-620

  Gokhale, Chaitanya S ^a   Iwasa, Yoh ^b   Nowak, Martin A ^c   Traulsen, Arne ^a  

^a MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^b KYUSHU UNIVERSITY   (Japan)

^c HARVARD UNIVERSITY   (United States)

Author keywords

Evolutionary speed; Finite populations; Stochastic tunneling

Indexed keywords

EVOLUTION; FITNESS; MUTATION; POPULATION SIZE; STOCHASTICITY;

ARTICLE; EVOLUTION; GENE MUTATION; MATHEMATICAL MODEL; MUTATION RATE; POPULATION GENETICS; POPULATION SIZE; PRIORITY JOURNAL;

ADAPTATION, PHYSIOLOGICAL; COMPUTER SIMULATION; EVOLUTION; GENETICS, POPULATION; HUMANS; MUTATION; POPULATION DENSITY; POPULATION DYNAMICS; STOCHASTIC PROCESSES;

EID: 67649961277     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.04.011     Document Type: Article

References (47)

1. Antal T., and Scheuring I. Fixation of strategies for an evolutionary game in finite populations. Bull. Math. Biol. 68 (2006) 1923-1944
2. Armitage P., and Doll R. The age distribution of cancer and a multi-stage theory of carcinogenesis. Br. J. Cancer 8 (1954) 1-12
3. Atwood K.C., Schneider K.L., and Ryan F.J. Periodic selection in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 37 (1951) 146-155
4. Beerenwinkel N., Antal T., Dingli D., Traulsen A., Kinzler K.W., Velculescu V.E., Vogelstein B., and Nowak M.A. Genetic progression and the waiting time to cancer. PLoS Comput. Biol. 3 (2007) e225
5. Chao L., and McBroom S.M. Evolution of transposable elements: an IS10 insertion increases fitness in Escherichia coli. Mol. Biol. Evol. 2 (1985) 359-369
6. Cooper T., Rozen D., and Lenski R.E. Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 100 3 (2003) 1072-1077
7. Crow J.F., and Kimura M. An Introduction to Population Genetics Theory (1970), Harper & Row, New York
8. DePristo M.A., Hartl D.L., and Weinreich D.M. Mutational reversions during adaptive protein evolution. Mol. Biol. Evol. 24 (2007) 1608-1610
9. Eigen M., McCaskill J., and Schuster P. The molecular quasi-species. Adv. Chem. Phys. 75 (1989) 149-263
10. Eigen M., and Schuster P. The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. Die Naturwiss. 64 (1977) 541-565
11. Ewens W.J. Mathematical Population Genetics (2004), Springer, New York
12. Fisher J. Multiple-mutation theory of carcinogenesis. Nature 181 (1959) 651-652
13. Fisher, R.A., 1930. The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
14. Frank S.A. Evolutionary Dynamics of Cancer (2007), Princeton University Press, Princeton, NJ
15. Gerrish P.J., and Lenski R.E. The fate of competing beneficial mutations in a asexual population. Genetica 102/103 (1998) 127-144
16. Gerstung, M., Beerenwinkel, N., 2008. Waiting time models of cancer progression. Mathematical Population Studies, to appear. arXiv:0807.3638.
17. Gillespie J.H. Some properties of finite populations experiencing strong selection and weak mutation. Am Nat. 121 5 (1983) 691-708
18. Gillespie J.H. Population Genetics: A Concise Guide. second ed (2004), The Johns Hopkins University Press
19. Goel N., and Richter-Dyn N. Stochastic Models in Biology (1974), Academic Press, New York
20. Iwasa Y., Michor F., and Nowak M.A. Stochastic tunnels in evolutionary dynamics. Genetics 166 (2004) 1571-1579
21. Jain K., and Krug J. Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes. Genetics 175 (2007) 1275-1288
22. Jones S., Chen W.-D., Parmigiani G., Diehl F., Beerenwinkel N., Antal T., Traulsen A., Nowak M.A., Siegel C., Velculescu V.E., Kinzler K.W., Vogelstein B., Willis J., and Markowitz S.D. Comparative lesion sequencing provides insights into tumor evolution. Proc. Natl. Acad. Sci. U.S.A. 105 11 (2008) 4283-4288
23. Jones S., Zhang X., Parsons D.W., Lin J.C.-H., Leary R.J., Angenendt P., Mankoo P., Carter H., Kamiyama H., Jimeno A., Hong S.-M., Fu B., Lin M.-T., Calhoun E.S., Kamiyama M., Walter K., Nikolskaya T., Nikolsky Y., Hartigan J., Smith D.R., Hidalgo M., Leach S.D., Klein A.P., Jaffee E.M., Goggins M., Maitra A., Iacobuzio-Donahue C., Eshleman J.R., Kern S.E., Hruban R.H., Karchin R., Papadopoulos N., Parmigiani G., Vogelstein B., Velculescu V.E., and Kinzler K.W. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321 5897 (2008) 1801-1806
24. Karlin S., and Taylor H.M.A. A First Course in Stochastic Processes. second ed (1975), Academic Press, London
25. Knudson A.G. Mutation and cancer: statistical study of retinoblastoma. Proc. Natl. Acad. Sci. U.S.A. 68 (1971) 820-823
26. Lee T.H., DSouza L.M., and Fox G.E. Equally parsimonious pathways through an RNA sequence space are not equally likely. J. Mol. Evol. 45 (1997) 278-284
27. Michor F., Iwasa Y., and Nowak M.A. Dynamics of cancer progression. Nat. Rev. Cancer 4 (2004) 197-205
28. Moran P.A.P. The Statistical Processes of Evolutionary Theory (1962), Clarendon Press, Oxford
29. Muller H.J. Some genetic aspects of sex. Am. Nat. 66 703 (1932) 118-138
30. Nordling C. A new theory on cancer inducing mechanism. Br. J. Cancer 7 (1953) 68-72
31. Nowak M.A. What is a quasispecies?. Trends in Ecology and Evolution 7 (1992) 118-121
32. Nowak M.A. Evolutionary Dynamics (2006), Harvard University Press, Cambridge, MA
33. Nowak M.A., Michor F., Komarova N.L., and Iwasa Y. Evolutionary dynamics of tumor suppressor gene inactivation. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 10635-10638
34. Park S.-C., and Krug J. Clonal interference in large populations. Proc. Natl. Acad. Sci. U.S.A. 104 46 (2007) 18135-18140
35. Poelwijk F.J., Kiviet D.J., Weinreich D.M., and Tans S.J. Empirical fitness landscales reveal accessible evolutionary paths. Nature 445 (2007) 383-386
36. Press W.H., Teukolsky S.A., Vetterling W.T., and Flannery B.P. Numerical Recipes 3rd Edition: The Art of Scientific Computing (2007), Cambridge University Press, New York
37. Sjöblom T., Jones S., Wood L., Parsons D., Lin J., Barber T., Mandelker D., Leary R., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S., Willis J., Dawson D., Willson J., Gazdar A., Hartigan J., Wu L., Liu C., Parmigiani G., Park B., Bachman K., Papadopoulos N., Vogelstein B., Kinzler K., and Velculescu V. The consensus coding sequences of human breast and colorectal cancers. Science 314 (2006) 268-274
38. Traulsen A., Iwasa Y., and Nowak M.A. The fastest evolutionary trajectory. J. Theor. Biol. 249 3 (2007) 617-623
39. van Nimwegen E., and Crutchfield J. Metastable evolutionary dynamics: crossing fitness barriers or escaping via neutral paths?. Bull. Math. Biol. 62 (2000) 799-848
40. Vogelstein B., and Kinzler K. Cancer genes and the pathways they control. Nat. Med. 10 (2004) 789-799
41. Weinreich D. The rank ordering of genotypic fitness values predicts genetic constraint on natural selection on landscapes lacking sign epistasis. Genetics 171 (2005) 1397-1405
42. Weinreich D., Delaney N., DePristo M., and Hartl D. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312 (2006) 111-114
43. Weinreich D.M., and Chao L. Rapid evolutionary escape by large populations from local fitness peaks is likely in nature. Evolution 59 (2005) 1175-1182
44. Weinreich D.M., Watson R., and Chao L. Perspective: sign epistasis and genetic constraint on evolutionary trajectories. Evolution 56 6 (2005) 1165-1174
45. Wilke C. The speed of adaptation in large asexual populations. Genetics 167 (2004) 2045-2053
46. Wilke C. Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5 (2005) 44
47. Wood L.D., Parsons D.W., Jones S., Lin J., Sjöblom T., Leary R.J., Shen D., Boca S.M., Barber T., Ptak J., Silliman N., Szabo S., Dezso Z., Ustyanksky V., Nikolskaya T., Nikolsky Y., Karchin R., Wilson P.A., Kaminker J.S., Zhang Z., Croshaw R., Willis J., Dawson D., Shipitsin M., Willson J.K.V., Sukumar S., Polyak K., Park B.H., Pethiyagoda C.L., Pant P.V.K., Ballinger D.G., Sparks A.B., Hartigan J., Smith D.R., Suh E., Papadopoulos N., Buckhaults P., Markowitz S.D., Parmigiani G., Kinzler K.W., Velculescu V.E., and Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science 318 5853 (2007) 1108-1113