Predictability of evolution depends nonmonotonically on population size

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 2, 2013, Pages 571-576

  Szendro, Ivan G ^a   Franke, Jasper ^a   De Visser, J Arjan G M ^b   Krug, Joachim ^a  

^a UNIVERSITY OF COLOGNE   (Germany)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Clonal interference; Epistasis; Experimental evolution

Indexed keywords

AMPLITUDE MODULATION; ARTICLE; ASPERGILLUS NIGER; CLONE; ENTROPY; EPISTASIS; GENE LOCUS; MICROORGANISM; MOLECULAR EVOLUTION; MUTATION; MUTATION RATE; NONHUMAN; POPULATION SIZE; PRIORITY JOURNAL;

ADAPTATION, BIOLOGICAL; ASPERGILLUS NIGER; BIOLOGICAL EVOLUTION; COMPUTER SIMULATION; ENTROPY; GENETIC FITNESS; MODELS, THEORETICAL; MUTATION RATE; POPULATION DENSITY;

ASPERGILLUS NIGER; FUNGI;

EID: 84872198240     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1213613110     Document Type: Article

References (52)

1. Beatty J (2006) Replaying life's tape. J Philos 7:336-362.
2. Conway Morris S (2010) Evolution: Like any other science it is predictable. Philos Trans R Soc Lond B Biol Sci 365(1537):133-145.
3. Gould SJ (1989) Wonderful Life (Norton, New York).
4. Conway Morris S (2003) Life's Solution: Inevitable Humans in a Lonely Universe (Cambridge Univ Press, Cambridge, UK).
5. Travisano M, Mongold JA, Bennett AF, Lenski RE (1995) Experimental tests of the roles of adaptation, chance, and history in evolution. Science 267(5194):87-90.
6. Cooper TF, Rozen DE, Lenski RE (2003) Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proc Natl Acad Sci USA 100(3):1072-1077.
7. Blount ZD, Borland CZ, Lenski RE (2008) Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci USA 105(23):7899-7906.
8. Saxer G, Doebeli M, Travisano M (2010) The repeatability of adaptive radiation during long-term experimental evolution of Escherichia coli in a multiple nutrient environment. PLoS One 5(12):e14184.
9. Wichman HA, Brown CJ (2010) Experimental evolution of viruses: Microviridae as a model system. Philos Trans R Soc Lond B Biol Sci 365(1552):2495-2501.
10. Weinreich DM, Delaney NF, Depristo MA, Hartl DL (2006) Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312(5770):111-114.
11. Lozovsky ER, et al. (2009) Stepwise acquisition of pyrimethamine resistance in the malaria parasite. Proc Natl Acad Sci USA 106(29):12025-12030.
12. Salverda MLM, et al. (2011) Initial mutations direct alternative pathways of protein evolution. PLoS Genet 7(3):e1001321.
13. Toprak E, et al. (2012) Evolutionary paths to antibiotic resistance under dynamically sustained drug selection. Nat Genet 44(1):101-105.
14. Schenk MF, Szendro IG, Krug J, de Visser JAGM (2012) Quantifying the adaptive potential of an antibiotic resistance enzyme. PLoS Genet 8(6):e1002783.
15. Roy SW (2009) Probing evolutionary repeatability: Neutral and double changes and the predictability of evolutionary adaptation. PLoS One 4(2):e4500.
16. Wahl LM, Krakauer DC (2000) Models of experimental evolution: The role of genetic chance and selective necessity. Genetics 156(3):1437-1448.
17. Jain K, Krug J (2007) Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes. Genetics 175(3):1275-1288.
18. Lobkovsky AE, Wolf YI, Koonin EV (2011) Predictability of evolutionary trajectories in fitness landscapes. PLoS Comput Biol 7(12):e1002302.
19. Gillespie JH (1983) A simple stochastic gene substitution model. Theor Popul Biol 23(2):202-215.
20. Gillespie JH (1984) Molecular evolution over the mutational landscape. Evolution 38:1116-1129.
21. Orr HA (2002) The population genetics of adaptation: The adaptation of DNA sequences. Evolution 56(7):1317-1330.
22. Weinreich DM, Watson RA, Chao L (2005) Perspective: Sign epistasis and genetic constraint on evolutionary trajectories. Evolution 59(6):1165-1174.
23. Poelwijk FJ, Kiviet DJ, Weinreich DM, Tans SJ (2007) Empirical fitness landscapes reveal accessible evolutionary paths. Nature 445(7126):383-386.
24. Carneiro M, Hartl DL (2010) Colloquium papers: Adaptive landscapes and protein evolution. Proc Natl Acad Sci USA 107(Suppl 1):1747-1751.
25. da Silva J, Coetzer M, Nedellec R, Pastore C, Mosier DE (2010) Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region. Genetics 185(1):293-303.
26. Franke J, Klözer A, de Visser JAGM, Krug J (2011) Evolutionary accessibility of mutational pathways. PLoS Comput Biol 7(8):e1002134.
27. Szendro IG, Schenk MF, Franke J, Krug J, de Visser JAGM (2012) Quantitative analyses of empirical fitness landscapes. arXiv:1202.4378.
28. Gerrish PJ, Lenski RE (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102-103(1-6):127-144.
29. Wilke CO (2004) The speed of adaptation in large asexual populations. Genetics 167(4):2045-2053.
30. Park SC, Krug J (2007) Clonal interference in large populations. Proc Natl Acad Sci USA 104(46):18135-18140.
31. Park SC, Simon D, Krug J (2010) The speed of evolution in large asexual populations. J Stat Phys 138:381-410.
32. Rozen DE, de Visser JAGM, Gerrish PJ (2002) Fitness effects of fixed beneficial mutations in microbial populations. Curr Biol 12(12):1040-1045.
33. Schiffels S, Szöllosi GJ, Mustonen V, Lässig M (2011) Emergent neutrality in adaptive asexual evolution. Genetics 189(4):1361-1375.
34. Orr HA (2003) A minimum on the mean number of steps taken in adaptive walks. J Theor Biol 220(2):241-247.
35. Jain K, Krug J, Park SC (2011) Evolutionary advantage of small populations on complex fitness landscapes. Evolution 65(7):1945-1955.
36. Rozen DE, Habets MGJL, Handel A, de Visser JAGM (2008) Heterogeneous adaptive trajectories of small populations on complex fitness landscapes. PLoS One 3:e1715.
37. Handel A, Rozen DE (2009) The impact of population size on the evolution of asexual microbes on smooth versus rugged fitness landscapes. BMC Evol Biol 9:236.
38. Iwasa Y, Michor F, Nowak MA (2004) Stochastic tunnels in evolutionary dynamics. Genetics 166(3):1571-1579.
39. Weinreich DM, Chao L (2005) Rapid evolutionary escape by large populations from local fitness peaks is likely in nature. Evolution 59(6):1175-1182.
40. Weissman DB, Desai MM, Fisher DS, Feldman MW (2009) The rate at which asexual populations cross fitness valleys. Theor Popul Biol 75(4):286-300.
41. Aita T, et al. (2000) Analysis of a local fitness landscape with a model of the rough Mt. Fuji-type landscape: Application to prolyl endopeptidase and thermolysin. Biopolymers 54(1):64-79.
42. Lenski RE, Ofria C, Pennock RT, Adami C (2003) The evolutionary origin of complex features. Nature 423(6936):139-144.
43. Østman B, Hintze A, Adami C (2012) Impact of epistasis and pleiotropy on evolutionary adaptation. Proc R Soc B Biol Sci 279(1727):247-256.
44. Jain K, Krug J (2005) Evolutionary trajectories in rugged fitness landscapes. J Stat Mech 2005:P04008.
45. Miller CR, Joyce P, Wichman HA (2011) Mutational effects and population dynamics during viral adaptation challenge current models. Genetics 187(1):185-202.
46. Woods RJ, et al. (2011) Second-order selection for evolvability in a large Escherichia coli population. Science 331(6023):1433-1436.
47. de Visser JAGM, Hoekstra RF, van den Ende H (1997) Test of interaction between genetic markers that affect fitness in Aspergillus niger. Evolution 51:1499-1505.
48. Kimura M (1962) On the probability of fixation of mutant genes in a population. Genetics 47:713-719.
49. Orr HA (2005) The probability of parallel evolution. Evolution 59(1):216-220.
50. Joyce P, Rokyta DR, Beisel CJ, Orr HA (2008) A general extreme value theory model for the adaptation of DNA sequences under strong selection and weak mutation. Genetics 180(3):1627-1643.
51. Kouyos RD, et al. (2012) Exploring the complexity of the HIV-1 fitness landscape. PLoS Genet 8(3):e1002551.
52. Schoustra SE, Bataillon T, Gifford DR, Kassen R (2009) The properties of adaptive walks in evolving populations of fungus. PLoS Biol 7(11):e1000250.