Emergence of species in evolutionary ́simulated annealinǵ

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

Volumn 106, Issue 6, 2009, Pages 1869-1874

  Heo, Muyoung ^a   Kang, Louis ^a   Shakhnovich, Eugene I ^a  

^a HARVARD UNIVERSITY   (United States)

Author keywords

Digital life; Fitness landscape; Molecular evolution; Mutation rates; Protein interaction networks

Indexed keywords

DNA;

ARTICLE; ASEXUAL REPRODUCTION; FITNESS; GENE SEQUENCE; MOLECULAR EVOLUTION; MUTATION RATE; POPULATION DYNAMICS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION;

ANIMALS; COMPUTER SIMULATION; EVOLUTION; EVOLUTION, MOLECULAR; GENETIC SPECIATION; KINETICS; MODELS, GENETIC; MUTATION; POPULATION DYNAMICS; PROTEINS; REPRODUCTION, ASEXUAL; SELECTION (GENETICS);

EID: 60549115416     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0809852106     Document Type: Article

References (40)

1. Mayr E (1942) Systematics and the origin of species (Columbia Univ Press, New York).
2. De Queiroz K (2007) Species concepts and species delimitation. Syst Biol 56:879-886.
3. Eigen M (1971) Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58:465-523.
4. Fersht A (1999) Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding (W.H. Freeman, New York).
5. Bolon DN, Grant RA, Baker TA, Sauer RT (2005) Specificity versus stability in computational protein design. Proc Natl Acad Sci USA 102:12724-12729.
6. Taverna DM, Goldstein RA (2002) Why are proteins so robust to site mutations? J Mol Biol 315:479-484.
7. Zeldovich KB, Chen P, Shakhnovich EI (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci USA 104:16152-16157.
8. Drake JW, Holland JJ (1999) Mutation rates among RNA viruses. Proc Natl Acad Sci USA 96:13910-13913.
9. Anderson JP, Daifuku R, Loeb LA (2004) Viral error catastrophe by mutagenic nucleosides. Annu Rev Microbiol 58:183-205.
10. Denamur E, Matic I (2006) Evolution of mutation rates in bacteria. Mol Microbiol 60:820-827.
11. Earl DJ, Deem MW (2004) Evolvability is a selectable trait. Proc Natl Acad Sci USA 101:11531-11536.
12. Sniegowski PD, Gerrish PJ, Lenski RE (1997) Evolution of high mutation rates in experimental populations of E. coli. Nature 387:703-705.
13. Shaver AC, et al. (2002) Fitness evolution and the rise of mutator alleles in experimental Escherichia coli populations. Genetics 162:557-566.
14. Matic I, et al. (1997) Highly variable mutation rates in commensal and pathogenic Escherichia coli. Science 277:1833-1834.
15. Zeldovich KB, Chen P, Shakhnovich BE, Shakhnovich EI (2007) A first-principles model of early evolution: Emergence of gene families, species, and preferred protein folds. PLoS Comp Biol 3:e139.
16. Shakhnovich EI, Gutin A (1990) Enumeration of all compact conformations of copolymers with random sequence links. J Chem Phys 93:5967-5971.
17. Fraser HB, et al. (2002) Evolutionary rate in the protein interaction network. Science 296:750-752.
18. Jain K, Krug J (2005) Adaptation in simple and complex fitness landscapes. q-bio PE/0508008.
19. Eigen M, McCaskill J, Schuster P (1989) The Molecular Quasi-Species. Adv Chem Phys 75:149-263.
20. Fontana W, Schuster P (1998) Continuity in evolution: On the nature of transitions. Science 280:1451-1455.
21. Huynen MA, Stadler PF, Fontana W (1996) Smoothness within ruggedness: The role of neutrality in adaptation. Proc Natl Acad Sci USA 93:397-401.
22. Forster R, Adami C, Wilke CO (2006) Selection for mutational robustness in finite populations. J Theor Biol 243:181-190.
23. Zhang J, Maslov S, Shakhnovich EI (2008) Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol Syst Biol 4:210.
24. Novella IS, et al. (1995) Exponential increases of RNA virus fitness during large population transmissions. Proc Natl Acad Sci USA 92:5841-5844.
25. Elena SF, Cooper VS, Lenski RE (1996) Punctuated evolution caused by selection of rare beneficial mutations. Science 272:1802-1804.
26. Elena SF, Lenski RE (2003) Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation. Nat Rev Genet 4:457-469.
27. Wilke CO, Campos PR, Fontanari JF (2002) Genealogical process on a correlated fitness landscape. J Exp Zool 294:274-284.
28. Crotty S, Cameron CE, Andino R (2001) RNA virus error catastrophe: Direct molecular test by using ribavirin. Proc Natl Acad Sci USA 98:6895-6900.
29. Drake JW (1999) The distribution of rates of spontaneous mutation over viruses, prokaryotes, and eukaryotes. Ann N Y Acad Sci 870:100-107.
30. Zeldovich KB, Shakhnovich EI (2008) Understanding protein evolution: From protein physics to Darwinian selection. Annu Rev Phys Chem 59:105-127.
31. Orr HA (2000) The rate of adaptation in asexuals. Genetics 155:961-968.
32. Andre JB, Godelle B (2006) The evolution of mutation rate in finite asexual populations. Genetics 172:611-626.
33. Sniegowski PD, Gerrish PJ, Johnson T, Shaver A (2000) The evolution of mutation rates: Separating causes from consequences. Bioessays 22:1057-1066.
34. Gerrish PJ, Colato A, Perelson AS, Sniegowski PD (2007) Complete genetic linkage can subvert natural selection. Proc Natl Acad Sci USA 104:6266-6271.
35. Taddei F, et al. (1997) Role of mutator alleles in adaptive evolution. Nature 387:700-702.
36. Taverna DM, Goldstein RA (2000) The distribution of structures in evolving protein populations. Biopolymers 53:1-8.
37. Takeuchi N, Poorthuis PH, Hogeweg P (2005) Phenotypic error threshold; additivity and epistasis in RNA evolution. BMC Evol Biol 5:9.
38. van Nimwegen E, Crutchfield JP, Huynen M (1999) Neutral evolution of mutational robustness. Proc Natl Acad Sci USA 96:9716-9720.
39. Wilke CO (2001) Adaptive evolution on neutral networks. Bull Math Biol 63:715-730.
40. Maslov S, Ispolatov I (2007) Propagation of large concentration changes in reversible protein-binding networks. Proc Natl Acad Sci USA 104:13655-13660.