Climbing mount probable: Mutation as a cause of nonrandomness in evolution

Journal of Heredity

Volumn 100, Issue 5, 2009, Pages 637-647

  Stoltzfus, Arlin ^a,b   Yampolsky, Lev Y ^a,c  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^c EAST TENNESSEE STATE UNIVERSITY   (United States)

Author keywords

Evolution; Genomics; Mutation bias; Population genetics

Indexed keywords

AMINO ACID SUBSTITUTION; CODON; COMPARATIVE GENOMIC HYBRIDIZATION; CONCEPTION; GENE; GENE FREQUENCY; GENETIC VARIABILITY; GENOMICS; HUMAN; MODULATION; MOLECULAR EVOLUTION; MUTATION; NONHUMAN; PRIORITY JOURNAL; REVIEW; VARIANCE;

EVOLUTION, MOLECULAR; GENETIC DRIFT; GENETIC VARIATION; GENETICS, POPULATION; MODELS, GENETIC; MUTATION;

PAN;

EID: 69249205499     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esp048     Document Type: Review

References (56)

1. Ayala FJ. 1970. Teleological explanations in evolutionary biology. Phil Sci. 37:1-15.
2. Beatty J. 2008. Chance variation and evolutionary contingency: darwin, Simpson, the Simpsons, and Gould. In: Ruse M, editor. Oxford handbook of the philosophy of biology. Oxford: Oxford University Press.
3. Bookstein FL. 1987. Random walk and the existence of evolutionary rates. Paleobiology. 13:446-464.
4. Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics. 129:897-907
5. Chuzhanova NA, Anassis EJ, Ball EV, Krawczak M, Cooper DN. 2003. Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum Mutat. 21:28-44.
6. Cornish-Bowden A. 2004. Fundamentals of enzyme kinetics. London: Portland Press.
7. Ebersberger I, Metzler D, Schwarz C, Paabo S. 2002. Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet. 70:1490-1497.
8. Emlen DJ. 2000. Integrating development with evolution: a case study with Beetle Horns. BioScience. 50:403.
9. Ford EB. 1971. Ecological genetics. London: Chapman & Hall.
10. Freeman S, Herron JC. 1998. Evolutionary analysis. Upper Saddle River (NJ): Prentice-Hall.
11. Gillespie JH. 1991. The causes of molecular evolution. New York: Oxford University Press.
12. Gould SJ. 1989. Wonderful life: the Burgess shale and the nature of history. New York: Norton.
13. Gould SJ. 2002. The structure of evolutionary theory. Cambridge (MA): Harvard University Press.
14. Gu X, Hewett-Emmett D, Li WH. 1998. Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria. Genetica. 103:383-391.
15. Hermisson J, Pennings PS. 2005. Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics. 169:2335-2352.
16. Hwang DG, Green P. 2004. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci USA. 101:13994-14001.
17. Johnson PA, Lenski RE, Hoppensteadt FC. 1995. Theoretical analysis of divergence in mean fitness between initially identical populations. Proc R Soc Lond B Biol Sci. 259:125-130.
18. Kacser H, Burns JA. 1973. The control of flux. Symp Soc Exp Biol. 27:65-104.
19. Kauffman SA. 1993. The origins of order: self-organization and evolution. New York: Oxford University Press.
20. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
21. King JL. 1971. The role of mutation in evolution. In: Le Cam LM, Newman J, Scott EL, editors. Sixth Berkeley Symposium on Mathematical Statistics and Probability. Berkeley (CA): University of California Press. p. 69-88.
22. Knight RD, Freeland SJ, Landweber LF. 2001. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol. 2:research0010.0011- research0010.0013.
23. Kondrashov AS. 2003. Direct estimates of human per nucleotide mutation rates at 20 loci causing Mendel Ian diseases. Hum Mutat. 21:12-27.
24. Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH. 1999. Protease composition and codon usage in spirochetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res. 27:1642-1649.
25. Lenski RE, Travisano M. 1994. Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci USA. 91:6808-6814.
26. Lynch M, Koskella B, Schaack S. 2006. Mutation pressure and the evolution of organelle genomic architecture. Science. 311:1727-1730.
27. Mani GS, Clarke BC. 1990. Mutational order: a major stochastic process in evolution. Proc R Soc Lond B Biol Sci. 240:29-37.
28. Maynard Smith J. 1983. Evolution and development. In: Goodwin BC, Holder N, Wylie CC, editors. Development and evolution. New York: Cambridge University Press. p. 33-46.
29. Mayr E. Response to John Beatty. Biol Phil. 9:357-358.
30. Mayr EM. 1961. Cause and effect in biology. Science. 134:1501-1506.
31. Monod J. 1972. Chance and necessity: an on the natural philosophy of modern biology. New York: Vintage Books.
32. Nachman MW, Crowell SL. 2000. Estimate of the mutation rate per nucleotide in humans. Genetics. 156:297-304.
33. Ng PC, Henikoff S. 2003. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31:3812-3814.
34. Orr HA. 2002. The population genetics of adaptation: the adaptation of DNA sequences. Evil Into J Org Evil. 56:1317-1330.
35. Orr HA. 2005. Theories of adaptation: what they do and don't say. Genetica. 123:3-13.
36. Reeve HK, Sherman PW. 1993. Adaptation and the goals of evolutionary research. Quart Rev Biol. 68:1-32.
37. Rokyta DR, Joyce P, Caudle SB, Wichman HA. 2005. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet. 37:441-444.
38. Smith NG, Webster MT, Ellegren H. 2003. A low rate of simultaneous double-nucleotide mutations in primates. Mol Biol Evil. 20: 47-53.
39. Sober E. 1984. The nature of selection: evolutionary theory in philosophical focus. Cambridge (MA): MIT Press.
40. Sober E. 1994. From a biological point of view. New York: Cambridge University Press.
41. Stoltzfus A. 1999. On the possibility of constructive neutral evolution. J Mol Evol. 49:169-181.
42. Stoltzfus A. 2006a. Mutation-biased adaptation in a protein NK model. Mol Biol Evol. 23:1852-1862.
43. Stoltzfus A. 2006b. Mutationism and the dual causation of evolutionary change. Evol Dev. 8:304-317.
44. Sueoka N. 1988. Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA. 85:2653-2657.
45. Thomson KS. 1985. Essay review: the relationship between development and evolution. Oxford Surv Evol Biol. 2:220-233.
46. Vrba ES, Eldredge N. 1984. Individuals, hierarchies and processes: towards a more complete evolutionary theory. Paleobiology. 10: 146-171.
47. Wahl LM, Krakauer DC. 2000. Models of experimental evolution: the role of genetic chance and selective necessity. Genetics. 156: 1437-1448.
48. Weinreich DM, Delaney NF, Depristo MA, Hartl DL. 2006. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science. 312:111-114.
49. Whelan S, Goldman N. 2004. Estimating the frequency of events that cause multiple-nucleotide changes. Genetics. 167:2027-2043.
50. Wolfe KH. 1991. Mammalian DNA replication: mutation biases and the mutation rate. J Theor Biol. 149:441-451.
51. Yampolsky LY, Kondrashov FA, Kondrashov AS. 2005. Distribution of the strength of selection against amino acid replacements in human proteins. Hum Mol Genet. 14:3191-3201.
52. Yampolsky LY, Stoltzfus A. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev. 3:73-83.
53. Yampolsky LY, Stoltzfus A. 2005. The exchangeability of amino acids in proteins. Genetics. 170:1459-1472.
54. Yang Z, Nielsen R. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol. 25:568-579.
55. Zhang Z, Gerstein M. 2003. Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res. 31:5338-5348.
56. Zuckerkandl E, Pauling L. 1965. Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ, editors. Evolving genes and proteins. New York: Academic Press.