Purifying selection, drift, and reversible mutation with arbitrarily high mutation rates

Genetics

Volumn 198, Issue 4, 2014, Pages 1587-1602

  Charlesworth, Brian ^a   Jain, Kavita ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b JAWAHARLAL NEHRU CENTRE FOR ADVANCED SCIENTIFIC RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA SEQUENCE; EPIGENETICS; GENE FREQUENCY; GENETIC DRIFT; GENETIC VARIABILITY; MUTATION; MUTATION RATE; POPULATION MODEL; POPULATION SIZE; PURIFYING SELECTION; REVERSIBLE MUTATION; ALGORITHM; BIOLOGICAL MODEL; GENETIC SELECTION; MOLECULAR EVOLUTION; POPULATION GENETICS;

ALGORITHMS; EVOLUTION, MOLECULAR; GENETIC DRIFT; GENETICS, POPULATION; MODELS, GENETIC; MUTATION; MUTATION RATE; SELECTION, GENETIC;

EID: 84915748002     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.114.167973     Document Type: Article

References (59)

1. Abramowitz, M., and I. A. Stegun, 1965 Handbook of Mathematical Functions. Dover, New York.
2. Aris-Brosou, S., and L. Excoffier, 1996 The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Mol. Biol. Evol. 13: 494-504.
3. Becker, C., J. Hagmann, J. Mueller, D. Koenig, O. Stegle et al., 2011 Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480: 245-249.
4. Bertorelle, G., and M. Slatkin, 1995 The number of segregating sites in expanding human populations with implications for estimates of demographic parameters. Mol. Biol. Evol. 12: 887- 892.
5. Bulmer, M. G., 1991 The selection-mutation-drift theory of synonomous codon usage. Genetics 129: 897-907.
6. Charlesworth, B., 2013 Stabilizing selection, purifying selection and mutational bias in finite populations. Genetics 194: 955- 971.
7. Charlesworth, B., and D. Charlesworth, 2010 Elements of Evolutionary Genetics. Roberts & Co., Greenwood Village, CO.
8. Cutter, A. D., G.-X. Wang, H. Ai, and Y. Peng, 2012 Influence of finite-sites mutations, population subdivision and sampling schemes on patterns of nucleotide polymorphism for species with molecular hyperdiversity. Mol. Ecol. 21: 1345-1359.
9. Cutter, A. D., R. Jovelin, and D. Dey, 2013 Molecular hyperdiversity and evolution in very large populations. Mol. Ecol. 22: 2074-2095.
10. Desai, M., and J. B. Plotkin, 2008 The polymorphism frequency spectrum of finitely many sites under selection. Genetics 180: 2175-2191.
11. Dey, A., C. K. W. Chan, C. G. Thomas, and A. D. Cutter, 2013 Molecular hyperdiversity defines populations of the nematode Caenorhabditis brenneri. Proc. Natl. Acad. Sci. USA 110: 11056- 11060.
12. Eory, L., D. L. Halligan, and P. D. Keightley, 2010 Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol. Biol. Evol. 27: 177-192.
13. Evans, B. J., K. Zeng, J. A. Esselstyn, B. Charlesworth, and D. J. Melnick, 2014 Reduced representation genome sequencing suggests low diversity on the sex chromosomes of Tonkean macaque monkeys. Mol. Biol. Evol. 31: 2425-2440.
14. Ewens, W. J., 2004 Mathematical Population Genetics. 1. Theoretical Introduction. Springer-Verlag, New York.
15. Eyre-Walker, A., 1992 The effect of constraint on the rate of evolution in neutral models with biased mutation. Genetics 131: 233-234.
16. Fisher, R. A., 1922 On the dominance ratio. Proc. R. Soc. Edinb. 42: 321-341.
17. Fisher, R. A., 1930 The distribution of gene ratios for rare mutations. Proc. R. Soc. Edinb. 50: 205-220.
18. Fu, Y.-X., and W.-H. Li, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
19. Grossniklaus, U., B. Kelly, A. Ferguson-Smith, M. Pembry, and S. Lindquist, 2013 Transgenerational epigenetic inheritance: How important is it? Nat. Rev. Genet. 14: 228-235.
20. Haldane, J. B. S., 1927 A mathematical theory of natural and artificial selection. Part V. Selection and mutation. Proc. Camb. Philos. Soc. 23: 838-844.
21. Halligan, D. L., A. Eyre-Walker, P. Andolfatto, and P. D. Keightley, 2004 Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Res. 14: 273-279.
22. Hudson, R. R., 1990 Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 7: 1-45.
23. Jenkins, P. A., and Y. S. Song, 2011 The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele. Theor. Popul. Biol. 80: 158-173.
24. Jenkins, P. A., J. W. Mueller, and Y. S. Song, 2014 General triallelic frequency spectrum under demographic models with variable population size. Genetics 196: 295-311.
25. Johannes, F., E. Porcher, F. Texeira, V. Saliba-Colombani, M. Simon et al., 2009 Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet. 6: e1000530.
26. Kimura, M., 1962 On the probability of fixation of a mutant gene in a population. Genetics 47: 713-719.
27. Kimura, M., 1968 Evolutionary rate at the molecular level. Nature 217: 624-626.
28. Kimura, M., 1971 Theoretical foundations of population genetics at the molecular level. Theor. Popul. Biol. 2: 174-208.
29. Kimura, M., 1981 Possibility of extensive neutral evolution under stabilizing selection with special reference to non-random usage of synonymous codons. Proc. Natl. Acad. Sci. USA 78: 454-458.
30. Kimura, M., T. Maruyama, and J. F. Crow, 1963 The mutation load in small populations. Evolution 48: 1303-1312.
31. Klironomos, F., J. Berg, and S. Collins, 2013 How epigenetic mutations can affect genetic evolution: model and mechanism. Bio- Essays 35: 571-578.
32. Kondrashov, F. A., A. Y. Ogurtsov, and A. S. Kondrashov, 2006 Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. J. Theor. Biol. 240: 616-626.
33. Langley, S. A., G. H. Karpen, and C. H. Langley, 2014 Nucleosomes shape DNA polymorphism and divergence. PLoS Genet. 10: e1004457.
34. Lauria, M., S. Piccinni, R. Pirona, G. Lund, A. Viotti et al., 2014 Epigenetic variation, inheritance, and parent-of-origin effects of cytosine methylation in maize (Zea mays). Genetics 196: 653-666.
35. Laval, G., and L. Excoffier, 2004 SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics 20: 2485-2487.
36. Lawrie, D. S., D. A. Petrov, and P. W. Messer, 2011 Faster than neutral evolution of constrained sequences: the complex interplay of mutational biases and weak selection. Genome Biol. Evol. 3: 383-395.
37. Leffler, E. M., K. Bullaughey, D. R. Matute, W. K. Meyer, L. Ségurel et al., 2012 Revisiting an old riddle: What determines genetic diversity levels within a species? PLoS Biol. 10: e1001388.
38. Li, W.-H., 1987 Models of nearly neutral mutations with particular implications for non-random usage of synonymous codons. J. Mol. Evol. 24: 337-345.
39. McVean, G. A. T., and B. Charlesworth, 1999 A population genetic model for the evolution of synonymous codon usage: patterns and predictions. Genet. Res. 74: 145-158.
40. Mizawa, K., and F. Tajima, 1997 Estimation of the amount of genetic variation when the mutation rate varies among sites. Genetics 147: 1959-1964.
41. Richards, E. J., 2006 Inherited epigenetic variation: revisiting soft inheritance. Nat. Rev. Genet. 7: 395-401.
42. Sargsyan, O., 2014 A framework including recombination for analyzing the dynamics of within-host HIV genetic diversity. PLoS Genet. 9: e87655.
43. Schmitz, R. J., and J. R. Ecker, 2012 Epigenetic and epigenomic variation in Arabidopsis thaliana. Trends Plant Sci. 17: 149- 154.
44. Schmitz, R. J., M. D. Schultz, M. G. Lewsey, R. C. O'Malley, M. A. Urich et al., 2011 Transgenerational epigenetic instability is a source of novel methylation variants. Science 334: 369- 373.
45. Schmitz, R. J., M. D. Schultz, M. A. Urich, J. P. Nery, M. Pelizola et al., 2013 Patterns of population epigenomic diversity. Nature 495: 193-198.
46. Sharp, P. M., L. B. Emery, and K. Zeng, 2010 Forces that influence the evolution of codon bias. Philos. Trans. R. Soc. B 365: 1203- 1212.
47. Slatkin, M., and R. R. Hudson, 1991 Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 143: 579-587.
48. Staedler, T., B. Haubold, C. Merino, W. Stephan, and P. Pfaffelhuber, 2009 The impact of sampling schemes on the site frequency spectrum in nonequilibrium subdivided populations. Genetics 182: 205-216.
49. Tajima, F., 1983 Evolutionary relationship of DNA sequences in a finite population. Genetics 105: 437-460.
50. Tajima, F., 1989a The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
51. Tajima, F., 1989b Statistical method for testing the neutral mutation hypothesis. Genetics 123: 585-595.
52. Tajima, F., 1996 The amount of DNA polymorphism maintained in a finite population when the neutral mutation rate varies among sites. Genetics 143: 1457-1465.
53. Wakeley, J., 2000 The effects of subdivision on the genetic divergence of populations and species. Evolution 54: 1092-1101.
54. Wakeley, J., 2008 Coalescent Theory. An Introduction. Roberts & Co., Greenwood Village, CO.
55. Watterson, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
56. Wright, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.
57. Wright, S., 1937 The distribution of gene frequencies in populations. Proc. Natl. Acad. Sci. USA 23: 307-320.
58. Yang, Z., 1996 Statistical properties of a DNA sample under the finite-sites model. Genetics 144: 1941-1959.
59. Zeng, K., 2010 A simple multiallele model and its application to identifying preferred-unpreferred codons using polymorphism data. Mol. Biol. Evol. 27: 1327-1337.