Selective sweeps in multilocus models of quantitative traits

Genetics

Volumn 192, Issue 1, 2012, Pages 225-239

  Pavlidis, Pavlos ^a,b   Metzler, Dirk ^a   Stephan, Wolfgang ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; DIALLEL ANALYSIS; FITNESS; GENE FREQUENCY; GENE LOCUS; GENE MUTATION; GENEALOGY; GENETIC EPISTASIS; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HETEROZYGOSITY; HOMOZYGOTE; PHENOTYPE; PRIORITY JOURNAL; PROBABILITY; QUANTITATIVE TRAIT LOCUS; SELECTIVE SWEEP; SINGLE NUCLEOTIDE POLYMORPHISM;

ALLELES; EVOLUTION, MOLECULAR; GENETIC FITNESS; HUMANS; MODELS, GENETIC; PHENOTYPE; POLYMORPHISM, GENETIC; QUANTITATIVE TRAIT LOCI; SELECTION, GENETIC;

EID: 84866134251     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.142547     Document Type: Article

References (53)

1. Barton, N. H., 1990 Pleiotropic models of quantitative variation. Genetics 124: 773-782.
2. Bodmer, W. F., and J. Felsenstein, 1967 Linkage and selection: theoretical analysis of the deterministic two locus random mating model. Genetics 57: 237-265.
3. Bulmer, M. G., 1973 The maintenance of the genetic variability of polygenic characters by heterozygous advantage. Genet. Res. 22: 9-12.
4. Bürger, R., 1998 Mathematical properties of mutation-selection models. Genetica 102: 279-298.
5. Bürger, R., 2000 The Mathematical Theory of Selection, Recombination, and Mutation. Wiley, Hoboken, NJ.
6. Bürger, R., 2002 On a genetic model of intraspecific competition and stabilizing selection. Am. Nat. 160: 661-682.
7. Bürger, R., and A. Gimelfarb, 1999 Genetic variation maintained in multilocus models of additive quantitative traits under stabilizing selection. Genetics 152: 807-820.
8. Bürger, R., and A. Gimelfarb, 2004 The effects of intraspecific competition and stabilizing selection on a polygenic trait. Genetics 167: 1425-1443.
9. Chevin, L.-M., and F. Hospital, 2008 Selective sweep at a quantitative trait locus in the presence of background genetic variation. Genetics 180: 1645-1660.
10. Cleveland, W., 1979 Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc. 74: 829-836.
11. Endler, J., 1986 Natural Selection in the Wild. Princeton University Press, Princeton.
12. Ewing, G., and J. Hermisson, 2010 MSMS: a coalescent simulation program including recombination, demographic structure and selection at a single locus. Bioinformatics 26: 2064-2065.
13. Fay, J. C., and C. I. Wu, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
14. Fisher, R., 1930 The Genetical Theory of Natural Selection. Clarendon Press, Oxford.
15. Gavrilets, S., and A. Hastings, 1994 Maintenance of multilocus variability under strong stabilizing selection. J. Math. Biol. 32: 287-302.
16. Gerhardt, H., 1994 The evolution of vocalization in frogs and toads. Annu. Rev. Ecol. Syst. 25: 293-324.
17. Gillespie, J. H., 1984 Pleiotropic overdominance and the maintenance of genetic variation in polygenic characters. Genetics 107: 321-330.
18. Gillespie, J. H., and M. Turelli, 1989 Genotype-environment interactions and the maintenance of polygenic variation. Genetics 121: 129-138.
19. Gimelfarb, A., 1998 Stable equilibria in multilocus genetic systems: a statistical investigation. Theor. Popul. Biol. 54: 133-145.
20. Hill, W. G., and P. D. Keightley, 1988 Interrelations of mutation, population size, artificial and natural selection, pp. 57-70 in Proceedings of the Second International Conference on Quantitative
21. Kaplan, N. L., R. R. Hudson, and C. H. Langley, 1989 The "Hitchhiking Effect" revisited. Genetics 123: 887-899.
22. Karlin, S., and M. W. Feldman, 1970 Linkage and selection: two locus symmetric viability model. Theor. Popul. Biol. 1: 39-71.
23. Kim, Y., and R. Nielsen, 2004 Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.
24. Kim, Y., and W. Stephan, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
25. Kimura, M., 1962 On the probability of fixation of mutant genes in a population. Genetics 47: 713-719.
26. Kimura, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
27. Kirby, D. A., and W. Stephan, 1996 Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster. Genetics 144: 635-645.
28. Lande, R., 1976 The maintenance of genetic variability by mutation in a polygenic character with linked loci. Genet. Res. 26: 221-235.
29. Lande, R., 1983 The response to selection on major and minor mutations affecting a metrical trait. Heredity 50: 47-65.
30. Li, H., 2011 A new test for detecting recent positive selection that is free from the confounding impacts of demography. Mol. Biol. Evol. 28: 365-375.
31. Li, H., and W. Stephan, 2006 Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet. 2: e166.
32. Ludwig, M. Z., C. Bergman, N. H. Patel, and M. Kreitman, 2000 Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567.
33. Mauricio, R., and M. Rausher, 1997 Experimental manipulation of putative selective agents provides evidence for the role of natural enemies in the evolution of plant defense. Evolution 51: 1435-1444.
34. Maynard Smith, J., and J. Haigh, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
35. Nielsen, R., S. Williamson, Y. Kim, M. J. Hubisz, A. G. Clark et al., 2005 Genomic scans for selective sweeps using SNP data. Genome Res. 15: 1566-1575.
36. Pavlidis, P., J. D. Jensen, and W. Stephan, 2010 Searching for footprints of positive selection in whole-genome SNP data from nonequilibrium populations. Genetics 185: 907-922.
37. Perrett, D. I., K. A. May, and S. Yoshikawa, 1994 Facial shape and judgements of female attractiveness. Nature 368: 239-242.
38. Robertson, A., 1956 The effect of selection against extreme deviants based on deviation or on homozygosis. J. Genet. 54: 236-248.
39. Sabeti, P. C., D. E. Reich, J. M. Higgins, H. Z. Levine, D. J. Richter et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
40. Stephan, W., 2010 Genetic hitchhiking vs. background selection: the controversy and its implications. Philos. Trans. R. Soc. Lond. B Biol. Sci. 365: 1245-1253.
41. Stephan, W., Y. S. Song, and C. H. Langley, 2006 The hitchhiking effect on linkage disequilibrium between linked neutral loci. Genetics 172: 2647-2663.
42. Tajima, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
43. Tang, K., K. R. Thornton, and M. Stoneking, 2007 A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 5: e171.
44. Teshima, K. M., and H. Innan, 2009 mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. BMC Bioinformatics 10: 166.
45. Tufto, J., 2000 Quantitative genetic models for the balance between migration and stabilizing selection. Genet. Res. 76: 285-293.
46. Turelli, M., 1984 Heritable genetic variation via mutation-selection balance: Lerch's zeta meets the abdominal bristle. Theor. Popul. Biol. 25: 138-193.
47. Vignieri, S. N., J. G. Larson, and H. E. Hoekstra, 2010 The selective advantage of crypsis in mice. Evolution 64: 2153-2158.
48. Voight, B. F., S. Kudaravalli, X. Wen, and J. K. Pritchard, 2006 A map of recent positive selection in the human genome. PLoS Biol. 4: e72.
49. Wakeley, J., 2008 Coalescent Theory. Roberts, Greenwood Village, CO.
50. Willensdorfer, M., and R. Bürger, 2003 The two-locus model of Gaussian stabilizing selection. Theor. Popul. Biol. 64: 101-117.
51. Zhang, X.-S., and W. G. Hill, 2002 Joint effects of pleiotropic selection and stabilizing selection on the maintenance of quantitative genetic variation at mutation-selection balance. Genetics 162: 459-471.
52. Zhao, Z., N. Yu, Y.-X. Fu, and W.-H. Li, 2006 Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations. Genetics 174: 399-409.
53. Zhivotovsky, L. A., and S. Gavrilets, 1992 Quantitative variability and multilocus polymorphism under epistatic selection. Theor. Popul. Biol. 42: 254-283.