Skip to main content

Detecting Hitchhiking from Patterns of DNA Polymorphism

  • Chapter
Selective Sweep

Part of the book series: Molecular Biology Intelligence Unit ((MBIU))

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

eBook
USD 16.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Ewens WJ. Mathematical population genetics. Springer-Verlag: 1979.

    Google Scholar 

  2. Kimura M, Ohta T. The average number of generations until extinction of an individual mutant gene in a finite population. Genetics 1969; 63(3):701–709.

    PubMed  CAS  Google Scholar 

  3. Simonsen KL, Churchill GA, Aquadro CF. Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 1995; 141(1):413–429.

    PubMed  CAS  Google Scholar 

  4. Wiehe THE, Stephan W. Analysis of a genetic hitchhiking model, and its application to DNA polymorphism data from Drosophila melanogaster. Mol Biol Evol 1993; 10(4):842–854.

    PubMed  CAS  Google Scholar 

  5. Maynard-Smith J, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res 1974; 23(1):23–35.

    Google Scholar 

  6. Kaplan NL, Hudson RR, Langley CH. The “hitchhiking effect” revisited. Genetics 1989; 123(4):887–899.

    PubMed  CAS  Google Scholar 

  7. Barton NH. The effect of hitch-hiking on neutral genealogies. Genet Res 1998; 72:123–133.

    Article  CAS  Google Scholar 

  8. Barton NH. Genetic hitchhiking. Philos Trans R Soc Lond B Biol Sci 2000; 355(1403):1553–1562.

    Article  PubMed  CAS  Google Scholar 

  9. Stephan W, Wiehe THE, Lenz MW. The effect of stongly selected substitutions on neutral polymorphism: Analytical results based on diffusion theory. Theor Popul Biol 1992; 41:237–254.

    Article  Google Scholar 

  10. Hudson RR, Kreitman M, Aguade M. A test of neutral molecular evolution based on nucleotide data. Genetics 1987; 116(1): 153–159.

    PubMed  CAS  Google Scholar 

  11. Moriyama EN, Powell JR. Intraspecific nuclear DNA variation in Drosophila. Mol Biol Evol 1996; 13(1):261–277.

    PubMed  CAS  Google Scholar 

  12. Wakeley J. The variance of pairwise nucleotide differences in two populations with migration. Theor Popul Biol 1996; 49(1):39–57.

    Article  PubMed  CAS  Google Scholar 

  13. Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics 1993; 134(4): 1289–1303.

    PubMed  CAS  Google Scholar 

  14. Aguade M, Miyashita N, Langley CH. Polymorphism and divergence in the Mst26A male accessory gland gene region in Drosophila. Genetics 1992; 132(3):755–770.

    PubMed  CAS  Google Scholar 

  15. Fay JC, Wu C-I. Hitchhiking under positive Darwinian selection. Genetics 2000; 155(3):1405–1413.

    PubMed  CAS  Google Scholar 

  16. Hudson RR, Bailey K, Skarecky D et al. Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 1994; 136(4):1329–1340.

    PubMed  CAS  Google Scholar 

  17. Hudson RR, Saez AG, Ayala FJ. DNA variation at the Sod locus of Drosophila melanogaster: An unfolding story of natural selection. Proc Natl Acad Sci USA 1997; 94(15):7725–7729.

    Article  PubMed  CAS  Google Scholar 

  18. Nurminsky D, Aguiar DD, Bustamante CD et al. Chromosomal effects of rapid gene evolution in Drosophila melanogaster. Science 2001; 291(5501): 128–130.

    Article  PubMed  CAS  Google Scholar 

  19. Kim Y, Stephan W. Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 2002; 160(2):765–777.

    PubMed  CAS  Google Scholar 

  20. Tajima F. The effect of change in population size on DNA polymorphism. Genetics 1989; 123(3):597–601.

    PubMed  CAS  Google Scholar 

  21. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics 1983; 105(2):437–460.

    PubMed  CAS  Google Scholar 

  22. Watterson GA. On the number of segregating sites in genetical models without recombination. Theor Popul Biol 1975; 7(2):256–276.

    Article  PubMed  CAS  Google Scholar 

  23. Andolfatto P, Przeworski M. A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 2000; 156(1):257–268.

    PubMed  CAS  Google Scholar 

  24. Fu YX. Statistical properties of segregating sites. Theor Popul Biol 1995; 48(2):172–197.

    Article  PubMed  CAS  Google Scholar 

  25. Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and back ground selection. Genetics 1997; 147(2):915–925.

    PubMed  CAS  Google Scholar 

  26. Fay JC. Detecting natural selection from patterns of DNA polymorphism and divergence. PhD thesis, University of Chicago; 2001.

    Google Scholar 

  27. Kim Y, Stephan W. Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 2000; 155(3): 1415–1427.

    PubMed  CAS  Google Scholar 

  28. Przeworski M. The signature of positive selection at randomly chosen Loci. Genetics 2002; 160(3):1179–1189.

    PubMed  Google Scholar 

  29. Galtier N, Depaulis F, Barton NH. Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 2000; 155(2):981–987.

    PubMed  CAS  Google Scholar 

  30. Thomson G. The effect of a selected locus on linked neutral loci. Genetics 1977; 85(4):753–788.

    PubMed  CAS  Google Scholar 

  31. Kirby DA, Stephan W. Haplotype test reveals departure from neutrality in a segment of the white gene of Drosophila melanogaster. Genetics 1995; 141(4):1483–1490.

    PubMed  CAS  Google Scholar 

  32. Lewontin RC. The interaction of selection and linkage. I. General considerations heterotic models. Genetics 1964; 49:49–67.

    PubMed  CAS  Google Scholar 

  33. Depaulis F, Veuille M. Neutrality tests based on the distribution of haplotypes under an infinite-site model. Mol Biol Evol 1998; 15(12):1788–1790.

    PubMed  CAS  Google Scholar 

  34. Slatkin M, Wiehe T. Genetic hitch-hiking in a subdivided population. Genet Res 1998; 71(2):155–160.

    Article  PubMed  CAS  Google Scholar 

  35. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989; 123(3):585–595.

    PubMed  CAS  Google Scholar 

  36. Pluzhnikov A, DiRienzo A, Hudson RR. Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics 2002; 161(3):1209–1218.

    PubMed  Google Scholar 

  37. Pritchard JK, Przeworski M. Linkage disequilibrium in humans: Models and data. Am J Hum Genet 2001; 69(1):1–14.

    Article  PubMed  CAS  Google Scholar 

  38. Wall JD. Detecting ancient admixture in humans using sequence polymorphism data. Genetics 2000; 154(3):1271–1279.

    PubMed  CAS  Google Scholar 

  39. Andolfatto P. Adaptive hitchhiking effects on genome variability. Curr Opin Genet Dev 2001; 11(6):635–641.

    Article  PubMed  CAS  Google Scholar 

  40. Williams EJ, Hurst LD. Is the synonymous substitution rate in mammals gene-specific? Mol Biol Evol 2002; 19(8):1395–1398.

    PubMed  CAS  Google Scholar 

  41. Braverman JM, Hudson RR, Kaplan NL et al. The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 1995; 140(2):783–796.

    PubMed  CAS  Google Scholar 

  42. Andolfatto P, Przeworski M. Regions of lower crossing over harbor more rare variants in African populations of Drosophila melanogaster. Genetics 2001; 158(2):657–665.

    PubMed  CAS  Google Scholar 

  43. Charlesworth D, Charlesworth B, Morgan MT. The pattern of neutral molecular variation under the background selection model. Genetics 1995; 141(4):1619–1632.

    PubMed  CAS  Google Scholar 

  44. Begun DJ, Aquadro CF. Evolution at the tip and base of the X chromosome in an African population of Drosophila melanogaster. Mol Biol Evol 1995; 12(3):382–390.

    PubMed  CAS  Google Scholar 

  45. Berry AJ, Ajioka JW, Kreitman M. Lack of polymorphism on the Drosophila fourth chromosome resulting from selection. Genetics 1991; 129(4):1111–1117.

    PubMed  CAS  Google Scholar 

  46. Hamblin MT, Aquadro CF. High nucleotide sequence variation in a region of low recombination in Drosophila simulans is consistent with the background selection model. Mol Biol Evol 1996; 13(8):1133–1140.

    PubMed  CAS  Google Scholar 

  47. Jensen MA, Charlesworth B, Kreitman M. Patterns of genetic variation at a chromosome 4 locus of Drosophila melanogaster and D. simulans. Genetics 2002; 160(2):493–507.

    CAS  Google Scholar 

  48. Langley CH, Lazzaro BP, Phillips W et al. Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome. Genetics 2000; 156(4):1837–1852.

    PubMed  CAS  Google Scholar 

  49. Wayne ML, Kreitman M. Reduced variation at concertina, a heterochromatic locus in Drosophila. Genet Res 1996; 68(2):101–108.

    Article  PubMed  CAS  Google Scholar 

  50. Ohta T. Statistical analyses of Drosophila and human protein polymorphism. Proc Natl Acad Sci USA 1975; 72:3194–3196.

    Article  Google Scholar 

  51. Fay JC, Wyckoff GJ, Wu C-I. Positive and negative selection on the human genome. Genetics 2001; 158(3):1227–1234.

    PubMed  CAS  Google Scholar 

  52. Fay JC, Wyckoff GJ, Wu C-I. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 2001; 415(6875): 1024–1026.

    Article  CAS  Google Scholar 

  53. Gordo I, Navarro A, Charlesworth B. Muller’s Ratchet and the Pattern of Variation at a Neutral Locus. Genetics 2002; 161(2):835–848.

    PubMed  Google Scholar 

  54. Williamson S, Orive ME. The genealogy of a sequence subject to purifying selection at multiple sites. Mol Biol Evol 2002; 19(8):1376–1384.

    PubMed  CAS  Google Scholar 

  55. Gilad Y, Segre D, Skorecki K et al. Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes. Nat Genet 2000; 26(2):221–224.

    Article  PubMed  CAS  Google Scholar 

  56. Stephan W, Xing L, Kirby DA et al. A test of the background selection hypothesis based on nucleotide data from Drosophila ananassae. Proc Natl Acad Sci USA 1998; 95(10):5649–5654.

    Article  PubMed  CAS  Google Scholar 

  57. Frisse L, Hudson RR, Bartoszewicz A et al. Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am J Hum Genet 2001; 69(4):831–843.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Eurekah.com and Kluwer Academic/Plenum Publishers

About this chapter

Cite this chapter

Fay, J.C., Wu, CI. (2005). Detecting Hitchhiking from Patterns of DNA Polymorphism. In: Nurminsky, D. (eds) Selective Sweep. Molecular Biology Intelligence Unit. Springer, Boston, MA. https://doi.org/10.1007/0-387-27651-3_6

Download citation

Publish with us

Policies and ethics