A coalescent model for a sweep of a unique standing variant

Genetics

Volumn 201, Issue 2, 2015, Pages 707-725

  Berg, Jeremy J ^a,b   Coop, Graham ^b  

^a Population Biology Graduate Group   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Coalescent theory; Genetic hitchhiking; Natural selection; Soft sweep; Standing variation

Indexed keywords

ALLELE; ARTICLE; BALANCING SELECTION; CLADISTICS; CLASSIC HARD SWEEP; COALESCENT THEORY; EFFECTIVE POPULATION SIZE; ENVIRONMENTAL CHANGE; GENE FREQUENCY; GENE LOCUS; GENE MUTATION; GENEALOGY; GENETIC DISTANCE; GENETIC MODEL; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HAPLOTYPE; HETEROZYGOTE; HOMOZYGOTE; HUMAN; MATHEMATICAL PARAMETERS; MULTIPLE MUTATION SOFT SWEEP; NONHUMAN; PRIORITY JOURNAL; SELECTIVE SWEEP; STANDING VARIATION; ADAPTATION; BIOLOGICAL MODEL; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; MUTATION; POPULATION GENETICS;

ADAPTATION, PHYSIOLOGICAL; ALLELES; EVOLUTION, MOLECULAR; GENETICS, POPULATION; HAPLOTYPES; HUMANS; MODELS, GENETIC; MUTATION; POLYMORPHISM, GENETIC; SELECTION, GENETIC;

EID: 84943601236     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.178962     Document Type: Article

References (69)

1. Anderson, J. T., C.-R. Lee, C. A. Rushworth, R. I. Colautti, and T. Mitchell-Olds, 2013 Genetic trade-offs and conditional neutrality contribute to local adaptation. Mol. Ecol. 22(3): 699-708.
2. Andolfatto, P., 2007 Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res. 17(12): 1755-1762.
3. Bank, C., G. B. Ewing, A. Ferrer-Admettla, M. Foll, and J. D. Jensen, 2014 Thinking too positive? Revisiting current methods of population genetic selection inference. Trends Genet. 30(12): 540-546.
4. Barrett, R. D. H., and D. Schluter, 2008 Adaptation from standing genetic variation. Trends Ecol. Evol. 23(1): 38-44.
5. Barton, N. H., 1998 The effect of hitch-hiking on neutral genealogies. Genet. Res. 72: 123-133.
6. Chen, H., N. Patterson, and D. Reich, 2010 Population differentiation as a test for selective sweeps. Genome Res. 20(3): 393-402.
7. Colosimo, P. F., 2005 Widespread parallel evolution in sticklebacks by repeated fixation of ectodysplasin alleles. Science 307(5717): 1928-1933.
8. Coop, G., and P. Ralph, 2012 Patterns of neutral diversity under general models of selective sweeps. Genetics 192: 205-224.
9. Domingues, V. S., Y.-P. Poh, B. K. Peterson, P. S. Pennings, J. D. Jensen et al., 2012 Evidence of adaptation from ancestral variation in young populations of beach mice. Evolution 66(10): 3209-3223.
10. Durrett, R., and J. Schweinsberg, 2004 Approximating selective sweeps. Theor. Popul. Biol. 66(2): 129-138.
11. Durrett, R., and J. Schweinsberg, 2005 A coalescent model for the effect of advantageous mutations on the genealogy of a population. Stoch. Proc. Appl. 115(10): 1628-1657.
12. Elyashiv, E., S. Sattath, T. T. Hu, A. Strustovsky, G. McVicker et al., 2014 A genomic map of the effects of linked selection in Drosophila. arXiv:1408.5461: 1-100.
13. Etheridge, A., P. Pfaffelhuber, and A. Wakolbinger, 2006 An approximate sampling formula under genetic hitchhiking. Ann. Appl. Probab. 16(2): 685-729.
14. Ewens, W. J., 1972 The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 112: 87-112.
15. Ewing, G., J. Hermisson, P. Pfaffelhuber, and J. Rudolf, 2011 Selective sweeps for recessive alleles and for other modes of dominance. J. Math. Biol. 63(3): 399-431.
16. Eyre-Walker, A., and P. D. Keightley, 2009 Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol. Biol. Evol. 26 (9): 2097-2108.
17. Fay, J. C., and C. I. Wu, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
18. Garud, N. R., and N. A. Rosenberg, 2015 Enhancing the mathematical properties of new haplotype homozygosity statistics for the detection of selective sweeps. Theor. Popul. Biol. 92: 94-101.
19. Garud, N. R., P. W. Messer, E. O. Buzbas, and D. A. Petrov, 2015 Recent selective sweeps in North American Drosophila melanogaster show signatures of soft sweeps. PLoS Genet. 11 (2): e1005004.
20. Griffiths, R. C., 1980 Lines of descent in the diffusion approximation of neutral Wright-Fisher models. Theor. Popul. Biol. 17(1): 37-50.
21. Griffiths, R. C., 2003 The frequency spectrum of a mutation, and its age, in a general diffusion model. Theor. Popul. Biol. 64(2): 241-251.
22. Griffiths, R. C., and S. Tavare, 1998 The age of a mutation in a general coalescent tree. Stoch. Models 14(12): 273-295.
23. Griffiths, R. C., and S. Tavare, 1999 The ages of mutations in gene trees. Ann. Appl. Probab. 9: 567-590.
24. Hermisson, J., and P. S. Pennings, 2005 Soft sweeps: molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335-2352.
25. Hermisson, J., and P. Pfaffelhuber, 2008 The pattern of genetic hitchhiking under recurrent mutation. Electron. J. Probab. 13: 2069-2106.
26. Innan, H., and Y. Kim, 2004 Pattern of polymorphism after strong artificial selection in a domestication event. Proc. Natl. Acad. Sci. USA 101(29): 10667-10672.
27. Innan, H., and Y. Kim, 2008 Detecting local adaptation using the joint sampling of polymorphism data in the parental and derived populations. Genetics 179: 1713-1720.
28. Innan, H., and M. Nordborg, 2003 The extent of linkage disequilibrium and haplotype sharing around a polymorphic site. Genetics 165: 437-444.
29. Jensen, J. D., 2014 On the unfounded enthusiasm for soft selective sweeps. Nat. Commun. 5: 5281.
30. Jones, B. L., T. O. Raga, A. Liebert, P. Zmarz, E. Bekele et al., 2013 Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep. Am. J. Hum. Genet. 93(3): 538-544.
31. Kaplan, N. L., R. R. Hudson, and C. H. Langley, 1989 The “hitchhiking effect” revisited. Genetics 123: 887-899.
32. Karasov, T., P. W. Messer, and D. A. Petrov, 2010 Evidence that adaptation in Drosophila is not limited by mutation at single sites. PLoS Genet. 6(6): e1000924.
33. Kimura, M., and J. F. Crow, 1964 The number of alleles that can be maintained in a finite population. Genetics 49: 725-738.
34. Li, H., and R. Durbin, 2011 Inference of human population history from individual whole-genome sequences. Nature 475(7357): 493-496.
35. Magwire, M. M., F. Bayer, C. L. Webster, C. Cao, and F. M. Jiggins, 2011 Successive increases in the resistance of Drosophila to viral infection through a transposon insertion followed by a duplication. PLoS Genet. 7(10): e1002337.
36. Maynard Smith, J., and J. Haigh, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23(1): 23-35.
37. McVean, G., 2006 The structure of linkage disequilibrium around a selective sweep. Genetics 175: 1395-1406.
38. Menozzi, P., M. A. Shi, A. Lougarre, Z. H. Tang, and D. Fournier, 2004 Mutations of acetylcholinesterase which confer insecticide resistance in Drosophila melanogaster populations. BMC Evol. Biol. 4: 4.
39. Messer, P. W., and R. A. Neher, 2012 Estimating the strength of selective sweeps from deep population diversity data. Genetics 191(2): 593-605.
40. Messer, P. W., and D. A. Petrov, 2013 Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol. Evol. 28(11): 659-669.
41. Nagasawa, M., and T. Maruyama, 1979 An application of time reversal of Markov processes to a problem of population genetics. Adv. Appl. Probab. 11(3): 457-478.
42. Nair, S., D. Nash, D. Sudimack, A. Jaidee, M. Barends et al., 2006 Recurrent gene amplification and soft selective sweeps during evolution of multidrug resistance in malaria parasites. Mol. Biol. Evol. 24(2): 562-573.
43. 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(11): 1566-1575.
44. Orr, H. A. and A. J. Betancourt, 2001 Haldane’s sieve and adaptation from the standing genetic variation. Genetics 157: 875-884.
45. Patterson, N. J., 2005 How old is the most recent ancestor of two copies of an allele? Genetics 169: 1093-1104.
46. Paul, J. S., M. Steinrücken, and Y. S. Song, 2011 An accurate sequentially Markov conditional sampling distribution for the coalescent with recombination. Genetics 187: 1115-1128.
47. Pennings, P. S., and J. Hermisson, 2006a Soft sweeps II-molecular population genetics of adaptation from recurrent mutation or migration. Mol. Biol. Evol. 23(5): 1076-1084.
48. Pennings, P. S., and J. Hermisson, 2006b Soft sweeps III: the signature of positive selection from recurrent mutation. PLoS Genet. 2(12): e186.
49. Peter, B. M., E. Huerta-Sanchez, and R. Nielsen, 2012 Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genet. 8(10): e1003011.
50. Pokalyuk, C., 2012 The effect of recurrent mutation on the linkage disequilibrium under a selective sweep. J. Math. Biol. 64(12): 291-317.
51. Przeworski, M., G. Coop, and J. D. Wall, 2005 The signature of positive selection on standing genetic variation. Evolution 59 (11): 2312-2323.
52. Ralph, P., and G. Coop, 2010 Parallel adaptation: One or many waves of advance of an advantageous allele? Genetics 186: 647-668.
53. Rannala, B., 1997 On the genealogy of a rare allele. Theor. Popul. Biol. 52(3): 216-223.
54. Rasmussen, M. D., M. J. Hubisz, I. Gronau, and A. Siepel, 2014 Genome-wide inference of ancestral recombination graphs. PLoS Genet. 10(5): e1004342.
55. Roesti, M., S. Gavrilets, A. P. Hendry, W. Salzburger, and D. Berner, 2014 The genomic signature of parallel adaptation from shared genetic variation. Mol. Ecol. 23(16): 3944-3956.
56. Sabeti, P. C., D. E. Reich, J. M. Higgins, H. Z. P. Levine, D. J. Richter et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419 (6909): 832-837.
57. Salgueiro, P., J. L. Vicente, C. Ferreira, V. Teófilo, A. Galvão et al., 2010 Tracing the origins and signatures of selection of antifolate resistance in island populations of Plasmodium falciparum. BMC Infect. Dis. 10(1): 163.
58. Schmidt, J. M., R. T. Good, B. Appleton, J. Sherrard, G. C. Raymant et al., 2010 Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus. PLoS Genet. 6(6): e1000998.
59. Schrider, D. R., F. K. Mendes, M. W. Hahn, and A. D. Kern, 2015 Soft shoulders ahead: spurious signatures of soft and partial selective sweeps result from linked hard sweeps. Genetics 200: 267-284.
60. Schweinsberg, J., and R. Durrett, 2005 Random partitions approximating the coalescence of lineages during a selective sweep. Ann. Appl. Probab. 15(3): 1591-1651.
61. Sheehan, S., K. Harris, and Y. S. Song, 2013 Estimating variable effective population sizes from multiple genomes: a sequentially Markov conditional sampling distribution approach. Genetics 194: 647-662.
62. Studer, A., Q. Zhao, J. Ross-Ibarra, and J. Doebley, 2011 Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 43(11): 1160-1163.
63. 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(3): e72.
64. Watterson, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7 (2): 256-276.
65. Watterson, G. A., 1984 Lines of descent and the coalescent. Theor. Popul. Biol. 26(1): 77-92.
66. Wiehe, T. H., and W. Stephan, 1993 Analysis of a genetic hitchhiking model, and its application to DNA polymorphism data from Drosophila melanogaster. Mol. Biol. Evol. 10(4): 842-854.
67. Wilson, B. A., D. A. Petrov, and P. W. Messer, 2014 Soft selective sweeps in complex demographic scenarios. Genetics 198: 669-684.
68. Wiuf, C., 2000 On the genealogy of a sample of neutral rare alleles. Theor. Popul. Biol. 58(1): 61-75.
69. Wiuf, C., and P. Donnelly, 1999 Conditional genealogies and the age of a neutral mutant. Theor. Popul. Biol. 56(2): 183-201.