Linkage disequilibrium as a signature of selective sweeps

Genetics

Volumn 167, Issue 3, 2004, Pages 1513-1524

  Kim, Yuseob ^a,b   Neilsen, Rasmus ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALLELE; ARTICLE; DNA SEQUENCE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC MODEL; POPULATION GENETICS; PRIORITY JOURNAL;

COMPUTER SIMULATION; GENE FREQUENCY; GENETICS, POPULATION; HAPLOTYPES; LIKELIHOOD FUNCTIONS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MUTATION; POLYMORPHISM, GENETIC; SELECTION (GENETICS);

EID: 3843073210     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.025387     Document Type: Article

References (34)

1. AGUADÉ, M., N. MIYASHITA and C. H. LANGLEY, 1992 Polymorphism and divergence in the Mst26A male accessory gland gene region in Drosophila. Genetics 132: 755-770.
2. BARTON, N. H., 1998 The effect of hitch-hiking on neutral genealogies. Genet. Res. 72: 123-133.
3. BUSTAMANTE, C. D., R. NIELSEN, S. A. SAWYER, K. M. OLSEN, M. D. PURUGGANAN et al., 2002 The cost of inbreeding in Arabidopsis. Nature 416: 531-534.
4. DEPAULIS, F., and M. VEUILLE, 1998 Neutrality tests based on the distribution of haplotypes under an infinite-site model. Mol. Biol. Evol. 15: 1788-1790.
5. FAY, J. C., and C.-I WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
6. FAY, J. C., G. J. WYCKOFF and C.-I WU, 2001 Positive and negative selection on the human genome. Genetics 158: 1227-1234.
7. HARR, B., M. KAUER and C. SCHLÖTTERER, 2002 Hitchhiking mapping: a population-based fine-mapping strategy for adaptive mutations in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99: 12949-12954.
8. HILL, W. G., and A. ROBERTSON, 1968 Linkage disequilibrium in finite populations. Theor. Appl. Genet. 38: 473-485.
9. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
10. HUDSON, R. R., M. KREITMAN and M. AGUADÉ, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
11. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The 'hitch-hiking effect' revisited. Genetics 123: 887-899.
12. KELLY, J. K., 1997 A test of neutrality based on interlocus associations. Genetics 146: 1197-1206.
13. KIM, Y., and W. STEPHAN, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
14. MCVEAN, G. A. T., 2002 A genealogical interpretation of linkage disequilibrium. Genetics 162: 987-991.
15. MAYNARD SMITH, J., 1971 What use is sex? J. Theor. Biol. 30: 319-335.
16. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
17. NIELSEN, R., 2000 Estimation of population parameters and recombination rates using single nucleotide polymorphisms. Genetics 154: 931-942.
18. NIELSEN, R., and Z. YANG, 2003 Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol. Biol. Evol. 20: 1231-1239.
19. NORDBORG, M., and S. TAVARE, 2002 Linkage disequilibrium: what history has to tell us. Trends Genet. 18: 83-90.
20. PARSCH, J., C. D. MEIKLEJOHN and D. L. HARTL, 2001 Patterns of DNA sequence variation suggest the recent action of positive selection in the janus-ocnus region of Drosophila simulans. Genetics 159: 647-657.
21. PIGANEAU, G., and A. EYRE-WALKER, 2003 Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock. Proc. Natl. Acad. Sci. USA 100: 10335-10340.
22. PRZEWORSKI, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
23. PRZEWORSKI, M., 2003 Estimating the time since the fixation of a beneficial allele. Genetics 164: 1667-1676.
24. QUESADA, H., U. E. M. RAMÍREZ, J. ROZAS and M. AGUADÉ, 2003 Large-scale adaptive hitchhiking upon high recombination in Drosophila simulans. Genetics 165: 895-900.
25. SABETI, P. C., D. E. REICH, J. M. HIGGINS, H. C. LEVINE, D. J. RICHTER et al., 2002 Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832-837.
26. SCHLENKE, T. A., and D. J. BEGUN, 2004 Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc. Natl. Acad. Sci. USA 101: 1626-1631.
27. SMITH, N. G. C., and A. EYRE-WALKER, 2002 Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.
28. STEPHAN, W., 1995 An improved method for estimating the rate of fixation of favorable mutations based on DNA polymorphism data. Mol. Biol. Evol. 12: 959-962.
29. STEPHAN, W., T. H. E. WIEHE and M. W. LENZ, 1992 The effect of strongly selected substitutions on neutral polymorphism: analytical results based on diffusion theory. Theor. Popul. Biol. 41: 237-254.
30. TAJIMA, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
31. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis. Genetics 123: 585-595.
32. VIGOUROUX, Y., M. MCMULLEN, C. T. HITTINGER, K. HOUCHINS, L. SCHULZ et al., 2002 Identifying genes of agronomic importance in maize by screening microsatellites for evidence of selection during domestication. Proc. Natl. Acad. Sci. USA 99: 9650-9655.
33. WATTERSON, G. A., 1975 On the number of segregating sites. Theor. Popul. Biol. 7: 256-276.
34. WOOTTON, J. C., X. FENG, M. T. FERDIG, R. A. COOPER, J. MU et al., 2002 Genetic diversity and chloroquine selective sweeps in Plasmodium fakiparum. Nature 418: 320-323.