Distinguishing between selective sweeps and demography using DNA polymorphism data

Genetics

Volumn 170, Issue 3, 2005, Pages 1401-1410

  Jensen, Jeffrey D ^a   Kim, Yuseob ^b,c   DuMont, Vanessa Bauer ^a   Aquadro, Charles F ^a   Bustamante, Carlos D ^b  

^a Department of Obstetrics Gynecology   (United States)

^b Plant Breeding and Genetics Section in the School of Integrative Plant Science   (United States)

^c UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; ARTICLE; BOTTLENECK POPULATION; COMPOSITE LIKELIHOOD RATIO; DEMOGRAPHY; DIRECTED MOLECULAR EVOLUTION; DNA POLYMORPHISM; FITNESS; GENE MUTATION; GENETIC FITNESS; GENETIC SELECTION; GOODNESS OF FIT TEST; POPULATION STRUCTURE; PRIORITY JOURNAL; STATISTICAL ANALYSIS; STATISTICAL MODEL;

COMPUTER SIMULATION; DEMOGRAPHY; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; POLYMORPHISM, GENETIC; REPRODUCIBILITY OF RESULTS; SELECTION (GENETICS);

EID: 23344438911     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.038224     Document Type: Article

References (30)

1. AGUADÉ, M., N. MIYASHITA and C. H. LANGLEY, 1992 Polymorphism and divergence in the Mst26a male accessory gland gene region. Genetics 132: 755-777.
2. BARTON, N. H., 1998 The effect of hitch-hiking on neutral genealogies. Genet. Res. 72: 123-133.
3. BAUDRY, E., B. VIGINIER and M. VEUILLE, 2004 Non-African populations of Drosophila melanogaster have a unique origin. Mol. Biol. Evol. 21: 1482-1491.
4. BRAVERMAN, J. M., R. R. HUDSON, N. L. KAPLAN, C. H. LANGLEY and W. STEPHAN, 1995 The hitchhiking effect on the site frequency spectrum of DNA polymorphisms. Genetics 140: 783-796.
5. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
6. DEPAULIS, F., S. MOUSSET and M. VEUILLE, 2003 Power of neutrality tests to detect bottlenecks and hitchhiking. J. Mol. Evol. 57 (Suppl. 1): S190-S200.
7. FAY, J., and C.-I. WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
8. FU, Y.-X., 1997 Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
9. FU, Y.-X., and W.-H. LI, 1993 Statistical tests of neutral mutations. Genetics 133: 693-709.
10. GRIFFITHS, R. C., and P. MARJORAM, 1996a Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3: 479-502.
11. GRIFFITHS, R. C., and P. MARJORAM, 1996b An ancestral recombination graph, pp. 257-270 in IMA Volume on Mathematical Population Genetics, edited by P. DONNELLY and S. TAVARE. Springer-Verlag, Berlin/Heidelberg, Germany/New York.
12. HAMBLIN, M. T., E. E. THOMPSON and A. DI RIENZO, 2002 Complex signatures of natural selection at the Duffy blood group locus. ,Am. J. Hum. Genet. 70: 369-383.
13. 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.
14. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model. Bioinformatics 18: 337-338.
15. HUDSON, R. R., M. KREITMAN and M. AGUADÉ, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
16. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 "The hitch-hiking effect" revisited. Genetics 123: 887-899.
17. KIM, Y., and R. NIELSEN, 2004 Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.
18. KIM, Y., and W. STEPHAN, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
19. LLOPART, A., J. M. COMERON, F. G. BRUNET, D. LACHAISE and M. LONG, 2002 Intron presence-absence polymorphism in Drosophila driven by positive Darwinian selection. Proc. Natl. Acad. Sci. USA 99: 8121-8126.
20. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favorable gene. Genet. Res. 23: 23-35.
21. MEIKLEJOHN, C. D., Y. KIM, D. L. HARTL and J. PAKSCH, 2004 Identification of a locus under complex positive selection in Drosophila simulans by haplotype mapping and composite-likelihood estimation. Genetics 168: 265-279.
22. PRZEWORSKI, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
23. QUESADA, H., U. E. RAMIREZ, J. ROZAS and M. AGUADÉ, 2003 Large-scale adaptive hitchhiking upon high recombination in Drosophila simulans. Genetics 165: 895-900.
24. 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.
25. TAJIMA, F., 1989a Statistical method for testing the neutral mutation hypothesis. Genetics 123: 437-460.
26. TAJIMA, F., 1989b The effect of change in population size on DNA polymorphism. Genetics 123: 597-601.
27. 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.
28. WAKELEY, J., 2003 Polymorphism and divergence for island-model species. Genetics 163: 411-420.
29. WAKELEY, J., and N. ALICAR, 2001 Gene genealogies in a metapopulation. Genetics 159: 893-905.
30. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.