Identification of a locus under complex positive selection in Drosophila simulans by haplotype mapping and composite-likelihood estimation

Genetics

Volumn 168, Issue 1, 2004, Pages 265-279

  Meiklejohn, Colin D ^a   Kim, Yuseob ^b,d   Hartl, Daniel L ^a   Parsch, John ^c  

^a HARVARD UNIVERSITY   (United States)

^b Department of Obstetrics Gynecology   (United States)

^c UNIVERSITY OF MUNICH   (Germany)

^d UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME BANDING PATTERN; CONTROLLED STUDY; DNA POLYMORPHISM; DROSOPHILA SIMULANS; GENE; GENE LOCUS; GENETIC RECOMBINATION; GENETIC SELECTION; HAPLOTYPE; JANUS GENE; NONHUMAN; OCNUS GENE; PRIORITY JOURNAL; SERENDIPITY GENE;

ANIMALS; BASE SEQUENCE; COMPUTER SIMULATION; DROSOPHILA; DROSOPHILA PROTEINS; GENETICS, POPULATION; HAPLOTYPES; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

DROSOPHILA SIMULANS; JANUS; OCNUS;

EID: 5144229755     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.025494     Document Type: Article

References (64)

1. ADAMS, M. D., S. E. CELNIKER, R. A. HOLT, C. A. EVANS, J. D. GOCAYNE et al., 2000 The genome sequence of Drosophila melanogaster. Science 287: 2185-2195.
2. AGUADÉ, M., N. MIYASHITA and C. H. LANGLEY, 1989 Reduced variation in the yellow-achaete-scute region in natural populations of Drosophila melanogaster. Genetics 122: 607-615.
3. AKASHI, H., 1997 Codon bias evolution in Drosophila. Population genetics of mutation-selection drift. Gene 205: 269-278.
4. ANDOLFATTO, P., and M. PRZEWORSKI, 2000 A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156: 257-268.
5. ANDOLFATTO, P., and M. PRZEWORSKI, 2001 Regions of lower crossing over harbor more rare variants in African populations of Drosophila melanogaster. Genetics 158: 657-665.
6. ANDOLFATTO, P., J. D. WALL and M. KREITMAN, 1999 Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster. Genetics 153: 1297-1311.
7. BARTON, N. H., 1998 The effect of hitch-hiking on neutral genealogies. Genet. Res. 72: 123-133.
8. BEGUN, D. J., and P. WHITLEY, 2000 Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc. Natl. Acad. Sci. USA 97: 5960-5965.
9. BENASSI, V., F. DEPAULIS, G. K. MEGHLAOUI and M. VEUILLE, 1999 Partial sweeping of variation at the Fbp2 locus in a West African population of Drosophila melanogaster. Mol. Biol. Evol. 16: 347-353.
10. 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.
11. 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.
12. CACCONE, A., E. N. MORIYAMA, J. M. GLEASON, L. NIGRO and J. R. POWELL, 1996 A molecular phylogeny for the Drosophila melanogaster subgroup and the problem of polymorphism data. Mol. Biol. Evol. 13: 1224-1232.
13. CHARLESWORTH, B., and D. L. HARTL, 1978 Population dynamics of the segregation distorter polymorphism of Drosophila melanogaster. Genetics 89: 171-192.
14. CIRERA, S., and M. AGUADÉ, 1997 Evolutionary history of the sex-peptide (Acp70A) gene region in Drosophila melanogaster. Genetics 147: 189-197.
15. CIVETTA, A., and R. S. SINGH, 1998 Sex-related genes, directional sexual selection, and speciation. Mol. Biol. Evol. 15: 901-909.
16. CLARK, A. G., D. J. BEGUN and T. PROUT, 1999 Female X male interactions in Drosophila sperm competition. Science 283: 217-220.
17. FAY, J. C., and C.-I WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
18. FAY, J. C., G. L. WYCKOFF and C.-I WU, 2002 Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415: 1024-1026.
19. FU, Y.-X., and W.-H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
20. GILLESPIE, J. H., 2000 Genetic drift in an infinite population. The pseudohitchhiking model. Genetics 155: 909-919.
21. HEY, J., and R. M. KLIMAN, 1993 Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex. Mol. Biol. Evol. 10: 804-822.
22. HEY, J., and J. WAKELEY, 1997 A coalescent estimator of the population recombination rate. Genetics 145: 833-846.
23. HUDSON, R. R., 1987 Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50: 245-250.
24. HUDSON, R. R., K. BAILEY, D. SKARECKY, J. KWIATOWSKI and F. J. AYALA, 1994 Evidence for positive selection in the superoxide dismutase (Sod) region of Drosophila melanogaster. Genetics 136: 1329-1340.
25. KAPLAN, N. L., T. DARDEN and R. R. HUDSON, 1988 The coalescent process in models with selection. Genetics 120: 819-829.
26. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The "hitch-hiking effect" revisited. Genetics 123: 887-899.
27. KIM, Y., and R. NIELSEN, 2004 Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.
28. KIM, Y., and W. STEPHAN, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
29. KIMURA, M., 1968 Evolutionary rate at the molecular level. Nature 217: 624-626.
30. 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.
31. LACHAISE, D., M.-L. CARIOU, J. R. DAVID, F. LEMEUNIER, L. TSACAS et al., 1988 Historical biogeography of the Drosophila melanogaster species subgroup. Evol. Biol. 22: 159-225.
32. LEWONTIN, R. C., 1974 The Genetic Basis of Evolutionary Change. Columbia University Press, New York.
33. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
34. MCDONALD, J. H., 1996 Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol. Biol. Evol. 13: 253-260.
35. MCDONALD, J. H., 1998 Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol. Biol. Evol. 15: 377-384.
36. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
37. MORIYAMA, E. N., and J. R. POWELL, 1996 Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13: 261-277.
38. NACHMAN, M. W., and S. L. CROWELL, 2000 Contrasting evolutionary histories of two introns of the Duchenne Muscular Dystrophy gene, Dmd, in humans. Genetics 155: 1855-1864.
39. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
40. OHTA, T., and M. KIMURA, 1971 On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1: 18-25.
41. PARSCH, J., C. D. MEIKLEJOHN and D. L. HARTL, 2001a Patterns of DNA sequence variation suggest the recent action of positive selection in the janus-ocnus region of Drosophila simulans. Genetics 159: 647-657.
42. PARSCH, J., C. D. MEIKLEJOHN, E. HAUSCHTECK-JUNGEN, P. HUNZIKER and D. L. HARTL, 2001b Molecular evolution of the ocnus and janus genes in the Drosophila melanogaster species subgroup. Mol. Biol. Evol. 18: 801-811.
43. PRZEWORSKI, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
44. QUESADA, H., U. E. RAMIREZ, J. ROZAS and M. AGUADÉ, 2003 Largescale adaptive hitchhiking upon high recombination in Drosophila simulans. Genetics 165: 895-900.
45. RAND, D. M., and L. M. KANN, 1996 Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Mol. Biol. Evol. 13: 735-748.
46. RICE, W. R., 1984 Sex chromosomes and the evolution of sexual dimorphism. Evolution 38: 735-742.
47. ROZAS, J., M. GULLAUD, G. BLANDIN and M. AGUADÉ, 2001 DNA variation at the rp49 gene region of Drosophila simulans: evolutionary inferences from an unusual haplotype structure. Genetics 158: 1147-1155.
48. ROZAS, J., J. C. SANCHEZ-DELBARRIO, X. MESSEGUER and R. ROZAS, 2003 DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
49. SADETI, 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: 832-837.
50. 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.
51. SMITH, N. G. C., and A. EYRE-WALKER, 2002 Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.
52. 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.
53. SWANSON, W. J., and V. D. VACQUIER, 2002 Reproductive protein evolution. Annu. Rev. Ecol. Syst. 33: 161-179.
54. TAJIMA, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
55. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
56. THOMPSON, J. D., T. J. GIBSON, F. PLEWNIAK, F. JEANMOUGIN and D. G. HIGGINS, 1997 The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 4876-4882.
57. TRUE, J. R., J. M. MERCER and C. C. LAURIE, 1996 Differences in crossover frequency and distribution among three sibling species of Drosophila. Genetics 142: 507-523.
58. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
59. WALL, J. D., P. ANDOLFATTO and M. PRZEWORSKI, 2002 Testing models of selection and demography in Drosophila simulans. Genetics 162: 203-216.
60. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
61. WEINREICH, D. M., and D. M. RAND, 2000 Contrasting patterns of nonneutral evolution in proteins encoded in nuclear and mitochondrial genomes. Genetics 156: 385-399.
62. YANICOSTAS, C., and J.-A. LEPESANT, 1990 Transcriptional and translational cis-regulatory sequences of the spermatocyte-specific Drosophila janusB gene are located in the 3′ exonic region of the overlapping janusA gene. Mol. Gen. Genet. 224: 450-458.
63. YANICOSTAS, C., A. VINCENT and J.-A. LEPESANT, 1989 Transcriptional and posttranscriptional regulation contributes to the sex-regulated expression of two sequence-related genes at the janus locus of Drosophila melanogaster. Mol. Cell. Biol. 9: 2526-2535.
64. ZAPATA, C., C. NUÑEZ and T. VELASCO, 2002 Distribution of nonrandom associations between pairs of protein loci along the third chromosome of Drosophila melanogaster. Genetics 161: 1539-1550.