Multiple signatures of positive selection downstream of Notch on the X chromosome in Drosophila melanogaster

Genetics

Volumn 171, Issue 2, 2005, Pages 639-653

  DuMont, Vanessa Bauer ^a   Aquadro, Charles F ^a  

^a Cornell University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NOTCH RECEPTOR;

ALLELE; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DNA SEQUENCE; GENE LOCUS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; X CHROMOSOME;

ANIMALS; BASE SEQUENCE; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GENE COMPONENTS; GENETICS, POPULATION; LIKELIHOOD FUNCTIONS; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; MUTATION; POLYMORPHISM, GENETIC; RECEPTORS, NOTCH; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; X CHROMOSOME;

ANIMALIA; DROSOPHILA MELANOGASTER;

EID: 31544435449     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.104.038851     Document Type: Article

References (74)

1. AKASHI, H., 1994 Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136: 927-935.
2. ANDOLFATTO, P., 2001a Adaptive hitchhiking effects on genome variability. Curr. Opin. Genet. Dev. 11: 635-641.
3. ANDOLFATTO, P., 2001b Contrasting pattern of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 18: 279-290.
4. AQUADRO, C. F., D. J. BEGUN and E. C. KINDAHL, 1994 Selection, recombination, and DNA polymorphism in Drosophila, pp 46-56 in Non-neutral Evolution: Theories and Molecular Data, edited by BRIAN GOLDING. Chapman & Hall, New York.
5. AQUADRO, C. F., V. BAUER DUMONT and F. A. REED, 2001 Genomewide variation in the human and fruitfly: a comparison. Curr. Opin. Genet. Dev. 11: 627-634.
6. BACHTROG, D., M. AGIS, M. IMHOG and C. SCHLÖTTERER, 2000 Microsatellite variability differs between dinucleotide repeat motifs - evidence from Drosophila melanogaster. Mol. Biol. Evol. 17: 1277-1285.
7. BAUDRY, E., B. VIGINIER and M. VEUILLE, 2004 Non-African populations of Drosophila melanogaster have a unique origin. Mol. Biol. Evol. 8: 1482-1491.
8. BAUER DUMONT, V., J. C. FAY, P. P. CALABRESE, and C. F. AQUADRO 2004 DNA variability and divergence at the Notch locus in Drosophila melanogaster and D. simulans: a case of accelerated synonymous site divergence. Genetics 167: 171-185.
9. BEGUN, D. J., and C. F. AQUADRO, 1991 Molecular population genetics of the distal portion of the X chromosome in Drosophila: evidence for genetic hitchhiking of the yellow-achaete region. Genetics 129: 1147-1158.
10. BEGUN, D. J., and C. F. AQUADRO, 1992 Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356: 519-520.
11. BEGUN, D. J., and C. F. AQUADRO, 1993 African and North American populations of Drosophila melanogaster are very different at the DNA level. Nature 365: 548-550.
12. BEGUN, D. J., and C. F. AQUADRO, 1994 Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of Drosophila: selection and geographic differentiation. Genetics 136: 155-171.
13. BEGUN, D. J., and C. F. AQUADRO, 1995 Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. Genetics 140: 1019-1032.
14. BEGUN, D. J., and P. WHITLEY, 2000a Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc. Natl. Acad. Sci. USA 97: 5960-5965.
15. BEGUN, D.J., and P. WHITLEY, 2000b Adaptive evolution of Relish,a Drosophila NF-kappaB/IkappaB protein. Genetics 154: 1231-1238.
16. BIERNE, N., and A. EYRE-WALKER, 2004 The genomic rate of adaptive amino acid substitution in Drosophila. Mol. Biol. Evol. 21: 1350-1360.
17. BRINKMANN, B., M. KLINTSCHAR, F. NEUHUBER, J. HÜHNE and B. ROLF, 1998 Mutation rate in human microsatellites: influence of the structure and length of the tandem repeat. Am. J. Hum. Genet. 62: 1408-1415.
18. CASTILLO-DAVIS, C. I., D. L. HARTL and G. ACHAZ, 2004 cis-regulatory and protein evolution in orthologous and duplicate genes. Genome Res. 14: 1530-1536.
19. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
20. CORNUET, J. M., and G. LUIKART, 1996 Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
21. DAVID, J. R., and P. CAPY, 1988 Genetic variation of Drosophila melanogaster natural populations. Trends Genet. 4: 106-111.
22. DUVERNELL, D. D., P. S. SCHMIDT and W. F. EANES, 2003 Clines and adaptive evolution in the methuselah gene region in Drosophila melanogaster. Mol. Ecol. 12: 1277-1285.
23. ELLEGREN, H., 2000 Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet. 16: 551-558.
24. EYRE-WALKER, A., 2002 Changing effective population size and the McDonald-Kreitman test. Genetics 162: 2017-2024.
25. FAY, J. C., and C.-I WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
26. FlyBase Consortium, 2003 The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 31: 172-175.
27. FU, Y-X., and W-H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
28. GLINKA, S., L. OMETTO, S. MOUSSET, W. STEPHAN and D. DE LORENZO, 2003 Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach. Genetics 165: 1269-1278.
29. GU, Z., D. NICOLAE, H. H-S. LU and W-H. LI, 2002 Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet. 18: 609-613.
30. HADDRILL, P. R., K. R. THORNTON, B. CHARLESWORTH and P. ANDOLFATTO, 2005 Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res. 15: 790-799.
31. 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.
32. HEY, J., and R. M. KLIMAN, 2002 Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160: 595-608.
33. HUDSON, R.R., 2002 Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
34. HUDSON, R. R., and N. L. KAPLAN, 1995 Deleterious background selection with recombination. Genetics 141: 1605-1617.
35. HUDSON, R. R., M. KREITMAN and M. AGUADÉ, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
36. JENSEN, J. D., Y. KIM, V. BAUER DUMONT, C. F. AQUADRO and C. D. BUSTAMANTE, 2005 Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410.
37. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The "hitchhiking effect" revisited. Genetics 123: 887-899.
38. KAUER, M., B. ZANGERL, D. DIERINGER and C. SCHLÖTTERER, 2002 Chromosomal patterns of microsatellite variability contrast sharply in African and non-African populations of Drosophila melanogaster. Genetics 160: 247-256.
39. KAUER, M. O., D. DIERINGER and C. SCHLÖTTERER, 2003 A microsatellite variability screen for positive selection associated with the "out of Africa" habitat expansion of Drosophila melanogaster. Genetics 165: 1137-1148.
40. KAYSER, M., S. BRAUER and M. STONEKING, 2003 A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol. Biol. Evol. 20: 893-900.
41. KIM, Y., and W. STEPHAN, 2000 Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155: 1415-1427.
42. KIM, Y., and W. STEPHAN, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
43. KLIMAN, R. M., and J. HEY, 1993 Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol. Biol. Evol. 10: 1239-1258.
44. KOHN, M. H., H.-J. PELZ and R. K. WAYNE, 2000 Natural selection mapping of the warfarin-resistance gene. Proc. Natl. Acad. Sci. USA 97: 7911-7915.
45. KREITMAN, M., 1983 Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melangoaster. Nature 304: 412-417.
46. LACHAISE, D., M. CARIOU, J. R. DAVID, F. LEMEUNIER, L. TSACAS et al., 1988 Historical biogeography of the Drosophila melanogaster species subgroup, pp. 159-225 in Evolutionary Biology, edited by M. K. HECHT, B. WALLACE and G. T. PRANCE. Plenum, New York.
47. a) region of the Drosophila melanogaster X chromosome. Genetics 156: 1837-1852.
48. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 20: 652-654.
49. NACHMAN, M. W., 2001 Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17: 481-485.
50. NURMINSKY, D., D. DE AGUIAR, C. D. BUSTAMANTE and D. L. HARTL, 2001 Chromosomal effects of rapid gene evolution in Drosophila melanogaster. Science 291: 128-130.
51. ODGERS, W. A., C. F. AQUADRO, C. W. COPPIN, M. J. HEALY and J. G. OAKESHOTT, 2002 Nucleotide polymorphism in the Est6 promoter, which is widespread in derived populations of Drosophila melanogaster, changes the level of Esterase 6 expressed in the male ejaculatory duct. Genetics 162: 785-797.
52. ORENGO, D. J., and M. AGUADÉ, 2004 Detecting the footprint of positive selection in a European population of Drosophila melanogaster: multilocus pattern of variation and distance to coding regions. Genetics 167: 1759-1766.
53. PAYSEUR, B. A., A. D. CUTTER and M. W. NACHMAN, 2002 Searching for evidence of positive selection in the human genome using patterns of microsatellite variability. Mol. Biol. Evol. 19: 1143-1153.
54. PRZEWORSKI, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 162: 1179-1189.
55. PRZEWORSKI, M., 2003 Estimating the time since the fixation of a beneficial allele. Genetics 164: 1667-1676.
56. ROZAS, J., and R. ROZAS, 1997 DnaSP version 2.0: A novel software package for extensive molecular population genetics analysis. Comput. Appl. Biosci. 13: 307-311.
57. SAIKI, R. K., D. H. GELFAND, D. STOFFEL, S. J. SCHARF, R. HIGUCHI et al., 1988 Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.
58. Schlenke, T. A., and D. J. Begun, 2003 Natural selection drives Drosophila immune system evolution. Genetics 164: 1471-1480.
59. 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.
60. SCHLÖFL, G., and C. SCHLÖTTERER, 2004 Patterns of microsatellite variability among X chromosomes and autosomes indicate a high frequency of beneficial mutations in non-African D. simulans. Mol. Biol. Evol. 21: 1384-1390.
61. SCHLÖTTERER, C., 2002a Towards a molecular characterization of adaptation in local populations. Curr. Opin. Genet. Dev. 12: 683-687.
62. SCHLÖTTERER, C., 2002b A microsatellite-based multilocus screen for the identification of local selective sweeps. Genetics 160: 753-763.
63. SCHMIDT, P. S., D. D. DUVERNELL and W. F. EANES, 2000 Adaptive evolution of a candidate gene for aging in Drosophila. Proc. Natl. Acad. Sci. USA 97: 10861-10865.
64. SCHUG, M. D., C. M. HUTTER, K. A. WETTERSTRAND, M. S. GAUDETTE, T. F. C. MACKAY et al., 1998 The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster. Mol. Biol. Evol. 15: 1751-1760.
65. SHIELDS, D. C., P. M. SHARP, D. G. HIGGINS and F. WRIGHT, 1988 "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol. 5: 704-716.
66. STORZ, J. F., B. A. PAYSEUR and M. W. NACHMAN, 2004 Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol. Biol. Evol. 21: 1800-1811.
67. SWANSON, W. J., and V. D. VACQUIER, 2002 The rapid evolution of reproductive proteins. Nat. Rev. Genet. 3: 137-144.
68. SWANSON, W. J., Z. YANG, M. F. WOLFNER and C. F. AQUADRO, 2001 Positive Darwinian selection drives the evolution of female reproductive proteins in mammals. Proc. Natl. Acad. Sci. USA 98: 2509-2514.
69. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
70. TAKAHASHI, A., S.-C. TSAUR, J. A. COYNE and C.-I WU, 2001 The nucleotide changes governing cuticular hydrocarbon variation and their evolution in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 98: 3920-3925.
71. TSAUR, S.-C., and C.-I WU, 1997 Positive selection and the molecular evolution of a gene of male reproduction, Acp26Aa in Drosophila. Mol. Biol. Evol. 14: 544-549.
72. VERRELLI, B. C., and W. F. EANES, 2000 Extensive amino acid polymorphism at the Pgm locus is consistent with adaptive protein evolution in Drosophila melanogaster. Genetics 156: 1737-1752.
73. WAKELEY, J., 2003 Polymorphism and divergence for island-model species. Genetics 163: 411-420.
74. WAKELEY, J., and N. ALIACAR, 2001 Gene genealogies in a metapopulation. Genetics 159: 893-905.