History and structure of sub-saharan populations of Drosophila melanogaster

Genetics

Volumn 174, Issue 2, 2006, Pages 915-929

  Pool, John E ^a   Aquadro, Charles F ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DROSOPHILA MELANOGASTER; FEMALE; GENE STRUCTURE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GEOGRAPHIC DISTRIBUTION; NONHUMAN; PALEARCTIC; PRIORITY JOURNAL; SIMULATION;

AFRICA SOUTH OF THE SAHARA; ANIMALS; DROSOPHILA MELANOGASTER; EVOLUTION; FEMALE; GENETICS, POPULATION; MOLECULAR SEQUENCE DATA; NATURAL HISTORY; VARIATION (GENETICS);

DROSOPHILA MELANOGASTER;

EID: 33750464822     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.058693     Document Type: Article

References (65)

1. ANDOLFATTO, P., 2005 Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
2. AULARD, S., J. R. DAVID and F. LEMEUNIER, 2002 Chromosomal inversion polymorphism in Afrotropical populations of Drosophila melanogaster. Genet. Res. 79: 49-63.
3. BAILEY, T. L., and M. GRIBSKOV, 1998 Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14: 48-54.
4. BAUDRY, E., B. VIGINIER and M. VEUILLE, 2004 Non-African populations of Drosophila melanogaster have a unique origin. Mol. Biol. Evol. 21: 1482-1491.
5. BAUDRY, E., N. DEROME, M. HUET and M. VEUILLE, 2006 Contrasted polymorphism patterns in a large sample of populations from the evolutionary genetics model Drosophila simulans. Genetics 173: 759-767.
6. BAUER DUMONT, V., and C. F. AQUADRO, 2005 Multiple signatures of positive selection downstream of Notch on the X chromosome in Drosophila melanogaster. Genetics 171:639-653.
7. 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.
8. 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.
9. BÉNASSI, V., and M. VEUILLE, 1995 Comparative population structuring of molecular and allozyme variation of Drosophila melanogaster Adh between Europe, West Africa, and East Africa. Genet. Res. 65: 95-103.
10. BERGMAN, C. M., and M. KREITMAN, 2001 Analysis of conserved non-coding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences. Genome Res. 11: 1335-1345.
11. CAPY, P., M. VEUILLE, M. PAILLETTE, J.-M. JALLON, J. VOUIDIBIO et al., 2000 Sexual isolation of genetically differentiated sympatric populations of Drosophila melanogaster in Brazzaville, Congo: The first step towards speciation? Heredity 84: 468-475.
12. CARACRISTI, G., and C. SCHLÖTTERER, 2003 Genetic differentiation between American and European Drosophila melanogaster populations could be attributed to admixture of African alleles. Mol. Biol. Evol. 20: 792-799.
13. DAVID, J. R., and P. CAPY, 1988 Genetic variation of Drosophila melanogaster natural populations. Trends Genet. 4: 106-111.
14. DEAN, M. D., and J. W. O. BALLARD, 2004 Linking phylogenetics with population genetics to reconstruct the geographic origin of a species. Mol. Phylogenet. Evol. 32: 998-1009.
15. DEPAULIS, F., S. MOUSSET and M. VEUILLE, 2003 Power of neutrality tests to detect bottlenecks and hitchhiking. J. Mol. Evol. 57: S190-S200.
16. DIERINGER, D., V. NOLTE and C. SCHLÖTTERER, 2005 Population structure in African Drosophila melanogaster revealed by microsatellite analysis. Mol. Ecol. 14: 563-573.
17. EXCOFFIER, L., P. E. SMOUSE and J. M. QUATTRO, 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
18. EXCOFFIER, L., G. LAVAL and S. SCHNEIDER, 2005 Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol. Bioinformatics Online 1: 47-50.
19. FALUSH, D., M. STEPHENS and J. K. PRITCHARD, 2003 Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
20. FAY, J. C., and C. I. WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
21. FU, Y.-X., 1995 Statistical properties of segregating sites. Theor. Popul. Biol. 48: 172-197.
22. FU, Y.-X., and W.-H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
23. GIRDLER, R. W., 1991 The Afro-Arabian rift system - an overview. Tectonophysics 197: 139-153.
24. 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.
25. 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.
26. HEY, J., and R. M. KLIMAN, 2002 Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160: 595-608.
27. HUDSON, R. R., 2000 A new statistic for detecting genetic differentiation. Genetics 155: 2011-2014.
28. HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
29. HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model. Bioinformatics 18: 337-338.
30. HUDSON, R. R., M. KREITMAN and M. AGUADÉ, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
31. HUDSON, R. R., M. SLATKIN and W. P. MADDISON, 1992 Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
32. 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.
33. KASTANIS, P., E. ELIOPOULOS, G. GOULIELMOS, S. TSAKAS and M. LOUKAS, 2003 Macroevolutionary relationships of species of Drosophila melanogaster group based on mtDNA sequences. Mol. Phylogenet. Evol. 28: 518-528.
34. 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.
35. KAUER, M., D. DIERINGER and C. SCHLÖTTERER, 2003 Non-neutral admixture of immigrant genotypes in African Drosophila melanogaster populations from Zimbabwe. Mol. Biol. Evol. 20: 1329-1337.
36. KERN, A. D., and D. J. BEGUN, 2005 Patterns of polymorphism and divergence from noncoding sequences of Drosophila melanogaster and D. simulans: evidence for nonequilibrium processes. Mol. Biol. Evol. 22: 51-62.
37. KIM, Y., and W. STEPHAN, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
38. KINDAHL, E. C., 1994 Recombination and DNA polymorphism on the third chromosome of Drosophila melanogaster. Ph.D. Thesis, Cornell University, Ithaca, NY.
39. KO, W.-Y., R. M. DAVID and H. AKASHI, 2003 Molecular phylogeny of the Drosophila melanogaster species subgroup. J. Mol. Evol. 57: 562-573.
40. KOPP, A., and J. R. TRUE, 2002 Phylogeny of oriental Drosophila melanogaster species group: a multilocus reconstruction. Syst. Biol. 51: 786-805.
41. KUMAR, S., K. TAMURA and M. NEI, 2004 MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinformatics 5: 150-163.
42. LACHAISE, D., and J.-F. SILVAIN, 2004 How two Afrotropical endemics made two cosmopolitan human commensals: the Drosophila melanogaster-D. simulans palaeogeographic riddle. Genetica 120: 17-39.
43. 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, Vol. 22, edited by M. K. HECHT, B. WALLACE and G. T. PRANCE. PLENUM Press, New York.
44. LACHAISE, D., M. HARRY, M. SOLIGNAC, F. LEMEUNIER, V. BÉNASSI et al., 2000 Evolutionary novelties in islands: Drosophila santomea, a new melanogaster sister species from São Tomé. Proc. R. Soc. Lond. Ser. B 267: 1487-1495.
45. LEMEUNIER, F., and S. AULARD, 1992 Inversion polymorphism in Drosophila melanogaster, pp. 339-405 in Drosophila Inversion Polymorphism, edited by C. B. KRIMBAS and J. R. POWELL. CRC Press, Cleveland.
46. MANTEL, N., 1967 The detection of disease clustering and a generalized regression approach. Cancer Res. 27: 209-220.
47. MICHALAKIS, Y., and M. VEUILLE, 1996 Length variation of CAG/CAA trinucleotide repeats in natural populations of Drosophila melanogaster and its relation to the recombination rate. Genetics 145: 1713-1725.
48. OMETTO, L., S. GLINKA, D. DE LORENZO and W. STEPHAN, 2005 Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. Mol. Biol. Evol. 22: 2119-2130.
49. ORENGO, D. J., and M. AGUADÉ, 2004 Detecting the footprint of selection in a European population of Drosophila melanogaster: multilocus pattern of variation and distance to coding regions. Genetics 167: 1759-1766.
50. POOL, J. E., V. BAUER DUMONT, J. L. MUELLER and C. F. AQUADRO, 2006 A scan of molecular variation leads to the narrow localization of a selective sweep affecting both Afrotropical and cosmopolitan populations of Drosophila melanogaster. Genetics 172: 1093-1105.
51. PRITCHARD, J. K., M. STEPHENS and P. DONNELLY, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
52. REICH, D. E., M. CARGILL, S. BOLK, J. IRELAND, P. C. SABETI et al., 2001 Linkage disequilibrium in the human genome. Nature 411: 199-204.
53. ROSENBERG, N. A., 2004 DISTRUCT: a program for the graphical display of population structure. Mol. Ecol. Notes 4: 137.
54. ROZAS, J., J. C. SÁNCHEZ-DELBARRIO, X. MESSEGUER and R. ROZAS, 2003 DnaSP: DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496-2497.
55. RUSSO, C. A. M., N. TAKEZAKI and M. NEI, 1995 Molecular phylogeny and divergence times of Drosophilid species. Mol Biol. Evol. 12: 391-404.
56. SCHLÖTTERER, C., H. NEUMEIER, C. SOUSA and V. NOLTE, 2006 Highly structured Asian Drosophila melanogaster populations: A new tool for hitchhiking mapping? Genetics 172: 287-292.
57. STANLEY, S. M., P. A. PARSONS, G. E. SPENCE and L. WEBER, 1980 Resistance of species of the Drosophila melanogaster subgroup to environmental extremes. Aust. J. Zool. 28: 413-421.
58. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
59. TAMURA, K., S. SUBRAMANIAN and S. KUMAR, 2004 Temporal pattern of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol. Biol. Evol. 21: 36-44.
60. THORNTON, K., 2003 libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics 19: 2325-2327.
61. THORNTON, K., and P. ANDOLFATTO, 2006 Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
62. VAN HERREWEGE, J., and J. R. DAVID, 1997 Starvation and dessication tolerances in Drosophila: comparison of species from different climatic origins. Ecoscience 4: 151-157.
63. VEUILLE, M., E. BAUDRY, M. COBB, N. DEROME and E. GRAVOT, 2004 Historicity and population genetics of Drosophila melanogaster and D. simulans. Genetica 120: 61-70.
64. VOUIDIBIO, J, P. CAPY, D. DEFAYE, E. PLA, J. SANDRIN et al., 1989 Short-range genetic structure of Drosophila melanogaster populations in an Afrotropical urban area and its significance. Proc. Natl. Acad. Sci. USA 86: 8442-8446.
65. WALL, J. D., P. ANDOLFATTO and M. PRZEWORSKI, 2002 Testing models of selection and demography in Drosophila simulans. Genetics 162: 203-216.