Non-African populations of Drosophila melanogaster have a unique origin

Molecular Biology and Evolution

Volumn 21, Issue 8, 2004, Pages 1482-1491

  Baudry, Emmanuelle ^a   Viginier, Barbara ^a   Veuille, Michel ^a  

^a PSL RESEARCH UNIVERSITY   (France)

Author keywords

African; Bottleneck; DNA polymorphism; Drosophila melanogaster; Geographic subdivision

Indexed keywords

ARTICLE; BOTTLENECK POPULATION; DNA FOOTPRINTING; DNA POLYMORPHISM; DNA SEQUENCE; DROSOPHILA MELANOGASTER; GENE LOCUS; GENETIC VARIABILITY; HAPLOTYPE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; X CHROMOSOME;

AFRICA; ANIMALS; BASE SEQUENCE; DROSOPHILA MELANOGASTER; EVOLUTION, MOLECULAR; GENES, INSECT; HAPLOTYPES; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; X CHROMOSOME;

ARACHNIDA; DROSOPHILA MELANOGASTER; HEXAPODA; MELANOGASTER;

EID: 3242760033     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh089     Document Type: Article

References (66)

1. Aguadé, M. 1998. Different forces drive the evolution of the Acp26Aa and Acp26Ab accessory gland genes in the Drosophila melanogaster species complex. Genetics 150:1079-1089.
2. -. 1999. Positive selection drives the evolution of the Acp29AB accessory gland protein in Drosophila. Genetics 152:543-551.
3. Andolfatto, P. 2001. Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 18:279-290.
4. Andolfatto, P., and M. Kreitman. 2000. Molecular variation at the In(2L)t proximal breakpoint site in natural populations of Drosophila melanogaster and D. simulans. Genetics 154: 1681-1691.
5. Aulard, S., J. David, and F. Lemeunier. 2002. Chromosomal inversion polymorphism in Afrotropical populations of Drosophila melanogaster. Genet. Res. 79:49-63.
6. Balakirev, E., V. Chechetkin, V. Lobzin, and F. Ayala. 2003. DNA polymorphism in the beta-Esterase gene cluster of Drosophila melanogaster. Genetics 164:533-544.
7. Balakirev, E. S., E. I. Balakirev, and F. J. Ayala. 2002. Molecular evolution of the Est-6 gene in Drosophila melanogaster: contrasting patterns of DNA variability in adjacent functional regions. Gene 288:167-177.
8. Begun, D., and C. Aquadro. 1993. African and North American populations of Drosophila melanogaster are very different at the DNA level. Nature 365:548-550.
9. -. 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.
10. -. 1995. Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. Genetics 140:1019-1032.
11. Begun, D., C. Aquadro, and P. Whitley. 2000. Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc. Natl. Acad. Sci. U.S.A. 97:5960-5965.
12. 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.
13. 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.
14. Charlesworth, B. 1996. Background selection and patterns of genetic diversity in Drosophila. Genet. Res. 68:131-149.
15. -. 1998. Measures of divergence between populations and the effect of forces that reduce variability. Mol. Biol. Evol. 15:538-543.
16. Charlesworth, B., M. T. Morgan, and D. Charlesworth. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289-1303.
17. Cirera, S., and M. Aguadé. 1997. Evolutionary history of the sex-peptide (Acp70A) gene region in Drosophila melanogaster. Genetics 147:189-197.
18. Comeron, J. M., M. Kreitman, and M. Aguadé. 1999. Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151: 239-149.
19. David, J. R., and P. Capy. 1988. Genetic variation of Drosophila melanogaster natural populations. Trends Genet. 4: 106-111.
20. Depaulis, F., S. Mousset, and M. Veuille. 2003. Power of neutrality tests to detect bottlenecks and hitchhiking J. Mol. Evol. 57(Suppl. 1):S190-200.
21. Fay, J. C., and C. I. Wu. 2000. Hitchhiking under positive Darwinian selection. Genetics 155:1405-1413.
22. Filatov, D. A. 2002. ProSeq: A software for preparation and evolutionary analysis of DNA sequence data sets. Mol. Ecol. Notes 2:621-624.
23. Fu, Y. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147:915-925.
24. Hale, L. R., and R. S. Singh. 1987. Mitochondrial DNA variation and genetic structure in populations of Drosophila melanogaster Mol. Biol. Evol. 4:622-637.
25. -. 1991. A comprehensive study of genic variation in natural populations of Drosophila melanogaster. IV. Mitochondrial DNA variation and the role of history vs. selection in the genetic structure of geographic populations. Genetics. 129:103-117.
26. Hudson, R. R., D. D. Boos, and N. L. Kaplan. 1992. A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9:138-151.
27. Hudson, R. R., and N. L. Kaplan. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-164.
28. -. 1995. Deleterious background selection with recombination. Genetics 141:1605-1617.
29. Hudson, R. R., M. Slatkin, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583-589.
30. Kaplan, N. L., R. R. Hudson, and C. H. Langley. 1989. The "hitchhiking effect" revisited. Genetics 123:887-899.
31. Kauer, M., B. Zangerl, D. Dieringer, and C. Schlötterer. 2001. Chromosomal patterns of microsatellite variability contrast sharply in African and non-African populations of Drosophila melanogaster. Genetics 160:247-256.
32. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
33. Kirby, D. A., and W. Stephan. 1995. Haplotype test reveals departures from neutrality in a segment of the white gene of Drosophila melanogaster. Genetics 141:1483-1490.
34. -. 1996. Multi-locus selection and the structure of variation at the white gene of Drosophila melanogaster. Genetics 144:635-645.
35. Kliman, R. M., and J. Hey. 1993. Reduced natural selection associated with low recombination in Drosophila melanogaster. Mol. Biol. Evol. 10:1239-1258.
36. Kreitman, M., and R. R. Hudson. 1991. Inferring the evolutionary histories of the Adh and Adh-dup loci in Drosophila melanogaster from patterns of polymorphism and divergence. Genetics 127:565-582.
37. Kumar, S., K. Tamura, and M. Nei. 1993. MEGA: Molecular evolutionary genetics analysis.
38. Lachaise, D., M. Cariou, J. R. David, F. Lemeunier, L. Tsacas, and M. Ashburner. 1988. Historical biogeography of the Drosophila melanogaster species subgroup. Pp. 159-225 in M.K. Hecht, B. Wallace, and G. T. Prance, eds. Evolutionary biology, Vol. 22. Plenum Press, New York.
39. Langley, C., B. Lazzaro, W. Phillips, E. Heikkinen, and J. Braverman. 2000. Linkage disequilibria and the site frequency spectra in the su(s) and su(w(a)) regions of the Drosophila melanogaster X chromosome. Genetics 156:1837-1852.
40. Lazzaro, B., and A. Clark. 2001. Evidence for recurrent paralogous gene conversion and exceptional allelic divergence in the Attacin genes of Drosophila melanogaster. Genetics 159:659-71.
41. Lemeunier F., S. Aulard, V. Benassi, and M. Veuille. 1994. Fruitfly origins. Nature 365:548-550.
42. Lemeunier, F., J. David, L. Tsacas, and L. Ashburner 1985. The Drosophila melanogaster species group. Pp. 147-256 in M. Ashburner and H. Carson, Jr., eds. The genetics and biology of Drosophila, Vol. 3. Academic Press, New York.
43. Lewontin R. C. 1974. The genetics basis of evolutionary change. Columbia University Press, New York.
44. Li, W. H. 1997. Molecular evolution. Sinauer Associates, Sunderland, Mass.
45. Maynard Smith, J., and J. Haigh. 1974. The hitch-hiking effect of a favourable gene. Genet. Res. 23:23-35.
46. 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 143:1713-1725.
47. Mousset S., L. Brazier, M. M. Cariou, F. Chartois, F. Depaulis, and M. Veuille. 2003. Evidence of a high rate of selective sweeps in African Drosophila melanogaster. Genetics. 163:599-609.
48. Navarro, A., A. Barbadilla, and A. Ruiz. 2000. Effect of inversion polymorphism on the neutral nucleotide variability of linked chromosomal regions in Drosophila. Genetics: 155:685-698.
49. Odgers, W. A., C. F. Aquadro, C. W. Coppin, M. J. Healy, and J. G. Oakeshott. 2001. 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.
50. Posada, D., and K. Crandall. 2002. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54:396-402.
51. Roders, R. A., and H. Harpending. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol. Biol. Evol. 9:552-569.
52. Rozas, J., and R. Rozas. 1999. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15:174-175.
53. Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
54. Schlötterer, C., C. Vogl, and D. Tautz. 1997. Polymorphism and locus-specific effects on polymorphism at microsatellite loci in natural Drosophila melanogaster populations. Genetics 146:309-320.
55. Singh, R., M. Choudhary, and J. David. 1987. Contrasting patterns of geographic variation in the cosmopolitan sibling species Drosophila melanogaster and Drosophila simulans. Biochem. Genet. 4:27-40.
56. Slatkin, M., and R. R. Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555-562.
57. 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.
58. Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105:437-460.
59. -. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585-595.
60. Teeter, K., M. Naeemuddin, R. Gasperini, E. Zimmerman, K. White, R. Hoskins, and G. Gibson. 2000. Haplotype dimorphism in a SNP collection from Drosophila melanogaster. J. Exp. Zool. 288:63-75.
61. Teissier, G. 1957. Discriminative biometrical characters in French and Japanese Drosophila melanogaster. Proceedings of the XIVth International Genetics Symposia, 502-506.
62. Veuille M., V. Benassi, S. Aulard, and F. Depaulis. 1998. Allele-specific population structure of Drosophila melanogaster alcohol dehydrogenase at the molecular level. Genetics 149:971-981.
63. Wall, J. D. 1999. Recombination and the power of statistical tests of neutrality. Genet. Res. 74:65-79.
64. Wall, J. D., P. Andolfatto, and M. Przeworski. 2002. Testing models of selection and demography in Drosophila simulans. Genetics 162:203-216.
65. Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7:256-276.
66. Zurovcova, M., and F. Ayala. 2002. Polymorphism patterns in two tightly linked developmental genes, Idgf1 and Idgf3, of Drosophila melanogaster. Genetics. 162:177-188.