Recombination, Dominance and Selection on Amino Acid Polymorphism in the Drosophila Genome: Contrasting Patterns on the X and Fourth Chromosomes

Genetics

Volumn 165, Issue 3, 2003, Pages 1195-1208

  Sheldahl, Lea A ^a   Weinreich, Daniel M ^a   Rand, David M ^a  

^a BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

AMINO ACID ANALYSIS; DNA SEQUENCE; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; FLY; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETIC SELECTION; GENOME; HAPLOTYPE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; POPULATION SIZE; POPULATION STRUCTURE; PRIORITY JOURNAL; REVIEW; X CHROMOSOME;

AMINO ACIDS; ANIMALS; BASE SEQUENCE; CHROMOSOMES; DNA PRIMERS; DROSOPHILA; GENOME; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC; SELECTION (GENETICS); X CHROMOSOME;

ARABIDOPSIS; DROSOPHILA MELANOGASTER; DROSOPHILA SIMULANS; MELANOGASTER;

EID: 0346361874     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (68)

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-achete-scute region in natural populations of Drosophila melanogaster. Genetics 122: 607-615.
3. AKASHI, H., 1995 Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139: 1067-1076.
4. ANDOLFATTO, P., 2001 Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 18: 279-290.
5. AQUADRO, C. F., D. J. BEGUN and E. C. KINDAHL (Editors), 1994 Selection, Recombination, and DNA Polymorphism in Drosophila. Chapman & Hall, New York.
6. ASHBURNER, M., 1989 Drosophila: A Laboratory Handbook. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
7. BALLARD, J. W. O., 2000 Comparative genomics of mitochondrial DNA in members of the Drosophila melanogaster subgroup. J. Mol. Evol. 51: 48-63.
8. BEGUN, D. J., 1996 Population genetics of silent and replacement variation in Drosophila simulans and D. melanogaster: X/autosome differences? Mol. Biol. Evol. 13: 1405-1407.
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 occuring 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 Drosphila melanogaster are very different at the DNA level. Nature 356: 519-520.
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, 2000 Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc. Natl. Acad. Sci. USA 97: 5960-5965.
15. BERRY, A. J., J. W. AJIOKA and M. KREITMAN, 1991 Lack of polymorphism on the Drosophila fourth chromosome resulting form selection. Genetics 129: 1111-1117.
16. BETANCOURT, A. J., D. C. PRESGRAVES and W. J. SWANSON, 2002 A test for faster X evolution in Drosophila. Mol. Biol. Evol. 19: 1816-1819.
17. 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.
18. 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.
19. CHARLESWORTH, B., 1996 Background selection and patterns of genetic diversity in Drosophila melanogaster. Genet. Res. 68: 131-149.
20. CHARLESWORTH, B., 1998 Measures of divergence between populations and the effect of forces that reduce variability. Mol. Biol. Evol. 15: 538-543.
21. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
22. COMERON, J., 1999 K-estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals. Bioinformatics 15: 763-764.
23. COMERON, J., and M. KREITMAN, 2002 Population, evolutionary and genomic consequences of interference selection. Genetics 161: 389-410.
24. COMERON, J., M. KREITMAN and M. AGUADE, 1999 Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151: 239-249.
25. CROW, J. F., and M. KIMURA, 1970 An Introduction to Population Genetics Theory. Harper & Row, New York.
26. EXCOFFIER, L., 2002 Arlequin: Software for Population Genetics Analysis. (http://lgb.unige.ch/arlequin/).
27. FAY, J. C., and C.-I WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
28. FAY, J. C., G. J. WYCKOFF and C.-I WU, 2002 Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415: 1024-1026.
29. FELSENSTEIN, J., 1974 The evolutionary advantage of recombination. Genetics 78: 737-756.
30. FU, Y.-X., and W.-H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
31. GILLESPIE, J. H., 1997. Junk ain't what junk does: neutral alleles in a selected context. Gene 205: 291-299.
32. GILLESPIE, J. H., 2000 Genetic drift in an infinite population: the pseudohitchhiking model. Genetics 155: 909-919.
33. GLOOR, G., and W. R. ENGELS, 1991 Single fly DNA preps for PCR. Dros. Inf. Newsl. 1 (flybase.bio.indiana.edu/docs/news/DIN/dinvol1.txt).
34. HEY, J., and R. M. KLIMAN, 2002 Interactions between natural selection, recombination and gene density in the genes of Drosophila. Genetics 160: 595-608.
35. HILL, W. G., and A. ROBERTSON, 1966 The effect of linkage on limits of artificial selection. Genet. Res. 8: 269-294.
36. 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.
37. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
38. HUDSON, R. R., D. D. BOOS and N. L. KAPLAN, 1992 A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9: 138-151.
39. JENSEN, M. A., B. CHARLESWORTH and M. KREITMAN, 2002 Patterns of genetic variation at a chromosome 4 locus of Drosophila melanogaster and D. simulans. Genetics 160: 493-507.
40. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The "hitchhiking effect" revisited. Genetics 123: 887-899.
41. KIM, Y., and W. STEPHAN, 2000 Joint effects of genetic hitchhiking and background selection on neutral variation. Genetics 155: 1415-1427.
42. KIMURA, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
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. LANGLEY, C. H., B. P. LAZZARO, W. PHILLIPS, E. HEIKKINEN and J. M. 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.
45. LI, W.-H., and D. GRAUR, 1991 Fundamentals of Molecular Evolution. Sinauer Associates, Sunderland, MA.
46. MALCOLM, C. M., G. J. WYCKOFF and B. T. LAHN, 2003 Genic mutation rates in mammals: local similarity, chromosomal heterogeneity, and X-versus-autosome disparity. Mol. Biol. Evol. 20: 1633-1641.
47. MARAIS, G., D. MOUCHIROUD and L. DURET, 2001 Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc. Natl. Acad. Sci. USA 98: 5688-5692.
48. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
49. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
50. MCVEAN, G. A., and B. CHARLESWORTH, 2000 The effects of Hill-Robertson interference between weakly selected mutations on patterns of molecular evolution and variation. Genetics 155: 929-944.
51. NACHMAN, M. W., 1998 Deleterious mutations in animal mitochondrial DNA. Genetica 102/103: 61-69.
52. NACHMAN, M. W., 2001 Single nucleotide polymorphisms and recombination rate in humans. Trends Genet. 17: 481-485.
53. PAYSEUR, B. A., and M. W. NACHMAN, 2000 Microsatellite variation and recombination rate in the human genome. Genetics 156: 1285-1298.
54. RAND, D. M., 2001 The units of selection on mitochondrial DNA. Annu. Rev. Ecol. Syst. 32: 415-448.
55. 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.
56. RAND, D. M., and L. M. KANN, 1998 Mutation and selection at silent and replacement sites in the evolution of animal mitochondrial DNA. Genetica 102/103: 393-407.
57. RAND, D. M., D. M. WEINREICH and B. O. CEZAIRLIYAN, 2000 Neutrality tests of conservative-radical amino acid changes in nuclear- and mitochondrially-encoded proteins. Gene 261: 115-125.
58. ROZAS, J., and R. ROZAS, 1999 DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
59. SAWYER, S. A., and D. L. HARTL, 1992 Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
60. SIMONSEN, K. L., G. A. CHURCHILL and C. F. AQUADRO, 1995 Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141: 413-429.
61. SOKAL, R. R., and F. J. ROHLF, 1981 Biometry, W. H. Freeman, San Francisco.
62. SOLIGNAC, M., M. MONNEROT and J.-C. MOUNOLOU, 1986 Mitochondrial DNA evolution in the melanogaster species subgroup of Drosophila. J. Mol. Evol. 23: 31-40.
63. STEPHAN, W., and C. H. LANGLEY, 1998 DNA polymorphism in lycopersicon and crossing-over per physical length. Genetics 150: 1585-1593.
64. STEPHAN, W., L. XING, D. A. KIRBY and J. M. BRAVERMAN, 1998 A test of the background selection hypothesis based on nucleotide data from Drosophila ananassae. Proc. Natl. Acad. Sci. USA 10: 5649-5654.
65. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
66. WANG, W., K. THORNTON, A. BERRY and M. LONG, 2002 Nucleotide variation along the Drosophila melanogaster fourth chromosome. Science 295: 134-137.
67. WEINREICH, D. M., and D. M. RAND, 2000 Contrasting patterns of non-neutral evolution in proteins encoded in nuclear and mitochondrial genomes. Genetics 156: 385-399.
68. WYCKOFF, G. J., W. WANG and C.-I WU, 2000 Rapid evolution of male reproductive genes in the descent of man. Nature 403: 304-309.