DNA variability and recombination rates at X-linked loci in humans

Genetics

Volumn 150, Issue 3, 1998, Pages 1133-1141

  Nachman, Michael W ^a   Bauer, Vanessa L ^b   Crowell, Susan L ^a   Aquadro, Charles F ^b  

^a University of Arizona   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; CHIMPANZEE; GENETIC RECOMBINATION; GENETIC VARIABILITY; HETEROZYGOSITY; HUMAN; INTRON; NEUTRAL GENE THEORY; NONHUMAN; ORANG UTAN; PRIORITY JOURNAL; X CHROMOSOME; X CHROMOSOME LINKAGE;

ANIMALS; DNA; GENOME; GENOME, HUMAN; HUMANS; LINKAGE (GENETICS); PAN TROGLODYTES; POLYMORPHISM, GENETIC; PONGO PYGMAEUS; RECOMBINATION, GENETIC; VARIATION (GENETICS); X CHROMOSOME;

EID: 0031770039     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (69)

1. AGUADE, M., and C. H. LANGLEY, 1994 Polymorphism and divergence in regions of low recombination in Drosophila, pp. 67-76 in Non-Neutral Evolution: Theories and Molecular Data, edited by B. GOLDING. Chapman & Hall, New York.
2. AQUADRO, C. F., 1992 Why is the genome variable? Insights from Drosophila. Trends Genet. 8: 355-362.
3. AQUADRO, C. F., 1997 Insights into the evolutionary process from patterns of DNA sequence variability. Curr. Opin. Genet. Devel. 7: 835-840.
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 B. GOLDING. Chapman & Hall, New York.
5. 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.
6. 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.
7. BIRD, A. P., 1995 Gene number, noise reduction and biological complexity. Trends Genet. 11: 94-100.
8. 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 polymorphism. Genetics 140: 783-796.
9. CHARLESWORTH, B., 1994 The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63: 213-227.
10. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
11. CHARLESWORTH, D., B. CHARLESWORTH and M. T. MORGAN, 1995 The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619-1632.
12. CLARK, A. G., K. M. WEISS, D. A. NICKERSON, S. L. TAYLOR, A. BUCHANAN et al., 1998 Haplotype structure and population genetic inferences from nucleotide sequence variation in human lipoprotein lipase. Am. J. Hum. Genet. 63: 595-612.
13. DIB, C., S. FAURE, C. FIZAMES, D. SAMSON, N. DROUOT et al., 1996 A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380: 152-154.
14. DIEHL, H. J., M. SCHAIGH, R. M. BUDZINSKI and W. STOFFEL, 1986 Individual exons encode the integral membrane domains of human myelin proteolipid protein. Proc. Natl. Acad. Sci. USA 83: 9807-9811.
15. DORIT, R. L., H. AKASHI and W. GILBERT, 1995 Absence of polymorphism at the Zfy locus on the human Y chromosome. Science 268: 1183-1185.
16. DRAKE, J. W., B. CHARLESWORTH, D. CHARLESWORTH and J. F. CROW, 1998 Rates of spontaneous mutation. Genetics 148: 1667-1686.
17. EDWARDS, A., H. VOSS, P. RICE, A. CIVITELLO, J. STEGEMANN et al., 1990 Automated DNA sequencing of the human HPRT locus. Genomics 6: 593-608.
18. EXCOFFIER, L., 1990 Evolution of human mitochondrial DNA: evidence for departure from a pure neutral model of populations at equilibrium. J. Mol. Evol. 30: 125-139.
19. FU, Y. X., 1996 Estimating the age of the common ancestor of a DNA sample using the number of segregating sites. Genetics 144: 829-838.
20. FU, Y. X., and W. H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
21. FU, Y. X., and W. H. LI, 1997 Estimating the age of the common ancestor of a sample of DNA sequences. Mol. Biol. Evol. 14: 195-199.
22. FULLERTON, S. M., 1996 Allelic sequence variation at the human β-globin locus, pp. 225-241 in Molecular Biology and Human Diversity, edited by A. J. BOYCE and C. G. N. MASCIE-TAYLOR. Cambridge University Press, Cambridge, UK.
23. FULLERTON, S. M., R. M. HARDING, A. J. BOYCE and J. B. CLEGG, 1994 Molecular and population genetic analysis of allelic sequence diversity at the human β-globin locus. Proc. Natl. Acad. Sci. USA 91: 1805-1809.
24. GUO, W., K. WORLEY, V. ADAMS, J. MASON, D. SYLVESTER-JACKSON et al., 1993 Genomic scanning for expressed sequences in Xp21 identifies the glycerol kinase gene. Nat. Genet. 4: 367-372.
25. HAMMER, M., 1995 A recent common ancestry for human Y chromosomes. Nature 378: 376-378.
26. HARDING, R. M., S. M. FULLERTON, R. C. GRIFFITHS, J. BOND, M. J. COX et al., 1997 Archaic African and Asian lineages in the genetic ancestry of modern humans. Am. J. Hum. Genet. 60: 772-789.
27. HARTL, D. L., and A. G. CLARK 1997 Principles of Population Genetics, Ed. 3, Sinauer Associates, Inc., Sunderland, MA.
28. HEY, J., 1997 Mitochondrial and nuclear genes present conflicting portraits of human origins. Mol. Biol. Evol. 14: 166-172.
29. HEY, J., and J. WAKELEY, 1997 A coalescent estimator of the population recombination rate. Genetics 145: 833-846.
30. HUANG, W., Y. X. FU, B. H. J. CHANG, X. GU, L. B. JORDE et al., 1998 Sequence variation in Zfx introns in human populations. Mol. Biol. Evol. 15: 138-142.
31. HUDSON, R. R., 1994 How can the low levels of DNA sequence variation in regions of the Drosophila genome with low recombination rates be explained? Proc. Natl. Acad. Sci. USA 91: 6815-6818.
32. HUDSON, R. R., and N. L. KAPLAN, 1994 Gene trees with background selection, pp. 140-153 in Non-Neutral Evolution: Theories and Molecular Data, edited by B. GOLDING. Chapman and Hall, New York.
33. HUDSON, R. R., and N. L. KAPLAN, 1995 Deleterious background selection with recombination. Genetics 141: 1605-1617.
34. HUDSON, R. R., M. KREITMAN and M. AGUADE, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
35. KAPLAN, N. L., R. R. HUDSON and C. H. LANGLEY, 1989 The "hitch-hiking effect" revisited. Genetics 123: 887-899.
36. KOIKE, K., Y. URATA, S. MATSUO and M. KOIKE, 1990 Characterization and nucleotide sequence of the gene encoding the human pyruvate dehydrogenase α-subunit. Gene 93: 307-311.
37. KREITMAN, M., 1983 Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412-417.
38. KREITMAN, M., and H. AKASHI, 1995 Molecular evidence for natural selection. Annu. Rev. Ecol. Syst. 26: 403-422.
39. LEWONTIN, R. C., 1964 The interaction of selection and linkage. I. General considerations: heterotic models. Genetics 43: 419-434.
40. LEWONTIN, R. C., 1995 The detection of linkage disequilibrium in molecular sequence data. Genetics 140: 377-388.
41. LI, W. H., and L. A. SADLER, 1991 Low nucleotide diversity in man. Genetics 129: 513-523.
42. LU, F., J. LU, R. L. CLINGAN, M. A. WENTLAND, D. M. MUNZY et al., 1994 Complete DNA sequence of the human iduronate sulphate sulphatase (Ids) locus. Unpublished. GenBank accession no. L35485.
43. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
44. MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
45. MCVEAN, G. T., and L. D. HURST, 1997 Evidence for a selectively favourable reduction in the mutation rate of the X chromosome. Nature 386: 388-392.
46. MORIYAMA, E. N., and J. R. POWELL, 1996 Intraspecific nuclear DNA variation in Drosophila. Mol. Biol. Evol. 13: 261-277.
47. NACHMAN, M. W., 1997 Patterns of DNA variability at X-linked loci in Mus domesticus. Genetics 147: 1303-1316.
48. NACHMAN, M. W., W. M. BROWN, M. STONEKING and C. F. AQUADRO, 1996 Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics 142: 953-963.
49. NAGARAJA, R., S. MACMILLAN, J. KERE, C. JONES, S. GRIFFIN et al., 1997 X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content. Genome Res. 7: 210-222.
50. NEI, M., and W.-H. LI, 1979 Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76: 5269-5273.
51. NICKERSON, D. A., S. L. TAYLOR, K. M. WEISS, A. G. CLARK, R. G. HUTCHINSON et al., 1998 DNA sequence diversity in a 9.7 kb region of the human lipoprotein lipase gene. Nat. Genet. 19: 233-240.
52. NOGUCHI, M., S. ADELSTEIN, X. CAO and W. J. LEONARD, 1993 Characterization of the human interleukin-2 receptor γ chain gene. J. Biol. Chem. 268: 13601-13608.
53. OUDET, C., A. HANAUER, P. CLEMENS, T. CASKEY and J. L. MANDEL, 1992 Two hot spots of recombination in the DMD gene correlate with the deletion prone regions. Hum. Mol. Genet. 1: 599-603.
54. RICHARDS, S., 1992 Sequence analysis of a deletion hotspot in intron 44 of the Dystrophin gene. Unpublished. GenBank accession no. M86524.
55. ROEST CROLLIUS, H., M. T. ROSS, A. GRIGORIEV, C. J. KNIGHTS, E. HOLLOWAY et al., 1996 An integrated YAC map of the human X chromosome. Genome Res. 6: 943-955.
56. SAIKI, R. K., D. H. GELFAND, S. STOFFEL, S. J. SCHARF, R. HIGUCHI et al., 1988 Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239: 487-491.
57. SANGER, F., S. NICKLON and A. R. COULSON, 1977 DNA sequencing with chain terminating inhibitors. Proc. Natl. Acad. Sci. USA 74: 5463-5467.
58. SCHAEFFER, S. W., and E. L. MILLER, 1993 Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura. Genetics 135: 541-552.
59. SHIMMIN, L. C., B. H. J. CHANG and W. H. LI, 1993 Male-driven evolution of DNA sequences. Nature 362: 745-747.
60. SIMONSEN, K. L., G. A. CHURCHILL and C. F. AQUADRO, 1995 Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141: 413-439.
61. STEPHAN, W., 1994 Effects of genetic recombination and population subdivision on nucleotide sequence variation in Drosophila ananassae, pp. 57-66 in Non-Neutral Evolution: Theories and Molecular Data, edited by B. GOLDING. Chapman and Hall, New York.
62. STEPHAN, W., 1995 An improved method for estimating the rate of fixation of favorable mutations based on DNA polymorphism data. Mol. Biol. Evol. 12: 959-962.
63. TAJIMA, F., 1983 Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460.
64. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
65. WANG, L. H., A. COLLINS, S. LAWRENCE, B. J. KEATS and N. E. MORTON, 1994 Integration of gene maps: chromosome X. Genomics 22: 590-604.
66. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Pop. Biol. 7: 256-276.
67. WHITFIELD, L. S., J. E. SULSTON and P. E. GOODFELLOW, 1995 Sequence variation of the human Y chromosome. Nature 378: 379-380.
68. WHITTAM, T. S., A. G. CLARK, M. STONEKING, R. L. CANN and A. C. WILSON, 1986 Allelic variation in human mitochondrial genes based on patterns of restriction site polymorphism. Proc. Natl. Acad. Sci. USA 83: 9611-9615.
69. WIEHE, T. H. E., and W. STEPHAN, 1993 Analysis of a genetic hitch-hiking model, and its application to DNA polymorphism data from Drosophila melanogaster. Mol. Biol. Evol. 10: 842-855.