Heterogeneous patterns of variation among multiple human X-linked loci: The possible role of diversity-reducing selection in non-Africans

Genetics

Volumn 167, Issue 4, 2004, Pages 1841-1853

  Hammer, Michael F ^a,b   Garrigan, Daniel ^a,b   Wood, Elizabeth ^a,b   Wilder, Jason A ^a,b   Mobasher, Zahra ^a   Bigham, Abigail ^a   Krenz, James G ^b   Nachman, Michael W ^b  

^a UNIVERSITY OF ARIZONA   (United States)

^b The University of Arizona   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA POLYMORPHISM; DNA SEQUENCE; GENE LOCUS; GENETIC HETEROGENEITY; GENETIC MODEL; GENETIC RECOMBINATION; GENETIC SELECTION; GENETIC VARIABILITY; HUMAN; HUMAN CELL; MALE; MOLECULAR MODEL; MUTATION RATE; NATURAL SELECTION; NEGRO; NONHUMAN; POPULATION GENETICS; PRIORITY JOURNAL; X CHROMOSOME; X CHROMOSOME LINKAGE;

AFRICAN AMERICANS; BASE SEQUENCE; CHROMOSOMES, HUMAN, X; CONTINENTAL POPULATION GROUPS; CROSS-CULTURAL COMPARISON; DNA; EUROPEAN CONTINENTAL ANCESTRY GROUP; HUMANS; INDIANS, NORTH AMERICAN; JEWS; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; SELECTION (GENETICS); UNITED STATES; VARIATION (GENETICS);

EID: 4644354737     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.103.025361     Document Type: Article

References (72)

1. ALONSO, S., and J. A. ARMOUR, 2001 A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outside Africa. Proc. Natl. Acad. Sci. USA 98: 864-869.
2. ALTSHULER, D., V. J. POLLARA, C. R. COWLES, W. J. VAN ETTEN, J. BALDWIN et al., 2000 An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407: 513-516.
3. ANDOLFATTO, P., and M. PRZEWORSKI, 2001 Regions of lower crossing over harbor more rare variants in African populations of Drosophila melanogaster. Genetics 158: 657-665.
4. AQUADRO, C. F., D. J. BEGUN and E. C. KINDAHL, 1994 Selection, recombination, and DNA polymorphism in Drosophila, pp. 46-55 in Non-neutral Evolution: Theories and Molecular Data, edited by B. GOLDING. Chapman & Hall, New York.
5. AVERY, P. J., 1984 The population genetics of haplo-diploids and X-linked genes. Genet. Res. 44: 321-341.
6. 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.
7. BEGUN, D. J., and P. WHITLEY, 2000 Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc. Natl. Acad. Sci. USA 97: 5960-5965.
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 polymorphisms. Genetics 140: 783-796.
9. CARLSON, C. S., M. A. EBERLE, M. J. RIEDER, J. D. SMITH, L. KRUGLYAK et al., 2003 Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat. Genet. 33: 518-521.
10. CHARLESWORTH, B., J. COYNE and N. BARTON, 1987 The relative rates of evolution of sex chromosomes and autosomes. Am. Nat. 130: 113-146.
11. CHARLESWORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
12. EXCOFFIER, L., 2002 Human demographic history: refining the recent African origin model. Curr. Opin. Genet. Dev. 12: 675-682.
13. FAY, J. C., and C.-I WU, 1999 A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation. Mol. Biol. Evol. 16: 1003-1005.
14. FAY, J. C., and C.-I WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
15. FEARNHEAD, P., and P. DONNELLY, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
16. FRISSE, L., R. R. HUDSON, A. BARTOSZEWICZ, J. D. WALL, J. DONFACK et al., 2001 Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels. Am. J. Hum. Genet. 69: 831-843.
17. FU, Y. X., and W.-H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
18. GILAD, Y., S. ROSENBERG, M. PRZEWORSKI, D. LANCET and K. SKORECKI, 2002 Evidence for positive selection and population structure at the human MAO-A gene. Proc. Natl. Acad. Sci. USA 99: 862-867.
19. HALUSHKA, M. K., J. B. FAN, K. BENTLEY, L. HSIE, N. SHEN et al., 1999 Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet. 22: 239-247.
20. HAMMER, M. F., 1995 A recent common ancestry for human Y chromosomes. Nature 378: 376-378.
21. HAMMER, M. F., T. M. KARAFET, A. J. REDD, H. JARJANAZI, S. SANTACHIARA-BENERECETTI et al., 2001 Hierarchical patterns of global human Y-chromosome diversity. Mol. Biol. Evol. 18: 1189-1203.
22. HAMMER, M. F., F. BLACKMER, D. GARRIGAN, M. W. NACHMAN and J. A. WILDER, 2003 Human population structure and its effects on sampling Y chromosome sequence variation. Genetics 164: 1495-1509.
23. 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.
24. HARDISON, R. C., K. M. ROSKIN, S. YANG, M. DIEKHANS, W. J. KENT et al., 2003 Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution. Genome Res. 13: 13-26.
25. HARPENDING, H., and A. ROGERS, 2000 Genetic perspectives on human origins and differentiation. Annu. Rev. Genomics Hum. Genet. 1: 361-385.
26. HARPENDING, H. C., M. A. BATZER, M. GURVEN, L. B. JORDE, A. R. ROGERS et al., 1998 Genetic traces of ancient demography. Proc. Natl. Acad. Sci. USA 95: 1961-1967.
27. HARRIS, E. E., and J. HEY, 1999 X chromosome evidence for ancient human histories. Proc. Natl. Acad. Sci. USA 96: 3320-3324.
28. HARRIS, E. E., and J. HEY, 2001 Human populations show reduced DNA sequence variation at the factor IX locus. Curr. Biol. 11: 774-778.
29. HELLMANN, I., I. EBERSBERGER, S. E. PTAK, S. PAABO and M. PRZEWORSKI, 2003 A neutral explanation for the correlation of diversity with recombination rates in humans. Am. J. Hum. Genet. 72: 1527-1535.
30. HEY, J., 1997 Mitochondrial and nuclear genes present conflicting portraits of human origins. Mol. Biol. Evol. 14: 166-172.
31. HUDSON, R. R., M. KREITMAN and M. AGUADÉ, 1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
32. HUDSON, R. R., M. SLATKIN and W. P. MADDISON, 1992 Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
33. JARUZELSKA, J., E. ZIETKIEWICZ, M. BATZER, D. E. COLE, J. P. MOISAN et al., 1999 Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: analysis of the haplotype structure and genealogy. Genetics 152: 1091-1101.
34. KAESSMANN, H., F. HEISSIG, A. VON HAESELER and S. PAABO, 1999 DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat. Genet. 22: 78-81.
35. 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.
36. KITANO, T., C. SCHWARZ, B. NICKEL and S. PAABO, 2003 Gene diversity patterns at 10 X-chromosomal loci in humans and chimpanzees. Mol. Biol. Evol. 20: 1281-1289.
37. KONG, A., D. F. GUDBJARTSSON, J. SAINZ, G. M. JONSDOTTIR, S. A. GUDJONSSON et al., 2002 A high-resolution recombination map of the human genome. Nat. Genet. 31: 241-247.
38. LERCHER, M. J., and L. D. HURST, 2002 Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18: 337-340.
39. LI, W. H., and L. A. SADLER, 1991 Low nucleotide diversity in man. Genetics 129: 513-523.
40. MAYNARD SMITH, J., and J. HAIGH, 1974 The hitch-hiking effect of a favourable gene. Genet. Res. 23: 23-35.
41. MISHMAR, D., E. RUIZ-PESINI, P. GOLIK, V. MACAULAY, A. G. CLARK et al., 2003 Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. USA 100: 171-176.
42. NACHMAN, M. W., and S. L. CROWELL, 2000 Contrasting evolutionary histories of two introns of the Duchenne muscular dystrophy gene, Dmd, in humans. Genetics 155: 1855-1864.
43. NACHMAN, M. W., V. L. BAUER, S. L. CROWELL and C. F. AQUADRO, 1998 DNA variability and recombination rates at X-linked loci in humans. Genetics 150: 1133-1141.
44. NACHMAN, M. W., S. L. D'AGOSTINO, C. R. TILLQUIST, Z. MOBASHER and M. F. HAMMER, 2004 Nucleotide variation at Msn and Alas2, two genes flanking the centromere of the X chromosome in humans. Genetics 167: 423-437.
45. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
46. 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.
47. 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.
48. PLUZHNIKOV, A., A. DI RIENZO and R. R. HUDSON, 2002 Inferences about human demography based on multilocus analyses of non-coding sequences. Genetics 161: 1209-1218.
49. PRZEWORSKI, M., 2002 The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
50. PRZEWORSKI, M., R. R. HUDSON and A. DI RIENZO, 2000 Adjusting the focus on human variation. Trends Genet. 16: 296-302.
51. PRZEWORSKI, M., J. D. WALL and P. ANDOLFATTO, 2001 Recombination and the frequency spectrum in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 18: 291-298.
52. PTAK, S. E., and M. PRZEWORSKI, 2002 Evidence for population growth in humans is confounded by fine-scale population structure. Trends Genet. 18: 559-563.
53. 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.
54. ROGERS, A. R., 2001 Order emerging from chaos in human evolutionary genetics. Proc. Natl. Acad. Sci. USA 98: 779-780.
55. ROMUALDI, C., D. BALDING, I. S. NASIDZE, G. RISCH, M. ROBICHAUX et al., 2002 Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res. 12: 602-612.
56. ROZAS, J., and R. ROZAS, 1999 DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
57. SAUNDERS, M. A., M. F. HAMMER and M. W. NACHMAN, 2002 Nucleotide variability at g6pd and the signature of malarial selection in humans. Genetics 162: 1849-1861.
58. SHEN, P., F. WANG, P. A. UNDERHILL, C. FRANCO, W. H. YANG et al., 2000 Population genetic implications from sequence variation in four Y chromosome genes. Proc. Natl. Acad. Sci. USA 97: 7354-7359.
59. STEPHENS, J. C., J. A. SCHNEIDER, D. A. TANGUAY, J. CHOI, T. ACHARYA et al., 2001 Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.
60. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
61. TISHKOFF, S. A., E. DIETZSCH, W. SPEED, A. J. PAKSTIS, J. R. KIDD et al., 1996 Global patterns of linkage disequilibrium at the CD4 locus and modern human origins. Science 271: 1380-1387.
62. VIGILANT, L., M. STONEKING, H. HARPENDING, K. HAWKES and A. C. WILSON, 1991 African populations and the evolution of human mitochondrial DNA. Science 253: 1503-1507.
63. WAKELEY, J., 1999 Nonequilibrium migration in human history. Genetics 153: 1863-1871.
64. WALL, J. D., and M. PRZEWORSKI, 2000 When did the human population size start increasing? Genetics 155: 1865-1874.
65. WATERSTON, R. H., K. LINDBLAD-TOH, E. BIRNEY, J. ROGERS, J. F. ABRIL et al., 2002 Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
66. WATTERSON, G. A., 1975 On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7: 256-276.
67. WHITFIELD, L. S., J. E. SULSTON and P. N. GOODFELLOW, 1995 Sequence variation of the human Y chromosome. Nature 378: 379-380.
68. WOODING, S., and A. ROGERS, 2000 A Pleistocene population X-plosion? Hum. Biol. 72: 693-695.
69. Y CHROMOSOME CONSORTIUM, 2002 A nomenclature system for the tree of Y chromosomal binary haplogroups. Genome Res. 12: 339-348.
70. YU, N., F. C. CHEN, S. OTA, L. B. JORDE, P. PAMILO et al., 2002a Larger genetic differences within Africans than between Africans and Eurasians. Genetics 161: 269-274.
71. YU, N., Y. X. FU and W. H. LI, 2002b DNA polymorphism in a worldwide sample of human X chromosomes. Mol. Biol. Evol. 19: 2131-2141.
72. ZIETKIEWICZ, E., V. YOTOVA, M. JARNIK, M. KORAB-LASKOWSKA, K. K. KIDD et al., 1997 Nuclear DNA diversity in worldwide distributed human populations. Gene 205: 161-171.