Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: Analysis of the haplotype structure and genealogy

Genetics

Volumn 152, Issue 3, 1999, Pages 1091-1101

  Jaruzelska, Jadwiga ^a   Zietkiewicz, Ewa ^b   Batzer, Mark ^d   Cole, David E C ^e   Moisan, Jean Paul ^f   Scozzari, Rosaria ^g   Tavaré, Simon ^h   Labuda, Damian ^b,c  

^a INSTITUTE OF HUMAN GENETICS   (Poland)

^b UNIVERSITY OF MONTREAL   (Canada)

^c UNIVERSITÉ DE MONTRÉAL   (Canada)

^d LOUISIANA STATE UNIV MEDICAL CENTER   (United States)

^e UNIVERSITY OF TORONTO   (Canada)

^f HÔTEL DIEU   (France)

^g SAPIENZA UNIVERSITY OF ROME   (Italy)

^h UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; PROTEIN ZFX; UNCLASSIFIED DRUG;

AGE DETERMINATION; ALLELE; ARTICLE; EVOLUTION; GENEALOGY; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; INTRON; PRIORITY JOURNAL;

ALOCASIA MACRORRHIZOS;

EID: 0032789358     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (67)

1. AKALIN, N., E. ZIETKIEWICZ, W. MAKALOWSKI and D. LABUDA, 1994 Are CpG sites mutation hot spots in the dystrophin gene? Hum. Mol. Genet. 3: 1425-1426.
2. BATZER, M. A., M. STONEKING, M. ALEGRIA-HARTMAN, H. BAZAN, D. H. KASS et al., 1994 African origin of human-specific polymorphic Alu insertions. Proc. Natl. Acad. Sci. USA 91: 12288-12292.
3. BATZER, M. A., S. S. ARCOT, J. W. PHINNEY, M. ALEGRIA-HARTMAN, D. H. KASS et al., 1996 Genetic variation of recent Alu insertions in human populations. J. Mol. Evol. 42: 22-29.
4. BOWCOCK, A. M., J. KIDD, J. L. MOUNTAIN, J. M. HEBERT, L. CAROTENUTO et al., 1991 Drift, admixture, and selection in human evolution: a study with DNA polymorphisms. Proc. Natl. Acad. Sci. USA 88: 839-843.
5. BOWCOCK, A. M., A. RUIZ-LINARES, J. TOMFOHRDE, E. MINCH, J. R. KIDD et al., 1994 High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
6. BROMAN, K. W., J. C. MURRAY, V. C. SHEFFIELD, R. L. WHITE and J. L. WEBER, 1998 Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63: 861-869.
7. CHAKRABORTY, R., 1990 Mitochondrial DNA polymorphism reveals hidden heterogeneity within some Asian populations. Am. J. Hum. Genet. 47: 87-94.
8. CHAKRABORTY, R., M. I. KAMBOH, M. NWANKWO and R. E. FERRELL, 1992 Caucasian genes in American Blacks: new data. Am. J. Hum. Genet. 50: 145-155.
9. CLARK, A., 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.
10. n polymorphisms in world populations. Am. J. Hum. Genet. 56: 461-474.
11. DI RIENZO, A., and A. C. WILSON, 1991 Branching pattern in the evolutionary tree for human mitochondrial DNA. Proc. Natl. Acad. Sci. USA 88: 1597-1601.
12. DI RIENZO, A., P. DONNELLY, C. TOOMAJIAN, B. SISK, A. HILL et al., 1998 Heterogeneity of microsatellite mutations within and between loci, and implications for human demographic histories. Genetics 148: 1269-1284.
13. 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.
14. EWENS, W. J., 1972 The sampling theory of selectively neutral alleles. Theor. Popul. Biol. 3: 87-112.
15. EXCOFFIER, L., P. SMOUSE and J. QUATTRO, 1992 Analysis of molecular variance inferred from metric distance among DNA haplotypes: application to human mitochondria DNA restriction data. Genetics 131: 479-491.
16. FOLEY, R., 1998 Genes, evolution and diversity: yet another look at the problem of modern human origins. Evol. Anthropol. 6: 191-193.
17. 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.
18. GRIFFITHS, R. C., and S. TAVARÉ, 1994 Ancestral inference in population genetics. Stat. Sci. 9: 307-319.
19. GRIFFITHS, R. C., and S. TAVARÉ, 1998 The age of a mutation in a general coalescent tree. Stochastic Models 14: 273-295.
20. GRIFFITHS, R. C., and S. TAVARÉ, 1999 The ages of mutations in gene trees. Ann. Appl. Prob. (in press).
21. HAMMER, M. F., and S. L. ZECURA, 1996 The role of the Y chromosome in human evolutionary studies. Evol. Anthropol. 5: 116-134.
22. HAMMER, M. F., T. KARAFET, A. RASANAYAGAM, E. T. WOOD, T. K. ALTHEIDE et al., 1998 Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol. Biol. Evol. 15(4): 427-441.
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. HAYASHI, K., 1991 PCR-SSCP: A simple and sensitive method for detection of mutations in the genomic DNA. PCR Methods Appl. 1: 34-38.
25. HEY, J., 1997 Mitochondrial and nuclear genes present conflicting portraits of human origins. Mol. Biol. Evol. 14: 166-172.
26. HORAI, S., K. HAYASAKA, R. KONDO, K. TSUGANE and N. TAKAHATA, 1995 Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. USA 92: 532-536.
27. HUANG, W., Y.-X. FU, B. H. CHANG, X. GU, L. B. JORDE et al., 1998 Sequence variation in ZFX introns in human populations. Mol. Biol. Evol. 15(2): 138-142.
28. JOBLING, M. A., and C. TYLER-SMITH, 1995 Fathers and sons: the Y chromosome and human evolution. Trends. Genet. 11: 449-456.
29. JORDE, L. B., M. J. BAMSHAD, W. S. WATKINS, R. ZENGER, A. E. FRALEY et al., 1995 Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data. Am. J. Hum. Genet. 57: 523-538.
30. JORDE, L. B., A. R. ROGERS, M. BAMSHAD, W. S. WATKINS, P. KRAKOWIAK et al., 1997 Microsatellite diversity and the demographic history of modern humans. Proc. Natl. Acad. Sci. USA 94: 3100-3103.
31. JORDE, L. B., M. BAMSHAD and A. R. ROGERS, 1998 Using mitochondrial and nuclear DNA markers to reconstruct human evolution. Bioessays 20: 126-136.
32. KIMMEL, M., R. CHAKRABORTY, J. P. KING, M. BAMSHAD, W. S. WATKINS et al., 1998 Signatures of population expansion in microsatellite repeat data. Genetics 148: 1921-1930.
33. KIMURA, M., and T. OHTA, 1973 The age of a neutral mutant persisting in a finite population. Genetics 75: 199-212.
34. LAHR, M. M., and R. FOLEY, 1998 Towards a theory of modern human origins: geography, demography and diversity in recent human evolution. Am. J. Phys. Anthropol. 27(Suppl.): 137-176.
35. MALASPINA, P., F. CRUCIANI, B. M. CIMINELLI, L. TERRANATO, P. SANTOIAMAZZA et al., 1998 Network analyses of Y-chromosomal types in Europe, Northern Africa, and Western Asia reveal specific patterns of geographic distribution. Am. J. Hum. Genet. 63: 847-860.
36. MOUNTAIN, J. L., and L. L. CAVALLI-SFORZA, 1994 Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc. Natl. Acad. Sci. USA 91: 6515-6519.
37. NEI, M., T. MARUYAMA and R. CHAKRABORTY, 1975 The bottleneck effect and genetic variability in populations. Evolution 29: 1-10.
38. NICKERSON, D. A., S. L. TAYLOR, K. M. WEISS, A. G. CLARK, T. G. HUTCHINSON et al., 1998 Genome resequencing and variation analysis in a 9.7 kb region of the human lipoprotein lipase gene. Nat. Genet. 19: 233-240.
39. POLONI, E. S., O. SEMINO, G. PASSARINO, A. S. SANTACHIARA-BENERECETTI, I. DUPANLOUP et al., 1997 Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics. Am. J. Hum. Genet. 61: 1015-1035.
40. RAVNIK-GLAVAC, M., D. GLAVAC and M. DEAN, 1994 Sensitivity of single-strand conformation polymorphism and heteroduplex method for mutation detection in the cystic fibrosis gene. Hum. Mol. Genet. 3: 801-807.
41. REICH, D. E., and D. B. GOLDSTEIN, 1998 Genetic evidence for a Paleolithic human population expansion in Africa. Proc. Natl. Acad. Sci. USA 95: 8119-8123.
42. RELETHFORD, J. H., 1995 Genetics and modern human origins. Evol. Anthropol. 4: 53-63.
43. RELETHFORD, J. H., and H. C. HARPENDING, 1995 Ancient differences in population size can mimic a recent African origin of modern humans. Curr. Anthropol. 36: 667-673.
44. ROGERS, A. R., and H. HARPENDINC, 1992 Population growth makes waves in the distribution of pairwise generic differences. Mol. Biol. Evol. 9: 552-569.
45. ROGERS, A. R., and L. B. JORDE, 1995 Genetic evidence on modern human origins. Hum. Biol. 67: 1-36.
46. ROGERS, A. R., and L. B. JORDE, 1996 Ascertainment bias in estimates of average heterozygosity. Am. J. Hum. Genet. 58: 1033-1041.
47. SCHNEIDER, S., J.-M. KUEFFER, D. ROESSLI and L. EXCOFFIER, 1997 Arlequin ver. 1.1: a software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
48. SCOZZARI, R., F. CRUCIANI, P. MALASPINA, P. SANTOLAMAZZA, B. M. CIMINELLI et al., 1997 Differential structuring of human populations for homologous X and Y microsatellite loci. Am. J. Hum. Genet. 61: 719-733.
49. SEIELSTAD, M. T., J. M. HEBERT, A. A. LIN, P. A. UNDERHILL, M. IBRAHIM et al., 1994 Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition. Hum. Mol. Genet. 3(12): 2159-2161.
50. SHIMMIN, L. C., B. H. CHANG and W. H. LI, 1993 Male-driven evolution of DNA sequences. Nature 362: 745-777.
51. SLATKIN, M., and R. R. HUDSON, 1991 Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
52. STONEKING, M., J. J. FONTIUS, S. L. CLIFFORD, H. SOODYALL, S. S. ARCOT et al., 1997 Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 7: 1061-1071.
53. TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
54. TAKAHATA, N., 1993 Allelic genealogy and human evolution. Mol. Biol. Evol. 10: 2-22.
55. TAKAHATA, N., 1994 Repeated failures that led to the eventual success in human evolution. Mol. Biol. Evol. 11: 803-805.
56. TATTERSALL, I., 1995 The Fossil Trail: How We Know What We Think We Know About Human Evolution. American Museum of Natural History. Oxford University Press, New York.
57. TAVARÉ, S., D. J. BALDING, R. C. GRIFFITHS and P. DONNELLY, 1997 Inferring coalescence times for molecular sequence data. Genetics 145: 505-518.
58. TEMPLETON, A. R., 1997 Out of Africa? What do genes tell us? Curr. Opin. Genet. Dev. 7: 841-847.
59. 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.
60. UNDERHILL, P. A., L. JIN, A. A. LIN, S. Q. MEHDI, T. JENKINS et al., 1997 Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 7: 996-1005.
61. WANG, T., Y. OKANO, R. C. EISENSMITH, M. L. HARVEY, W. H. Y. LO et al., 1991 Founder effect of a prevalent phenylketonuria mutation in the Oriental population. Proc. Natl. Acad. Sci. USA 88: 2146-2150.
62. WATTERSON, G. A., 1978 The homozygosity test of neutrality. Genetics 88: 405-417.
63. WELSH, J. A., K. CASTREN and K. H. VAHAKANGAS, 1997 Single-strand conformation polymorphism analysis to detect p53 mutations: characterisation and development of controls. Clin. Chem. 43: 2251-2255.
64. ZIETKIEWICZ, E., D. SINNETT, C. RICHER, G. MITCHELL, M. VANASSE et al., 1992a Single-strand conformational polymorphisms (SSCP): detection of useful polymorphisms at the dystrophin locus. Hum. Genet. 89: 453-456.
65. ZIETKIEWICZ, E., L. R. SIMARD, S. B. MELANÇON, M. VANASSE and D. LABUDA, 1992b Carrier status diagnosis in Duchenne muscular dystrophy with "conformational" DNA polymorphism. Lancet 339: 134.
66. 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.
67. ZIETKIEWICZ, E., V. YOTOVA, M. JARNIK, M. KORAB-LASKOWSKA, K. K. KIDD et al., 1998 Genetic structure of the ancestral population of modern humans. J. Mol. Evol. 47: 146-155.