The geographic distribution of human Y chromosome variation

Genetics

Volumn 145, Issue 3, 1997, Pages 787-805

  Hammer, M F ^a,b   Spurdle, A B ^b   Karafet, T ^c   Bonner, M R ^d   Wood, E T ^e   Novelletto, A ^f   Malaspina, P ^a   Mitchell, R J ^a   Horai, S ^b   Jenkins, T ^a   Zegura, S L ^a  

^a Laboratory of Molecular Systematics and Evolution   (United States)

^b UNIVERSITY OF ARIZONA   (United States)

^c UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^d UNIVERSITY OF ROME TOR VERGATA   (Italy)

^e LA TROBE UNIVERSITY   (Australia)

^f NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

MICROSATELLITE DNA; POLYADENYLIC ACID;

AFRICA; ARTICLE; ASIA; AUSTRALIA; BIODIVERSITY; CHROMOSOME POLYMORPHISM; CHROMOSOME VARIANT; CLINICAL PROTOCOL; EUROPE; EVOLUTION; FEMALE; GENE LOCUS; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; HUMAN; HUMAN CELL; MAJOR CLINICAL STUDY; MALE; MIGRATION; POINT MUTATION; POPULATION GENETICS; PRIORITY JOURNAL; Y CHROMOSOME;

GENE FREQUENCY; HAPLOTYPES; HUMANS; LIKELIHOOD FUNCTIONS; MALE; POLYMORPHISM, GENETIC; VARIATION (GENETICS); Y CHROMOSOME;

EID: 0031026061     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (104)

1. AMMERMAX, A. J., and L. L. GvVALLl-SFORZA, 1984 Neolithic Transition and the Genetics a/Populations in Europe. Princeton University Press, Princeton.
2. AOKI, K., and M. SIIIDA, 1996 A Monte Carlo simulation study of coalescence times in a successive colonization model with migration, pp. 66-71 in Prehistoric Alongoloid Dispersals, edited by T. AKAZAWA and E.J. E. SZATHMARY. Oxford University Press, Oxford.
3. AVISE, J. C., 1994 Molecular Markers, Natural History and Evolution. Chapman & Hall, New York.
4. BATZER, M. A., M. STONEKIXG, 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.
5. BOWCOCK, A. M.,J. R. KIDD.J. L. MOUNTAIN,J. M. HERBERT, 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.
6. BOWCOCK, A. M., A. RUIZ-LlNARES, J. TOMFOHRDE, E. MlNCH, J. R. KIDD et al., 1994 High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
7. CANN, R. L., M. STONEKING and A. C. WILSON, 1987 Mitochondrial DNA and human evolution. Nature 325: 31-36.
8. CASANOVA M., P. LEROY, C. BOUCEKKJNE, J. WEISSENBACH, C. BISHOP et al., 1985 A human Y-linked DNA polymorphism and its potential for estimating genetic and evolutionary distance. Science 230: 1403-1406.
9. CAVALLI-SFORZA, L. L., and W. F. BODMER, 1971 The Genetics of Human Populations. W. H. Freeman, San Francisco.
10. CAWLLI-SFORZA, L. L., A. PIAZZA, P. MENOZZI and J. MOUNTAIN, 1988 Reconstruction of human evolution: bringing together genetic, archaeological, and linguistic data. Proc. Natl. Acad. Sci. USA 85: 6002-6006.
11. CAWALLI-SFORZA, L. L., P. MENOZZI and A. PIAZZA, 1994 The History and Geography of Human Genes. Princeton University Press, Princeton.
12. CHARLES\VORTH, B., M. T. MORGAN and D. CHARLESWORTH, 1993 The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
13. CHEN, Y.-S., A. TORRONI, L. EXCOFFIER, A. S. SANTACHLVRA-BENERECETTI and D. C. WAI.IACE, 1995 Analysis of mtDNA variation in African populations reveals the most ancient of all human continent-specific haplogroups. Am. J. Hum. Genet. 57: 133-149.
14. ClMINELLI, B., F. POMPEI, P. MAIASFINA, M. F. HAMMER, F. PERSI-CHETTI et al., 1995 Recurrent simple tandem repeat mutations during human Y chromosome radiation in Caucasian subpopulations.J. Mol. Evol. 41: 966-976.
15. n polymorphisms in world populations. Am. J. Hum. Genet. 56: 461-474.
16. ESTOUP, A., L. GARNERY, M. SOLIGNAC and J.-M. CORNUET, 1995 Microsatellite variation in Honey Bee (Apis Mellifera L.) populations: hierarchical genetic structure and test of the infinite allele and stepwise mutation models. Genetics 140: 679-695.
17. EXCOFFIER, L., 1990 Evolution of human mitochondria! DNA: evidence for departure from a pure neutral model of populations at equilibrium. J. Mol. Evol. 30: 125-139.
18. EXCOFFIER, L., and A. LANGANEY, 1989 Origin and differentiation of human mitochondrial DNA. Am.J. Hum. Genet. 44: 73-85.
19. EXCOFFIER, L., B. PELLEGRINI, A. SANCHEZ-MAZAS, C. SIMON and A. LANGANEY, 1987 Genetics and history of sub-Saharan Africa. Yrbk. Phys. Anthropol. 30: 151-194.
20. FELSENSTEIN, J., 1981 Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376.
21. FELSENSTEIN, J., 1993 PHYLIP: Phylogeny Inference Package, Version 3.5p. Joseph Felsenstein and the University of Washington, Seattle.
22. FITCH, \V. M., and E. MARGOUASII, 1967 Construction of phylogenetic trees. Science 155: 279-284.
23. FRAYER, D. W., M. H. WOI.POFF, A. G. THORNE, F. H. SMITH and G. G. POPE, 1993 Theories of modern human origins: the paleontological test. Am. Anthropol. 95: 14-50.
24. Fu, Y.-X., and W.-H. Li, 1996 Estimating the age of the common ancestor of men from the ZfYintron. Science 272: 1356-1357.
25. GOLDSTEIN, D. B., A. R. LINARES, L. L. GXVALLI-SFORZA and M. W. FELDMAN, 1995 An evaluation of genetic distances for use ïvith microsatellite loci. GeneticsJ39: 463-471.
26. GOMOLKA, M., J. HUNDRIESER, P. NURNBERG, L. ROEWER, J. T. EPPLEN et al., 1994 Selected di- and tctranucleotide microsatellites from chromosomes 7, 12, 14, and Y in various Eurasian populations. Hum. Genet. 93: 592-596.
27. GREENBERG, J. H., C. G. TURNER and S. L. ZEGURA, 1986 The settlement of the Americas: a comparison of the linguistic, dental, and genetic evidence. Current Anthropol. 27: 477-497.
28. GRIFFITHS, R. G., and S. TAVARE, 1994 Ancestral inference in population genetics. Statistical Sci. 9: 307-319.
29. HAMMER, M. F., 1994 A recent insertion of an Alu element on the Y chromosome is a useful marker for human population studies. Mol. Biol. Evol. 11: 749-761.
30. HAMMER, M. F., 1995 A recent common ancestry for human Y chromosomes. Nature 378: 376-378.
31. HAMMER, M. F., and S. HORAI, 1995 Y chromosomal DNA variation and the peopling of Japan. Am. J. Hum. Genet. 56: 951-962.
32. HAMMER, M. F., and S. L. ZECURA, 1997 The role of the Y chromosome in human evolutionary studies. Evol. Anthropol. (in press),
33. HARPENDING, H., and A. ROGERS, 1984 Antana: A Package for Multivariate Data Analysis. Harpending & Rogers, Bosque Farms.
34. HARPENDING, H. C., S. T. SHERRY, A. R. ROGERS and M. STONEKING, 1993 The genetic structure of ancient human populations. Curr. Anthropol. 34: 483-496.
35. IKUTA, S., K. TAKAGI, R. B. WALI.ACE and K. ITAKURA, 1987 Dissociation kinetics of 19 base paired oligonucleotide-DNA duplexes containing different single mismatched base pairs. Nucleic Acids Res. 15: 797-811.
36. JOBLING, M. A., and C. TvLER-SMlTH, 1995 Fathers and sons: the Y chromosome and human evolution. Trends Genet. 11: 449-456.
37. KARAFET, T., S. L. ZEGURA, J. VUTURO-BRADY, O. POSUKH, L. OSIPOVA et al., 1997 Y chromosome markers and trans-Bering Strait dispersals. Am. J. Phys. Anthropol. (in press).
38. LAIIIRI, O.K., and J.I. NURNBERGER, 1991 A rapid non-enzymatic method for the preparation of HMW DNA from blood for RFLP studies. Nucleic Acids Res. 19: 5444.
39. LAHR, M. M., and R. FOLEY, 1995 Multiple dispersals and modern human origins. Evol. Anthropol. 3: 48-60.
40. LI, W.-H., 1977 Distribution of nucleotide differences between two randomly chosen cistrons in a finite population. Genetics 85: 331-337.
41. LI, W.-L., and D. GRAUR, 1991 Fundamentals of Molecular Evolution. Sinauer Associates, Inc., Sunderland, MA.
42. LUCOTTE, G., and N.Y. Nco, 1985 p49f, a highly polymorphic probe, that detects Taql RFLPs on the human Y chromosome. Nucleic Acids Res. 13: 82-85.
43. LUCOTTE, G., N. GERARD, R. KRISHNAMOORTHY, F. DAVID, A. AOUIZERATE et al., 1994 Reduced variability in Y-chromosome-specific haplotypes for some Central African populations. Hum. Biol. 66: 519-526.
44. MARTINSON, J.J., L. EXCOFFIER, C. SWINBURN, A. J. BOYCE, R. M. HARDING et al., 1995 High diversity of α-globin haplotypes in a Senegalese population, including many previously unreported vari.. ants. Am.J. Hum. Genet. 57: 1186-1198.
45. MATHIAS, N., M. BAYES and C. TYLER-SMITH, 1994 Highly informative compound haplotypes for the human Y chromosome. Hum. Mol. Genet. 3: 115-123.
46. MAYNARD-SMlTHj., 1990 The Y of human relationships. Nature 344: 591-592.
47. MELTON, T., R. PETERSON, A. J. REDD, N. SAIIA, A. S. M. SOFRO et al, 1995 Polynesian genetic affinities with southeast Asian populations as identified by mtDNA analysis. Am. J. Hum. Genet. 57: 403-414.
48. MERRIWETHER,D. A.,F.RoTHHAMMERandR. E.FERRELL, 1995 Distribution of the four founding lineage haplotypes in Native Americans suggests a single wave of migration for the New World. Am. J. Phys. Anthropol. 98: 411-430.
49. MICILALAKIS, Y., and L. EXCOFFIER, 1996 A generic estimation of population subdivision using distances between alleles with special references for microsatellite loci. Genetics 142: 1061 -1064.
50. MINUGH-PuRVis, N., 1995 The modern human origins controversy: 1984-1994. Evol. Anthropol. 4: 140-147.
51. MITCHELL, R.J., L. EARL and J. W. WILLIAMS, 1993 Two Y-chromosome-specific restriction fragment length polymorphisms (DYSI1 and DYZ8) in Italian and Greek migrants to Australia. Hum. Biol. 65: 387-399.
52. MOUNTAIN, J. L., and L. L. GWALI.I-SFORZA, 1994 Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc. Nail. Acad. Sci. USA 91: 6515-6519.
53. MULLER, S., M. GOMOI.KA and H. WALTER, 1994 The Y-specific SSLP of the locus DYS19 in four different European samples. Hum. Hered. 44: 298-300.
54. NEI, M., 1978 Estimation of average heterozygosity and genetic distance from small number of individuals. Genetics 89: 583-590.
55. NEI, M., 1987 Molecular Evolutionary Genetics. Columbia University Press, New York.
56. NEI, M., and A. K. ROYCHOUDHURY, 1982 Genetic relationships and evolution of human races. Evol. Biol. 14: 1-59.
57. NEI, M., and A. K. ROYCHOUDHURY, 1993 Evolutionary relationships of human populations on a global, scale. Mol. Biol. Evol. 10:927-943.
58. NYSTUEN, A., T. BUSINGA, R. CARMI, G. M. DUYK and V. C. SHEFFIELD, 1995 Identification of polymorphic markers for the Y chromosome and the use of these markers to determine the number of male founders in isolated populations. Am. J. Hum. Genet. 57 (Suppl.): A26.
59. PENA, S. D. J., F. R. SANTOS, N. O. BIANCIII, C. M. BRAVI, F. R. CARNESE et al, 1995 A major founder Y-chromosome haplotype in Amerindians. Nature Genet. 11: 15-16.
60. PENNY, D., M. STEEL, P.J. WADDEIJ. and M. D. HENDY, 1995 Improved analyses of human mitochondrial DNA sequences support a recent African origin for Homo sapiens. Mol. Biol. Evol. 12: 863-882.
61. PERNA, N. T., M. A. BATZER, P. L. DEININGER and M. STONEKING, 1992 Alu insertion polymorphism: a new type of marker for human population studies. Hum. Biol. 64: 641-648.
62. PERSICIIETTI, F., P. BI.ASI, M. HAMMER, P. MAIASPINA, C. IODICE et al., 1992 Disequilibrium of multiple markers on the human Y chromosome. Ann. Hum. Genet. 56: 303-310.
63. RELETIIFORD,J. H., 1995 Genetics and modern human origins. Evol. Anthropol. 4: 53-63.
64. RELETHFORD, J. H., 1996 Genetic drift can obscure population history: problem and solution. Hum. Biol. 68: 29-44.
65. RELETHFORD, J. H., and H. C. HARPENDING, 1994 Craniometric variation, genetic theory, and modern human origins. Am. J. Phys. Anthropol. 95: 249-270.
66. RELETHFORD, J. H., and H. C. H\RPENDING, 1995 Ancient differences in population size can mimic a recent African origin of modern humans. Curr. Anthropol. 36: 667-674.
67. REYNOLDS, J., B. S. WEIR and C. C. COCKERIIAM, 1983 Estimation of coancestry coefficient: Basis for short-term genetic distance. Genetics 105: 767-779.
68. RICHARDS, B., J. SKOLETSKY, A. P. SIIUBER, R. BALFOUR, R. C. STERN el al, 1993 Multiplex PCR amplification from the CFTR gene using DNA prepared from buccal brushes/swabs. Hum. Mol. Genet. 2: 159-163.
69. RICHARDS, M., H. CORTE-REAL, P. FORSTER, V. MACAUIAY, H. WII.KINSON-HERBOTS et al, 1996 Paleolithic and Neolithic lineages in the European mitochondria! gene pool. Am. J. Hum. Genet. 59: 185-203.
70. ROEWER, L., J. ARXEMANN, N. K. SPURR, K.-H. GRZESCHIK andj. T. EPPI.EN, 1992 Simple repeat sequences on the human Y chromosome are equally polymorphic as their autosomal counterparts. Hum. Genet. 89: 389-394.
71. ROGERS, A. R., and L. B. JORDE, 1995 Genetic evidence on modern human origins. Hum. Biol. 67: 1-36.
72. SAITOU, N., and M. NEI, 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
73. SALEM, A.-H., F. M. BADR, M. F. GABALLAH and S. PAABO, 1996 The genetics of traditional living: Y chromosomal and mitochondria! lineages in the Sinai Peninsula. Am. J. Hum. Genet. 59: 741 743.
74. SANTOS, F. R., S. D. J. PENA andj. T. EPPLEN, 1993 Genetic and population study of a Y-linked tetranucleotide repeat DNA polymorphism with a simple non-isotopic technique. Hum. Genet. 90: 655-656.
75. SANTOS, F. R., T. GERELSAIKIL\N, B. MUNKHTUJA, T. OYUNSUREN.J. E. EPPLEN et al, 199 Geographic differences in the allele frequencies of the human Y-linked tetranucleotide polymorphism DYS19. Hum. Genet. 97: 309-313.
76. SEIELSTAD, M. T., J. M. HEBERT, A. A. LIN, P. A. UNDERIIILL, M. IBRAHIM et al, 1994 Construction of human Y-chromosomal haplotypes using a new polymorphic A to G transition. Hum. Mol. Genet. 3: 2159-2161.
77. SHRIVF.R, M. D., L. JIN, R. CIUKRABORTY and E. BOERWINKLE, 1993 VNTRallele frequency distributions under the stepwise mutation model: a computer simulation approach. Genetics 134:983-993.
78. SIATKIN, M., 1995 A measure of population subdivision based on microsatellite allcle frequencies. Genetics 139: 457-462.
79. SOKAI., R. R., and C. D. MICIIENER, 1958 A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull. 28: 1409-1438.
80. SOODYAI.I, H., L. VIGIIANT, A. V. HII.I., M. STONEKIXG and T. JEXKIXS, 1996 mtDN'A control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans. Am. J. Hum. Genet. 58: 595-608.
81. SruRDLE, A. B., and T. JEXKIXS, 1992 Y chromosome probe p49a detects complex Pvu II haplotypes and many new Taq I haplotypes in southern African populations. Am. J. Hum. Genet. 50: 107-125.
82. SPURDI.E, A. B., and T. JEXKIXS, 1993 Complex polymorphisms are revealed by Y chromosome probe 49a with Bglll, Hind III, Pstl and Sstl. Ann. Hum. Genet. 57: 41-53.
83. SPURDLE, A. B., and T. JENKIXS, 1996 The origins of the Lemba "Black Jews" of southern Africa: evidence from /72/2and other Y chromosome markers. Am. J. Hum. Genet. 59: 1126-1133.
84. SPURDLE, A., M. F. HAMMER and T. JENKINS, 1994 The Y Alu polymorphism in Southern African populations, and its relationship to other Y-spccific polymorphisms. Am.J. Hum. Genet. 54: 319330.
85. STONEKING, M., 1993 DNA and recent human evolution. Evol. Anthropol. 2: 60-73.
86. STOXEKINC, M., 1994 In defense of "Eve"-a response to Templeton's critique. Am. Anthropol. 96: 131-141.
87. STOXEKIXG, M., and R. L. G\NX, 19S9 African origin of human mitochondria! DNA, pp. 17-30 in The Human Revolution: Behavioural and Biological Perspectives on the Origins of Modem Humans, edited by P. MELLARS and C. STRINGER. Princeton University Press, Princeton.
88. STOXEKIXG, M., and A. C. WILSON, 1989 Mitochondria! DNA, pp. 215-245 in The Colonization of the Pacific: A Genetic Trail, edited by A. V. S. HIM. and S. W. SERJEANTSOX. Oxford University Press, New York.
89. STRINGER, C., and C. GAMBLE, 1993 In Search of the Neanderthals: Solving the I'uzzle of Human Origins. Thames and Hudson, Inc., New York.
90. SZATIIMARY, E.J. E., 1993 Genetics of aboriginal North Americans. Evol. Anthropol. 1: 202-220.
91. TAKAIIATA, N., 1994 Repeated failures that led to the eventual success in human evolution. Mol. Biol. Evol. 11: 803-805.
92. TEMPLETON, A. R., 1993 The "Eve" hypothesis: a genetic critique and reanalysis. Am. AnthropoJ, 95: 51-72.
93. TEMPLETON, A. R., 1994 "Eve": hypothesis compatibility vs. hypothesis testing. Am. Anthropol. 96: 141-147.
94. TEMPLETON, A. R., 1996 Gene lineages and human evolution. Science 272: 1363.
95. TEMPLETON, A. R., E. ROUTMAN and C. A. PHILLIPS, 1995 Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondria! haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140: 762782.
96. TISIIKOFF, S. A., E. DIETZSCII, W. SPEF.D, 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.
97. TORRONI, A..Y.-S. CIIEN, O. SEMINO, A. S. SANTACIIIARA-BEXECERETTI, C. R. SCOTT et al., 1994a mtDNA and Y-chromosome polymorphisms in four Native American populations from southern Mexico. Am. J. Hum. Genet. 54: 303-318.
98. TORRONI, A., J. MILLER, I- G. MOORE, S. ZAMUUIO, J. ZIIUANG et al., 1994b Mitochondria! DNA analysis in Tibet: implications for the origin of the Tibetan population and its adaptation to high altitude. Am. J. Phys. Anthropol. 93: 189-199.
99. UNDERIIILL, P. A., L. JIN, R. ZEMAXS, P.J. OF.FNER and L. L. CAVALI.ISFORZA, 1996 A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. Proc. Natl. Acad. Sci. USA 93: 196-200.
100. VIGIIANT, L., M. STONEKING, H. HARPENDING, K. H.WKES and A. C. WILSON, 1991 African populations and the evolution of human mitochondrial DNA. Science 253: 1503-1507.
101. WAIXSCOAT.J. S., A. V. S. HILL, A. L. BOYCE, J. FLINT, M. HERNANDF.Z et al., 1986 Evolutionary relationships of human populations from an analysis of nuclear DNA polymorphisms. Nature 319: 491-493.
102. WEISS, G., and A. VON HAESEI.ER, 1996 Estimating the age of the common ancestor of men from the 2/T intron. Science 272: 1359-1360.
103. WEBER, J. L., and C. Woxc, 1993 Mutation in human short tandem repeats. Hum. Mol. Genet. 2: 1123-1128.
104. WEIR, B. S., 1990 Genetic Data Analysis. Sinatier Associates, Inc., Sunderland, MA.