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Hierarchical patterns of global human Y-chromosome diversity.

Hammer, Michael F., Karafet, Tatiana M., Redd, Alan J., Jarjanazi, Hamdi, Santachiara-Benerecetti, Silvana, Soodyall, Himla, Zegura, Stephen L.·2001·Molecular Biology and Evolution
DOI 10.1093/oxfordjournals.molbev.a003906
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Abstract

We examined 43 biallelic polymorphisms on the nonrecombining portion of the Y chromosome (NRY) in 50 human populations encompassing a total of 2,858 males to study the geographic structure of Y-chromosome variation. Patterns of NRY diversity varied according to geographic region and method/level of comparison. For example, populations from Central Asia had the highest levels of heterozygosity, while African populations exhibited a higher level of mean pairwise differences among haplotypes. At the global level, 36% of the total variance of NRY haplotypes was attributable to differences among populations (i.e., Phi(ST) = 0.36). When a series of AMOVA analyses was performed on different groupings of the 50 populations, high levels of among-groups variance (Phi(CT)) were found between Africans, Native Americans, and a single group containing all 36 remaining populations. The same three population groupings formed distinct clusters in multidimensional scaling plots. A nested cladistic analysis (NCA) demonstrated that both population structure processes (recurrent gene flow restricted by isolation by distance and long-distance dispersals) and population history events (contiguous range expansions and long-distance colonizations) were instrumental in explaining this tripartite division of global NRY diversity. As in our previous analyses of smaller NRY data sets, the NCA detected a global contiguous range expansion out of Africa at the level of the total cladogram. Our new results s…

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Research works printed but not linked: 70

  1. Allen B. S., H. Ostrer, 1994 Conservation of human Y chromosome sequences among male great apes: implications for the evolution of Y chromosomes J. Mol. Evol39:13-21 · DOI
  2. Bao W., S. Zhu, A. Pandya, T. Zerjal, J. Xu, Q. Shu, R. Du, H. Yang, C. Tyler-Smith, 2000 MSY2: a slowly evolving minisatellite on the human Y chromosome which provides a useful polymorphic marker in Chinese populations Gene244:29-33 · DOI
  3. Barbujani G., A. Magagni, E. Minch, L. L. Cavalli-Sforza, 1997 An apportionment of human DNA diversity Proc. Natl. Acad. Sci. USA94:4516-4519 · DOI · Paper page
  4. Batzer M. A., M. Stoneking, M. Alegria-Hartman, et al. (11 co-authors) 1994 African origin of human-specific polymorphic Alu insertions Proc. Natl. Acad. Sci. USA91:12288-12292 · DOI
  5. Bowcock A., L. L. Cavalli-Sforza, 1991 The study of variation in the human genome Genomics11:491-498 · DOI
  6. Carvajal-Carmona L. G., I. D. Soto, N. Pineda, et al. (11 co-authors) 2000 Strong Amerind/White sex bias and a possible Sephardic contribution among the founders of a population in northwest Colombia Am. J. Hum. Genet67:1287-1295 · DOI
  7. Cavalli-Sforza L. L., 2000 Genes, peoples, and languages North Point Press, New York
  8. Cavalli-Sforza L. L., P. Menozzi, A. Piazza, 1994 The history and geography of human genes Princeton University Press, Princeton, N.J
  9. Cavalli-Sforza L. L., E. Minch, 1997 Paleolithic and Neolithic lineages in the European mitochondrial gene pool Am. J. Hum. Genet61:247-254 · DOI
  10. Crawford M. H., 1998 The origins of Native Americans: evidence from anthropological genetics Cambridge University Press, Cambridge, England · DOI
  11. Deka R., M. D. Shriver, L. M. Yu, R. E. Ferrell, R. Chakraborty, 1995 Intra- and inter-population diversity at short tandem repeat loci in diverse populations of the world Electrophoresis16:1659-1664 · DOI
  12. Excoffier L., E. S. Poloni, S. Santachiara-Benerecetti, O. Semino, A. Langaney, 1996 The molecular diversity of the Niokholo Mandenkalu from Eastern Senegal: an insight into West Africa genetic history Pp. 141–155 in A. J. Boyce and C. G. N. Mascie-Taylors, eds. Molecular biology and human diversity. Cambridge University Press, Cambridge, England · DOI
  13. Excoffier L., P. E. Smouse, J. M. Quattro, 1992 Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data Genetics131:479-491 · DOI · Paper page
  14. Fix A., 1999 Migration and colonization in human microevolution Cambridge University Press, New York
  15. Fu Y., W.-H. Li, 1997 Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection Genetics147:915-925 · DOI
  16. Hammer M. F., 1995 A recent common ancestry for human Y-chromosomes Nature378:376-378 · DOI
  17. Hammer M. F., T. Karafet, A. Rasanayagam, E. T. Wood, T. K. Altheide, T. Jenkins, R. C. Griffiths, A. R. Templeton, S. L. Zegura, 1998 Out of Africa and back again: nested cladistic analysis of human Y chromosome variation Mol. Biol. Evol15:427-441 · DOI
  18. Hammer M. F., A. J. Redd, E. T. Wood, et al. (12 co-authors) 2000 Jewish and middle eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes Proc. Natl. Acad. Sci. USA97:6769-6774 · DOI · Paper page
  19. Hammer M. F., A. B. Spurdle, T. Karafet, et al. (11 co-authors) 1997 The geographic distribution of human Y chromosome variation Genetics145:787-805 · DOI
  20. Hammer M. F., S. L. Zegura, 1996 The role of the Y chromosome in human evolutionary studies Evol. Anthropol5:116-134 · DOI
  21. Hey J., 1997 Mitochondrial and nuclear genes present conflicting portraits of human origins Mol. Biol. Evol14:166-172 · DOI
  22. Jin L., R. Chakraborty, 1995 Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics Heredity74:274-285 · DOI
  23. Jobling M. A., V. Samara, A. Pandya, et al. (16 co-authors) 1996 Recurrent duplication and deletion polymorphisms on the long arm of the Y chromosome in normal males Hum. Mol. Genet5:1767-1775 · DOI
  24. Jobling M. A., C. Tyler-Smith, 1995 Fathers and sons: the Y chromosome and human evolution Trends Genet11:449-456 · DOI
  25. Jorde L. B., W. S. Watkins, M. J. Bamshad, M. E. Dixon, C. E. Ricker, M. T. Seielstad, M. A. Batzer, 2000 The distribution of human genetic diversity: a comparison of mitochondrial, autosomal, and Y-chromosome data Am. J. Hum. Genet66:979-988 · DOI
  26. Karafet T. M., S. L. Zegura, O. Posukh, et al. (14 co-authors) 1999 Ancestral Asian source(s) of New World Y-chromosome founder haplotypes Am. J. Hum. Genet64:817-831 · DOI
  27. Karafet T., S. L. Zegura, J. Vuturo-Brady, et al. (14 co-authors) 1997 Y chromosome markers and trans-Bering Strait dispersals Am. J. Phys. Anthropol102:301-314 · DOI
  28. Kittles R. A., A. W. Bergen, M. Urbanek, M. Virkkunen, M. Linnoila, D. Goldman, J. C. Long, 1999 Autosomal, mitochondrial, and Y chromosome DNA variation in Finland: evidence for a male-specific bottleneck Am. J. Phys. Anthropol108:381-399 · DOI
  29. Kruskal J. B., 1964 Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis Pyschometrika29:1-27 · DOI
  30. Labuda D., E. Zietkiewicz, V. Yotova, 2000 Archaic lineages in the history of modern humans Genetics156:799-808 · DOI
  31. Latter B. D. H., 1980 Genetic differences within and between populations of the major human subgroups Am. Nat116:220-237 · DOI
  32. Lewontin R. C., 1972 The apportionment of human diversity Evol. Biol6:381-398 · DOI · Paper page
  33. Melton T., C. Ginther, G. Sensabaugh, H. Soodyall, M. Stoneking, 1997 Extent of heterogeneity in mitochondrial DNA of sub-Saharan African populations J. Forensic Sci42:582-592 · DOI
  34. Mesa N. R., M. C. Mondragon, I. D. Soto, et al. (13 co-authors) 2000 Autosomal, mtDNA, and Y-chromosome diversity in Amerinds: pre- and post-Columbian patterns of gene flow in South America Am. J. Hum. Genet67:1277-1286 · DOI
  35. Mountain J. L., 1998 Molecular evolution and modern human origins Evol. Anthropol7:21-37 · DOI
  36. Murdock G. P., 1967 Ethnographic atlas University of Pittsburgh Press, Pittsburgh, Pa · DOI
  37. Nei M., 1987 Molecular evolutionary genetics Columbia University Press, New York · DOI
  38. Perez-Lezaun A., F. Calafell, D. Comas, et al. (12 co-authors) 1999 Sex-specific migration patterns in Central Asian populations, revealed by analysis of Y-chromosome short tandem repeats and mtDNA Am. J. Hum. Genet65:208-219 · DOI · Paper page
  39. Poloni E. S., O. Semino, G. Passarino, A. S. Santachiara-Benerecetti, I. Dupanloup, A. Langaney, L. Excoffier, 1997 Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics Am. J. Hum. Genet61:1015-1035 · DOI
  40. Posada D., K. A. Crandall, A. R. Templeton, 2000 GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes Mol. Ecol9:487-488 · DOI
  41. Pritchard J. K., M. T. Seielstad, A. Perez-Lezaun, M. W. Feldman, 1999 Population growth of human Y chromosomes: a study of Y chromosome microsatellites Mol. Biol. Evol16:1791-1798 · DOI
  42. Przeworski M., R. R. Hudson, A. Di Rienzo, 2000 Adjusting the focus on human variation Trends Genet16:296-302 · DOI
  43. Redd A. J., M. Stoneking, 1999 Peopling of Sahul: mtDNA variation in aboriginal Australian and Papua New Guinean populations Am. J. Hum. Genet65:808-828 · DOI · Paper page
  44. Relethford J. H., 1995 Genetics and modern human origins Evol. Anthropol4:53-63 · DOI
  45. Relethford J. H., H. C. Harpending, 1994 Craniometric variation, genetic theory, and modern human origins Am. J. Phys. Anthropol95:249-270 · DOI
  46. Santos F. R., A. Pandya, M. Kayser, et al. (13 co-authors) 2000 A polymorphic L1 retroposon insertion in the centromere of the human Y chromosome Hum. Mol. Genet9:421-430 · DOI
  47. Schaal B. A., K. M. Olsen, 2000 Gene genealogies and population variation in plants Proc. Natl. Acad. Sci. USA97:7024-7029 · DOI
  48. Scozzari R., F. Cruciani, P. Santolamazza, et al. (17 co-authors) 1999 Combined use of biallelic and microsatellite Y-chromosome polymorphisms to infer affinities among African populations Am. J. Hum. Genet65:829-846 · DOI
  49. Seielstad M. T., E. Minch, L. L. Cavalli-Sforza, 1998 Genetic evidence for a higher female migration rate in humans Nat. Genet20:278-280 · DOI · Paper page
  50. Semino O., G. Passarino, P. J. Oefner, et al. (17 co-authors) 2000 The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective Science290:1155-1159 · DOI
  51. Sheffield V. C., J. S. Beck, A. E. Kwitek, D. W. Sandstrom, E. M. Stone, 1993 The sensitivity of single-strand conformation polymorphism analysis for the detection of single base changes Genomics16:325-332 · DOI
  52. Shen P., F. Wang, P. A. Underhill, et al. (13 co-authors) 2000 Population genetic implications from sequence variation in four Y chromosome genes Proc. Natl. Acad. Sci. USA97:7354-7359 · DOI
  53. Shinka T., K. Tomita, T. Toda, S. E. Kotliarova, J. Lee, Y. Kuroki, D. K. Jin, K. Tokunaga, H. Nakamura, Y. Nakahori, 1999 Genetic variations on the Y chromosome in the Japanese population and implications for modern human Y chromosome lineage J. Hum. Genet44:240-245 · DOI
  54. Stoneking M., 1998 Women on the move Nat. Genet20:219-220 · DOI
  55. Stoneking M., J. J. Fontius, S. L. Clifford, H. Soodyall, S. S. Arcot, N. Saha, T. Jenkins, M. A. Tahir, P. L. Deininger, M. A. Batzer, 1997 Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa Genome Res7:1061-1071 · DOI
  56. Su B., J. Xiao, P. Underhill, et al. (21 co-authors) 1999 Y-Chromosome evidence for a northward migration of modern humans into Eastern Asia during the last Ice Age Am. J. Hum. Genet65:1718-1724 · DOI
  57. Templeton A. R., 1993 The “Eve” hypothesis: a genetic critique and reanalysis Am. Anthropol95:51-72 · DOI
  58. ———. 1997 Testing the out-of-Africa replacement hypothesis with mitochondrial DNA data Pp. 329–360 in G. A. Clark and C. Willermet, eds. Conceptual issues in modern human origins research. Aldine de Gruyter, Amsterdam
  59. ———. 1999 Human races: a genetic and evolutionary perspective Am. Anthropol100:632-650 · DOI
  60. Templeton A. R., E. Boerwinkle, C. F. Sing, 1987 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila.Genetics117:343-351 · DOI
  61. Templeton A. R., E. Routman, C. A. Phillips, 1995 Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum.Genetics140:767-782 · DOI
  62. Templeton A. R., C. F. Sing, 1993 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination Genetics134:659-669 · DOI
  63. Thomson R., J. K. Pritchard, P. Shen, P. J. Oefner, M. W. Feldman, 2000 Recent common ancestry of human Y chromosomes: evidence from DNA sequence data Proc. Natl. Acad. Sci. USA97:7360-7365 · DOI
  64. Turner T. F., J. C. Trexler, J. L. Harris, J. L. Haynes, 2000 Nested cladistic analysis indicates population fragmentation shapes genetic diversity in a freshwater mussel Genetics154:777-785 · DOI
  65. Underhill P. A., L. Jin, A. A. Lin, S. Q. Mehdi, T. Jenkins, D. Vollrath, R. W. Davis, L. L. Cavalli-Sforza, P. J. Oefner, 1997 Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography Genome Res7:996-1005 · DOI
  66. Underhill P. A., P. Shen, A. A. Lin, et al. (21 co-authors) 2000 Y chromosome sequence variation and the history of human populations Nat. Genet26:358-361 · DOI · Paper page
  67. Urbanek M., D. Goldman, J. C. Long, 1996 The apportionment of dinucleotide repeat diversity in Native Americans and Europeans: a new approach to measuring gene identity reveals asymmetric patterns of divergence Mol. Biol. Evol13:943-953 · DOI
  68. Vigilant L., M. Stoneking, H. Harpending, K. Hawkes, A. C. Wilson, 1991 African populations and the evolution of human mitochondrial DNA Science253:1503-1507 · DOI
  69. Vollrath D., S. Foote, A. Hilton, L. G. Brown, P. Beer-Romero, J. S. Bogan, D. C. Page, 1992 The human Y chromosome: a 43-interval map based on naturally occurring deletions Science258:52-59 · DOI
  70. Wright S., 1969 Evolution and the genetics of populations 2. the theory of gene frequencies University of Chicago Press, Chicago

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Metadata

Authors
Hammer, M. F., Karafet, T. M., Redd, A. J., Jarjanazi, H., Santachiara-Benerecetti, S., Soodyall, H., & Zegura, S. L.
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2001-07-01
Volume
18
Issue
7
Pages
1189-1203
ISSN
  • 1537-1719
  • 0737-4038
DOI
10.1093/oxfordjournals.molbev.a003906
Cited by
192
References
0
Language
en

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Hammer, M. F., Karafet, T. M., Redd, A. J., Jarjanazi, H., Santachiara-Benerecetti, S., Soodyall, H., & Zegura, S. L. (2001). Hierarchical patterns of global human Y-chromosome diversity. Molecular Biology and Evolution. https://doi.org/10.1093/oxfordjournals.molbev.a003906