Skip to main content
PMC home page
American Journal of Human Genetics logoLink to American Journal of Human Genetics
. 1999 Mar;64(3):817–831. doi: 10.1086/302282

Ancestral Asian source(s) of new world Y-chromosome founder haplotypes.

T M Karafet 1, S L Zegura 1, O Posukh 1, L Osipova 1, A Bergen 1, J Long 1, D Goldman 1, W Klitz 1, S Harihara 1, P de Knijff 1, V Wiebe 1, R C Griffiths 1, A R Templeton 1, M F Hammer 1
PMCID: PMC1377800  PMID: 10053017

Abstract

Haplotypes constructed from Y-chromosome markers were used to trace the origins of Native Americans. Our sample consisted of 2,198 males from 60 global populations, including 19 Native American and 15 indigenous North Asian groups. A set of 12 biallelic polymorphisms gave rise to 14 unique Y-chromosome haplotypes that were unevenly distributed among the populations. Combining multiallelic variation at two Y-linked microsatellites (DYS19 and DXYS156Y) with the unique haplotypes results in a total of 95 combination haplotypes. Contra previous findings based on Y- chromosome data, our new results suggest the possibility of more than one Native American paternal founder haplotype. We postulate that, of the nine unique haplotypes found in Native Americans, haplotypes 1C and 1F are the best candidates for major New World founder haplotypes, whereas haplotypes 1B, 1I, and 1U may either be founder haplotypes and/or have arrived in the New World via recent admixture. Two of the other four haplotypes (YAP+ haplotypes 4 and 5) are probably present because of post-Columbian admixture, whereas haplotype 1G may have originated in the New World, and the Old World source of the final New World haplotype (1D) remains unresolved. The contrasting distribution patterns of the two major candidate founder haplotypes in Asia and the New World, as well as the results of a nested cladistic analysis, suggest the possibility of more than one paternal migration from the general region of Lake Baikal to the Americas.

Full Text

The Full Text of this article is available as a PDF (398.0 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bamshad M. J., Watkins W. S., Dixon M. E., Jorde L. B., Rao B. B., Naidu J. M., Prasad B. V., Rasanayagam A., Hammer M. F. Female gene flow stratifies Hindu castes. Nature. 1998 Oct 15;395(6703):651–652. doi: 10.1038/27103. [DOI] [PubMed] [Google Scholar]
  2. Bianchi N. O., Bailliet G., Bravi C. M., Carnese R. F., Rothhammer F., Martínez-Marignac V. L., Pena S. D. Origin of Amerindian Y-chromosomes as inferred by the analysis of six polymorphic markers. Am J Phys Anthropol. 1997 Jan;102(1):79–89. doi: 10.1002/(SICI)1096-8644(199701)102:1<79::AID-AJPA7>3.0.CO;2-8. [DOI] [PubMed] [Google Scholar]
  3. Cann R. L., Stoneking M., Wilson A. C. Mitochondrial DNA and human evolution. Nature. 1987 Jan 1;325(6099):31–36. doi: 10.1038/325031a0. [DOI] [PubMed] [Google Scholar]
  4. Hammer M. F., Karafet T., Rasanayagam A., Wood E. T., Altheide T. K., Jenkins T., Griffiths R. C., Templeton A. R., Zegura S. L. Out of Africa and back again: nested cladistic analysis of human Y chromosome variation. Mol Biol Evol. 1998 Apr;15(4):427–441. doi: 10.1093/oxfordjournals.molbev.a025939. [DOI] [PubMed] [Google Scholar]
  5. Hammer M. F., Spurdle A. B., Karafet T., Bonner M. R., Wood E. T., Novelletto A., Malaspina P., Mitchell R. J., Horai S., Jenkins T. The geographic distribution of human Y chromosome variation. Genetics. 1997 Mar;145(3):787–805. doi: 10.1093/genetics/145.3.787. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Harding R. M., Fullerton S. M., Griffiths R. C., Bond J., Cox M. J., Schneider J. A., Moulin D. S., Clegg J. B. Archaic African and Asian lineages in the genetic ancestry of modern humans. Am J Hum Genet. 1997 Apr;60(4):772–789. [PMC free article] [PubMed] [Google Scholar]
  7. Harpending H. C., Batzer M. A., Gurven M., Jorde L. B., Rogers A. R., Sherry S. T. Genetic traces of ancient demography. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1961–1967. doi: 10.1073/pnas.95.4.1961. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Karafet T., Zegura S. L., Vuturo-Brady J., Posukh O., Osipova L., Wiebe V., Romero F., Long J. C., Harihara S., Jin F. Y chromosome markers and Trans-Bering Strait dispersals. Am J Phys Anthropol. 1997 Mar;102(3):301–314. doi: 10.1002/(SICI)1096-8644(199703)102:3<301::AID-AJPA1>3.0.CO;2-Y. [DOI] [PubMed] [Google Scholar]
  9. Karafet T., de Knijff P., Wood E., Ragland J., Clark A., Hammer M. F. Different patterns of variation at the X- and Y-chromosome-linked microsatellite loci DXYS156X and DXYS156Y in human populations. Hum Biol. 1998 Dec;70(6):979–992. [PubMed] [Google Scholar]
  10. Kolman C. J., Sambuughin N., Bermingham E. Mitochondrial DNA analysis of Mongolian populations and implications for the origin of New World founders. Genetics. 1996 Apr;142(4):1321–1334. doi: 10.1093/genetics/142.4.1321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lell J. T., Brown M. D., Schurr T. G., Sukernik R. I., Starikovskaya Y. B., Torroni A., Moore L. G., Troup G. M., Wallace D. C. Y chromosome polymorphisms in native American and Siberian populations: identification of native American Y chromosome haplotypes. Hum Genet. 1997 Oct;100(5-6):536–543. doi: 10.1007/s004390050548. [DOI] [PubMed] [Google Scholar]
  12. Lorenz J. G., Smith D. G. Distribution of the 9-bp mitochondrial DNA region V deletion among North American Indians. Hum Biol. 1994 Oct;66(5):777–788. [PubMed] [Google Scholar]
  13. Merriwether D. A., Rothhammer F., Ferrell R. E. Distribution of the four founding lineage haplotypes in Native Americans suggests a single wave of migration for the New World. Am J Phys Anthropol. 1995 Dec;98(4):411–430. doi: 10.1002/ajpa.1330980404. [DOI] [PubMed] [Google Scholar]
  14. Morell V. Kennewick Man's trials continue. Science. 1998 Apr 10;280(5361):190–192. doi: 10.1126/science.280.5361.190. [DOI] [PubMed] [Google Scholar]
  15. Reed T. E. Caucasian genes in American Negroes. Science. 1969 Aug 22;165(3895):762–768. doi: 10.1126/science.165.3895.762. [DOI] [PubMed] [Google Scholar]
  16. Santos F. R., Rodriguez-Delfin L., Pena S. D., Moore J., Weiss K. M. North and South Amerindians may have the same major founder Y chromosome haplotype. Am J Hum Genet. 1996 Jun;58(6):1369–1370. [PMC free article] [PubMed] [Google Scholar]
  17. Seielstad M. T., Minch E., Cavalli-Sforza L. L. Genetic evidence for a higher female migration rate in humans. Nat Genet. 1998 Nov;20(3):278–280. doi: 10.1038/3088. [DOI] [PubMed] [Google Scholar]
  18. Shields G. F., Schmiechen A. M., Frazier B. L., Redd A., Voevoda M. I., Reed J. K., Ward R. H. mtDNA sequences suggest a recent evolutionary divergence for Beringian and northern North American populations. Am J Hum Genet. 1993 Sep;53(3):549–562. [PMC free article] [PubMed] [Google Scholar]
  19. Stone A. C., Stoneking M. mtDNA analysis of a prehistoric Oneota population: implications for the peopling of the New World. Am J Hum Genet. 1998 May;62(5):1153–1170. doi: 10.1086/301838. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Templeton A. R., Routman E., Phillips C. A. Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics. 1995 Jun;140(2):767–782. doi: 10.1093/genetics/140.2.767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Torroni A., Neel J. V., Barrantes R., Schurr T. G., Wallace D. C. Mitochondrial DNA "clock" for the Amerinds and its implications for timing their entry into North America. Proc Natl Acad Sci U S A. 1994 Feb 1;91(3):1158–1162. doi: 10.1073/pnas.91.3.1158. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Torroni A., Schurr T. G., Cabell M. F., Brown M. D., Neel J. V., Larsen M., Smith D. G., Vullo C. M., Wallace D. C. Asian affinities and continental radiation of the four founding Native American mtDNAs. Am J Hum Genet. 1993 Sep;53(3):563–590. [PMC free article] [PubMed] [Google Scholar]
  23. Torroni A., Schurr T. G., Yang C. C., Szathmary E. J., Williams R. C., Schanfield M. S., Troup G. A., Knowler W. C., Lawrence D. N., Weiss K. M. Native American mitochondrial DNA analysis indicates that the Amerind and the Nadene populations were founded by two independent migrations. Genetics. 1992 Jan;130(1):153–162. doi: 10.1093/genetics/130.1.153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Torroni A., Sukernik R. I., Schurr T. G., Starikorskaya Y. B., Cabell M. F., Crawford M. H., Comuzzie A. G., Wallace D. C. mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans. Am J Hum Genet. 1993 Sep;53(3):591–608. [PMC free article] [PubMed] [Google Scholar]
  25. Underhill P. A., Jin L., Lin A. A., Mehdi S. Q., Jenkins T., Vollrath D., Davis R. W., Cavalli-Sforza L. L., Oefner P. J. Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 1997 Oct;7(10):996–1005. doi: 10.1101/gr.7.10.996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Underhill P. A., Jin L., Zemans R., Oefner P. J., Cavalli-Sforza L. L. A pre-Columbian Y chromosome-specific transition and its implications for human evolutionary history. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):196–200. doi: 10.1073/pnas.93.1.196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Whitfield L. S., Sulston J. E., Goodfellow P. N. Sequence variation of the human Y chromosome. Nature. 1995 Nov 23;378(6555):379–380. doi: 10.1038/378379a0. [DOI] [PubMed] [Google Scholar]
  28. Zerjal T., Dashnyam B., Pandya A., Kayser M., Roewer L., Santos F. R., Schiefenhövel W., Fretwell N., Jobling M. A., Harihara S. Genetic relationships of Asians and Northern Europeans, revealed by Y-chromosomal DNA analysis. Am J Hum Genet. 1997 May;60(5):1174–1183. [PMC free article] [PubMed] [Google Scholar]

Articles from American Journal of Human Genetics are provided here courtesy of American Society of Human Genetics

RESOURCES