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Cited by 710

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New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

Karafet, Tatiana M., Mendez, Fernando L., Meilerman, Monica B., Underhill, Peter A., Zegura, Stephen L., Hammer, Michael F.·2008·Genome Research
DOI 10.1101/gr.7172008
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Abstract

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

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Research works printed but not linked: 57

  1. 10.1016/j.forsciint.2005.06.003 · DOI
  2. 10.1007/s00439-003-1073-7 · DOI
  3. 10.1101/gr.226502 · DOI
  4. Cann,, 2002, A human genome diversity cell line panel, Science, 296, 261, 10.1126/science.296.5566.261b · DOI
  5. 10.1086/318205 · DOI · Paper page
  6. 10.1007/s00439-003-1031-4 · DOI · Paper page
  7. Cox,, 2007, A Polynesian motif on the Y chromosome: Population structure in remote Oceania, Hum. Biol., 79, 525, 10.1353/hub.2008.0004 · DOI
  8. 10.1086/340257 · DOI
  9. Deng,, 2004, Evolution and migration history of the Chinese population inferred from Chinese Y-chromosome evidence, J. Hum. Genet., 49, 339, 10.1007/s10038-004-0154-3 · DOI
  10. 10.1146/annurev.anthro.31.040402.085413 · DOI
  11. Hammer,, 1998, Out of Africa and back again: Nested cladistic analysis of human Y chromosome variation, Mol. Biol. Evol., 15, 427, 10.1093/oxfordjournals.molbev.a025939 · DOI
  12. 10.1073/pnas.100115997 · DOI · Paper page
  13. Hammer,, 2001, Hierarchical patterns of global human Y-chromosome diversity, Mol. Biol. Evol., 18, 1189, 10.1093/oxfordjournals.molbev.a003906 · DOI · Paper page
  14. Hammer,, 2003, Human population structure and its effects on sampling Y chromosome sequence variation, Genetics, 164, 1495, 10.1093/genetics/164.4.1495 · DOI
  15. 10.1007/s10038-005-0322-0 · DOI
  16. 10.1126/science.1105436 · DOI
  17. 10.1073/pnas.0702928104 · DOI
  18. Hurles,, 2002, Y chromosomal evidence for the origins of Oceanic-speaking peoples, Genetics, 160, 289, 10.1093/genetics/160.1.289 · DOI
  19. Jobling,, 2003, The human Y chromosome: An evolutionary marker comes of age, Nat. Rev. Genet., 4, 598, 10.1038/nrg1124 · DOI
  20. 10.1086/323299 · DOI
  21. Karafet,, 2002, High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life, Hum. Biol., 74, 761, 10.1353/hub.2003.0006 · DOI · Paper page
  22. 10.1353/hub.2005.0030 · DOI
  23. 10.1126/science.1060011 · DOI
  24. King,, 2007, Thomas Jefferson’s Y chromosome belongs to a rare European lineage, Am. J. Phys. Anthropol., 132, 583, 10.1002/ajpa.20557 · DOI
  25. 10.1086/346068 · DOI
  26. Lahr,, 1998, Towards a theory of modern human origins: Geography, demography, and diversity in recent human evolution, Am. J. Phys Anthropol., 41, 137, 10.1002/(SICI)1096-8644(1998)107:27+<137::AID-AJPA6>3.0.CO;2-Q · DOI
  27. 10.1126/science.1109792 · DOI · Paper page
  28. 10.1046/j.1529-8817.2005.00174.x · DOI · Paper page
  29. 10.1111/j.1469-1809.2006.00343.x · DOI · Paper page
  30. 10.1159/000093774 · DOI
  31. 10.1038/ng1754 · DOI
  32. 10.1086/422196 · DOI
  33. 10.1038/sj.ejhg.5201748 · DOI
  34. 10.1093/molbev/msl028 · DOI
  35. 10.1126/science.290.5494.1155 · DOI
  36. 10.1086/338306 · DOI
  37. 10.1086/386295 · DOI
  38. 10.1086/499411 · DOI · Paper page
  39. 10.1126/science.311.5767.1544 · DOI
  40. 10.1073/pnas.97.13.7354 · DOI
  41. 10.1086/444436 · DOI
  42. Sims,, 2007, Sub-populations within the major European and African derived haplogroups R1b3 and E3a are differentiated by previously phylogenetically undefined Y-SNPs, Hum. Mutat., 28, 97, 10.1002/humu.9469 · DOI
  43. 10.1086/302680 · DOI
  44. 10.1073/pnas.97.15.8225 · DOI
  45. 10.1038/70539 · DOI
  46. Tang,, 2002, Frequentist estimation of coalescence times from nucleotide sequence data using a tree-based partition, Genetics, 161, 447, 10.1093/genetics/161.1.447 · DOI · Paper page
  47. 10.1016/S0960-9822(02)01336-2 · DOI
  48. 10.1146/annurev.genet.41.110306.130407 · DOI
  49. 10.1038/81685 · DOI · Paper page
  50. 10.1046/j.1469-1809.2001.6510043.x · DOI
  51. 10.1038/ng1428 · DOI · Paper page
  52. 10.1093/molbev/msh214 · DOI · Paper page
  53. 10.1038/sj.ejhg.5201408 · DOI
  54. 10.1534/genetics.105.054270 · DOI
  55. 10.1101/gr.217602 · DOI · Paper page
  56. Zegura,, 2004, High-resolution SNPs and microsatellite haplotypes point to a single, recent entry of Native American Y chromosomes into the Americas, Mol. Biol. Evol., 21, 164, 10.1093/molbev/msh009 · DOI
  57. 10.1007/s00439-006-0282-2 · DOI

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Metadata

Authors
Karafet, T. M., Mendez, F. L., Meilerman, M. B., Underhill, P. A., Zegura, S. L., & Hammer, M. F.
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2008-04-02
Volume
18
Issue
5
Pages
830-838
ISSN
1088-9051
DOI
10.1101/gr.7172008
Cited by
710
References
1
Language
en

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