D   M174/Page30, IMS-JST021355
�    D*   -
�    D1   M15
�   �    D1*   -
�   �    D1a   N1
�    D2   M55, M57, M64.1/Page44.1, M179/Page31, M359.1/P41.1, P37.1, P190, 12f2.2
�   �    D2*   -
�   �    D2a   M116.1
�   �    �    D2a*   -
�   �    �    D2a1   M125
�   �    �   �    D2a1*   -
�   �    �   �    D2a1a   P42
�   �    �   �    �    D2a1a*   -
�   �    �   �    �    D2a1a1   P12_1, P12_2, P12_3
�   �    �   �    D2a1b   CTS107/IMS-JST055457, IMS-JST022457
�   �    �   �    �    D2a1b*   -
�   �    �   �    �    D2a1b1   P53.2
�   �    �   �    �    D2a1b2   IMS-JST006841/Page3
�   �    �   �    �   �    D2a1b2*   -
�   �    �   �    �   �    D2a1b2a   Z1500
�   �    �   �    �   �    �    D2a1b2a*   -
�   �    �   �    �   �    �    D2a1b2a1   Z1524
�   �    �    D2a2   M151
�   �    �    D2a3   P120
�   �    �    D2a4   IMS-JST022456
�    D3   P99
�   �    D3*   -
�   �    D3a   P47
�   �    �    D3a*   -
�   �    �    D3a1   M533

Experimental D Tree by Ray Banks.

• Private SNP N3 is located under M174 and is known to be ancestral for SNPs N1 and M64.1. Listed 6 Apr 2006.
• N2 is downstream of N1. Listed 5 August 2012.

SNPs under Investigation - Additional testing is needed to confirm adequate positive samples and/or correct placement on the tree.

• Z1476 is at approximately IMS-JST022457. Listed 18 June 2012.
• Z1504 is downstream from IMS-JST022457 and parallel to P53.2. Listed 18 June 2012.
• IMS-JST119166 is at approximately IMS-JST006841. Listed 21 March 2013.
• IMS-JST75888-GC is at approximately M125. Listed 21 March 2013.
• M226.2 is located at approximately L1366, L1378. Listed 13 December 2013.

NOTES:

• Identical SNPs that were discovered separately are listed in alphabetical order, not necessarily in the order of discovery, and separated by "/". Examples: M359.1/P41.1.

Y-DNA haplogroup D is seen primarily in Central Asia, Southeast Asia, and in Japan and was established approximately 50,000 years ago. Sub-group D1 (D-M15) is seen in Tibet, Mongolia, Central Asia, and Southeast Asia, and the sub-groups D* (D-M174) and D3 (D-P47) are seen in Central Asia. The sub-group D2 (D-M55) is seen almost exclusively in Japan. The high frequency of haplogroup D in Tibet (about 50%) and in Japan (about 35%) implies some early migratory connection between these areas. Examination of the genetic diversity seen in sub-group D2 in Japan implies that this group has been isolated in Japan for between 12,000-20,000 years. The highest frequencies of D2 in Japan are seen among the Ainu and the Ryukyuans.

An isolated incidence of haplogroup D has also been seen in the Andaman Islands in the Indian Ocean. This implies that the group may once have had a much greater range, but has subsequently been displaced by more recent population events.

References:

Cristofaro et al, Afghan Hindu Kush: Where Eurasian Sub-Continent Gene Flows Converge. PLoS ONE 8(10): e76748. doi:10.1371/journal.pone.0076748, 2013.
Cruciani et al, A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes. American Journal of Human Genetics, 70:1197-1214, 2002.
Cruciani et al, Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out of Africa. (pdf) American Journal of Human Genetics, 74:1014-1022, 2004.
Deng et al, Evolution and Migration History of the Chinese Population Inferred from the Chinese Y-chromosome Evidence. (pdf) Journal of Human Genetics, 49:339-348, 2004.
Gayden et al, The Himalayas as a Directional Barrier to Gene Flow. American Journal of Human Genetics, 80(5):884-894, 2007.
Hammer et al, Dual Origins of the Japanese: Common Ground for Hunter-gatherer and Farmer Y Chromosomes. (abstract) Journal of Human Genetics, 51:47-58, 2006.
Karafet et al, New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree. Abstract. Genome Research, published online April 2, 2008. Supplementary Material.
Karafet et al, Paternal Population History of East Asia: Sources, Patterns, and Microevolutionary Processes. (pdf) American Journal of Human Genetics, 69:615-628, 2001.
Li et al, Paternal Genetic Affinity between Western Austronesians and Daic Populations BMC Evolutionary Biology, Vo. 15(8), p. 146, 2008.
Naitoh S, et al, Assignment of Y-chromosomal SNPs Found in Japanese Population to Y-chromosomal Haplogroup tree. Journal of Human Genetics, 2013 Feb 7. doi: 10.1038/jhg.2012.159, 2013.
Nonaka et al, Y Chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms. (abstract) Annals of Human Genetics, 71:480-495, 2007.
Rozen et al, Remarkably Little Variation in Proteins Encoded by the Y Chromosome's Single-Copy Genes, Implying Effective Purifying Selection. American Journal of Human Genetics. 2009 December 11; 85(6): 923-928.
Sengupta et al, Polarity and Temporality of High Resolution Y-chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists. (pdf) American Journal of Human Genetics, 78:202-221, 2006.
Shi et al, Y-Chromosome Evidence of Earliest Modern Human Settlement in East Asia and Multiple Origins of Tibetan and Japanese Populations. (abstract) BMC Biology 2008, 6:45, 2008.
Su et al, Y-chromosome Evidence for a Northward Migration of Modern Humans into Eastern Asia during the Last Ice Age, (pdf), American Journal of Human Genetics, 65:1718-1724, 1999.
Thangaraj et al, Genetic Affinities of the Andaman Islanders, a Vanishing Human Population. (pdf) Current Biology, 13:86-93, 2003.
Xue et al, A Spatial Analysis of Genetic Structure of Human Populations in China Reveals Distinct Difference between Maternal and Paternal Lineages. European Journal of Human Genetics, 16:705-17, 2008.

Additional Resources:
ISOGG Wiki - What you need to know about Genetic Genealogy.
D Haplogroup (YDNA) Project, Ray Banks.

Corrections/Additions made since 1 January 2013:

• Added Naitoh et al (2013) on 21 March 2013.
• Added CTS107/IMS-JST055457, IMS-JST022456, IMS-JST006841 to tree; added IMS-JST75888-GC, IMS-JST119166, to Investigation on 21 March 2013.
• Added Experimental D Tree by Ray Banks on 7 May 2013.
• Added M533 to tree; added Cristofaro et al (2013) on 30 November 2013.
• Added M226.2 to Investigation on 13 December 2013.
• Added Z1500, Z1524 to tree on 31 December 2013.

Contact Person for Haplogroup D: Ray H. Banks

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