Y-DNA Haplogroup D and its Subclades - 2014

Because of continuing research, the structure of the Y-DNA Haplogroup Tree changes and ISOGG does its best to keep the tree updated with the latest developments in the field. The viewer may observe other versions of the tree on the Web. Email Alice Fairhurst if the differences need clarification or if you find any broken links on this page.

The criteria for a representative SNP printed in bold for a subclade is: traditional usage, testing one in multiple labs, and/or being found in the area of the chromosome used in recent research studies.

SNPs listed below in italics (colored black or red) are quality variants from next-generation sequencing reports consistently showing as representing that subgroup.

Contact Person for Haplogroup C: Ray H. Banks

Link to Experimental Composite Y-DNA Haplogroup D Tree by Ray Banks.

D   M174/Page30, CTS94, CTS1014.2, CTS1171, CTS1582, CTS7660, CTS8880/Z1613, F975, F1034, F1066, F1137/Z1591, F1278, F1306, F1344, F1379, F1439, F1447, F1533, F1612, F1620, F1690, F1927, F2062, F2147/Z1608, F2161/Z1610, F2318, F2325, F2455, F2510, F2662/Z1612, F2765, F2923, F2956, F3289, F3321, F3328/Z1620, F3370, F3519, F3572, F3666, F3707, F3835, F3845/Z1588, F3920, F4030, IMS-JST021355
• D*   -
• D1   CTS11577
• • D1*   -
• • D1a   M15
• • • D1a*   -
• • • D1a1   N1
• • D1b   M64.1/Page44.1, M55, M57, M179/Page31, M359.1/P41.1, P37.1, P190, 12f2.2
• • • D1b*   -
• • • D1b1   M116.1
• • • • D1b1*   -
• • • • D1b1a   M125
• • • • • D1b1a*   -
• • • • • D1b1a1   P42
• • • • • • D1b1a1*   -
• • • • • • D1b1a1a   P12_1, P12_2, P12_3
• • • • • D1b1a2   IMS-JST022457, CTS107/IMS-JST055457
• • • • • • D1b1a2*   -
• • • • • • D1b1a2a   P53.2
• • • • • • D1b1a2b   IMS-JST006841/Page3
• • • • • • • D1b1a2b*   -
• • • • • • • D1b1a2b1   CTS3397, CTS1982/Z1498, CTS3197, CTS4606/Z1499, Z3611, Z3642, Z3643
• • • • • • • • D1b1a2b1*   -
• • • • • • • • D1b1a2b1a   Z1500, CTS8181, CTS9242/Z1502, CTS10268, CTS10511/Z1503, Z1501, Z3603, Z3605, Z3607, Z3610, Z3617, Z3636, Z3651, Z14780, Z14781
• • • • • • • • • D1b1a2b1a*   -
• • • • • • • • • D1b1a2b1a1   Z1504, CTS1434, CTS8093, Z14779
• • • • • • • • • • D1b1a2b1a1*   -
• • • • • • • • • • D1b1a2b1a1a   CTS5406, Z14778
• • • • D1b1b   M151
• • • • D1b1c   P120
• • • • D1b1d   CTS6609
• • • • • D1b1d*   -
• • • • • D1b1d1   CTS1897/Z1574, CTS504/Z1569, CTS741, CTS906/Z1570, CTS2296, CTS2798, CTS3097/Z1575, CTS3906, CTS4219, CTS4305, CTS4517, CTS6090, CTS7590/Z1576, CTS8368, CTS8666, CTS10807, Z1568, Z1571, Z1572, Z1573, Z1578, Z1579, Z3838, Z3840, Z3844, Z3851, Z14867, Z14868, Z14869, Z14870, Z14871, Z14872, Z14873, Z14874, Z14875, Z14876, Z14877, Z14878, Z14879, Z14880
• • • • • • D1b1d1*   -
• • • • • • D1b1d1a   CTS218/Z1527, CTS321/Z1528, CTS621, CTS1228/Z1533, CTS1670/Z1546, CTS2078/Z1547, CTS2378/Z1548, CTS2482, CTS3489/Z1549, CTS3636/Z1550, CTS5307, CTS5862/Z1552, CTS6303/Z1553, CTS6392, CTS6499, CTS6572/Z1554, CTS6859, CTS7234/Z1555, CTS7398, CTS7543, CTS7615/Z1556, CTS7999/Z1557, CTS8230, CTS8960/Z1558, CTS9028, CTS9335, CTS9902, CTS10793/Z1566, CTS11032, CTS11048, CTS11071/Z1567, CTS12720, IMS-JST022456, PF7228, Z1529, Z1530, Z1531, Z1534, Z1535, Z1538, Z1539, Z1540, Z1541, Z1542, Z1560, Z1561, Z1562, Z1563, Z1564, Z1565, Z3834, Z3839, Z3841, Z3843, Z3847, Z3849, Z3850, Z3852, Z3854, Z3855, Z3856, Z14820, Z14821, Z14822, Z14823, Z14824, Z14825, Z14826, Z14827, Z14828, Z14829, Z14830, Z14831, Z14832, Z14833, Z14834, Z14835, Z14836, Z14837, Z14838, Z14839, Z14840, Z14841, Z14842, Z14843, Z14844, Z14845, Z14846, Z14847, Z14848, Z14849, Z14850, Z14851, Z14852, Z14853, Z14854, Z14855, Z14856, Z14857, Z14858, Z14859, Z14860, Z14861, Z14862, Z14863, Z14864, Z14865, Z14866
• • • • • • • D1b1d1a*   -
• • • • • • • D1b1d1a1   CTS6909, CTS356/Z1532, CTS1614/Z1545, CTS4617, Z14802, Z14804, Z14805, Z14806, Z14807, Z14809, Z14810, Z14811, Z14812, Z14814, Z14818
• • • • • • D1b1d1b   CTS1964, CTS6511, M6525, Z14881, Z14882, Z14883, Z14884, Z14885, Z14886, Z14887, Z14888
• • • D1b2   CTS583/Z1516, CTS131, CTS881/Z1517, CTS1352, CTS1592, CTS2098/Z1520, CTS2712, CTS2820, CTS3798, CTS3808, CTS3879, CTS4645/Z1521, CTS6144/Z1522, CTS6908, CTS7457, CTS7467, CTS8057/Z1523, CTS8075, CTS8327, CTS8635, CTS9143, CTS11368, Z1515, Z1518, Z1519, Z1524, Z1526, Z3801, Z3810, Z3811, Z3822, Z3823, Z3824, Z3827, Z3832, Z3833, Z14793, Z14794, Z14795, Z14796, Z14797, Z14798, Z14799, Z14800, Z17170, Z17171
• • • • D1b2*   -
• • • • D1b2a   CTS220, CTS709, CTS1333, CTS1439/Z1505, CTS2259, CTS2940, CTS3320/Z1508, CTS4158/Z1509, CTS5302, CTS5941, CTS6287/Z1510, CTS6342/Z1511, CTS10054, CTS10126, CTS11474, CTS11619, L495.2/Z2788.2, Z1506, Z1507, Z1514, Z3807, Z3814, Z3819, Z14782, Z14783, Z14784, Z14785, Z14786, Z14787, Z14788, Z14789, Z14790, Z14791, Z14792, Z17172, Z17174, Z17175
• • • • • D1b2a*   -
• • • • • D1b2a1   CTS10495, Z17173, Z17176
• • • • • D1b2a2   CTS11285, Z17254, Z17255, Z17256, Z17257, Z17258
• • D1c   P99
• • • D1c*   -
• • • D1c1   P47
• • • • D1c1*   -
• • • • D1c1a   M533
• D2   L1366, L1378, M226.2

Private SNPs are being removed from the tree and placed in the following category:
Private SNPs - After having been investigated, these SNPs have not met the population distribution criteria for placement on the tree. Either too few confirmed positive testers have been found OR multiple confirmed testers were confined to either a single surname or to a small group of related males.

• 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.
• IMS-JST119166 is at approximately IMS-JST006841. Listed 21 March 2013.
• IMS-JST75888-GC is at approximately M125. Listed 21 March 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. Subgroup D-M15 is seen in Tibet, Mongolia, Central Asia, and Southeast Asia, and the subgroup D-P47 is seen in Central Asia. The subgroup 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 subgroup D-M55 in Japan implies that this group has been isolated in Japan for between 12,000-20,000 years. The highest frequencies of D-M55 in Japan are seen among the Ainu and the Ryukyuans. Subgroup D-L1366 is so far noted only in the Philippines.

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 2014:

• Corrected SNP name; Z1524 should say Z1504; moved Z1504 from Investigation to tree on 4 February 2014.
• Added CTS1434, CTS1982/Z1498, CTS3197, CTS4606/Z1499, CTS8093, CTS8181, CTS9242/Z1502, CTS10268, CTS10511/Z1503, Z1501, Z3603, Z3605, Z3607, Z3610, Z3611, Z3617, Z3636, Z3642, Z3643, Z3651, Z14780, Z14781, Z14779, Z14778 to tree on 7 February 2014.
• Added CTS504/Z1569, CTS741, CTS906/Z1570, CTS1897/Z1574, CTS2296, CTS2798, CTS3097/Z1575, CTS3906, CTS4219, CTS4305, CTS4517, CTS6090, CTS6609, CTS7590/Z1576, CTS8368, CTS8666, CTS10807, Z1568, Z1571, Z1572, Z1573, Z1578, Z1579, Z3838, Z3840, Z3844, Z3851, Z14867, Z14868, Z14869, Z14870, Z14871, Z14872, Z14873, Z14874, Z14875, Z14876, Z14877, Z14878, Z14879, Z14880 to tree on 13 February 2014.
• Added CTS218/Z1527, CTS321/Z1528, CTS621, CTS1228/Z1533, CTS1670/Z1546, CTS2078/Z1547, CTS2378/Z1548, CTS2482, CTS3489/Z1549, CTS3636/Z1550, CTS5307, CTS5862/Z1552, CTS6303/Z1553, CTS6392, CTS6499, CTS6572/Z1554, CTS6859, CTS7234/Z1555, CTS7398, CTS7543, CTS7615/Z1556, CTS7999/Z1557, CTS8230, CTS8960/Z1558, CTS9028, CTS9335, CTS9902, CTS10793/Z1566, CTS11032, CTS11048, CTS11071/Z1567, CTS12720, PF7228, Z1529, Z1530, Z1531, Z1534, Z1535, Z1538, Z1539, Z1540, Z1541, Z1542, Z1560, Z1561, Z1562, Z1563, Z1564, Z1565, Z3834, Z3839, Z3841, Z3843, Z3847, Z3849, Z3850, Z3852, Z3854, Z3855, Z3856, Z14820, Z14821, Z14822, Z14823, Z14824, Z14825, Z14826, Z14827, Z14828, Z14829, Z14830, Z14831, Z14832, Z14833, Z14834, Z14835, Z14836, Z14837, Z14838, Z14839, Z14840, Z14841, Z14842, Z14843, Z14844, Z14845, Z14846, Z14847, Z14848, Z14849, Z14850, Z14851, Z14852, Z14853, Z14854, Z14855, Z14856, Z14857, Z14858, Z14859, Z14860, Z14861, Z14862, Z14863, Z14864, Z14865, Z14866 to tree on 13 February 2014.
• Added CTS6909, Z14802, Z14804, Z14805, Z14806, Z14807, Z14809, Z14810, Z14811, Z14812, Z14814, Z14818 to tree on 13 February 2014.
• Added CTS1964, CTS6511, M6525, Z14881, Z14882, Z14883, Z14884, Z14885, Z14886, Z14887, Z14888 to tree on 13 February 2014.
• Added CTS131, CTS583/Z1516, CTS881/Z1517, CTS1352, CTS1592, CTS2098/Z1520, CTS2712, CTS2820, CTS3798, CTS3808, CTS3879, CTS4645/Z1521, CTS6144/Z1522, CTS6908, CTS7457, CTS8057/Z1523, CTS8075, CTS8327, CTS8635, CTS9143, CTS11368, Z1515, Z1518, Z1519, Z1524, Z1526, Z3801, Z3810, Z3811, Z3822, Z3823, Z3824, Z3827, Z3832, Z3833, Z14793, Z14794, Z14795, Z14796, Z14797, Z14798, Z14799, Z14800 to tree on 22 February 2014.
• Added CTS220, CTS709, CTS1333, CTS1439/Z1505, CTS2259, CTS2940, CTS3320/Z1508, CTS5302, CTS6287/Z1510, CTS6342/Z1511, CTS10054, CTS11474, CTS11619, L495.2/Z2788.2, Z1506, Z1507, Z1514, Z3807, Z3814, Z3819, Z14782, Z14783, Z14784, Z14785, Z14786, Z14787, Z14788, Z14789, Z14790, Z14791, Z14792 to tree on 22 February 2014.
• Added L1366, L1378 to tree; moved M226.2 from Investigation to tree on 9 March 2014.
• Added CTS94, CTS1014.2, CTS1171, CTS1582, CTS3334/M5459/PF1432, CTS7660, F975, F986/M5402, F1034, F1066, F1137/Z1591, F1278, F1306, F1344, F1379, F1439, F1447, F1533, F1612, F1620, F1690, F1927, F2062, F2147/Z1608, F2161/Z1610, F2318, F2325, F2455, F2510, F2662/Z1612, F2765, F2923, F2956, F3289, F3321, F3370, F3519, F3572, F3666, F3707, F3835, F3845/Z1588, F3920, F4030 to tree on 26 April 2014.
• Added CTS11577 to tree and revised haplogroup description on 23 May 2014.
• Added CTS4158/Z1509, CTS7467, CTS10126, CTS10495, CTS11285, Z17170, Z17171, Z17172, Z17173, Z17174, Z17175, Z17176, Z17254, Z17255, Z17256, Z17257, Z17258 to tree on 14 August 2014.
• Removed CTS3334/M5459/PF1432, F986/M5402 from D and placed in DE on 15 September 2014.
• Added Experimental Composite Y-DNA Haplogroup D Tree by Ray Banks on 5 October 2014.
• Added CTS356/Z1532, CTS1614/Z1545, CTS5941, CTS4617, CTS8880/Z1613, F3328/Z1620 to tree on 25 October 2014.

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