Root (Y-Adam)
�    A00   AF4, AF5, AF6/L1284, AF7, AF8, AF9, AF10, AF13, L1086, L1087, L1088, L1091,
                 L1092, L1094, L1096, L1097, L1102, L1103, L1104, L1106, L1107, L1108, L1109,
                 L1110, L1111, L1113, L1114, L1115, L1117, L1119, L1122, L1126, L1131, L1133,
                 L1134, L1138, L1139, L1140, L1141, L1144, L1146, L1147, L1148, L1151, L1152,
                 L1154, L1156, L1157, L1158, L1159, L1160, L1161, L1163, L1233, L1234, L1236
�    A0-T   AF3, L1085, L1089, L1090, L1093, L1095, L1098, L1099, L1101, L1105, L1116,
                  L1118, L1120, L1121, L1123, L1124, L1125, L1127, L1128, L1129, L1130, L1132,
                  L1135, L1136, L1137, L1142, L1143, L1145, L1150, L1155, L1235
�   �    A0   L529.2, L896, L982, L984, L990, L991, L993, L995, L997, L998, L999, L1000, L1001,
                   L1006, L1008, L1010, L1012, L1016, L1018, L1055, V148, V149, V154, V164, V165,
                   V166, V167, V172, V173, V176, V177, V190, V196, V223, V225, V229, V233, V239
�   �    A1   L985, L986, L989, L1002, L1003, L1004, L1005, L1009, L1013, L1053, L1084, L1112,
                   L1153, P305, V161.2, V168, V171, V174, V238, V241, V250
�   �    �    A1*   -
�   �    �    A1a   M31, P82, V4, V14, V15, V25, V26, V28, V30, V40, V48, V57, V58, V63, V191,
                          V201, V204, V215
�   �    �    A1b   P108, V221
�   �    �   �    A1b*   -
�   �    �   �    A1b1   L419/PF712
�   �    �   �    BT    L413/PF1409/V31, L418, L438, L440, L604/PF1243, L957, L962, L969,
                              L970/PF1065, L971, L977, L1060/PF1021, L1061/PF1101, L1062/PF302, M42,
                              M91, M94/PF1081, M139, M299, P97, SPage65.1/SRY1532.1/SRY10831.1,
                              V29/PF1408, V59/PF1411, V64/PF1412, V102/PF1406, V187/PF1403,
                              V202/PF1406, V235PF1410
�   �    �   �    �    B   M60, M181/Page32, M247/P85, P90
�   �    �   �    �    CT    M168/PF1416, M294, P9.1
�   �    �   �    �   �    DE    M1/YAP, M145/P205/PF1444, M203/Page36/PF1435, P144/PF1436, P153,
                                         P165/PF1439, P167, P183/PF1424
�   �    �   �    �   �    �    D    M174/Page30
�   �    �   �    �   �    �    E     L339, L504/PF1803, L507/PF1874, L511, L537/PF1507,
                                            L614/PF1898/YSC0000032, L856, M40/SRY4064/SRY8299,
                                            M96/PF1823, P29/PF1643, P150/PF1704, P152/PF1646, P154,
                                            P155/PF1687, P156,P162/PF1496, P168, P169/Page54, P170/PF1656,
                                            P171/PF1903, P172/PF1510, P173, P174, P175, P176/PF1678
�   �    �   �    �   �    CF   P143
�   �    �   �    �   �    �    C    IMS-JST029149, IMS-JST037816-80, M130/Page51/RPS4Y711, M216,
                                            P184, P255/P325, P260/P324, Page85, V77, V183, V199, V232
�   �    �   �    �   �    �    F     L132.1, M89/PF2746, M213/P137/Page38, M235/Page80/PF2665,
                                            P14/PF2704, P133, P134, P135/PF2741, P136/PF2762, P138/PF2655,
                                            P139, P140, P141/PF2602, P142, P145/PF2617, P146/PF2623,
                                            P148/PF2734, P149, P151/PF2625, P157, P158/PF2706, P159/PF2717,
                                            P160/PF2618, P161, P163, P166/PF2702, P187/PF2632, P316
�   �    �   �    �   �    �   �    G     L116/PF2955/S284, L154/PF3139, L204/PF2825, L240,
                                                L269/PF3135, L402, L519, L520/PF2892, L521/PF2899,
                                                L522/PF3011, L523/PF3027, L605/PF3023,
                                                L769/CTS11294/PF3104, L770, L836, L837, L1258, L1407/Z3439
                                                M201/PF2957, P257/PF2950/U6, Page94/PF3137/U17,
                                                PF2952/S314/U2, PF2956/U3, PF2958/U7, U12, U20, U21, U23,
                                                PF3134/U33
�   �    �   �    �   �    �   �    H    M69/Page45, M370
�   �    �   �    �   �    �   �    IJK    L15/M523/PF3492/S137, L16/M522/PF3493/S138
�   �   ; �   �    �   �    �   �    �    IJ   M429/P125, P123/PF3554, P124/PF3553, P126,
                                                      P127/PF3526, P129, P130/PF3525/S22, S2
�   �    �   �    �   �    �   �    �   �    I     L41/PF3787, M170/PF3715, M258, P19_1, P19_2, P19_3,
                                                         P19_4, P19_5, P38, P212, U179
�   �    �   �    �   �    �   �    �   �    J     12f2.1, L134/PF4539, M304/Page16/PF4609, P209/PF4584,
                                                          S6/L60, S34, S35
�   �    �   �    �   �    �   �    �    K     M9, P128/PF5504, P131/PF5493, P132/PF5480
�   �    �   �    �   �    �   �    �   �    LT   CTS2888/PF5543, CTS3648, CTS4783/PF5548,
                                                          CTS5175/PF5549, CTS6888, CTS753/PF5525, PF5519,
                                                          PF5526, PF5531, PF5535, PF5536, PF5566, PF5586,
                                                          L298/P326, L811
�   �    �   �    �   �    �   �    �   �    �    L    L855, L863, L878/PF5524, L879/PF5697, M11, M20/PF5570, M61/Page43,
                                                              M185/PF5755
�   �    �   �    �   �    �   �    �   �    �    T     L445, L452, L455/PF5670, L810,
                                                                M184/Page34/USP9Y+3178, M272/PF5667,
                                                                Page129
�   �    �   �    �   �    �   �    �   �    K(xLT)   M526/PF5979
�   �    �   �    �   �    �   �    �   �    �    M    P256, Page93/S322
�   �    �   �    �   �    �   �    �   �    �    NO    M214/Page39, P188, P192, P193, P194, P195
�   �    �   �    �   �    �   �    �   �    �   �    N     M231/Page91
�   �    �   �    �   �    �   �    �   �    �   �    O     M175, P186, P191, P196
�   �    �   �    �   �    �   �    �   �    �    P    92R7_1, 92R7_2, L138, L268, L405, L471/PF5989,
                                                              L536/PF5860, L721/PF6020, L741,
                                                              L768/PF5976/YSC0000274, L779/PF5907/YSC0000251,
                                                              L781/PF5875/YSC0000255, M45/PF5962, M74/N12,
                                                              P27.1_1/P207, P27.1_2, P69, P226/PF5879, P228/PF5927,
                                                              P230/PF5925, P235/PF5946, P237/PF5873, P239,
                                                              P240/PF5897, P243/PF5874, P244, P281/PF5941,
                                                              P282/PF5932, P283/PF5966, P284, P295/PF5866/S8,
                                                              Page83, V231
�   �    �   �    �   �    �   �    �   �    �   �    Q     M242
�   �    �   �    �   �    �   �    �   �    �   �    R     M207/Page37/UTY2, P224, P227, P229/PF6019,
                                                                     P232, P280, P285, S4, S9
�   �    �   �    �   �    �   �    �   �    �    S    M230,P202, P204    

NOTES:

• Identical SNPs that were discovered separately are listed in alphabetical order, not necessarily in the order of discovery, and separated by "/". Examples: SRY1532.1/SRY10831.1, M1/YAP, M40/SRY4064/SRY8299, M130/RPS4Y711, M213/P137, L15/S137, L16/S138, M429/P125, M74/N12, M207/UTY2, M306/S1, and M184/USP9Y+3178.
• The naming conventions of the subclades at the beginning of the tree come from the supplement to Mendez et al (2013). Listed 5 March 2013.

Y-DNA haplogroup descriptions are provided on each haplogroup page. The combined haplogroups are the only ones whose description appears on this page.

The root of the Y haplogroup tree is the so-called "Y-Chromosome Adam," the most recent patrineal ancestor of all people living today, who is believed to have lived 60,000 to 90,000 years ago. He was not the only man living at that time, he simply was the only man with an unbroken male line of descent to the present day. The A haplogroup is thought to have been defined about 60,000 years bp. The BT haplogroup split from the root of the Y haplogroup tree 55,000 years before present (bp), probably in North East Africa. The CF(xDE) haplogroup was the common ancestor of all people who migrated outside of Africa until recent times. The defining mutation occurred 31-55,000 years bp in North East Africa and is still most common in Africa today in Ethiopia and Sudan. The DE haplogroup appeared approximately 50,000 years bp in North East Africa and subsequently split into haplogroup E that spread to Europe and Africa and haplogroup D that rapidly spread along the coastline of India and Asia to North Asia. The IJ haplogroup characterizes part of the second wave of emigration from Africa that occurred via the Middle East 45,000 years bp and defines two branches I and J that emigrated northwards and eastwards into Europe. The J branch subsequently split again and contributed to the current North African population. The NO haplogroup appeared approximately 35,000-40,000 years bp in a region east of the Aral sea; subsequent branches spread to North Asia (N) and another branch (O) to South Asia via North India.

References:

Butler, Recent Developments in Y-Short Tandem Repeat and Y-Single Nucleotide Polymorphism Analysis. (pdf) Forensic Science Review, Vol. 15, No. 2, 100-111, 2003.
Chandrasekar et al, YAP Insertion Signature in South Asia. Annals of Human Biology, 34(5);582-6, 2007.
Charoni et al, Y Chromosome Diversity, Human Expansion, Drift, and Cultural Evolution. PNAS, 106 (48); 20174-20179, 2009.
Cruciani et al, A Revised Root for the Human Y Chromosomal Phylogenetic Tree--The Origin of Patrilineal Diversity in Africa. The American Journal of Human Genetics, doi:10.1016/j.ajhg.2011.05.002, 2011.
Hammer et al, Hierarchical Patterns of Global Human Y-Chromosome Diversity. (pdf) Molecular Biology and Evolution, 18:1189-1203, 2001.
Hammer et al, Population Structure of Y chromosome SNP Haplogroups in the United States and Forensic Implications for Constructing Y Chromosome STR Databases. Forensic Science International, (in press), 2005.
Jobling et al, The Human Y Chromosome: An Evolutionary Marker Comes of Age. Nature/Reviews/Genetics, 4:598-612, 2003.
Karafet et al, Major East-West Division Underlies Y Chromosome Stratification Across Indonesia. Abstract. Molecular Biology and Evolution, doi:10.1093/molbev/msq063. 2010.
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.
Kayser et al, Melanesian and Asian Origins of Polynesians: mtDNA and Y-Chromosome Gradients across the Pacific. MBE Advance Access published August 21, 2006.
Mendez et al, An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree. (abstract) American Journal of Human Genetics 28 February 2013.
Rootsi S, Human Y Chromosomal Variations in European Populations (dissertation) Council of the Institute of Molecular and Cell Biology, University of Tartu, Oct 2004.
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.
Underhill et al, The Phylogeography of Y Chromosome Binary Haplotypes and the Origins of Modern Human Populations. (pdf) Annals of Human Genetics, 65:43-62, 2001.
Underhill et al, New Phylogenetic Relationships for Y-chromosome Haplogroup I: Reappraising its Phylogeography and Prehistory. in Rethinking the Human Evolution, Mellars P, Boyle K, Bar-Yosef O, Stringer C, Eds. McDonald Institute for Archaeological Research, Cambridge, UK, pp. 33-42, 2007b.
Underhill et al, Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations. (abstract) Annual Review Genetics, 41:539-564, December 1, 2007a.
Underhill et al, Y Chromosome Sequence Variation and the History of Human Populations. (pdf) Nature Genetics, 26: 358-361, November 2000.
Y Chromosome Consortium (YCC), A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups. Genome Research: 12:339-348, 2002.

Corrections/Additions made since 1 January 2013:

• Added PF1081, PF1403, PF1408, PF1411, PF1412, PF1416, PF1424, PF1435, PF1436, PF1439, PF1444, PF2602, PF2607, PF2618, PF2623, PF2625, PF2632, PF2655, PF2665, PF2702, PF2704, PF2706, PF2717, PF2734, PF2741, PF2746, PF2762, PF3492, PF3493, PF3525, PF3526, PF3553, PF3554, PF3715, F3787, PF5480, PF5493, PF5504, PF5570, PF5667, PF5670, PF5755, PF5860, PF5866, PF5873, PF5874, PF5875, PF5879, PF5897, PF5907, PF5925, PF5927, PF5932, PF5941, PF5946, PF5962, PF5966, PF5976, PF5979, PF5989, PF6020, YSC0000251, YSC0000255, YSC0000274 on 4 January 2013.
• Added CTS11294, PF2825, PF2892, PF2899, PF2950, PF2952, PF2955, PPF2956, PF2957, PF2958, PF3011, PF3023, PF3027, PF3104, PR3134, PF3135, PF3137, PF3139 on 5 January 2013.
• Added PF1496, PF1507, PF1510, PF1643, PF1646, PF1656, PF1678, PF1687, PF1704, PF1803, PF1823, PF1874, PF1898, PF1903, YSC0000032 on 6 January 2013.
• Added PF4539, PF4584, PF4609, PF6019 on 7 January 2013.
• Added L1060/PF1021, L1061/PF1101, L1062/PF302, V102/PF1406 on 25 February 2013.
• Added PF1409; added Mendez et al (2013) on 1 March 2013.
• Added .2 to V161; added note on naming conventions on 5 March 2013.
• Added AF3, AF4, AF5, AF6, AF7, AF8, AF9, AF10, AF13 on 5 March 2013.
• Added L529.2, L896, L982, L984, L986, L990, L991, L993, L995, L996, L997, L998, L999, L1000, L1001, L1005, L1006, L1008, L1010, L1012, L1016, L1018, L1055, L1084, L1085, L1086, L1087, L1088, L1089, L1090, L1091, L1092, L1093, L1094, L1095, L1096, L1097, L1098, L1099, L1101, L1102, L1103, L1104, L1105, L1106, L1107, L1108, L1109, L1110, L1111, L1112, L1113, L1114, L1115, L1116, L1117, L1118, L1119, L1120, L1121, L1122, L1123, L1124, L1125, L1126, L1127, L1128, L1129, L1130, L1131, L1132, L1133, L1134, L1135, L1136, L1137, L1138, L1139, L1140, L1141, L1142, L1143, L1144, L1145, L1146, L1147, L1148, L1150, L1151, L1152, L1153, L1154, L1155, L1156, L1157, L1158, L1159, L1160, L1161, L1163, L1233, L1234, L1235, L1236, V15, V26, V28, V30, V40, V48, V57, V58, V63, V191, V201, V204, V215 on 5 March 2013.
• Added PF1065, PF1243, PF1410 on 8 March 2013.
• Removed Page56/S323 from N on 21 March 2013.
• Added L1407/Z3439 on 12 May 2013.
• Removed outdated Additional Resources from Kerchner and Scott on 12 August 2013.
• Added CTS2888/PF5543, CTS3648, CTS4783/PF5548, CTS5175/PF5549, CTS6888, CTS753/PF5525, PF5519, PF5526, PF5531, PF5535, PF5536, PF5566, PF5586 on 19 August 2013.
• Added PF5524, PF5697 on 20 August 2013.
• Added L1284 on 22 August 2013.
• Added V77, V183, V199, V232 on 3 October 2013.

Contact person for Haplogroup Main Tree: David Reynolds

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