Y-DNA Haplogroup A and its Subclades - 2015

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 Ray H. Banks 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.

Paragroups, subclades ending with an asterisk (*) indicate that some individuals do not test positive for any snps downstream. Since this fact is commonly known, paragroups are being omitted to simplify the display of SNPs.

Contact Person for Haplogroup A: Bonnie Schrack

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

Y   Root (Y-Adam)
• A00   AF6/L1284, AF4, AF5, 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   L1085, AF3, 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   CTS2809/L991, L529.2, L896, L982, L984, L990, L993, L995, L997, L998, L999, L1000, L1001, L1006, L1008, L1010, L1012, L1016, L1018, L1055, V148, V149, V154, V165, V166, V172, V173, V176, V177, V190, V196, V223, V225, V229, V233, V239
• • • A0a   L979, L980, L987, L996, L1011, L1015, L1017
• • • • A0a1   L1070, L1072, L1073, L1075, L1076, L1078, L1079, L1080, L1081, L1082, V150, V153, V157, V158, V159, V162, V164, V170
• • • • • A0a1a   P114, V151, V152, V161.1, V169, V181, V195
• • • • • A0a1b   L1289
• • • • A0a2   L981, L983, L988, L994, L1007, L1014, V203
• • • A0b   L92.2, L1035, L1036, L1037, L1038, L1039, L1040, L1041, L1042, L1043, L1044, L1045, L1046, L1047, L1048, L1049, L1050, L1051, L1052, L1054, L1056, L1057, L1058
• • A1   L985, L986, L1002, L1003, L1004, L1005, L1084, L1112, L1153, P305, V161.2, V168, V171, V174, V238, V241, V250
• • • A1a   M31, P82, V4, V14, V15, V25, V26, V28, V30, V40, V48, V57, V58, V63, V191, V201, V204, V215
• • • A1b   P108, FGC8027, L989, L1009, L1013, L1053, M11301/Z11908, V221, Z11891, Z11892, Z11893, Z11894, Z11895, Z11896, Z11897, Z11898, Z11899, Z11900, Z11901, Z11902, Z11903, Z11904, Z11905, Z11906, Z11907, Z11909, Z11910, Z11911, Z11912, Z11913, Z11914, Z11915, Z11916, Z11917, Z11918, Z11919, Z17890, Z17891, Z17892, Z17893, Z17894, Z17895, Z17896, Z17897, Z17898, Z17899, Z17900
• • • • A1b1   L419/PF712
• • • • • A1b1a   L602, V50, V82, V198, V224
• • • • • • A1b1a1   M14, M23, L968/M29/P3/PN3, M71, M135, M141, M206, M276/P247, M277/P248, MEH1, P4, P5, P36.1, Page71, Page87, Page95
• • • • • • • A1b1a1a   M6, M49/Page41, M196
• • • • • • • • A1b1a1a1   P28
• • • • • • • • A1b1a1a2   L963
• • • • • • • • • A1b1a1a2a   M114, M212
• • • • • • • • • A1b1a1a2b   P262
• • • • • A1b1b   M32
• • • • • • A1b1b1   M28
• • • • • • A1b1b2   L427, L430, M144, M190/Page35/PF1373, M220, M305/Page17, P289/PF1372, Page50, PF1365/V160
• • • • • • • A1b1b2a   M51/Page42, M229, M239/Page89, P71, P100
• • • • • • • • A1b1b2a1   P291
• • • • • • • • • A1b1b2a1a   P102
• • • • • • • A1b1b2b   M13/PF1374, M63/PF1079, M127, M202, M219, Page53, Page77/PF1364/V10
• • • • • • • • A1b1b2b1   M118
• • • • BT   M91, CTS5903/M9174/PF795/S1572, CTS7503/M9219, L413/PF1409/V31, L418, L438, L440, L604/PF1243, L962, L969, L1060/PF1021, L1061/PF1101, L1062/PF302, L1071/M8945, L1220/M9212, M42, M94/PF1081, M139, M251/M9122/PF699, M299, M8947, M8949, M8951, M8952, M8953/PF1405/V216, M8954, M8955/PF12, M8956, M8957, M8958/PF196, M8959, M8961/PF201, M8967, M8968/PF207, M8969/PF1407/V21, M8970/PF208, M8971, M8972, M8973, M8976/PF215, M8977, M8979/PF226, M8980/PF229, M8983/PF230, M8985/PF232, M8986, M8988, M8993, M8994, M8995, M8997/PF260, M8999, M9000, M9001, M9003, M9004/PF270, M9005, M9006, M9008, M9009, M9010, M9011, M9015, M9016, M9017/PF282, M9019/PF286, M9020/PF287, M9021/PF288, M9025, M9026, M9027, M9028/PF298, M9030, M9031, M9032/PF304, M9034, M9036/PF308, M9037, M9038/PF313, M9039, M9041/PF319, M9042, M9043, M9045, M9046/PF324, M9054, M9056, M9057, M9064/PF350, M9065/PF351, M9066, M9069/PF635, M9070, M9075, M9076, M9077, M9079, M9080, M9081, M9083, M9086/PF648, M9087, M9089/PF653, M9094/PF671, M9095, M9097/PF672, M9098, M9099/PF674, M9100, M9102, M9103/PF679, M9105, M9109, M9110/PF684, M9111, M9112, M9113, M9114, M9115, M9116/PF688, M9117, M9118/Page81, M9121, M9123, M9124/PF701, M9125, M9126/PF703, M9127, M9128, M9129/PF707, M9130/PF708, M9131, M9133/PF715, M9135, M9136/PF724, M9138, M9139, M9140, M9141, M9142/PF731, M9143/PF732, M9145/PF733, M9146, M9148/PF744, M9151, M9152, M9155/PF762, M9156/PF764, M9157/PF766, M9159/PF767, M9160/Page24, M9162, M9163/PF777, M9165, M9166/PF785, M9169, M9172, M9173/PF794, M9176, M9177, M9178, M9179, M9180, M9182, M9187, M9188, M9189, M9192, M9193, M9194.3/PF825.3, M9195, M9196, M9197, M9198, M9199/PF834, M9200/PF835, M9202, M9203/PF837, M9204, M9209, M9210, M9213, M9214, M9215/PF847, M9216, M9217/PF857, M9218/PF860, M9220, M9221, M9223/PF865, M9225/PF868, M9226/PF869, M9227, M9228, M9230/PF870, M9231/PF876, M9234, M9235/PF886, M9237/PF890, M9238, M9239, M9240/PF896, M9242/PF899, M9244, M9245, M9246, M9248, M9249, M9251/PF913, M9252, M9253/PF914, M9254, M9255/PF925, M9257, M9258, M9260, M9261/PF931, M9262/PF932, M9263, M9265, M9266/PF946, M9267/PF948, M9269, M9271, M9277, M9278/PF969, M9280, M9282, M9283/PF973, M9284, M9285, M9286, M9287, M9288/PF985, M9289/PF988, M9290/PF989, M9291, M9292, M9293/PF997, M9295/PF1000, M9296, M9298/Z12093, M9300, M9301/PF1015, M9302, M9303, M9306, M9310, M9311/PF1030, M9312, M9314, M9315/PF1033, M9316/PF1034, M9317, M9318, M9319, M9321/PF1045, M9322/PF1049, M9323/PF1050, M9325, M9326, M9327, M9328/PF1053, M9331/PF1057, M9334, M9335/PF1060, M9336/Page26, M9338/PF1064, M9340, M9341/PF1072, M9343, M9344, M9346, M9347, M9348/PF1093, M9349, M9352/PF1100, M9353, M9356, M9357/PF1209, M9359, M9360, M9361, M9362, M9365/PF1218, M9366, M9367, M9368, M9369, M9370, M9372, M9373, M9374/Z4690, M9376, M9377/PF1421, M9378, M9379/PF1253, M9380/PF1256, M9382/PF1257, M9387, M9389, M9390/PF1262, M9393, M9394/PF1271, M9396, M9397, M9398/PF1279, M9399/PF1283, M9405, M9406, M9408/PF1296, M9410, M9411/PF1315, M9412, M9417, M9420, M9421, M9425, M11752, M11753/PF243, M11754, M11755/PF280, M11756/PF301, M11757/PF327, M11759, M11760, M11762, M11767, M11773/PF809, M11779/PF1027, M11780/PF1044, M11781, M11787/PF1311, M11789/PF1332, P97, Page65.1/SRY1532.1/SRY10831.1, PF16, PF20, PF28, PF51, PF69, PF72, PF73, PF79, PF122, PF127, PF133, PF135, PF149, PF161, PF162, PF167, PF175, PF177, PF236, PF338, PF420, PF462, PF468, PF509, PF585, PF591, PF592, PF601, PF620, PF622, PF626, PF627, PF632, PF713, PF918, PF1026, PF1042, PF1096, PF1143, PF1178, PF1184, PF1196, PF1201, PF1247, PF1248, PF1249, PF1252, PF1274, PF1318, PF1325, V29/PF1408, V59/PF1411, V64/PF1412, V102/PF1406, V187/PF1403, V202/PF1404, V235/PF1410, Z11924, Z11926, Z11927, Z11929, Z11930, Z11931, Z11932, Z11933, Z11937, Z11938, Z11939, Z11940, Z11941, Z11943, Z11945, Z11948, Z11970, Z11971, Z11978, Z11979, Z11980, Z11981, Z11983, Z11984, Z11985, Z11986, Z11987, Z11988, Z11989, Z11990, Z11991, Z11993, Z11997, Z11999, Z12001, Z12002, Z12003, Z12004, Z12005, Z12006, Z12007, Z12008, Z12031, Z12047, Z12070, Z12071, Z12077, Z12094, Z12095, Z12096, Z12110, Z12111, Z12128, Z12129, Z12138, Z12139, Z17332, Z17333, Z17334, Z17335, Z17336, Z17337, Z17338, Z17339, Z17340, Z17341, Z17342, Z17343, Z17344, Z17345, Z17346, Z17347, Z17348, Z17349, Z17350, Z17351, Z17352, Z17353, Z17354, Z17355, Z17356, Z17357, Z17358, Z17359, Z17360, Z17361, Z17362, Z17363, Z17364, Z17365, Z17366, Z17367, Z17368, Z17369, Z17370, Z17371, Z17372, Z17373, Z17374, Z17375, Z17376, Z17377, Z17378, Z17379, Z17380, Z17381, Z17382, Z17383, Z17384, Z17385, Z17386, Z17387, Z17388, Z17389, Z17390

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.

• M59 found in the same sample from Ethiopia. Listed 15 February 2012.
• M171 found in a single A3a2 (the former A3b2, positive for M13 or its equivalents) sample from Sudan. Listed 15 February 2012.
• L1100 and L1149 are located downstream of L1086. Reported in Perry surname. Listed 5 March 2013.

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

• L600, L601, L603 are downstream from V50. These SNPs were found in an A-V50 individual by Thomas Krahn. Listed 15 February 2012
• V53, V214, V236. These SNPs were found in an A-M31+ sample by Cruciani (2011). Listed 15 February 2012
• Page110 is downstream of Page41, Page71, Page87, and Page95, but it needs to be tested to find out where it belongs in relation to other SNPs. It may be private. Listed 15 February 2012
• PF3627.1/V218.1, V60, V61, V70, V72, V79, V80, V81, V180, V188, V192, V200, V228, V242. The V SNPs were found in an A-P262 sample by Cruciani (2011). Listed 15 February 2012
• V97 is found dowstream of M212. This SNP was found in an A-M114 sample by Trombetta (2010) and has been found derived in A-P262+ sample. Listed 15 February 2012
• M9462/PF1361/V1, PF1358/V193, PF1362/V156, PF1363/V155, M9531/PF1366/V230, PF1367/V243, PF1368/V194, PF1369/V51, PF1370/V66, PF1371/V56. The V SNPs were found in an A-M13* sample by Cruciani (2011). Listed 15 February 2012
• V89/PF1359, V98. These SNPs were found in an A-M13* by Trombetta (2010). Listed 15 February 2012
• V67 is found downstream of V161,2. Listed 15 February 2012.
• L411/PF11, L412, L414, L420, L421, L422, L423, L424, L425, L426, L428, L429, L436/PF962, L437/PF965, L439, L441/PF1287, L442/PF1300. These SNPs were found in an A-M13 WTY participant. They are being tested in more samples to determine where they belong in the tree. Listed 15 February 2012
• Page52.3 has been found derived in the current hg A-P262 WTY sample from the U of A. It is ancestral in A-L896 and in A-M13. Listed 15 February 2012.
• PK1 may be philogenically equivalent to BT. Listed 10 July 2012.
• Page10 may be philogenically equivalent to M144. Listed 10 July 2012.
• V139.1 and V141 are located at approximately M14. Listed 26 February 2013.
• L949, L950, L951, L952, L954, L955, L956, L958, L959, L961, L964, L965, L966, L973, L974, L975, and L976 are located at approximately P262. Listed 26 February 2013.
• PF825.1 is located at approximately V148. Listed 26 June 2013.

NOTES:

• Identical SNPs that were discovered separately are listed in alphabetical order, not necessarily in the order of discovery, and separated by "/". Examples: M29/P3/PN3, M276/P247 and M277/P248.
• PK1 (formerly A2) and M63 (formerly A3b2) were removed from the tree due to the uncertainty of their placement.
• A0 is being used to emphasize that this constitutes a haplogroup distinct from A1 and downstream clades, although for practical reasons, the letter A will still be used in its name, following the precedent of the addition of L0 and its subclades to the mtDNA phylogenetic tree. Listed 15 February 2012.
• There is some uncertainty about the position of M14, M29/P3/PN3, M71, M135, M141, M206, M276/P247, M277/P248, MEH1, P4, P5, P36.1, Page71, Page87, and Page95, since although they have been considered equivalent to M23 in the past, they have not yet been tested in the A2* sample in which V50, V82, etc, are derived and M23 is ancestral. Listed 15 February 2012.
• BT is shown on this tree, though it is not considered to be a part of Haplogroup A, in order to make it clear that, as a sibling clade with A1b1 and A1b2, BT and all other haplogroups are downstream of A1b. Listed 15 February 2012.
• 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 A contains lineages deriving from the earliest branching in the human Y chromosome tree. The oldest branching event, separating A0-P305 and A1-V161, is thought to have occurred about 140,000 years ago. Haplogroups A0-P305, A1a-M31 and A1b1a-M14 are restricted to Africa and A1b1b-M32 is nearly restricted to Africa. The haplogroup that would be named A1b2 is composed of haplogroups B through T. The internal branching of haplogroup A1-V161 into A1a-M31, A1b1, and BT (A1b2) may have occurred about 110,000 years ago. A0-P305 is found at low frequency in Central and West Africa. A1a-M31 is observed in northwestern Africans; A1b1a-M14 is seen among click language-speaking Khoisan populations. A1b1b-M32 has a wide distribution including Khoisan speaking and East African populations, and scattered members on the Arabian Peninsula.

References:

Batini et al, Signatures of the Preagricultural Peopling Processes in Sub-Saharan Africa as Revealed by the Phylogeography of Early Y Chromosome Lineages. (abstract) Molecular Biology and Evolution. 28 (9): 2603-2613, 2011.
Behar et al, Genome-Wide Structure of the Jewish People. Nature, 446:238-42, 2010.
Cinnioglu et al, Excavating Y-chromosome Haplotype Strata in Anatolia. (pdf) Human Genetics. 114:127-148, 2004.
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, 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.
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.
Francalacci et al, Low-Pass DNA Sequencing of 1200 Sardinians Reconstructs European Y-Chromosome Phylogeny. Science: Vol. 341 no. 6145, pp. 565-569, DOI: 10.1126/science.1237947, 2 August 2013.
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.
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.
Mohyuddin et al, Detection of Novel Y SNPs Provides Further Insights into Y Chromosomal Variation in Pakistan. Journal of Human Genetics, 2006.
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.
Schuster et al, Complete Khoisan and Bantu Genomes from Southern Africa. (abstract) Nature 463, 943-947, 18 February 2010.
Scozzari et al, An Unbiased Resource of Novel SNP Markers Provides a New Chronology for the Human Y Chromosome and Reveals a Deep Phylogenetic Structure in Africa, Genome Research, Vol. doi:10.1101/gr.160788.113, 2014.
Semino et al, Ethiopians and Khoisan Share the Deepest Clades of the Human Y-Chromosome Phylogeny. (pdf) American Journal of Human Genetics, 70:265-268, 2002.
Shen et al, Reconstruction of Patrilineages and Matrilineages of Samaritans and other Israeli Populations from Y-Chromosome and Mitochondrial DNA Sequence Variation. (pdf) Human Mutation, 24:248-260, 2004.
Valone et al, Y SNP Typing of African-American and Caucasian Samples Using Allele-Specific Hybridization and Primer Extension. (pdf) Journal of Forensic Science, 49:4, July 2004.

Additional Resources:
ISOGG Wiki - What you need to know about Genetic Genealogy.
Y Haplogroup A, Bonnie Schrack.
The African DNA Project (A), Dr. Ana Oquendo Pabon.

Corrections/Additions made since 1 January 2015:

• Added Experimental Composite Y-DNA Haplogroup A Tree by Ray Banks on 28 January 2015.
• Added Z12093 on 28 January 2015.

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