Human Y-chromosome DNA haplogroup
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In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by mutations in the non-recombining portions of DNA from the Y chromosome (called Y-DNA). Mutations that are shared by many people are called single-nucleotide polymorphisms (SNPs).
The human Y-chromosome accumulates roughly two mutations per generation. Y-DNA haplogroups represent major branches of the Y-chromosome phylogenetic tree that share hundreds or even thousands of mutations unique to each haplogroup.
The Y-chromosomal most recent common ancestor (Y-MRCA, informally known as Y-chromosomal Adam) is the most recent common ancestor (MRCA) from whom all currently living men are descended patrilineally. Y-chromosomal Adam is estimated to have lived roughly 236,000 years ago in Africa. By examining other bottlenecks all Eurasian men are descended from a man who lived 69,000 years ago. Another major bottleneck occurred about 5,000 years ago and subsequently most Eurasian men can trace their ancestry back to a dozen ancestors who lived 5,000 years ago.
- 1 Naming convention
- 2 Phylogenetic structure
- 3 Major Y-DNA haplogroups
- 3.1 Haplogroups A & B
- 3.2 Haplogroup CT (P143)
- 3.3 Haplogroup C (M130)
- 3.4 Haplogroup D (M174)
- 3.5 Haplogroup E (M96)
- 3.6 Haplogroup F (M89)
- 3.7 Haplogroup G (M201)
- 3.8 Haplogroup H (M69)
- 3.9 Haplogroup I (M170)
- 3.10 Haplogroup J (M304)
- 3.11 Haplogroup K (M9)
- 3.12 Haplogroups L & T (K1)
- 3.13 Haplogroup K2 (K-M526)
- 3.14 Haplogroups K2a, K2a1, NO & NO1
- 3.15 Haplogroup N
- 3.16 Haplogroup O
- 3.17 Haplogroups K2b1, M & S
- 3.18 Haplogroup P (K2b2)
- 3.19 Haplogroup Q M242
- 3.20 Haplogroup R (M207)
- 4 Chronological development of haplogroups
- 5 See also
- 6 References
- 7 Further reading
- 8 External links
Y-DNA haplogroups are defined by the presence of a series of Y-DNA SNP markers. Subclades are defined by a terminal SNP, the SNP furthest down in the Y-chromosome phylogenetic tree. The Y Chromosome Consortium (YCC) developed a system of naming major Y-DNA haplogroups with the capital letters A through T, with further subclades named using numbers and lower case letters (YCC longhand nomenclature). YCC shorthand nomenclature names Y-DNA haplogroups and their subclades with the first letter of the major Y-DNA haplogroup followed by a dash and the name of the defining terminal SNP.
Y-DNA haplogroup nomenclature is changing over time to accommodate the increasing number of SNPs being discovered and tested, and the resulting expansion of the Y-chromosome phylogenetic tree. This change in nomenclature has resulted in inconsistent nomenclature being used in different sources. This inconsistency, and increasingly cumbersome longhand nomenclature, has prompted a move towards using the simpler shorthand nomenclature. In September 2012, Family Tree DNA provided the following explanation of its changing Y-DNA haplogroup nomenclature to individual customers on their Y-DNA results pages (note that the haplogroup mentioned below relates to a specific individual):
Long time customers of Family Tree DNA have seen the YCC-tree of Homo Sapiens evolve over the past several years as new SNPs have been discovered. Sometimes these new SNPs cause a substantial change in the "longhand" explanation of your terminal Haplogroup. Because of this confusion, we introduced a shorthand version a few years ago that lists the branch of the tree and your terminal SNP, i.e. J-L147, in lieu of J1c3d. Therefore, in the very near term, Family Tree DNA will discontinue showing the current "longhand" on the tree and we will focus all of our discussions around your terminal defining SNP.
This changes no science – it just provides an easier and less confusing way for us all to communicate.
Major Y-DNA haplogroups
Haplogroups A & B
Haplogroup A is the NRY macrohaplogroup from which all modern paternal haplogroups descend. It is sparsely distributed in Africa, being concentrated among Khoisan populations in the southwest and Nilotic populations toward the northeast in the Nile Valley. BT is a subclade of haplogroup A; more precisely of the A1b clade (A2-T in Cruciani et al. 2011), as follows:
- Haplogroup A
Haplogroup CT (P143)
- Haplogroup DE (M1, M145, M203)
- Haplogroup CF (P143)
Haplogroup C (M130)
- Haplogroup C (M130, M216) Found in Asia, Oceania, and North America
- Haplogroup C1 (F3393/Z1426)
- Haplogroup C1a (CTS11043)
- Haplogroup C1b (F1370, Z16480)
- Haplogroup C1b1 (AM00694/K281)
- Haplogroup C1b2 (B477/Z31885)
- Haplogroup C2 (M217, P44) Found throughout Eurasia and North America, but especially among Mongols, Kazakhs, Tungusic peoples, Paleosiberians, and Na-Dené-speaking peoples
- Haplogroup C1 (F3393/Z1426)
Haplogroup D (M174)
- Haplogroup D (M174) Found in Japan, China (especially Tibet), the Andaman Islands
- D1 (CTS11577)
- D1a (Z27276, Z27283, Z29263)
- Haplogroup D1b (M55, M57, M64.1, M179, P12, P37.1, P41.1 (M359.1), 12f2.2) Found mainly in Japan
- D2 (L1366, L1378, M226.2) Found in Mactan Island, Philippines
- D1 (CTS11577)
Haplogroup E (M96)
- Haplogroup E (M40, M96) Found in Africa and parts of Middle East and Europe
- Haplogroup E1 (P147)
- Haplogroup E1a (M33, M132) formerly E1
- Haplogroup E1b (P177)
- Haplogroup E2 (M75)
- Haplogroup E1 (P147)
Haplogroup F (M89)
The groups descending from haplogroup F are found in some 90% of the world's population, but almost exclusively outside of sub-Saharan Africa.
F xG,H,I,J,K is rare in modern populations and peaks in South Asia, especially Sri Lanka. It also appears to have long been present in South East Asia. has been reported at rates of 4–5% in Sulawesi and Lembata. One study, which did not comprehensively screen for other subclades of F-M89 (including some subclades of GHIJK), found that Indonesian men with the SNP P14/PF2704 (which is equivalent to M89), comprise 1.8% of men in West Timor, 1.5% of Flores 5.4% of Lembata 2.3% of Sulawesi and 0.2% in Sumatra. F* (F xF1,F2,F3) has been reported among 10% of males in Sri Lanka and South India, 5% in Pakistan, as well as lower levels among the Tamang people (Nepal), and in Iran. F1 (P91), F2 (M427) and F3 (M481; previously F5) are all highly rare and virtually exclusive to regions/ethnic minorities in Sri Lanka, India, Nepal, South China, Thailand, Burma, and Vietnam. In such cases, however, the possibility of misidentification is considered to be relatively high and some may belong to misidentified subclades of Haplogroup GHIJK.
Haplogroup G (M201)
It is found in many ethnic groups in Eurasia; most common in the Caucasus, Iran, Anatolia and the Levant. Found in almost all European countries, but most common in Gagauzia, southeastern Romania, Greece, Italy, Spain, Portugal, Tyrol, and Bohemia with highest concentrations on some Mediterranean islands; uncommon in Northern Europe.
- Haplogroup G1
- Haplogroup G2
Haplogroup H (M69)
Haplogroup H (M69) probably emerged in South Asia, about 48,000 years BP, and remains prevalent there, in the forms of H1 (M69) and H3 (Z5857).
Haplogroup I (M170)
- Haplogroup I1 (M253) Found mainly in northern Europe
- Haplogroup I2 (P215) Found mainly in southeast Europe and Sardinia save for I2B1 (m223) which is primarily found in Western, Central, and Northern Europe.
Haplogroup J (M304)
- Haplogroup J* (J-M304*) is rare outside the island of Socotra.
- Haplogroup J1 (M267) is associated with Northeast Caucasian peoples in Dagestan and Semitic languages speaking people in the Middle East, Ethiopia, and North Africa and also found in Mediterranean Europe in smaller frequencies much like haplogroup T.
- Haplogroup J2 (M172) is found mainly in the Semitic-speaking peoples, Anatolia, Greece, the Balkans, Italy, Iran, South/Central Asia and the Caucasus.
Haplogroup K (M9)
Haplogroups L & T (K1)
Haplogroup L (M20) is found in South Asia, Central Asia, South-West Asia, and the Mediterranean.
Haplogroup T (M184, M70, M193, M272) is found at high levels in the Horn of Africa (mainly Afro-Asiatic-speaking peoples), parts of South Asia, the Middle East, and the Mediterranean. T-M184 is also found in significant minorities of Sciaccensi, Stilfser, Fulbe, Egyptians, Omanis, Sephardi Jews, Ibizans (Eivissencs), and Toubou. It is also found at low frequencies in other parts of the Mediterranean and South Asia.
Haplogroup K2 (K-M526)
The only living males reported to carry the basal paragroup K2* are indigenous Australians. Major studies published in 2014 and 2015 suggest that up to 27% of Aboriginal Australian males carry K2*, while others carry a subclade of K2.
Haplogroups K2a, K2a1, NO & NO1
Haplogroup N possibly originated in eastern Asia and spread both west into Siberia and north, being the most common group found in some Uralic speaking peoples. Haplogroup O is found at its highest frequency in East Asia and Southeast Asia, with lower frequencies in the South Pacific, Central Asia, and South Asia.
Haplogroup O (M175) is found in East Asia, Southeast Asia, and the South Pacific.
- Haplogroup O1 (F265/M1354, CTS2866, F75/M1297, F429/M1415, F465/M1422)
- Haplogroup O1a (M119, CTS31, F589/Page20, L246, L466) Found in eastern and southern China, Taiwan, and Southeast Asia, especially among Austronesian and Tai–Kadai peoples
- Haplogroup O1b (P31, M268)
- Haplogroup O2 (M122) Found throughout East Asia, Southeast Asia, and Austronesia including Polynesia
Haplogroups K2b1, M & S
Its primary subclades are two major haplogroups:
- Haplogroup S (B254) also known as K2b1a: found in the highlands of Papua New Guinea and;
- Haplogroup M (P256) also known as K2b1b: found in New Guinea and Melanesia.
Haplogroup P (K2b2)
P*, P1* and P2 are found together only on the island of Luzon, in The Philippines. In particular, P* and P1* are found at significant rates among members of the Aeta (or Agta) people of Luzon. While, P1* is now more common among living individuals in Eastern Siberia and Central Asia, it is also found at low levels in mainland South East Asia and South Asia. Considered together, these distributions tend to suggest that P* emerged from K2b in South East Asia.
P1 is also the parent node of two primary clades:
- Haplogroup Q (Q-M242) and;
- Haplogroup R (R-M207). These share the common marker M45 in addition to at least 18 other SNPs.
Haplogroup Q M242
Q is defined by the SNP M242. It is believed to have arisen in Central Asia approximately 32,000 years ago. The subclades of Haplogroup Q with their defining mutation(s), according to the 2008 ISOGG tree are provided below. ss4 bp, rs41352448, is not represented in the ISOGG 2008 tree because it is a value for an STR. This low frequency value has been found as a novel Q lineage (Q5) in Indian populations
The 2008 ISOGG tree
- Q (M242)
- Q1 (P36.2)
- Q1a (MEH2)
- Q1a1 (M120, M265/N14) Found with low frequency among Dungans, Han Chinese, Hazaras, Japanese, Koreans, and Tibetans
- Q1a2 (M25, M143) Found at low to moderate frequency among some populations of Southwest Asia, Central Asia, and Siberia
- Q1a3 (M346)
- Q1a4 (P48)
- Q1a5 (P89)
- Q1a6 (M323) Found in a significant minority of Yemeni Jews
- Q1b (M378) Found at low frequency among samples of Hazara and Sindhis
Haplogroup R (M207)
Haplogroup R is defined by the SNP M207. The bulk of Haplogroup R is represented in descendant subclade R1, which likely originated on the Eurasian Steppes. R1 has two descendant subclades: R1a and R1b.
Haplogroup R1b is the dominant haplogroup of Western Europe and also found sparsely distributed among various peoples of Asia and Africa. Its subclade R1b1a2 (M269) is the haplogroup that is most commonly found among modern Western European populations, and has been associated with the Italo-Celtic and Germanic peoples.
- Haplogroup R1 (M173) Found throughout western Eurasia
- Haplogroup R2 (M124) Found in South Asia, Caucasus, Central Asia, and Eastern Europe
Chronological development of haplogroups
|Haplogroup||Possible time of origin||Possible place of origin||Possible TMRCA|
|A00||235,900 years ago||Africa||235,900 years ago|
|BT||130,700 years ago||Africa||88,000 years ago|
|CT||88,000 years ago||Africa||68,500 years ago|
|F||65,900 years ago||Eurasia||48,800 years ago|
|E||65,200 years ago||East Africa or Asia||53,100 years ago|
|G||48,500 years ago||Middle East||26,200 years ago|
|IJ||47,200 years ago||Middle East||42,900 years ago|
|K||47,200 years ago||Asia||45,400 years ago|
|P||45,400 years ago||Asia||31,900 years ago|
|J||42,900 years ago||Middle East||31,600 years ago|
|I||42,900 years ago||Europe||27,500 years ago|
|E-M215 (E1b1b)||42,400 years ago||East Africa||34,800 years ago|
|N||36,800 years ago||Asia||22,100 years ago|
|E1b1b-M35||34,800 years ago||East Africa||24,100 years ago|
|R||31,900 years ago||Asia||28,200 years ago|
|J-M267 (J1)||31,600 years ago||Middle East||18,500 years ago|
|J-M172 (J2)||31,600 years ago||Middle East||27,800 years ago|
|R-M173 (R1)||28,200 years ago||Asia||22,800 years ago|
|I-M253 (I1)||27,500 years ago||Europe||4,600 years ago|
|I-M438 (I2)||27,500 years ago||Europe||21,800 years ago|
|R-M420 (R1a)||22,800 years ago||Eurasia||18,300 years ago|
|R-M343 (R1b)||22,800 years ago||Eurasia||20,400 years ago|
|I2-L460 (I2a)||21,800 years ago||Europe||21,100 years ago|
|I2a-P37||21,100 years ago||Europe||18,500 years ago|
|E1b1b-M78||19,800 years ago||Northeast Africa||13,400 years ago|
|I2a-M423||18,500 years ago||Europe||13,500 years ago|
|I2a-M223||17,400 years ago||Europe||12,100 years ago|
|N1c-M178||14,200 years ago||Asia||11,900 years ago|
|R1a-M17||14,100 years ago||Eastern Europe||8,500 years ago|
|R1b-M269||13,300 years ago||Eastern Europe||6,400 years ago|
|E1b1b-V12||11,800 years ago||North Africa||9,900 years ago|
|E1b1b-V13||7,600 years ago||Middle East||5,100 years ago|
|R1b-L151||5,800 years ago||Eastern Europe||4,800 years ago|
|R1a-Z280||5,000 years ago||Eastern Europe||4,600 years ago|
|R1a-M458||4,700 years ago||Eastern Europe||4,700 years ago|
- Y-chromosome haplogroups in populations of the world
- Y-DNA haplogroups in populations of Europe
- Genetic history of Europe
- List of Y-DNA single-nucleotide polymorphisms
- List of Y-STR markers
- Human mitochondrial DNA haplogroups
- * (haplogroup)
- Molecular phylogeny
- Genetic genealogy
- Genealogical DNA test
- Conversion table for Y chromosome haplogroups
|Phylogenetic tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]|
|A00||A0-T [χ 3]|
|A0||A1 [χ 4]|
|I||J||LT [χ 5]||K2|
|L||T [χ 6]||K2a [χ 7]||K2b [χ 8]||K2c||K2d||K2e [χ 9]|
|K2a1||K2b1 [χ 10]||P [χ 11]|
|NO||S [χ 12]||M [χ 13]||P1||P2|
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- Karmin; et al. (2015). "A recent bottleneck of Y chromosome diversity coincides with a global change in culture". Genome Research. 25 (4): 459–66. doi:10.1101/gr.186684.114. PMC . PMID 25770088. "we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males."
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Y-chromosome DNA (Y-DNA) haplogroups are the major branches on the human paternal family tree. Each haplogroup has many subbranches. These are subclades.
- "myFTDNA 2.0 User Guide: Y-DNA: What is the Y-DNA – Matches page?". Family Tree DNA. Retrieved 31 March 2013.
A terminal SNP determines the terminal (final) subbranch on the Y-DNA Tree to which someone belongs.
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- "Family Tree DNA – Genetic Testing for Ancestry, Family History & Genealogy". familytreedna.com.
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- Chuan-Chao Wang; Li Hui (2014-05-03). "Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates". bioRxiv .
- Karafet, TM; Mendez, FL; Meilerman, MB; Underhill, PA; Zegura, SL; Hammer, MF (2008). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Research. 18 (5): 830–38. doi:10.1101/gr.7172008. PMC . PMID 18385274.
- Chiaroni, Jacques; Underhill, Peter A.; Cavalli-Sforza, Luca L. (1 December 2009). "Y chromosome diversity, human expansion, drift, and cultural evolution". Proceedings of the National Academy of Sciences of the United States of America. 106 (48): 20174–79. doi:10.1073/pnas.0910803106. PMC . PMID 19920170.
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- This was, for instance, the case with the original subclade F3 (M96), which has since been renamed Haplogroup H2.
- Passarino G, Cavalleri GL, Lin AA, Cavalli-Sforza LL, Børresen-Dale AL, Underhill PA (2002). "Different genetic components in the Norwegian population revealed by the analysis of mtDNA and Y chromosome polymorphisms". European Journal of Human Genetics. 10 (9): 521–29. doi:10.1038/sj.ejhg.5200834. PMID 12173029.
- Karlsson, Andreas O; Wallerström, Thomas; Götherström, Anders; Holmlund, Gunilla (2006). "Y-chromosome diversity in Sweden – A long-time perspective". European Journal of Human Genetics. 14 (8): 963–70. doi:10.1038/sj.ejhg.5201651. PMID 16724001.
- Nogueiro, Inês (2009). "Phylogeographic analysis of paternal lineages in NE Portuguese Jewish communities". American Journal of Physical Anthropology. 141: 373–81. doi:10.1002/ajpa.21154.
- ISOGG, 2016, Y-DNA Haplogroup P and its Subclades – 2016 (20 June 2016).
- Tumonggor, Meryanne K; Karafet, Tatiana M; Downey, Sean; Lansing, J Stephen; Norquest, Peter; Sudoyo, Herawati; Hammer, Michael F; Cox, Murray P (31 July 2014). "Isolation, contact and social behavior shaped genetic diversity in West Timor". Journal of Human Genetics. 59 (9): 494–503. doi:10.1038/jhg.2014.62. PMC . PMID 25078354.
- Tatiana M Karafet; et al. (2015). "Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia" (PDF). European Journal of Human Genetics. 23: 369–73. doi:10.1038/ejhg.2014.106. PMC . PMID 24896152.
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Since the first studies, it has been found that extant Native American populations exhibit almost exclusively five "mtDNA haplogroups" (A–D and X)6 classified in the autochthonous haplogroups A2, B2, C1, D1, and X2a.7 Haplogroups A–D are found all over the New World and are frequent in Asia, supporting a northeastern Asian origin of these lineages
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- "Y-DNA Haplogroup Tree 2010". International Society of Genetic Genealogy. Retrieved July 2010. Check date values in:
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- Underhill et al
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- "Y-Haplogroup A Phylogenetic Tree". March 2013. Retrieved 30 March 2013. (chart highlighting new branches added to the A phylotree in March 2013)
|Wikimedia Commons has media related to Human Y-DNA haplogroups.|
- ISOGG Y-DNA Haplogroup Tree
- FTDNA (2008) Y-Chromosome Phylogenetic Tree
- Chart of the speed of different Y chromosomal STR mutation rates
- Map of Y Haplogroups
- Atlas of the Human Journey, from the Genographic Project, National Geographic
- DNA Heritage's Y-haplogroup map
- Video tutorial on Discovering Paternal Ancestry with Y-Chromosomes
- Haplogroup Predictor
- Semino O, Passarino G, Oefner PJ, et al. (November 2000). "The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective". Science. 290 (5494): 1155–9. doi:10.1126/science.290.5494.1155. PMID 11073453. As PDF Paper that defined "Eu" haplogroups
- Y-DNA Haplogroup and Sub-clade Projects
- Kerchner's YDNA Haplogroup Descriptions, Projects & Links
- Y-DNA Testing Company STR Marker Comparison Chart
- Y-DNA Ethnographic and Genographic Atlas and Open-Source Data Compilation
- Y Chromosome Consortium