Human Y-chromosome DNA haplogroup explained

In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by mutations in the non-recombining portions of DNA from the male-specific Y chromosome (called Y-DNA). Many people within a haplogroup share similar numbers of short tandem repeats (STRs) and types of mutations called single-nucleotide polymorphisms (SNPs).[1]

The human Y-chromosome accumulates roughly two mutations per generation.[2] 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 humans are descended patrilineally. Y-chromosomal Adam is estimated to have lived roughly 236,000 years ago in Africa. By examining other bottlenecks most Eurasian men (men from populations outside of Africa) are descended from a man who lived in Africa 69,000 years ago (Haplogroup CT). Southeast Asia has been suggested as the origin for all non-African human Y chromosomes,[3] however, this has cited as being unlikely.[4] Other major bottlenecks occurred about 50,000 and 5,000 years ago and subsequently the ancestry of most Eurasian men can be traced back to four ancestors who lived 50,000 years ago, who were descendants of African (E-M168).[5] [6]

Naming convention

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.[7] [8] 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.[9]

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.[1] This inconsistency, and increasingly cumbersome longhand nomenclature, has prompted a move toward using the simpler shorthand nomenclature.

Phylogenetic structure

Phylogenetic tree of Y-DNA haplogroups [10]

Major Y-DNA haplogroups

Haplogroups A and B

Haplogroup A is the NRY (non-recombining Y) 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 CT (P143)

See main article: Haplogroup CT (Y-DNA). The defining mutations separating CT (all haplogroups except for A and B) are M168 and M294. The site of origin is likely in Africa. Its age has been estimated at approximately 88,000 years old,[11] [12] and more recently at around 100,000[13] or 101,000 years old.[14]

Haplogroup C (M130)

See main article: Haplogroup C (Y-DNA).

Haplogroup D (CTS3946)

See main article: Haplogroup D (Y-DNA).

See main article: Haplogroup D-M174.

Haplogroup E (M96)

See main article: Haplogroup E (Y-DNA).

Haplogroup F (M89)

See main article: Haplogroup F (Y-DNA). 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.[10] It also appears to have long been present in South East Asia; it 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.[15] [16] 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.[17]

Haplogroup G (M201)

See main article: Haplogroup G (Y-DNA).

Haplogroup G (M201) originated some 48,000 years ago and its most recent common ancestor likely lived 26,000 years ago in the Middle East. It spread to Europe with the Neolithic Revolution.

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.[18] [19]

G-M201 is also found in small numbers in northwestern China and India, Bangladesh, Pakistan, Sri Lanka, Malaysia, and North Africa.

Haplogroup H (M69)

See main article: Haplogroup H (Y-DNA). Haplogroup H (M69) probably emerged in Southern Central Asia, South Asia or West Asia, about 48,000 years BP, and remains largely prevalent there in the forms of H1 (M69) and H3 (Z5857). Its sub-clades are also found in lower frequencies in Iran, Central Asia, across the middle-east, and the Arabian peninsula.

However, H2 (P96) is present in Europe since the Neolithic and H1a1 (M82) spread westward in the Medieval era with the migration of the Roma people.

Haplogroup I (M170)

See main article: Haplogroup I (Y-DNA).

Haplogroup I (M170, M258) is found mainly in Europe and the Caucasus.

Haplogroup J (M304)

See main article: Haplogroup J (Y-DNA).

Haplogroup J (M304, S6, S34, S35) is found mainly in the Middle East, Caucasus and South-East Europe.

Haplogroup K (M9)

See main article: Haplogroup K (Y-DNA).

Haplogroup K (M9) is spread all over Eurasia, Oceania and among Native Americans.

K(xLT,K2a,K2b) – that is, K*, K2c, K2d or K2e – is found mainly in Melanesia, Aboriginal Australians, India, Polynesia and Island South East Asia.

Haplogroups L and T (K1)

See main article: Haplogroup LT.

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 Cushitic-speaking peoples), parts of South Asia, the Middle East, and the Mediterranean. T-M184 is also found in significant minorities of Sciaccensi, Stilfser, Egyptians, Omanis, Sephardi Jews,[20] Ibizans (Eivissencs), and Toubou. It is also found at low frequencies in other parts of the Mediterranean and South Asia.

Haplogroup K2 (K-M526)

See main article: Haplogroup K2. 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

See main article: Haplogroup K2a (Y-DNA).

Haplogroup N

See main article: Haplogroup N (Y-DNA).

Haplogroup N (M231) is found in northern Eurasia, especially among speakers of the Uralic languages.

Haplogroup N possibly originated in eastern Asia and spread both northward and westward into Siberia, being the most common group found in some Uralic-speaking peoples.

Haplogroup O

See main article: Haplogroup O (Y-DNA).

Haplogroup O (M175) is found with its highest frequency in East Asia and Southeast Asia, with lower frequencies in the South Pacific, Central Asia, South Asia, and islands in the Indian Ocean (e.g. Madagascar, the Comoros).

Haplogroups K2b1, M & S

See main article: Haplogroup K2b1 (Y-DNA).

No examples of the basal paragroup K2b1* have been identified. Males carrying subclades of K2b1 are found primarily among Papuan peoples, Micronesian peoples, indigenous Australians, and Polynesians.

Its primary subclades are two major haplogroups:

Haplogroup P (K2b2)

See main article: Haplogroup P (Y-DNA).

Haplogroup P (P295) has two primary branches: P1 (P-M45) and the extremely rare P2 (P-B253).[21]

P*, P1* and P2 are found together only on the island of Luzon in the Philippines.[21] In particular, P* and P1* are found at significant rates among members of the Aeta (or Agta) people of Luzon.[22] 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.[22] [23]

P1 is also the parent node of two primary clades:

Haplogroup Q (MEH2, M242, P36) found in Siberia and the AmericasHaplogroup R (M207, M306): found in Europe, West Asia, Central Asia, and South Asia

Haplogroup Q M242

See main article: Haplogroup Q (Y-DNA).

Q is defined by the SNP M242. It is believed to have arisen in Central Asia approximately 32,000 years ago.[24] [25] The subclades of Haplogroup Q with their defining mutation(s), according to the 2008 ISOGG tree[26] 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[27]

The 2008 ISOGG tree

Haplogroup R (M207)

See main article: Haplogroup R (Y-DNA).

Haplogroup R is defined by the SNP M207. The bulk of Haplogroup R is represented in the descendant subclade R1 (M173), which originated in Siberia. R1 has two descendant subclades: R1a and R1b.

R1a is associated with the proto-Indo-Iranian and Balto-Slavic peoples, and is now found predominantly in Central Asia, South Asia, and Eastern Europe.

Haplogroup R1b is the dominant haplogroup of Western Europe and is 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.

Chronological development of haplogroups

HaplogroupPossible time of originPossible place of originPossible TMRCA[33]
235,900[34] or 275,000 years ago[35] Africa[36] 235,900 years ago
130,700 years ago 88,000 years ago
88,000 or 101-100,000 years ago 68,500 years ago
65,200, 69,000,[37] or 73,000 years ago[38] 53,100 years ago
65,900 years ago 48,800 years ago
48,500 years ago 26,200 years ago
47,200 years ago 42,900 years ago
47,200 years ago 45,400 years ago
45,400 years ago 31,900 years ago
42,900 years ago[40] 31,600 years ago
42,900 years ago 27,500 years ago
E-M215 (E1b1b) 42,300 years ago 34,800 years ago
E-V38 (E1b1a) 42,300 years ago 40,100 years ago
36,800 years ago[41] 22,100 years ago
34,800 years ago[42] 24,100 years ago
31,900 years ago 28,200 years ago
J-M267 (J1) 31,600 years ago18,500 years ago
J-M172 (J2) 31,600 years ago 27,800 years ago[43]
R-M173 (R1)28,200 years ago 22,800 years ago
I-M253 (I1) 27,500 years ago 4,600 years ago
I-M438 (I2) 27,500 years ago[44] 21,800 years ago
R-M420 (R1a) 22,800 years ago[45] 18,300 years ago
R-M343 (R1b) 22,800 years ago[46] Eurasia[47] 20,400 years ago
I2-L460 (I2a) 21,800 years ago[48] 21,100 years ago
I2a-P37 21,100 years ago[49] 18,500 years ago
E1b1b-M78 19,800 years ago13,400 years ago
I2a-M423 18,500 years ago[50] 13,500 years ago
I2a-M223 17,400 years ago12,100 years ago
N1c-M178 14,200 years ago 11,900 years ago
R1a-M17 14,100 years ago[51] 8,500 years ago
R1b-M269 13,300 years ago 6,400 years ago[52]
E1b1b-V12 11,800 years ago 9,900 years ago
E-U175 (E1b1a8) 9,200 years ago 8,500 years ago
E1b1b-V13 8,100 years ago[53] Southern Europe4,800 years ago
E-M191 (E1b1a7) 7,400 years ago 6,400 years ago
E-U174 (E1b1a-U174) 6,400 years ago 5,300 years ago
R1b-L151 5,800 years ago 4,800 years ago
R1a-Z280 5,000 years ago 4,600 years ago[54]
R1a-M458 4,700 years ago 4,700 years ago

See also

References

Further reading

External links

Notes and References

  1. Web site: Understanding Haplogroups: How are the haplogroups named?. Family Tree DNA. 31 March 2013. dead. https://web.archive.org/web/20120621052330/http://www.familytreedna.com/understanding-haplogroups.aspx. 21 June 2012.
  2. Human mutation rate revealed. Nature. 2009. 18 September 2017. 10.1038/news.2009.864. Dolgin. Elie. free. "one mutation in every 30 million base pairs"
  3. Hallast . Pille . Agdzhoyan . Anastasia . Balanovsky . Oleg . Xue . Yali . Tyler-Smith . Chris . 2021 . A Southeast Asian origin for present-day non-African human Y chromosomes . Human Genetics . en . 140 . 2 . 299–307 . 10.1007/s00439-020-02204-9 . 0340-6717 . 32666166. 7864842 .
  4. Book: St. Clair, Michael . The Prehistory of Language: A Triangulated Y-Chromosome-Based Perspective . Genetic–Linguistic Interface . 2021 . 978-3-00-071045-2 . Stuttgart, Germany . 29 . en.
  5. Karmin . etal . 2015 . A recent bottleneck of Y chromosome diversity coincides with a global change in culture . . 25. 4. 459–66. 10.1101/gr.186684.114 . 25770088 . 4381518. "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."
  6. Web site: Something Weird Happened to Men 7,000 Years Ago, And We Finally Know Why . 31 May 2018 . Around 7000 years ago - all the way back in the Neolithic - something really peculiar happened to human genetic diversity. Over the next 2,000 years, and seen across Africa, Europe and Asia, the genetic diversity of the Y chromosome collapsed, becoming as though there was only one man for every 17 women..
  7. Web site: Understanding Results: Y-DNA Single Nucleotide Polymorphism (SNP): What is a Y-chromosome DNA (Y-DNA) haplogroup?. Family Tree DNA. Y-chromosome DNA (Y-DNA) haplogroups are the major branches on the human paternal family tree. Each haplogroup has many subbranches. These are subclades.. 31 March 2013.
  8. Web site: myFTDNA 2.0 User Guide: Y-DNA: What is the Y-DNA – Matches page?. Family Tree DNA. A terminal SNP determines the terminal (final) subbranch on the Y-DNA Tree to which someone belongs.. 31 March 2013.
  9. Web site: Understanding Results: Y-DNA Single Nucleotide Polymorphism (SNP): How are haplogroups and their subclades named?. Family Tree DNA. 31 March 2013.
  10. Web site: ISOGG 2015 Y-DNA Haplogroup Tree Trunk. Copyright 2015 ISOGG. isogg.org.
  11. Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations. Annu. Rev. Genet. . 2007 . 41. 1. 539–64 . 10.1146/annurev.genet.41.110306.130407 . Underhill and Kivisild . 18076332 . Kivisild . T .
  12. 10.1101/gr.7172008 . 18385274 . 2008 . Karafet . TM . Mendez . FL . Meilerman . MB . Underhill . PA . Zegura . SL . Hammer . MF . New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree . 18 . 5 . 830–38 . Genome Research . 2336805.
  13. Kamin M, Saag L, Vincente M, et al. . A recent bottleneck of Y chromosome diversity coincides with a global change in culture . Genome Research . 25 . 4 . 459–66 . April 2015 . 25770088 . 4381518 . 10.1101/gr.186684.114 .
  14. Haber M, Jones AL, Connel BA, Asan, Arciero E, Huanming Y, Thomas MG, Xue Y, Tyler-Smith C . A Rare Deep-Rooting D0 African Y-chromosomal Haplogroup and its Implications for the Expansion of Modern Humans Out of Africa . Genetics . 212 . 4 . 1421–28 . June 2019 . 31196864 . 6707464 . 10.1534/genetics.119.302368 .
  15. Chiaroni . Jacques . Underhill . Peter A. . Cavalli-Sforza . Luca L. . 1 December 2009 . 10.1073/pnas.0910803106 . 19920170 . 2787129 . 106 . 48 . Y chromosome diversity, human expansion, drift, and cultural evolution . . 20174–79. 2009PNAS..10620174C . free .
  16. 10.1038/jhg.2014.62 . 59 . 9 . Isolation, contact and social behavior shaped genetic diversity in West Timor . Journal of Human Genetics . 494–503 . Tumonggor . Meryanne K . 25078354 . 4521296 . 2014.
  17. This was, for instance, the case with the original subclade F3 (M96), which has since been renamed Haplogroup H2.
  18. 10.1038/sj.ejhg.5200834 . Passarino . Giuseppe . Cavalleri . Gianpiero L . Lin . Alice A . vanc. Cavalli-Sforza. 2002 . LL . Børresen-Dale . AL . Underhill . PA . Different genetic components in the Norwegian population revealed by the analysis of mtDNA and Y chromosome polymorphisms . . 10 . 9. 521–29 . 12173029 . free .
  19. 10.1038/sj.ejhg.5201651 . 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 . 16724001 . free .
  20. 10.1002/ajpa.21154 . 19918998 . 141 . 3 . Phylogeographic analysis of paternal lineages in NE Portuguese Jewish communities . American Journal of Physical Anthropology . 373–81 . Nogueiro . Inês . 2009. free .
  21. http://isogg.org/tree/ISOGG_HapgrpP.html ISOGG, 2016, Y-DNA Haplogroup P and its Subclades – 2016
  22. Tumonggor. Meryanne K. Karafet. Tatiana M. Downey. Sean. Lansing. J Stephen. Norquest. Peter. Sudoyo. Herawati. Hammer. Michael F. Cox. Murray P. Isolation, contact and social behavior shaped genetic diversity in West Timor. Journal of Human Genetics. 31 July 2014. 59. 9. 494–503. 10.1038/jhg.2014.62. 25078354. 4521296.
  23. Tatiana M Karafet. 2015. Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia. European Journal of Human Genetics. 23. 3. 369–73. etal. 10.1038/ejhg.2014.106. 24896152. 4326703.
  24. Fagundes . Nelson J.R. . Kanitz . Ricardo . Eckert . Roberta . Valls . Ana C.S. . Bogo . Mauricio R. . Salzano . Francisco M. . Smith . David Glenn . Silva . Wilson A. . Zago . Marco A. . Ribeiro-dos-Santos . Andrea K. . Santos . Sidney E.B. . Petzl-Erler . Maria Luiza . Maria Luiza Petzl-Erler . Bonatto . Sandro L. . 2008 . Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas . dead . American Journal of Human Genetics . 82 . 3 . 583–92 . 10.1016/j.ajhg.2007.11.013 . 2427228 . 18313026 . https://web.archive.org/web/20090325120035/http://www.familytreedna.com/pdf/Fagundes-et-al.pdf . 2009-03-25 . 2013-05-22 . 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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  30. Wen B, Li H, Lu D. etal . Genetic evidence supports demic diffusion of Han culture . Nature . 431 . 7006 . 302–05 . September 2004 . 15372031 . 10.1038/nature02878 . 2004Natur.431..302W . 4301581 .
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