Human Y-chromosome DNA haplogroup

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Dominant Y-chromosome haplogroups in pre-colonial world populations, with possible migration routes according to the Coastal Migration Model.
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In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by differences in the non-recombining portions of DNA from the Y chromosome (called Y-DNA). It represents human genetic diversity based on single-nucleotide polymorphisms (SNPs) on the Y chromosome.[1]

Y-DNA haplogroups represent major branches of the Y-chromosome phylogenetic tree. Y-chromosomal Adam is the name given by researchers to the patrilineal most recent common ancestor of all living humans at the root of this tree. Estimates of the date when Y-chromosomal Adam lived have varied significantly in different studies. Archaeological and genetic data suggest that the source populations of Paleolithic humans survived the glacial maxima (including the LGM) and human Y-DNA haplogroups emerged in sparsely wooded refugia, and dispersed through areas of high primary productivity while avoiding dense forest cover.[2]

Naming convention

Schematic illustration of Y-DNA haplogroups naming convention. Haplogroups are defined through mutations (SNPs).

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.[3][4] 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.[5]

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 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):[6]

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.

— 

Bennett Greenspan, Family Tree DNA
Dr. Michael F. Hammer, University of Arizona

Phylogenetic structure

Phylogenetic tree of Y-DNA haplogroups [7]
Y-DNA Adam

Major Y-DNA haplogroups

Haplogroups A & B

Using fast evolving SNPs, haplogroup A is the macrohaplogroup from which all modern paternal haplogroups descend. It is sparsely distributed in Africa. BT is a subclade of haplogroup A; more precisely of A1b (A2-T in Cruciani et al. 2011), as follows:

Haplogroup CT (P143)

Main article: Haplogroup CT (Y-DNA)

The defining mutations separating CT (all haplogroups excepting A and B) are M168 and M294. The site of origin is unknown and currently debated at this time; either occurring in Asia or Africa, approximately 70,000 years ago.[8]

Subclades:

  • Haplogroup CF (P143) Found outside of Africa, throughout Eurasia, Oceania, and the Americas
    • C-M130
    • F-M89
  • Haplogroup DE (M1, M145, M203) ca. 65 ka
    • D-M174
    • E-M96

Haplogroup C (M130)

Haplogroup F (M89)

Main article: Haplogroup F (Y-DNA)
The diversion of Haplogroup F and its descendants.

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.[7] 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.[9][10] 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.[11]

Haplogroup D (M174)

Haplogroup E (M96)

Haplogroup G (M201)

Haplogroup G (M201) originated in the Middle East or further east – possibly even the Wardak region of Afghanistan some 30,000 years BP. 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.[12][13]

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

Haplogroup H (M69)

Main article: Haplogroup H (Y-DNA)

Haplogroup H (M69) probably emerged in South Asia, about 30,000 to 40,000 years BP, and remains prevalent there, in the forms of H1 (M69) and H3 (Z5857).

However, H2 (P96) has been present in Europe since the Neolithic and H1a1 (M82) spread westward in the Medieval era with the migration of the Romani.

Haplogroup I (M170)

Main article: Haplogroup I (Y-DNA)

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

  • 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)

Main article: Haplogroup J (Y-DNA)

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

Haplogroup K (M9)

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 & T (K1)

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 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,[14] and Ibizans (Eivissencs). It is also found at low frequencies in other parts of the Mediterranean and South Asia.

Haplogroup K2 (K-M526)

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

Main article: Haplogroup K2a

Haplogroup N

Main article: Haplogroup N (Y-DNA)

Haplogroup N (M231) is found through northern Eurasia, especially among the Uralic peoples.

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

Main article: Haplogroup O (Y-DNA)

Haplogroup O (M175) is found in East Asia, Southeast Asia, and the South Pacific.

Haplogroups K2b1, M & S

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)

Main article: Haplogroup P (Y-DNA)

Haplogroup P (P295) has two primary branches: P1 (P-M45) and the extremely rare P2 (P-B253).[15]

P*, P1* and P2 are found together only on the island of Luzon, in The Philippines.[15] In particular, P* and P1* are found at significant rates among members of the Aeta (or Agta) people of Luzon.[16] 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.[16][17]

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

Haplogroup Q M242

Main article: Haplogroup Q (Y-DNA)

Q is defined by the SNP M242. It is believed to have arisen in Central Asia approximately 17,000 to 22,000 years ago.[18][19] The subclades of Haplogroup Q with their defining mutation(s), according to the 2008 ISOGG tree[20] 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[21]

The 2008 ISOGG tree

Haplogroup R (M207)

Main article: Haplogroup R (Y-DNA)
The divergence of Haplogroup R and its descendants.

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.

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

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.

Chronological development of haplogroups

Haplogroup Possible time of origin Possible place of origin Possible TMRCA[25][8]
A00 192–307,000 years ago
E 50-55,000 years ago[8][26] East Africa[27] or Asia[9] 27-59,000 years ago
F 38-56,000 years ago
IJ 30-46,000 years ago
K 40-54,000 years ago
E-M215 (E1b1b) 31-46,000 years ago[28] 39-55,000 years ago
P 27-41,000 years ago
J 19-44,500 years ago[29]
R 20-34,000 years ago
I 15-30,000 years ago
R-M173 (R1) 13-26,000 years ago
I-M438 (I2) 28-33,000 years ago[30] 16,000-20,000 years ago
E-M35 20,000-30,000 years ago[28] 15–21,000 years ago
J-M267 (J1) 15-34,000[29] years ago
R-M420 (R1a) 22,000 years ago[31] 8-10,000 years ago
R-M343 (R1b) 22,000 years ago[32] West Asia[33]
N at least 21,000 years ago (STR age)[34]
I-M253 (I1) 11-21,000[35] or 28-33,000 years ago[30] 3-5,000 years ago
J-M172 (J2) 15,000-22,000[29] years ago 19-24,000 years ago[36]
E-M78 15-20,000[28] or 17,500-20,000 years ago[37] Northeast Africa[37] at least 17,000 years ago[37]
E-V12 12,500-18,000 years ago[37]
R-M17 13 ,000[31] or 18,000 years ago[38] Eurasia
I-L460 (I2a) present 13,000 years ago[39]
I-M223 11-18,000 years ago[35]
E-V13 7-17,000 years ago[37] West Asia[37] 4,000-4,700 years ago (Europe)
6,800-17,000 years ago (Asia)[37]
R-Z280 11-14,000 years ago[40]
N-M46 (N1c1) at least 12,000 years ago (STR age)[34]
R-M458 11,000 years ago[40]
I-P37 6-16,000,[35] present 10,000 years ago[41]
I-M423 (I2a1b) present 10,000 years ago[41]
I-M26 (I2a1a) 2-17,000,[35] present 8,000 years ago[41]
R-M269 5,500-8,000 years ago[42]
R-L11, R-S116 3-5,000 years ago

See also

References

  1. ^ a b "Understanding Haplogroups: How are the haplogroups named?". Family Tree DNA. Retrieved 31 March 2013.
  2. ^ Gavashelishvili, A.; Tarkhnishvili, D. (2016). "Biomes and human distribution during the last ice age". Global Ecology and Biogeography. 25: 563–574. doi:10.1111/geb.12437.
  3. ^ "Understanding Results: Y-DNA Single Nucleotide Polymorphism (SNP): What is a Y-chromosome DNA (Y-DNA) haplogroup?". Family Tree DNA. Retrieved 31 March 2013. Y-chromosome DNA (Y-DNA) haplogroups are the major branches on the human paternal family tree. Each haplogroup has many subbranches. These are subclades.
  4. ^ "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.
  5. ^ "Understanding Results: Y-DNA Single Nucleotide Polymorphism (SNP): How are haplogroups and their subclades named?". Family Tree DNA. Retrieved 31 March 2013.
  6. ^ "Family Tree DNA - Genetic Testing for Ancestry, Family History & Genealogy". familytreedna.com.
  7. ^ a b Copyright 2015 ISOGG. "ISOGG 2015 Y-DNA Haplogroup Tree Trunk". isogg.org.{{cite web}}: CS1 maint: numeric names: authors list (link)
  8. ^ a b c 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): 830–8. doi:10.1101/gr.7172008. PMC 2336805. PMID 18385274.
  9. ^ a b 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): 20174–9. doi:10.1073/pnas.0910803106. PMC 2787129. PMID 19920170.
  10. ^ Tumonggor, Meryanne K (2014). "Isolation, contact and social behavior shaped genetic diversity in West Timor". Journal of Human Genetics. 59: 494–503. doi:10.1038/jhg.2014.62. PMC 4521296. PMID 25078354.
  11. ^ This was, for instance, the case with the original subclade F3 (M96), which has since been renamed Haplogroup H2.
  12. ^ Passarino, Giuseppe; Cavalleri, Gianpiero L; Lin, Alice A; 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): 521–529. doi:10.1038/sj.ejhg.5200834. PMID 12173029. {{cite journal}}: Unknown parameter |name-list-format= ignored (|name-list-style= suggested) (help)
  13. ^ 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): 963–970. doi:10.1038/sj.ejhg.5201651. PMID 16724001.
  14. ^ Nogueiro, Inês (2009). "Phylogeographic analysis of paternal lineages in NE Portuguese Jewish communities". American Journal of Physical Anthropology. 141: 373–381. doi:10.1002/ajpa.21154.
  15. ^ a b ISOGG, 2016, Y-DNA Haplogroup P and its Subclades – 2016 (20 June 2016).
  16. ^ a b 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 4521296. PMID 25078354.
  17. ^ 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: 369–373. doi:10.1038/ejhg.2014.106. PMC 4326703. PMID 24896152.
  18. ^ Fagundes, Nelson J.R.; Ricardo Kanitz; Roberta Eckert; Ana C.S. Valls; Mauricio R. Bogo; Francisco M. Salzano; David Glenn Smith; Wilson A. Silva; Marco A. Zago; Andrea K. Ribeiro-dos-Santos; Sidney E.B. Santos; Maria Luiza Petzl-Erler; Sandro L.Bonatto (2008). "Mitochondrial Population Genomics Supports a Single Pre-Clovis Origin with a Coastal Route for the Peopling of the Americas" (pdf). American Journal of Human Genetics. 82 (3): 583–592. doi:10.1016/j.ajhg.2007.11.013. PMC 2427228. PMID 18313026. 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
  19. ^ Zegura, S. L.; Karafet, TM; Zhivotovsky, LA; Hammer, MF (2003). "High-Resolution SNPs and Microsatellite Haplotypes Point to a Single, Recent Entry of Native American Y Chromosomes into the Americas" (PDF). Molecular Biology and Evolution. 21 (1): 164–75. doi:10.1093/molbev/msh009. PMID 14595095.
  20. ^ "Y-DNA Haplogroup Tree 2010". International Society of Genetic Genealogy. Retrieved July 2010. {{cite web}}: Check date values in: |accessdate= (help)
  21. ^ Sharma, Swarkar; Rai, Ekta; Bhat, Audesh K; Bhanwer, Amarjit S; Bamezaicorresponding, Rameshwar NK (2007). "A novel subgroup Q5 of human Y-chromosomal haplogroup Q in India". BMC Evol Biol. 7: 232. doi:10.1186/1471-2148-7-232. PMC 2258157. PMID 18021436.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  22. ^ Wen B, Li H, Lu D, et al. (September 2004). "Genetic evidence supports demic diffusion of Han culture" (Supplementary Table 2: NRY haplogroup distribution in Han populations). Nature. 431 (7006): 302–305. doi:10.1038/nature02878. PMID 15372031. {{cite journal}}: External link in |format= (help)
  23. ^ Wells RS, Yuldasheva N, Ruzibakiev R, et al. (August 2001). "The Eurasian heartland: a continental perspective on Y-chromosome diversity" (Table 1: Y-chromosome haplotype frequencies in 49 Eurasian populations, listed according to geographic region). Proc. Natl. Acad. Sci. U.S.A. 98 (18): 10244–9. doi:10.1073/pnas.171305098. PMC 56946. PMID 11526236. {{cite journal}}: External link in |format= (help)
  24. ^ Bortolini MC, Salzano FM, Thomas MG, et al. (September 2003). "Y-chromosome evidence for differing ancient demographic histories in the Americas". Am. J. Hum. Genet. 73 (3): 524–39. doi:10.1086/377588. PMC 1180678. PMID 12900798.
  25. ^ TMRCA
  26. ^ Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature 505, 87–91 (02 January 2014)
  27. ^ Semino, Ornella; Magri, Chiara; Benuzzi, Giorgia; Lin, Alice A.; Al-Zahery, Nadia; Battaglia, Vincenza; MacCioni, Liliana; Triantaphyllidis, Costas; et al. (2004). "Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area". The American Journal of Human Genetics. 74 (5): 1023–34. doi:10.1086/386295. PMC 1181965. PMID 15069642.
  28. ^ a b c Trombetta et al. 2015, Phylogeographic refinement and large scale genotyping of human Y chromosome haplogroup E provide new insights into the dispersal of early pastoralists in the African continent
  29. ^ a b c Semino, O; Magri, C; Benuzzi, G; et al. (May 2004). "Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area". Am. J. Hum. Genet. 74: 1023–34. doi:10.1086/386295. PMC 1181965. PMID 15069642. {{cite journal}}: Explicit use of et al. in: |last4= (help)
  30. ^ a b P.A. Underhill, N.M. Myres, S. Rootsi, C.T. Chow, A.A. Lin, R.P. Otillar, R. King, L.A. Zhivotovsky, O. Balanovsky, A. Pshenichnov, K.H. Ritchie, L.L. Cavalli-Sforza, T. Kivisild, R. Villems, S.R. Woodward, New Phylogenetic Relationships for Y-chromosome Haplogroup I: Reappraising its Phylogeography and Prehistory, in P. Mellars, K. Boyle, O. Bar-Yosef and C. Stringer (eds.), Rethinking the Human Evolution (2007), pp. pp. 33-42.
  31. ^ a b Sharma et al
  32. ^ ftDNA
  33. ^ Myres2010
  34. ^ a b http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066102
  35. ^ a b c d Rootsi, Siiri; et al. (2004). "Phylogeography of Y-Chromosome Haplogroup I Reveals Distinct Domains of Prehistoric Gene Flow in Europe" (PDF). American Journal of Human Genetics. 75: 128–137. doi:10.1086/422196. PMC 1181996. PMID 15162323.
  36. ^ "TMRCAs of major haplogroups in Europe estimated using two methods. : Large-scale recent expansion of European patrilineages shown by population resequencing : Nature Communications : Nature Publishing Group". www.nature.com. Retrieved 2015-05-20.
  37. ^ a b c d e f g Cruciani, F.; La Fratta, R.; Trombetta, B.; Santolamazza, P.; Sellitto, D.; Colomb, E. B.; Dugoujon, J.-M.; Crivellaro, F.; et al. (2007), "Tracing Past Human Male Movements in Northern/Eastern Africa and Western Eurasia: New Clues from Y-Chromosomal Haplogroups E-M78 and J-M12", Molecular Biology and Evolution, 24 (6): 1300–1311, doi:10.1093/molbev/msm049, PMID 17351267 Also see Supplementary Data
  38. ^ [1]
  39. ^ [2]
  40. ^ a b Underhill et al
  41. ^ a b c http://www.ancestraljourneys.org/mesolithicdna.shtml
  42. ^ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021592

Further reading

External links

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