Human Y-chromosome DNA haplogroup

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 (incl. 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

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

Major Y-DNA haplogroups

Major Y-chromosome haplogroups include:[7]

Tree view

Y─ DNA Adam

Haplogroup A00

Haplogroup A0

Haplogroup A1a

Haplogroup A1b1


BT

Haplogroup B


CT
DE

Haplogroup D

Haplogroup E



CF

Haplogroup C


F

Haplogroups F*, F1-F3

Haplogroup G

Haplogroup H


IJK
IJ

Haplogroup I

Haplogroup J



K

K*


LT (K1)

Haplogroup L

Haplogroup T



K2

Haplogroups K1-K3

Haplogroup M


NO

Haplogroup N

Haplogroup O



P

Haplogroup Q

Haplogroup R

Haplogroup S















Groups A and B

Haplogroup A is the African macrohaplogroup from which all modern haplogroups descend. BT is a subclade of haplogroup A, more precisely of A1b (A2-T in Cruciani et al. 2011), as follows:

Groups with mutation M168 (CT)

Main article: Haplogroup CT (Y-DNA)

The defining mutations separating CT (all haplogroups excepting A and B) are M168 and M294. These mutations predate the "Out of Africa" migration. The defining mutations of DE probably occurred in Northeastern Africa some 65,000 years ago.[8] The P143 mutation that defines Haplogroup CF may have occurred at that time, bringing modern humans to the southern coast of Asia.

Groups descended from Haplogroup F (G, H, IJ & K)

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. The mutation of IJ corresponds to a wave of migration out of the Middle East or South Asia some 45 ka that subsequently spread into Europe (Cro-Magnon). Haplogroup G originated in the Middle East or perhaps further east as far as Wardak region of Afghanistan some 30 ka, and spread to Europe with the Neolithic Revolution. Haplogroup H probably occurred in India some 30-40 ka, and remains prevalent there, spreading westwards in historical times with the Romani migration. Haplogroup K spread widely to Eurasia, Australia and the South Pacific.

Groups descended from Haplogroup K (M9)

Haplogroup L is mainly found in South Asia. Haplogroup M is most prevalent in Melanesia. The NO haplogroup appeared ca. 35-40 ka in Asia. Haplogroup N probably originated in Southeast Asia and spread north into Siberia and west, being the most common group found in Uralic 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 P gave rise to groups Q and R, and is rarely found in its undifferentiated stage. It probably originated in Central Asia or the Altai region. Haplogroup Q also originated in Central Asia, migrating east to North America.

Groups descended from Haplogroup NO (M214)

The NO haplogroup appeared ca. 35-40 ka in eastern Asia. 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.

Groups descended from Haplogroup P (M45)

Haplogroup P (M45) has two branches. They are Q-M242 and R-M207, which share the common marker M45 in addition to at least 18 other SNPs.

Haplogroup Q

Q is defined by the SNP M242. It is believed to have arisen in Central Asia approximately 17,000 to 22,000 years ago.[11][12] The subclades of Haplogroup Q with their defining mutation(s), according to the 2008 ISOGG tree[13] 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[14]

The 2008 ISOGG tree

Haplogroup R

The diversion 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.

Chronological development of haplogroups

Haplogroup Possible time of origin Possible place of origin Possible TMRCA[18][19]
A00 192–307,000 years ago
E 50-55,000 years ago[20][21]East Africa[22] or Asia[23] 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[24] 39-55,000 years ago
P 27-41,000 years ago
J 19-44,500 years ago[25]
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[26] 16,000-20,000 years ago
E-M35 20,000-30,000 years ago[24] 15–21,000 years ago
J-M267 (J1) 15-34,000[25] years ago
R-M420 (R1a) 22,000 years ago[27] 8-10,000 years ago
R-M343 (R1b) 22,000 years ago[28] West Asia[29]
N at least 21,000 years ago (STR age)[30]
I-M253 (I1) 11-21,000[31] or 28-33,000 years ago[26] 3-5,000 years ago
J-M172 (J2) 15,000-22,000[25] years ago 19-24,000 years ago[32]
E-M78 15-20,000[24] or 17,500-20,000 years ago[33] Northeast Africa[33] at least 17,000 years ago[33]
E-V12 12,500-18,000 years ago[33]
R-M17 13 ,000[27] or 18,000 years ago[34] India
I-L460 (I2a) present 13,000 years ago[35]
I-M223 11-18,000 years ago[31]
E-V13 7-17,000 years ago[33] West Asia[33] 4,000-4,700 years ago (Europe)
6,800-17,000 years ago (Asia)[33]
R-Z280 11-14,000 years ago[36]
N-M46 (N1c1) at least 12,000 years ago (STR age)[37]
R-M458 11,000 years ago[38]
I-P37 6-16,000,[31] present 10,000 years ago[39]
I-M423 (I2a1b) present 10,000 years ago[39]
I-M26 (I2a1a) 2-17,000,[31] present 8,000 years ago[39]
R-M269 5,500-8,000 years ago[40]
R-L11, R-S116 3-5,000 years ago

See also

Evolutionary tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]
"Y-chromosomal Adam"
A00 A0-T [χ 3]
A0 A1[χ 4]
A1a A1b
A1b1 BT
B CT
DE CF
D E C F
F1 F2 F3 GHIJK
G HIJK
H IJK
IJ K
I J LT [χ 5]  K2
L T NO [χ 6] K2b [χ 7]   K2c K2d K2e [χ 8]
N O K2b1 [χ 9]    P
M S [χ 10] Q R
  1. ↑ Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation 35 (2): 187–91. doi:10.1002/humu.22468. PMID 24166809.
  2. ↑ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
  3. ↑ Haplogroup A0-T is also known as A0'1'2'3'4.
  4. ↑ Haplogroup A1 is also known as A1'2'3'4.
  5. ↑ Haplogroup LT (L298/P326) is also known as Haplogroup K1.
  6. ↑ Haplogroup NO (M214) is also known as Haplogroup K2a (although the present Haplogroup K2e was also previously known as "K2a").
  7. ↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
  8. ↑ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a, also known as Haplogroup NO).
  9. ↑ Haplogroup K2b1 (P397/P399) is similar to the former Haplogroup MS, but has a broader and more complex internal structure.
  10. ↑ Haplogroup S (S-M230) was previously known as Haplogroup K5.

References

  1. 1 2 "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. 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. ↑ Copyright 2015 ISOGG. "ISOGG 2015 Y-DNA Haplogroup Tree Trunk". isogg.org.
  8. ↑ 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. ↑ 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): 521–529. doi:10.1038/sj.ejhg.5200834. PMID 12173029.
  10. ↑ 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.
  11. ↑ 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
  12. ↑ 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.
  13. ↑ "Y-DNA Haplogroup Tree 2010". International Society of Genetic Genealogy. Retrieved July 2010.
  14. ↑ 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.
  15. ↑ 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.
  16. ↑ 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.
  17. ↑ 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.
  18. ↑ TMRCA
  19. ↑ 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.
  20. ↑ Karafet, T. M.; Mendez, F. L.; Meilerman, M. B.; Underhill, P. A.; Zegura, S. L.; Hammer, M. F. (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.
  21. ↑ Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature 505, 87–91 (02 January 2014)
  22. ↑ 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.
  23. ↑ Chiaroni, J.; Underhill, P. A.; Cavalli-Sforza, L. L. (2009). "Y chromosome diversity, human expansion, drift, and cultural evolution". Proceedings of the National Academy of Sciences 106 (48): 20174–9. doi:10.1073/pnas.0910803106. PMC 2787129. PMID 19920170.
  24. 1 2 3 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
  25. 1 2 3 Semino et al 2004
  26. 1 2 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.
  27. 1 2 Sharma et al
  28. ↑ ftDNA
  29. ↑ Myres2010
  30. ↑ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066102
  31. 1 2 3 4 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.
  32. ↑ "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.
  33. 1 2 3 4 5 6 7 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
  34. ↑ [ https://books.google.com/books?id=3QYRAgAAQBAJ&pg=PT7&lpg=PT7&dq=r1a1+age&source=bl&ots=rnNgdeyfqa&sig=u4UdzEFjIJvd78mpb0BS609wnq4&hl=en&sa=X&ved=0ahUKEwjuyZj64sDMAhXFEywKHSdWAxUQ6AEIWDAJ#v=onepage&q=r1a1%20age&f=false]
  35. ↑
  36. ↑ Underhill et al
  37. ↑ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066102
  38. ↑ Underhill et al
  39. 1 2 3 http://www.ancestraljourneys.org/mesolithicdna.shtml
  40. ↑ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021592

Further reading

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