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.

Lua error in package.lua at line 80: module 'strict' not found. 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

File:Molecular lineage haplogroups.png
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]

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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

Haplogroup A00



Haplogroup A0



Haplogroup A1a



Haplogroup A1b1

BT

Haplogroup B

CT
DE

Haplogroup D


Haplogroup E


CF

Haplogroup C

F

Haplogroups F*, F1, F2, F3

GHIJK

Haplogroup G

HIJK

Haplogroup H

IJK
IJ

Haplogroup I


Haplogroup J


K

K*

LT (K1)

Haplogroup L


Haplogroup T


K2

K2*

NO

Haplogroup N


Haplogroup O


K2b

Haplogroup K2b1 – includes major haplogroups S and M


Haplogroup P (K2b2)















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)

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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.

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)

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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)

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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.

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Haplogroup I (M170)

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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)

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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)

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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)

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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)

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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.

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Haplogroups K2a, K2a1, NO & NO1

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Main article: Haplogroup K2a

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Haplogroup N

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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

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Main article: Haplogroup O (Y-DNA)

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

Haplogroups K2b1, M & S

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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:

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Haplogroup P (K2b2)

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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

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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)

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Main articles: Haplogroup R (Y-DNA) and 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] India
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


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. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  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. ↑ 1.0 1.1 Lua error in package.lua at line 80: module 'strict' not found.
  2. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  3. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  4. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  5. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  6. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  7. ↑ 7.0 7.1 Lua error in package.lua at line 80: module 'strict' not found.
  8. ↑ 8.0 8.1 8.2 Lua error in package.lua at line 80: module 'strict' not found.
  9. ↑ 9.0 9.1 Lua error in package.lua at line 80: module 'strict' not found.
  10. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  11. ↑ This was, for instance, the case with the original subclade F3 (M96), which has since been renamed Haplogroup H2.
  12. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  13. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  14. ↑ http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21154/abstract
  15. ↑ 15.0 15.1 ISOGG, 2016, Y-DNA Haplogroup P and its Subclades – 2016 (20 June 2016).
  16. ↑ 16.0 16.1 Lua error in package.lua at line 80: module 'strict' not found.
  17. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  18. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  19. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  20. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  21. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  22. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  23. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  24. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  25. ↑ TMRCA
  26. ↑ Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature 505, 87–91 (02 January 2014)
  27. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  28. ↑ 28.0 28.1 28.2 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. ↑ 29.0 29.1 29.2 Semino et al 2004
  30. ↑ 30.0 30.1 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. ↑ 31.0 31.1 Sharma et al
  32. ↑ ftDNA
  33. ↑ Myres2010
  34. ↑ 34.0 34.1 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066102
  35. ↑ 35.0 35.1 35.2 35.3 Lua error in package.lua at line 80: module 'strict' not found.
  36. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  37. ↑ 37.0 37.1 37.2 37.3 37.4 37.5 37.6 Lua error in package.lua at line 80: module 'strict' not found. Also see Supplementary Data
  38. ↑ [1]
  39. ↑ [2]
  40. ↑ 40.0 40.1 Underhill et al
  41. ↑ 41.0 41.1 41.2 http://www.ancestraljourneys.org/mesolithicdna.shtml
  42. ↑ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021592

Further reading

  • Lua error in package.lua at line 80: module 'strict' not found.
  • Lua error in package.lua at line 80: module 'strict' not found. (chart highlighting new branches added to the A phylotree in March 2013)

External links

Template:Y-chromosome haplogroups by population

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