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Human Y-chromosome DNA haplogroup

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This article is about the human Y-DNA haplogroup. For the human mtDNA haplogroup, see Human mitochondrial DNA haplogroup.

Human Y-DNA phylogeny and haplogroup distribution.[1](a) Phylogenetic tree. 'kya' means 'thousand years ago'. (b) Geographical distributions of haplogroups are shown in color. (c) Geographical color legend.
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In human genetics, a human Y-chromosome DNA haplogroup is a haplogroup defined by specific mutations in the non-recombining portions of DNA on the male-specific Y chromosome (Y-DNA). Individuals within a haplogroup share similar numbers of short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs).[2] The Y-chromosome accumulates approximately two mutations per generation,[3] and Y-DNA haplogroups represent significant branches of the Y-chromosome phylogenetic tree, each characterized by hundreds or even thousands of unique mutations.

The Y-chromosomal most recent common ancestor (Y-MRCA), often referred to as Y-chromosomal Adam, is the most recent common ancestor from whom all currently living humans are descended patrilineally. Y-chromosomal Adam is estimated to have lived around 236,000 years ago in Africa[citation needed]. By examining other population bottlenecks, most Eurasian men trace their descent from a man who lived in Africa approximately 69,000 years ago (Haplogroup CT). Although Southeast Asia has been proposed as the origin for all non-African human Y chromosomes,[4] this hypothesis is considered unlikely.[5] Other bottlenecks occurred roughly 50,000 and 5,000 years ago, and the majority of Eurasian men are believed to be descended from four ancestors who lived 50,000 years ago, all of whom were descendants of an African lineage (Haplogroup E-M168).[6][7][8]

Naming convention

[edit]
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 single-nucleotide polymorphisms genetic markers. Subclades are defined by a terminal SNP, the SNP furthest down in the Y-chromosome phylogenetic tree.[9][10] 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.[11]

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.[2] This inconsistency, and increasingly cumbersome longhand nomenclature, has prompted a move toward using the simpler shorthand nomenclature.[12]

Phylogenetic structure

[edit]
Migration route of Human Y-chromosome DNA haplogroups.
Phylogenetic tree of Y-DNA haplogroups [13]

Y-chromosomal Adam

Major Y-DNA haplogroups

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Haplogroups A and B

[edit]

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)

[edit]
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,[14][15] and more recently at around 100,000[16] or 101,000 years old.[17]

Haplogroup C (M130)

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Main article: Haplogroup C (Y-DNA)

Haplogroup D (CTS3946)

[edit]
Main article: Haplogroup D (Y-DNA)

Haplogroup E (M96)

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Main article: Haplogroup E (Y-DNA)

Haplogroup F (M89)

[edit]
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.[13] 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.[18][19] 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.[20]

Haplogroup G (M201)

[edit]
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.[21][22]

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

Haplogroup H (M69)

[edit]
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)

[edit]
Main article: Haplogroup I (Y-DNA)

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

  • Haplogroup I1 Nordid/Nordic Europids (M253) Found mainly in northern Europe
  • Haplogroup I2 Dinarid/Dinaric Europids (P215) Found mainly in Balkans, southeast Europe and Sardinia save for I2B1 (m223) which is found at a moderate frequency 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, Caucasus and South-East Europe.

Haplogroup K (M9)

[edit]
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)

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

Haplogroup K2 (K-M526)

[edit]
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

[edit]
Main article: Haplogroup K2a (Y-DNA)

Haplogroup N

[edit]
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

[edit]
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

[edit]
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)

[edit]
Main article: Haplogroup P (Y-DNA)

Haplogroup P (P295) has two primary branches: P1 (P-M45) and the extremely rare P2 (P-B253).[24]

P*, P1* and P2 are found together only on the island of Luzon in the Philippines.[24] In particular, P* and P1* are found at significant rates among members of the Aeta (or Agta) people of Luzon.[25] 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.[25][26]

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

[edit]
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.[27][28] The subclades of Haplogroup Q with their defining mutation(s), according to the 2008 ISOGG tree[29] 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[30]

The 2008 ISOGG tree

Haplogroup R (M207)

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

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

[edit]
Haplogroup Possible time of origin Possible place of origin Possible TMRCA[36][15]
A00 235,900[7] or 275,000 years ago[37] Africa[38] 235,900 years ago
BT 130,700 years ago[7] Africa 88,000 years ago
CT 88,000[7] or 101-100,000 years ago[16][17] Africa 68,500 years ago
E 65,200,[7] 69,000,[39] or 73,000 years ago[40] East Africa[41] or Asia[18] 53,100 years ago
F 65,900 years ago[7] Eurasia 48,800 years ago
G 48,500 years ago[7] Middle East 26,200 years ago
IJ 47,200 years ago[7] Middle East 42,900 years ago
K 47,200 years ago[7] Asia 45,400 years ago
P 45,400 years ago[7] Asia 31,900 years ago
J 42,900 years ago[7][42] Middle East 31,600 years ago
I 42,900 years ago[7] Europe 27,500 years ago
E-M215 (E1b1b) 42,300 years ago[7][43] East Africa 34,800 years ago
E-V38 (E1b1a) 42,300 years ago[7][43] East Africa 40,100 years ago
N 36,800 years ago[7][44] Asia 22,100 years ago
E1b1b-M35 34,800 years ago[7][43] East Africa 24,100 years ago
R 31,900 years ago[7] Asia 28,200 years ago
J-M267 (J1) 31,600 years ago[7][42] Middle East 18,500 years ago
J-M172 (J2) 31,600 years ago[7][42] Middle East 27,800 years ago[7][45]
R-M173 (R1) 28,200 years ago[7] Asia 22,800 years ago
I-M253 (I1) 27,500 years ago[7][46][47] Europe 4,600 years ago
I-M438 (I2) 27,500 years ago[7][47] Europe 21,800 years ago
R-M420 (R1a) 22,800 years ago[7][48] Eurasia 18,300 years ago
R-M343 (R1b) 22,800 years ago[7][49] Eurasia[50] 20,400 years ago
I2-L460 (I2a) 21,800 years ago[7][51] Europe 21,100 years ago
I2a-P37 21,100 years ago[7][46][52] Europe 18,500 years ago
E1b1b-M78 19,800 years ago[7][43][53] Northeast Africa[53] 13,400 years ago[7][53]
I2a-M423 18,500 years ago[7][52] Europe 13,500 years ago
I2a-M223 17,400 years ago[7] Europe 12,100 years ago
N1c-M178 14,200 years ago[7][44] Asia 11,900 years ago
R1a-M17 14,100 years ago[7][48][54] Eastern Europe 8,500 years ago
R1b-M269 13,300 years ago[7] Eastern Europe 6,400 years ago[55]
E1b1b-V12 11,800 years ago[7][53] North Africa 9,900 years ago
E-U175 (E1b1a8) 9,200 years ago[7][43] East Africa 8,500 years ago
E1b1b-V13 8,100 years ago[7][53] Southern Europe 4,800 years ago
E-M191 (E1b1a7) 7,400 years ago[7][43] East Africa 6,400 years ago
E-U174 (E1b1a-U174) 6,400 years ago[7][43] East Africa 5,300 years ago
R1b-L151 5,800 years ago[7] Eastern Europe 4,800 years ago
R1a-Z280 5,000 years ago[7] Eastern Europe 4,600 years ago[56]
R1a-M458 4,700 years ago[7] Eastern Europe 4,700 years ago[56]

See also

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References

[edit]
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  3. ^ Dolgin, Elie (2009). "Human mutation rate revealed". Nature. doi:10.1038/news.2009.864. Retrieved 18 September 2017. "one mutation in every 30 million base pairs"
  4. ^ 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. 140 (2): 299–307. doi:10.1007/s00439-020-02204-9. ISSN 0340-6717. PMC 7864842. PMID 32666166.
  5. ^ St. Clair, Michael (2021). The Prehistory of Language: A Triangulated Y-Chromosome-Based Perspective. Stuttgart, Germany: Genetic–Linguistic Interface. p. 29. ISBN 978-3-00-071045-2.
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  10. ^ "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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  20. ^ This was, for instance, the case with the original subclade F3 (M96), which has since been renamed Haplogroup H2.
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Further reading

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