Human Y-chromosome DNA haplogroup

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Human Y-DNA phylogeny and haplogroup distribution.[1] *(a) Phylogenetic tree. 'kya' means 'thousand years ago'. *(b) Geographical distributions of each haplogroups are shown in color. *(c) Geographical color legend.

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).[2]

The human Y-chromosome accumulates roughly two mutations per generation.[3] 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(E-M168).[citation needed] 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 descendendant of African (E-M168).[4][5][6][clarification needed]

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.[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.[2] 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):[10]

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.

Phylogenetic structure[]

Migraciones humanas en haplogrupos de ADN-Y.PNG

Phylogenetic tree of Y-DNA haplogroups [11]

Y-Chromosomal Adam

Haplogroup A

BT

Haplogroup B

CT
DE

Haplogroup D

Haplogroup E

CF

Haplogroup C

F

Haplogroup G

HIJK

Haplogroup H

IJK
IJ

Haplogroup I

Haplogroup J

K
LT

Haplogroup L

Haplogroup T

MNOPS
NO

Haplogroup N

Haplogroup O

MPS
MS

Haplogroup S

Haplogroup M

P

Haplogroup Q

Haplogroup R

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 A
    • Haplogroup A00
    • Haplogroup A0 (formerly also A1b)
    • Haplogroup A1 (also A1a-T)
      • Haplogroup A1a (M31)
      • Haplogroup A1b (also A2-T; P108, V221)
        • Haplogroup A1b1a1 (also A2; M14)
        • Haplogroup A1b1b (also A3; M32)
        • Haplogroup BT (M91, M42, M94, M139, M299)
          • Haplogroup B (M60)
          • Haplogroup CT

Haplogroup CT (P143)[]

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,[12][13] and more recently at around 100,000[14] or 101,000 years old.[15]

Haplogroup C (M130)[]

  • Haplogroup C (M130, M216) Found in Asia, Oceania, and North America
    • Haplogroup C1 (F3393/Z1426)
      • Haplogroup C1a (CTS11043)
      • Haplogroup C1b (F1370, Z16480)
        • Haplogroup C1b1 (AM00694/K281)
          • Haplogroup C1b1a (B66/Z16458)
            • (M356) Found with low frequency in South Asia, Southwest Asia, and northern China
            • Haplogroup C1b1a2 (B65)
              • Haplogroup C1b1a2a (B67) Found among Lebbo' people in Borneo, Indonesia
              • Haplogroup C1b1a2b (F725) Found among Han Chinese (Guangdong, Hunan, and Shaanxi), Dai people (Yunnan), Murut people (Brunei), Malay people (Singapore), and Aeta people (Philippines)
            • Haplogroup C1b1a3 (Z16582) Found with low frequency in Saudi Arabia and Iraq
          • Haplogroup C1b1b (B68) Found among Dusun people (Brunei)
        • Haplogroup C1b2 (C-Z16582)
        • Haplogroup C1b3 (B477/Z31885)
    • Haplogroup C2 (M217, P44) Found throughout Eurasia and North America, but especially among Mongols, Kazakhs, Tungusic peoples, Paleosiberians, and Na-Dené-speaking peoples

Haplogroup D (CTS3946)[]

  • Haplogroup D (CTS3946)

Haplogroup E (M96)[]

  • Haplogroup E (M40, M96) Found in Africa and parts of the Middle East and Europe
    • Haplogroup E1 (P147)
      • Haplogroup E1a (M33, M132) formerly E1
      • Haplogroup E1b (P177)
        • Haplogroup E1b1 (P2, DYS391p); formerly E3
          • Haplogroup E1b1a (V38)
            • Haplogroup E1b1a1 (M2) Found in Africa, especially among Niger–Congo-speaking populations.; formerly E3a
            • Haplogroup E1b1a2 (M329) Found in Africa, especially in Ethiopia among Omotic-speaking populations.; formerly E3*
          • Haplogroup E1b1b (M215)
            • Haplogroup E1b1b1 (M35) Found in Horn of Africa, North Africa, the Middle East, and Europe (especially in areas near the Mediterranean and the Balkans); formerly E3b
    • Haplogroup E2 (M75)

Haplogroup F (M89)[]

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.[11] 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.[16][17] 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.[18]

Haplogroup G (M201)[]

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.[19][20]

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

  • Haplogroup G1
  • Haplogroup G2
      • Haplogroup G2a1
        • Haplogroup G2a3a
          • Haplogroup G2a3b1
      • Haplogroup G2b
      • Haplogroup G2c (formerly Haplogroup G5)

Haplogroup H (M69)[]

Haplogroup H (M69) probably emerged in or South 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)[]

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)[]

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

Haplogroup K (M9)[]

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)[]

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

Haplogroup K2 (K-M526)[]

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[]

Haplogroup N[]

Haplogroup N (M231) is found through 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[]

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[]

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 S (B254) also known as K2b1a: found in the highlands of Papua New Guinea and;
  • Haplogroup M (P256) also known as K2b1b: found in New Guinea and Melanesia.

Haplogroup P (K2b2)[]

Haplogroup P (P295) has two primary branches: P1 (P-M45) and the extremely rare (P-B253).[22]

P*, P1* and P2 are found together only on the island of Luzon in the Philippines.[22] In particular, P* and P1* are found at significant rates among members of the Aeta (or Agta) people of Luzon.[23] 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.[23][24]

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[]

Q is defined by the SNP M242. It is believed to have arisen in Central Asia approximately 32,000 years ago.[25][26] The subclades of Haplogroup Q with their defining mutation(s), according to the 2008 ISOGG tree[27] 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[28]

The 2008 ISOGG tree

Haplogroup R (M207)[]

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 descendant subclade R1 (M173), 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.

  • Haplogroup R1 (M173) Found throughout western Eurasia
    • Haplogroup R1a (M420) Found in Central Asia, South Asia, and Central, Northern and Eastern Europe, Balkans
    • Haplogroup R1b (M343) Found in Western Europe, West Asia, Central Asia, North Africa, and northern Cameroon
  • Haplogroup R2 (M124) Found in South Asia, Caucasus, Central Asia, and Eastern Europe

Chronological development of haplogroups[]

Haplogroup Possible time of origin Possible place of origin Possible TMRCA[34][13]
A00 235,900[5] or 275,000 years ago[35] Africa[36] 235,900 years ago
BT 130,700 years ago[5] Africa 88,000 years ago
CT 88,000[5] or 101-100,000 years ago[14][15] Africa 68,500 years ago
E 65,200,[5] 69,000,[37] or 73,000 years ago[38] East Africa[39] or Asia[16] 53,100 years ago
F 65,900 years ago[5] Eurasia 48,800 years ago
G 48,500 years ago[5] Middle East 26,200 years ago
IJ 47,200 years ago[5] Middle East 42,900 years ago
K 47,200 years ago[5] Asia 45,400 years ago
P 45,400 years ago[5] Asia 31,900 years ago
J 42,900 years ago[5][40] Middle East 31,600 years ago
I 42,900 years ago[5] Europe 27,500 years ago
E-M215 (E1b1b) 42,300 years ago[5][41] East Africa 34,800 years ago
E-V38 (E1b1a) 42,300 years ago[5][41] East Africa 40,100 years ago
N 36,800 years ago[5][42] Asia 22,100 years ago
E1b1b-M35 34,800 years ago[5][41] East Africa 24,100 years ago
R 31,900 years ago[5] Asia 28,200 years ago
J-M267 (J1) 31,600 years ago[5][40] Middle East 18,500 years ago
J-M172 (J2) 31,600 years ago[5][40] Middle East 27,800 years ago[5][43]
R-M173 (R1) 28,200 years ago[5] Asia 22,800 years ago
I-M253 (I1) 27,500 years ago[5][44][45] Europe 4,600 years ago
I-M438 (I2) 27,500 years ago[5][45] Europe 21,800 years ago
R-M420 (R1a) 22,800 years ago[5][46] Eurasia 18,300 years ago
R-M343 (R1b) 22,800 years ago[5][47] Eurasia[48] 20,400 years ago
I2-L460 (I2a) 21,800 years ago[5][49] Europe 21,100 years ago
I2a-P37 21,100 years ago[5][44][50] Europe 18,500 years ago
E1b1b-M78 19,800 years ago[5][41][51] Northeast Africa[51] 13,400 years ago[5][51]
I2a-M423 18,500 years ago[5][50] Europe 13,500 years ago
I2a-M223 17,400 years ago[5] Europe 12,100 years ago
N1c-M178 14,200 years ago[5][42] Asia 11,900 years ago
R1a-M17 14,100 years ago[5][46][52] Eastern Europe 8,500 years ago
R1b-M269 13,300 years ago[5] Eastern Europe 6,400 years ago[53]
E1b1b-V12 11,800 years ago[5][51] North Africa 9,900 years ago
(E1b1a8) 9,200 years ago[5][41] East Africa 8,500 years ago
E1b1b-V13 8,100 years ago[5][51] Southern Europe 4,800 years ago
(E1b1a7) 7,400 years ago[5][41] East Africa 6,400 years ago
(E1b1a-U174) 6,400 years ago[5][41] East Africa 5,300 years ago
R1b-L151 5,800 years ago[5] Eastern Europe 4,800 years ago
R1a-Z280 5,000 years ago[5] Eastern Europe 4,600 years ago[54]
R1a-M458 4,700 years ago[5] Eastern Europe 4,700 years ago[54]

See also[]

Phylogenetic tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]
"Y-chromosomal Adam"
A00 A0-T [χ 3]
A0 A1 [χ 4]
A1a
BT
B CT
DE CF
D E C F
     GHIJK
G HIJK
IJK H
IJ K
I   J     LT [χ 5]       K2 [χ 6]
L     T    K2a [χ 7]        K2b [χ 8]            [χ 9]  
K-M2313 [χ 10]     K2b1 [χ 11] P [χ 12]
NO   S [χ 13]  M [χ 14]    P1     
N O Q R

References[]

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  18. ^ This was, for instance, the case with the original subclade F3 (M96), which has since been renamed Haplogroup H2.
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  25. ^ 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): 583–92. doi:10.1016/j.ajhg.2007.11.013. PMC 2427228. PMID 18313026. Archived from the original (PDF) on 2009-03-25. Retrieved 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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