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 mutations in the non-recombining portions of DNA from the Y chromosome (called Y-DNA). These mutations are commonly called single-nucleotide polymorphisms (SNPs).[1]

The human Y-chromosome accumulates roughly 2 mutations per generation.[2] Y-DNA haplogroups represent major branches of the Y-chromosome phylogenetic tree that share hundreds or even thousands of mutations unique to each haplogroup.

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.[3]

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 SNP markers. Subclades are defined by a terminal SNP, the SNP furthest down in the Y-chromosome phylogenetic tree.[4][5] 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.[6]

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):[7]

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[edit]

Phylogenetic tree of Y-DNA haplogroups [8]
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[edit]

Haplogroups A & B[edit]

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)[edit]

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.[9]

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)[edit]

Haplogroup F (M89)[edit]

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.[8] 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.[10][11] 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.[12]

Haplogroup D (M174)[edit]

Haplogroup E (M96)[edit]

Haplogroup G (M201)[edit]

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.[13][14]

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

Haplogroup H (M69)[edit]

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)[edit]

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)[edit]

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

Haplogroup K (M9)[edit]

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)[edit]

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

Haplogroup K2 (K-M526)[edit]

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]

Haplogroup N[edit]

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[edit]

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

Haplogroups K2b1, M & S[edit]

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]

Haplogroup P (P295) has two primary branches: P1 (P-M45) and the extremely rare P2 (P-B253).[16]

P*, P1* and P2 are found together only on the island of Luzon, in The Philippines;[16] in particular, P* and P1* are found at significant rates among members of the Aeta (or Agta) people of Luzon.[17] 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.[17][18]

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]

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

The 2008 ISOGG tree

Haplogroup R (M207)[edit]

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[edit]

Haplogroup Possible time of origin Possible place of origin Possible TMRCA[26][9]
A00 235,900 years ago[27] Africa[28] 235,900 years ago
E 65,200 years ago[27] East Africa[29] or Asia[10] 53,100 years ago
F 65,900 years ago[27] Eurasia 48,800 years ago
IJ 47,200 years ago[27] Middle East 42,900 years ago
K 47,200 years ago[27] Asia 45,400 years ago
E-M215 (E1b1b) 42,400 years ago[27][30] East Africa 34,800 years ago
P 45,400 years ago[27] Asia 31,900 years ago
J 42,900 years ago[27][31] Middle East 31,600 years ago
R 31,900 years ago[27] Asia 28,200 years ago
I 42,900 years ago[27] Europe 27,500 years ago
R-M173 (R1) 28,200 years ago Asia 22,800 years ago
I-M438 (I2) 28-33,000 years ago[32] 16,000-20,000 years ago
E-M35 20,000-30,000 years ago[30] 15–21,000 years ago
J-M267 (J1) 15-34,000[31] years ago
R-M420 (R1a) 22,000 years ago[33] 8-10,000 years ago
R-M343 (R1b) 22,000 years ago[34] West Asia[35]
N at least 21,000 years ago (STR age)[36]
I-M253 (I1) 11-21,000[37] or 28-33,000 years ago[32] 3-5,000 years ago
J-M172 (J2) 15,000-22,000[31] years ago 19-24,000 years ago[38]
E-M78 15-20,000[30] or 17,500-20,000 years ago[39] Northeast Africa[39] at least 17,000 years ago[39]
E-V12 12,500-18,000 years ago[39]
R-M17 13 ,000[33] or 18,000 years ago[40] Eurasia
I-L460 (I2a) present 13,000 years ago[41]
I-M223 11-18,000 years ago[37]
E-V13 7-17,000 years ago[39] West Asia[39] 4,000-4,700 years ago (Europe)
6,800-17,000 years ago (Asia)[39]
R-Z280 11-14,000 years ago[42]
N-M46 (N1c1) at least 12,000 years ago (STR age)[36]
R-M458 11,000 years ago[42]
I-P37 6-16,000,[37] present 10,000 years ago[43]
I-M423 (I2a1b) present 10,000 years ago[43]
I-M26 (I2a1a) 2-17,000,[37] present 8,000 years ago[43]
R-M269 5,500-8,000 years ago[44]
R-L11, R-S116 3-5,000 years ago

See also[edit]


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 A1b
A1b1 BT
B CT
DE CF
D E C F
F1  F2  F3  GHIJK
G HIJK
IJK H
IJ   K
I J     LT [χ 5]  K2
L     T [χ 6] K2a [χ 7] K2b [χ 8]   K2c   K2d  K2e [χ 9]  
K2a1                    K2b1 [χ 10]    P [χ 11]
NO S [χ 12]  M [χ 13]    P1     P2
N O Q     R

References[edit]

  1. ^ a b "Understanding Haplogroups: How are the haplogroups named?". Family Tree DNA. Retrieved 31 March 2013. 
  2. ^ "Human mutation rate revealed". Nature News. 2009. Retrieved 18 September 2017. 
  3. ^ 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. 
  4. ^ "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. 
  5. ^ "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. 
  6. ^ "Understanding Results: Y-DNA Single Nucleotide Polymorphism (SNP): How are haplogroups and their subclades named?". Family Tree DNA. Retrieved 31 March 2013. 
  7. ^ "Family Tree DNA - Genetic Testing for Ancestry, Family History & Genealogy". familytreedna.com. 
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  9. ^ a b 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. PMC 2336805Freely accessible. PMID 18385274. doi:10.1101/gr.7172008. 
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  12. ^ This was, for instance, the case with the original subclade F3 (M96), which has since been renamed Haplogroup H2.
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  26. ^ TMRCA
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Further reading[edit]

External links[edit]