Haplogroup A (Y-DNA)

Source: Wikipedia, the free encyclopedia.
This article is about the human Y-DNA haplogroup. For the unrelated human mtDNA haplogroup, see Haplogroup A (mtDNA).
Haplogroup A
Possible time of origin270,000 BP,
A1, A1a, A1b, A1b1 and BT
.)

Haplogroup A is a

Out of Africa migration of early modern humans
. The known branches of haplogroup A are A00, A0, A1a, and A1b1; these branches are only very distantly related, and are not more closely related to each other than they are to haplogroup BT.

Origin

Main article:
Y-MRCA
Tree showing relationship between branches of haplogroup A and haplogroup BT
Projected spatial frequency distribution of haplogroup A in Africa.

Though there are terminological challenges to define it as a haplogroup, haplogroup A has come to mean "the foundational haplogroup" (viz. of

kya) and the mutation defining haplogroup BT (estimated at some 140–150 kya),[8]
including any extant subclades that may yet to be discovered.

Bearers of haplogroup A (i.e. absence of the defining mutation of haplogroup BT) have been found in Southern Africa's hunter-gatherer inhabited areas, especially among the San people. In addition, the most basal mitochondrial DNA L0 lineages are also largely restricted to the San. However, the A lineages of Southern Africa are sub-clades of A lineages found in other parts of Africa, suggesting that A sub-haplogroups arrived in Southern Africa from elsewhere.[9]

The two most basal lineages of haplogroup A, A0 and A1 (prior to the announcement of the discovery of

haplogroup A00 in 2013), have been detected in West Africa, Northwest Africa and Central Africa. Cruciani et al. (2011) suggest that these lineages may have emerged somewhere in between Central and Northwest Africa.[10]
Scozzari et al. (2012) also supported "the hypothesis of an origin in the north-western quadrant of the African continent for the A1b [ i.e. A0 ] haplogroup".[11]

Haplogroup A1b1b2 has been found among ancient fossils excavated at Balito Bay in KwaZulu-Natal, South Africa, which have been dated to around 2149-1831 BP (2/2; 100%).[12]

Distribution

By definition of haplogroup A as "non-

Western Asia
.

The clade achieves its highest modern frequencies in the

patrilinear ancestor of modern humans) is believed to have originated. Estimates of its time depth have varied greatly, at either close to 190 kya or close to 140 kya in separate 2013 studies,[10][13] and with the inclusion of the previously unknown "A00" haplogroup to about 270 kya in 2015 studies.[14][15]

The clade has also been observed at notable frequencies in certain populations in

Mbuti Pygmies and the Khoisan.[19][20][21]

Haplogroup A frequencies
Africa
Study population Freq.
(in %)
[20] Tsumkwe San (Namibia) 66%
[20] Nama (Namibia) 64
[22]
Dinka
(Sudan) 		62
[22] Shilluk (Sudan) 53
[22]
Nuba
(Sudan) 		46
[23] Khoisan 44
[24][25]
Ethiopian Jews
 41
[20][24]
!Kung
/Sekele 		~40
[22] Borgu (Sudan) 35
[22] Nuer (Sudan) 33
[22] Fur (Sudan) 31
[20] Maasai (Kenya) 27
[26] Nara (Eritrea) 20
[22] Masalit (Sudan) 19
[27] Ethiopians 14
[20] Bantu (Kenya) 14
[22] Mandara (Cameroon) 14
[24] Hausa (Sudan) 13
[24]
Khwe
(South Africa) 		12
[20] Fulbe (Cameroon) 12
[28] Dama (Namibia) 11
[26] Oromo (Ethiopia) 10
[20] Kunama (Eritrea) 10
[27]
South Semitic
(Ethiopia) 		10
Arabs (Egypt) 3

In a composite sample of 3551 African men, Haplogroup A had a frequency of 5.4%.

Nilo-Saharans
from Sudan.

North America

1 African American Male out of Lacrosse, WI USA, Moses, Ramon, A00, A00-AF8

Africa

North Africa

In North Africa, haplogroup A is largely absent. Its subclade A1 has been observed at trace frequencies among Moroccans.

Upper Nile

Haplogroup A3b2-M13 is common among the Southern Sudanese (53%),[22] especially the Dinka Sudanese (61.5%).[30] Haplogroup A3b2-M13 also has been observed in another sample of a South Sudanese population at a frequency of 45% (18/40), including 1/40 A3b2a-M171.[23]

Further downstream around the Nile valley, the subclade A3b2 has also been observed at very low frequencies in a sample of Egyptian males (3%).

West Africa

Eight male individuals from

Cabo Verde carried haplogroup A1a.[31]

Central Africa

Haplogroup A3b2-M13 has been observed in populations of northern Cameroon (2/9 = 22%

Mbuti[20]
).

Haplogroup A-M91(xA1a-M31, A2-M6/M14/P3/P4, A3-M32) has been observed in the

Bakola people of southern Cameroon (3/33 = 9%).[20]

Without testing for any subclade, haplogroup A Y-DNA has been observed in samples of several populations of

Tsogo.[18]

East Africa

African Great Lakes

Bantus in Kenya (14%, Luis et al. 2004) and Iraqw in Tanzania (3/43 = 7.0% (Luis et al. 2004) to 1/6 = 17% (Knight et al. 2003)).

Horn of Africa

Haplogroup A is found at low to moderate frequencies in the Horn of Africa. The clade is observed at highest frequencies among the 41% of a sample of the Beta Israel, occurring among 41% of one sample from this population (Cruciani et al. 2002). Elsewhere in the region, haplogroup A has been reported in 14.6% (7/48) of an Amhara sample,[28] 10.3% (8/78) of an Oromo sample,[28] and 13.6% (12/88) of another sample from Ethiopia.[23]

Southern Africa

One 2005 study has found haplogroup A in samples of various Khoisan-speaking tribes with frequency ranging from 10% to 70%.[20] This particular haplogroup was not found in a sample of the

Khoisanid
population.

Asia

In Asia, haplogroup A has been observed at low frequencies in Asia Minor and the Middle East among Aegean Turks, Palestinians, Jordanians, Yemenites.[32]

Europe

A3a2 (A-M13; formerly A3b2), has been observed at very low frequencies in some Mediterranean islands. Without testing for any subclade, haplogroup A has been found in a sample of Greeks from

Lesvos[32] and in samples of Portuguese from southern Portugal, central Portugal, and Madeira.[33] The authors of one study have reported finding what appears to be haplogroup A in 3.1% (2/65) of a sample of Cypriots,[34] though they have not definitively excluded the possibility that either of these individuals may belong to a rare subclade of haplogroup BT, including haplogroup CT
.

Subclades

A00 (A00-AF6)

Mendez et al. (2013) announced the discovery of a previously unknown haplogroup, for which they proposed the designator "A00".

anatomically modern humans, such as Jebel Irhoud.[37]
A00 is also sometimes known as "Perry's Y-chromosome" (or simply "Perry's Y"). This previously unknown haplogroup was discovered in 2012 in the Y chromosome of an
African-American man who had submitted his DNA for commercial genealogical analysis.[38]
The subsequent discovery of other males belonging to A00 led to the reclassification of Perry's Y as A00a (A-L1149).

Researchers later found A00 was possessed by 11 Mbo males of Western Cameroon (Bantu) (out of a sample of 174 (6.32%).[39] Subsequent research suggested that the overall rate of A00 was even higher among the Mbo, i.e. 9.3% (8 of 86) were later found to fall within A00b (A-A4987).

Further research in 2015 indicates that the modern population with the highest concentration of A00 is the Bangwa [fr] (or Nweh), a Yemba-speaking group of Cameroon (Grassfields Bantu): 27 of 67 (40.3%) samples were positive for A00a (L1149). One Bangwa individual did not fit into either A00a or A00b.[40]

Geneticists sequenced genome-wide DNA data from four people buried at the site of

Mbuti pygmies. One individual carried the deeply divergent Y chromosome haplogroup A00.[41]

A0 (A-V148)

The haplogroup names "A-V148" and "A-CTS2809/L991" refer to the exact same haplogroup.

A0 is found only in Bakola Pygmies (South Cameroon) at 8.3% and Berbers from Algeria at 1.5%.[10] Also found in Ghana.[11][failed verification]

A1a (A-M31)

The subclade A1a (M31) has been found in approximately 2.8% (8/282) of a pool of seven samples of various ethnic groups in

Berbers from Morocco[24] and 2.3% (1/44) of a sample of unspecified ethnic affiliation from Mali.[23]

In 2007, seven men from Yorkshire, England sharing the unusual surname Revis were identified as being from the A1a (M31) subclade. It was discovered that these men had a common male-line ancestor from the 18th century, but no previous information about African ancestry was known.[29]

In 2023, Lacrosse, WI, 1 Male, A1a-M31, Moses, Ramon.[43]

A1b1a1a (A-M6)

The subclade A1b1a1a (M6; formerly A2 and A1b1a1a-M6) is typically found among Khoisan peoples. The authors of one study have reported finding haplogroup A-M6(xA-P28) in 28% (8/29) of a sample of Tsumkwe San and 16% (5/32) of a sample of

!Kung/Sekele, 9% (1/11) of a sample of Nama, and 6% (1/18) of a sample of Dama.[20] The authors of another study have reported finding haplogroup A2 in 15.4% (6/39) of a sample of Khoisan males, including 5/39 A2-M6/M14/M23/M29/M49/M71/M135/M141(xA2a-M114) and 1/39 A2a-M114.[23]

A1b1b (A-M32)

The clade A1b1b (M32; formerly A3) contains the most populous branches of haplogroup A and is mainly found in

Eastern Africa and Southern Africa
.

A1b1b1 (A-M28)

The subclade (appropriately considered as a distinct haplogroup) A1b1b1 (M28; formerly A3a) has only been rarely observed in the

Somalis.[16]
it has also been observed in Eastern, Central and Southern of Arabia. Current results, according to FTDNA, suggest that some branches such as A-V1127 originated in Arabia. Additionally, as suggested by experts as seen in TMRCA in Yfull tree, this haplogroup must have undergone a bottleneck time when people who represent this haplogroup suffered some sort of extinction and sharply decreased in number. Noteworthy, non semitic speakers don't have this haplogroup neither the koi-san or the nilots or the Cushites.

A1b1b2a (A-M51)

The subclade A1b1b2a (M51; formerly A3b1) occurs most frequently among Khoisan peoples (6/11 = 55%

Sotho–Tswana,[20] 3/53 = 6% non-Khoisan Southern Africans,[23] 4/80 = 5% Xhosa,[20] and 1/29 = 3% Zulu.[20]

A1b1b2b (A-M13)

The subclade A1b1b2b (M13; formerly A3b2) is primarily distributed among Nilotic populations in East Africa and northern Cameroon. It is different from the A subclades that are found in the Khoisan samples and only remotely related to them (it is actually only one of many subclades within haplogroup A). This finding suggests an ancient divergence.

In

Nuba of central Sudan, 25/90 = 27.8% of Western Sudanese, 4/32 = 12.5% of local Hausa people, and 5/216 = 2.3% of Northern Sudanese.[44]

In Ethiopia, one study has reported finding haplogroup A-M13 in 14.6% (7/48) of a sample of Amhara and 10.3% (8/78) of a sample of Oromo.[28] Another study has reported finding haplogroup A3b2b-M118 in 6.8% (6/88) and haplogroup A3b2*-M13(xA3b2a-M171, A3b2b-M118) in 5.7% (5/88) of a mixed sample of Ethiopians, amounting to a total of 12.5% (11/88) A3b2-M13.[23]

Haplogroup A-M13 also has been observed occasionally outside of Central and Eastern Africa, as in the

Palestinian Arabs (2/143 = 1.4%[46]), Sardinia (1/77 = 1.3%,[47] 1/22 = 4.5%[23]), the capital of Jordan, Amman (1/101=1%[48]), and Oman (1/121 = 0.8%[27]
).

Haplogroup A-M13 has been found among three Neolithic period fossils excavated from the Kadruka site in Sudan.[49]

Geographical frequency distribution of Haplogroup A3-M13.

Haplogroup A-M13 was also found in a male victim of the Mt. Vesuvius eruption in Pompeii.[50]

Phylogenetics

Phylogenetic history

Main article: Conversion table for Y chromosome haplogroups

Prior to 2002, there were in academic literature at least seven naming systems for the Y-Chromosome Phylogenetic tree. This led to considerable confusion. In 2002, the major research groups came together and formed the Y-Chromosome Consortium (YCC). They published a joint paper that created a single new tree that all agreed to use. Later, a group of citizen scientists with an interest in population genetics and genetic genealogy formed a working group to create an amateur tree aiming at being above all timely. The table below brings together all of these works at the point of the landmark 2002 YCC Tree. This allows a researcher reviewing older published literature to quickly move between nomenclatures.

The revised y-chromosome family tree by Cruciani et al. 2011 compared with the family tree from Karafet et al. 2008. (The "A1a-T" shown here is now known as A1 and "A2-T" is now known as A1b.)

Initial sequencing of the human Y-chromosome had suggested that first split in the Y-Chromosome family tree occurred with the mutations that separated

Haplogroup BT from Y-chromosomal Adam and haplogroup A more broadly.[51]
Subsequently, many intervening splits between Y-chromosomal Adam and BT, also became known.

A major shift in the understanding of the Y-DNA tree came with the publication of (Cruciani 2011). While the SNP marker M91 had been regarded as a key to identifying haplogroup BT, it was realised that the region surrounding M91 was a mutational hotspot, which is prone to recurrent back-mutations. Moreover, the 8T stretch of Haplogroup A represented the ancestral state of M91, and the 9T of haplogroup BT a derived state, which arose following the insertion of 1T. This explained why subclades A1b and A1a, the deepest branches of Haplogroup A, both possessed the 8T stretch. Similarly, the P97 marker, which was also used to identify haplogroup A, possessed the ancestral state in haplogroup A, but a derived state in haplogroup BT.[10] Ultimately the tendency of M91 to back-mutate and (hence) its unreliability, led to M91 being discarded as a defining SNP by ISOGG in 2016.[52] Conversely, P97 has been retained as a defining marker of Haplogroup BT.

YCC 2002/2008 (Shorthand) (α) (β) (γ) (δ) (ε) (ζ) (η) YCC 2002 (Longhand) YCC 2005 (Longhand) YCC 2008 (Longhand) YCC 2010r (Longhand) ISOGG 2006 ISOGG 2007 ISOGG 2008 ISOGG 2009 ISOGG 2010 ISOGG 2011 ISOGG 2012
A-M31 7 I 1A 1 – H1 A A1 A1 A1 A1a A1 A1 A1a A1a A1a A1a A1a
A-M6 27 I 2 3 – H1 A A2* A2 A2 A2 A2 A2 A2 A2 A2 A2 A1b1a1a
A-M114 27 I 2 3 – H1 A A2a A2a A2a A2a A2a A2a A2a A2a A2a A2a A1b1a1a1a
A-P28 27 I 2 4 – H1 A A2b A2b A2b A2b A2b A2b A2b A2b A2b A2b A1b1a1a1b
A-M32 * * * * * * * * A3 A3 A3 A3 A3 A3 A3 A3 A3 A1b1b
A-M28 7 I 1A 1 – H1 A A3a A3a A3a A3a A3a A3a A3a A3a A3a A3a A1b1b1
A-M51 7 I 1A 1 – H1 A A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A1b1b2a
A-M13 7 I 1A 2 Eu1 H1 A A3b2* A3b2 A3b2 A3b2 A3b2 A3b2 A3b2 A3b2 A3b2 A3b2 A1b1b2b
A-M171 7 I 1A 2 Eu1 H1 A A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a removed
A-M118 7 I 1A 2 Eu1 H1 A A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A1b1b2b1

The following research teams per their publications were represented in the creation of the YCC Tree.

Phylogenetic trees

The above phylogenetic tree is based on the

ISOGG,[17] YCC,[53]
and subsequent published research.

Y-chromosomal Adam
  A00 (AF6/L1284)

  • A00a (L1149, FGC25576, FGC26292, FGC26293, FGC27741)
  • A00b (A4987/YP3666, A4981, A4982/YP2683, A4984/YP2995, A4985/YP3292, A4986, A4988/YP3731)

  A0-T (L1085)

  • A0 (CTS2809/L991) formerly A1b
  • A1 (P305) formerly A1a-T, A0 and A1b
    • A1a (M31)
    • A1b (P108) formerly A2-T
      • A1b1 (L419/PF712)
        • A1b1a (L602, V50, V82, V198, V224)
          • A1b1a1 (M14) formerly A2
            • A1b1a1a (M6)
              • A1b1a1a1 (P28) formerly A1b1a1a1b and A2b
        • A1b1b (M32) formerly A3
          • A1b1b1 (M28) formerly A3a
          • A1b1b2 (L427)
            • A1b1b2a (M51/Page42) formerly A3b1
              • A1b1b2a1 (P291)
            • A1b1b2b (M13/PF1374) formerly A3b2
              • A1b1b2b1 (M118)
      • BT
         (M91)

See also
Y-DNA A subclades

References

  1. human Y-MRCA
    (see there); including the A00 lineage, Karmin et al. (2015) and Trombetta et al. (2015) estimate ages of 254,000 and 291,000 ybp, respectively.
  2. PMID 25770088
    . "we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males."
  3. PMID 27058445
    .
  4. PMID 31969706
    .
  5. PMID 26226630
    .
  6. ^ "A00 YTree".
  7. ^ According to Cruciani et al. 2011, the most basal lineages have been detected in
    Northwest and Central Africa
    , suggesting plausibility for the Y-MRCA living in the general region of North-Central Africa". In a sample of 2204 African Y-chromosomes, 8 chromosomes belonged to either haplogroup A1b or A1a. Haplogroup A1a was identified in two Moroccan Berbers, one Fulbe and one Tuareg people from Niger. Haplogroup A1b was identified in three Bakola pygmies from Southern Cameroon and one Algerian Berber. Cruciani, Fulvio; Trombetta, Beniamino; Massaia, Andrea; Destro-Bisol, Giovanni; Sellitto, Daniele; Scozzari, Rosaria (2011). "A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa". The American Journal of Human Genetics. 88 (6): 814–8.
    PMID 21601174
    . Scozzari et al. (2012) agreed with a plausible placement in "the north-western quadrant of the African continent" for the emergence of the A1b haplogroup: "the hypothesis of an origin in the north-western quadrant of the African continent for the A1b haplogroup, and, together with recent findings of ancient Y-lineages in central-western Africa, provide new evidence regarding the geographical origin of human MSY diversity". Scozzari R; Massaia A; D'Atanasio E; Myres NM; Perego UA; et al. (2012). Caramelli, David (ed.). "Molecular Dissection of the Basal Clades in the Human Y Chromosome Phylogenetic Tree". PLOS ONE. 7 (11): e49170.
    PMID 23145109
    .
  8. PMID 25770088
    .
  9. PMID 21478374
    .
  10. ^
    PMID 21601174
    .
  11. ^
    PMID 23145109
    .
  12. PMID 28971970
    .
  13. PMID 23908239
    . Cruciani et al. (2011) estimated 142 kya.
  14. ^
    PMID 25770088
    .
  15. ^
    PMID 26226630
    .
  16. ^
    PMID 19772609
    .
  17. ^ a b International Society of Genetic Genealogy. "Y-DNA Haplogroup Tree".
  18. ^
    PMID 19369595
    .
  19. ^
    PMID 17662131
    .
  20. ^
    PMID 15856073
    .
  21. S2CID 9441236
    .
  22. ^
    PMID 18618658
    .
  23. ^
    S2CID 12893406
    .
  24. ^
    PMID 11910562
    .
  25. ^
    S2CID 1571356
    .
  26. ^
    PMID 20051990
    .
  27. ^
    PMID 14973781
    .
  28. ^
    PMID 11719903
    .
  29. ^
    PMID 17245408
    .
    News article:     "Yorkshire clan linked to Africa". BBC News. 2007-01-24. Retrieved 2007-01-27.
  30. ^ 16/26, Hassan et al. 2008
  31. S2CID 11190055
    .
  32. ^
    PMID 12927125
    .
  33. S2CID 3229760
    .
  34. S2CID 25536759
    .
  35. PMID 23453668
    .
  36. PMID 23453668
    .
  37. ^ At first, via Mendez et al. (2013), this was announced as "extremely ancient" (95% confidence interval 237–581 kya for the age of the
    Y-MRCA
    including the lineage of this postulated haplogroup).
  38. slave born in the United States between ca. 1819–1827, lived in York County, South Carolina. See FamilyTreeDNA, Haplogroup A chart
  39. ^ Mendez et al. (2013), p. 455. Quote: "Upon searching a large pan-African database consisting of 5,648 samples from ten countries [...] we identified 11 Y chromosomes that were invariant and identical to the A00 chromosome at five of the six Y-STRs (2 of the 11 chromosomes carried DYS19-16, whereas the others carried DYS19-15). These 11 chromosomes were all found in a sample of 174 (~6.3%) Mbo individuals from western Cameroon (Figure 2). Seven of these Mbo chromosomes were available for further testing, and the genotypes were found to be identical at 37 of 39 SNPs known to be derived on the A00 chromosome (i.e., two of these genotyped SNPs were ancestral in the Mbo samples)".
  40. ^ Which of Cameroon's peoples have members of haplogroup A00? // experiment.com update of funded research (Schrack/Fomine Forka) available online[self-published source?] Quotes: We can now clearly see that with 40% A00, the Bangwa represent the epicentre of A00 in this region, and very possibly in the world. As I shared in the last Lab Note, we found that so far there are two main subgroups of A00, defined by different Y-SNP mutations, which, naturally, divide along ethnic lines: A00a among the Bangwa, and A00b among the Mbo. We also found the one Bangwa sample which didn't belong to either subgroup.".
  41. ^ Lipson Mark et al. Ancient Human DNA from Shum Laka (Cameroon) in the Context of African Population History // SAA 2019
  42. S2CID 63381583
    .
  43. ^ 23andme raw data
  44. ^ Hisham Y. Hassan et al. (2008). "Southern Sudanese" includes 26 Dinka, 15 Shilluk, and 12 Nuer. "Western Sudanese" includes 26 Borgu, 32 Masalit, and 32 Fur. "Northern Sudanese" includes 39 Nubians, 42 Beja, 33 Copts, 50 Gaalien, 28 Meseria, and 24 Arakien.
  45. S2CID 10763736.{{cite journal}}: CS1 maint: multiple names: authors list (link
    )
  46. PMID 11573163
    .
  47. PMID 11073453
    .
  48. PMID 16142507
    .
  49. ^ Yousif, Hisham; Eltayeb, Muntaser (July 2009). Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan (Thesis).
  50. PMID 35618734
    .
  51. PMID 18385274
    .
  52. ^ ISOGG, 2016, Y-DNA Haplogroup Tree 2016. (Access: 29 August 2017.)
  53. ^ Krahn, Thomas. "YCC Tree". FTDNA. Archived from the original on 2011-07-26.

Bibliography

Sources for conversion tables

External links

Wikimedia Commons has media related to Haplogroup A of Y-DNA.
Retrieved from "https://en.wikipedia.org/w/index.php?title=Haplogroup_A_(Y-DNA)&oldid=1219623055"