Haplogroup A is a human Y-chromosome DNA haplogroup, which includes all living human Y chromosomes. Bearers of extant sub-clades of haplogroup A are almost exclusively found in Africa (or among the African diaspora), in contrast with haplogroup BT, bearers of which participated in the 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

Though there are terminological challenges to define it as a haplogroup, haplogroup A has come to mean "the foundational haplogroup" (viz. of contemporary human populations); it is not defined by any mutation, but refers to any haplogroup which is not descended from the haplogroup BT; in other words, it is defined by the absence of the defining mutation of that group (M91). By this definition, haplogroup A includes all mutations that took place between the Y-chromosomal most recent common ancestor (estimated at some 270 kya) and the mutation defining haplogroup BT (estimated at some 140–150 kya), 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.

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. 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".

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%).

Distribution

By definition of haplogroup A as "non-BT", it is almost completely restricted to Africa, though a very small handful of bearers have been reported in Europe and Western Asia.

The clade achieves its highest modern frequencies in the Bushmen hunter-gatherer populations of Southern Africa, followed closely by many Nilotic groups in Eastern Africa. However, haplogroup A's oldest sub-clades are exclusively found in Central-Northwest Africa, where it (and by extension 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, Cruciani et al. (2011) estimated 142 kya. and with the inclusion of the previously unknown "A00" haplogroup to about 270 kya in 2015 studies.

The clade has also been observed at notable frequencies in certain populations in Ethiopia, as well as some Pygmy groups in Central Africa, and less commonly Niger–Congo speakers, who largely belong to the E1b1a clade. Haplogroup E in general is believed to have originated in Northeast Africa, and was later introduced to West Africa from where it spread around 5,000 years ago to Central, Southern and Southeastern Africa with the Bantu expansion. According to Wood et al. (2005) and Rosa et al. (2007), such relatively recent population movements from West Africa changed the pre-existing population Y chromosomal diversity in Central, Southern and Southeastern Africa, replacing the previous haplogroups in these areas with the now dominant E1b1a lineages. Traces of ancestral inhabitants, however, can be observed today in these regions via the presence of the Y DNA haplogroups A-M91 and B-M60 that are common in certain relict populations, such as the Mbuti people and the Khoisan.

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

In a composite sample of 3551 African men, haplogroup A had a frequency of 5.4%. The highest frequencies of haplogroup A have been reported among the Khoisan of Southern Africa, Beta Israel, and Nilo-Saharans from Sudan.

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%),28/53 (Dinka, Nuer, and Shilluk), especially the Dinka Sudanese (61.5%).16/26, Hassan et al. 2008 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.

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 Guinea Bissau, two male individuals from Niger, one male individual from Mali, and one male individual from Cabo Verde carried haplogroup A1a.

Central Africa

Haplogroup A3b2-M13 has been observed in populations of northern Cameroon (2/9 = 22% Tupuri, 4/28 = 14% Mandara, 2/17 = 12% Fulbe) and eastern DRC (2/9 = 22% Alur, 1/18 = 6% Hema, 1/47 = 2% Mbuti).

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%).

Without testing for any subclade, haplogroup A Y-DNA has been observed in samples of several populations of Gabon, including 9% (3/33) of a sample of Baka, 3% (1/36) of a sample of Ndumu, 2% (1/46) of a sample of Duma, 2% (1/57) of a sample of Nzebi, and 2% (1/60) of a sample of Tsogo.

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, 10.3% (8/78) of an Oromo sample, and 13.6% (12/88) of another sample from Ethiopia.

Southern Africa

One 2005 study has found haplogroup A in samples of various Khoisan-speaking tribes with frequency ranging from 10% to 70%. This particular haplogroup was not found in a sample of the Hadzabe from Tanzania, a population sometimes proposed as a remnant of a Late Stone Age 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.

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 Mitilini on the Aegean island of Lesvos and in samples of Portuguese from southern Portugal, central Portugal, and Madeira. The authors of one study have reported finding what appears to be haplogroup A in 3.1% (2/65) of a sample of Cypriots, 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)

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 to FamilyTreeDNA. He was identified as a descendent of Albert Perry, hence the name. Mendez et al. (2013) announced the discovery of this previously unknown haplogroup, for which they proposed the designator "A00". Perry's Y would later be renamed A00a after the discovery of a similar but different group from Cameroon.

A00 has an estimated age of around 275 kya, so is roughly contemporary with the known appearance of earliest known anatomically modern humans, such as Jebel Irhoud.

Researchers later found A00 was possessed by 11 Mbo males of Western Cameroon (Bantu) (out of a sample of 174; 6.32%).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)". Subsequent research suggested that the overall rate of A00 was even higher among the Mbo, i.e. 9.3% (8 of 86). The Mbo samples were later classified as its own subgroup, A00b (A-A4987).

Further research in 2015 indicates that the modern population with the highest concentration of A00 is the (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.Which of Cameroon's peoples have members of haplogroup A00? // experiment.com update of funded research (Schrack/Fomine Forka) available online 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".

Yet another A00 subtype is designated A00c. The modern sample from Cameroon reported to carry it, "YSEQ5368" is not linked to any paper.

Geneticists sequenced genome-wide DNA data from four people buried at the site of Shum Laka in Cameroon between 8000–3000 years ago, who were most genetically similar to Mbuti pygmies. One individual carried A00. ("At every subtype-specific site for which we had coverage, the Shum Laka A00 carries the ancestral allele."); Lipson Mark et al. Ancient Human DNA from Shum Laka (Cameroon) in the Context of African Population History // SAA 2019 Data for this individual from Shum Laka is now found in the Allen Ancient Genome Diversity Project / John Templeton Ancient DNA Atlas under the code "I10871". He seems to represent an earlier stage of A00 before the divergence into the three groups. The last common ancestor of A00a, A00b, and A00c (A00-Y125399) is 633 SNPs removed from him.

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%. Also found in Ghana.

A1a (A-M31)