Haplogroup A (Y-DNA)


Haplogroup A also known as A-V148 and A-CTS2809/L991 is a human Y-chromosome DNA haplogroup. It is the foundational haplogroup to all known patrilineal lineages carried by modern humans, and thus is the Y-chromosomal Adam.
Formerly also known as "clade I", bearers of extant sub-clades of haplogroup A are entirely found in Africa, in contrast with the descendant haplogroup BT bearers of which participated in the Out of Africa migration of anatomically modern humans.
The most basal subclades of haplogroup A are, by age of divergence, "A00", "A0", "A1" and "A2-T". Haplogroup BT, which is ancestral to all non-African haplogroups, is a subclade of A2-T.

Origin

There are terminological difficulties, but as "haplogroup A" has come to mean "the foundational haplogroup", haplogroup A is not defined by any mutation but refers to any haplogroup which is not descended from the haplogroup BT, i.e. defined by the absence of the defining mutation of that group. By this definition, haplogroup A includes all mutations that took place between the Y-MRCA and the mutation defining haplogroup BT, including any extant subclades that may yet to be discovered.
Bearers of haplogroup A have been found in Southern Africa's hunter-gatherer inhabited areas, especially among the San people. In addition, the most basal mitochondrial DNA 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, have been detected in West Africa, Northwest Africa and Central Africa. Cruciani et al. suggest that these lineages may have emerged somewhere in between Central and Northwest Africa.
Scozzari et al. also supported "the hypothesis of an origin in the north-western quadrant of the African continent for the A1b 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.

Distribution

By the 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 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,
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. and Rosa et al., 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 Pygmies and the Khoisan.
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

African Great Lakes

Bantus in Kenya and Iraqw in Tanzania to 1/6 = 17% ).

Central Africa

Haplogroup A3b2-M13 has been observed in populations of northern Cameroon and eastern DRC.
Haplogroup A-M91 has been observed in the Bakola people of southern Cameroon.
Without testing for any subclade, haplogroup A Y-DNA has been observed in samples of several populations of Gabon, including 9% of a sample of Baka, 3% of a sample of Ndumu, 2% of a sample of Duma, 2% of a sample of Nzebi, and 2% of a sample of Tsogo.

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. Elsewhere in the region, haplogroup A has been reported in 14.6% of an Amhara sample, 10.3% of an Oromo sample, and 13.6% of another sample from Ethiopia.

Tamazgha

In the Tamazgha, haplogroup 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, especially the Dinka Sudanese. Haplogroup A3b2-M13 also has been observed in another sample of a South Sudanese population at a frequency of 45%, 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.

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

Haplogroup A1a appears to have present among a very small number of phenotypically northern European males since pre-modern times – the best documented example are men with the surname Revis, which originated in Yorkshire, England.
A3a2, 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% 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. Other study found the presence of Y DNA A in 3,2% of total males from Central and Eastern Sicily.

Structure & subclade distribution

Phylogenetic structure

Y-chromosomal Adam

A00
A0-T
(The above phylogenetic tree is based on the ISOGG, YCC, and other, peer-reviewed research.

Subclade distribution

A00 (A00-AF6)

Mendez et al. announced the discovery of a previously unknown haplogroup, for which they proposed the designator "A00". It has an estimated age of around 270 kya, so postdates appearance of anatomically modern humans, such as Jebel Irhoud.
A00 is also sometimes known as "Perry's Y-chromosome" The subsequent discovery of other males belonging to A00 led to the reclassification of Perry's Y as A00a.
Researchers later found A00 was possessed by 11 Mbo males of Western Cameroon. Subsequent research suggested that the overall rate of A00 was even higher among the Mbo, i.e. 9.3% were later found to fall within A00b.
Further research in 2015 indicates that the modern population with the highest concentration of A00 is the Bangwa, a Yemba-speaking group of Cameroon : 27 of 67 samples were positive for A00a. One Bangwa individual did not fit into either A00a or A00b.
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 the deeply divergent Y chromosome haplogroup A00.

A0 (A-V148)

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

A1 (A-P305)

A1 is found only in Bakola Pygmies at 8.3% and Berbers from Algeria at 1.5%. Also found in Ghana.

A1a (A-M31)

The subclade A1a has been found in approximately 2.8% of a pool of seven samples of various ethnic groups in Guinea-Bissau, especially among the Papel-Manjaco-Mancanha. In an earlier study published in 2003, Gonçalves et al. have reported finding A1a-M31 in 5.1% of a sample from Guinea-Bissau and in 0.5% of a pair of samples from Cabo Verde. The authors of another study have reported finding haplogroup A1a-M31 in 5% of a sample of Mandinka from Senegambia and 2% of a sample of Dogon from Mali. Haplogroup A1a-M31 also has been found in 3% of a sample of Berbers from Morocco and 2.3% of a sample of unspecified ethnic affiliation from Mali.
In 2007, seven men from Yorkshire, England sharing the unusual surname Revis were identified as being from the A1a 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.

A1b1a1a (A-M6)

The subclade A1b1a1a is typically found among Khoisan peoples. The authors of one study have reported finding haplogroup A-M6 in 28% of a sample of Tsumkwe San and 16% of a sample of !Kung/Sekele, and haplogroup A2b-P28 in 17% of a sample of Tsumkwe San, 9% of a sample of !Kung/Sekele, 9% of a sample of Nama, and 6% of a sample of Dama. The authors of another study have reported finding haplogroup A2 in 15.4% of a sample of Khoisan males, including 5/39 A2-M6/M14/M23/M29/M49/M71/M135/M141 and 1/39 A2a-M114.

A1b1b (A-M32)

The clade A1b1b contains the most populous branches of haplogroup A and is mainly found in Eastern Africa and Southern Africa.

A1b1b1 (A-M28)

The subclade A1b1b1 has only been rarely observed in the Horn of Africa. In 5% of a mixed sample of speakers of South Semitic languages from Ethiopia, 1.1% of a sample of Ethiopians, and 0.5% in Somalis.

A1b1b2a (A-M51)

The subclade A1b1b2a occurs most frequently among Khoisan peoples. However, it also has been found with lower frequency among Bantu peoples of Southern Africa, including 2/28 = 7% Sotho–Tswana, 3/53 = 6% non-Khoisan Southern Africans, 4/80 = 5% Xhosa, and 1/29 = 3% Zulu.

A1b1b2b (A-M13)

The subclade A1b1b2b 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. This finding suggests an ancient divergence.
In Sudan, haplogroup A-M13 has been found in 28/53 = 52.8% of Southern Sudanese, 13/28 = 46.4% of the 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.
In Ethiopia, one study has reported finding haplogroup A-M13 in 14.6% of a sample of Amhara and 10.3% of a sample of Oromo. Another study has reported finding haplogroup A3b2b-M118 in 6.8% and haplogroup A3b2*-M13 in 5.7% of a mixed sample of Ethiopians, amounting to a total of 12.5% A3b2-M13.
Haplogroup A-M13 also has been observed occasionally outside of Central and Eastern Africa, as in the Aegean Region of Turkey, Yemenite Jews, Egypt, Palestinian Arabs, Sardinia, the capital of Jordan, Amman, and Oman.
Haplogroup A-M13 has been found among three Neolithic period fossils excavated from the Kadruka site in Sudan.

Nomenclature & taxonomical history

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. 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.
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. 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. 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. Ultimately the tendency of M91 to back-mutate and its unreliability, led to M91 being discarded as a defining SNP by ISOGG in 2016. Conversely, P97 has been retained as a defining marker of Haplogroup BT.
YCC 2002/2008 ''''''YCC 2002 YCC 2005 YCC 2008 YCC 2010r ISOGG 2006ISOGG 2007ISOGG 2008ISOGG 2009ISOGG 2010ISOGG 2011ISOGG 2012
A-M317I1A1–H1AA1A1A1A1aA1A1A1aA1aA1aA1aA1a
A-M627I23–H1AA2*A2A2A2A2A2A2A2A2A2A1b1a1a
A-M11427I23–H1AA2aA2aA2aA2aA2aA2aA2aA2aA2aA2aA1b1a1a1a
A-P2827I24–H1AA2bA2bA2bA2bA2bA2bA2bA2bA2bA2bA1b1a1a1b
A-M32********A3A3A3A3A3A3A3A3A3A1b1b
A-M287I1A1–H1AA3aA3aA3aA3aA3aA3aA3aA3aA3aA3aA1b1b1
A-M517I1A1–H1AA3b1A3b1A3b1A3b1A3b1A3b1A3b1A3b1A3b1A3b1A1b1b2a
A-M137I1A2Eu1H1AA3b2*A3b2A3b2A3b2A3b2A3b2A3b2A3b2A3b2A3b2A1b1b2b
A-M1717I1A2Eu1H1AA3b2aA3b2aA3b2aA3b2aA3b2aA3b2aA3b2aA3b2aA3b2aA3b2aremoved
A-M1187I1A2Eu1H1AA3b2bA3b2bA3b2bA3b2bA3b2bA3b2bA3b2bA3b2bA3b2bA3b2bA1b1b2b1

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