Haplogroup A (Y DNA)

Origin

There are terminological difficulties, but as "haplogroup A" has come to mean "the foundational haplogroup" (viz. of contemporary human population), haplogroup A is not defined by any mutation but refers to any haplogroup which is not descended from haplogroup BT, i.e. 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-MRCA (estimated at some 250 kya) and the mutation defining haplogroup BT (estimated at some 80–70 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-gatherers, 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 (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".

Distribution

By the definition of haplogroup A as "non-BT", it is largely restricted to Africa, though a 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, 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 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 —Central

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.

Africa —Eastern

Haplogroup A3b2-M13 is common among the Southern Sudanese (53%), especially the Dinka Sudanese (61.5%). 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. Haplogroup A also has been reported in 14.6% (7/48) of an Amhara sample, 10.3% (8/78) of an Oromo sample, 13.6% (12/88) of another sample from Ethiopia, and 41% of a sample of the Beta Israel (Cruciani et al. 2002), and important percentages are also shared by 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)).

Africa —Northern

The subclade A1 has been observed in Moroccan Berbers, while the subclade A3b2 has been observed in approximately 3% of Egyptian males.

Africa —Southern

One study has found haplogroup A in samples of various Khoisan-speaking tribes with frequency ranging from 10% to 70%. Surprisingly, this particular haplogroup was not found in a sample of the Hadzabe from Tanzania, a population traditionally considered an ancient remnant of Khoisans due to the presence of click consonants in their language.

Eurasia

Haplogroup A has been observed as A1 in European men in England. As A3b2, it has been observed with low frequency in Asia Minor, the Middle East, and some Mediterranean islands, among Aegean Turks, Sardinians, Palestinians, Jordanians, Yemenites, and Omanis. Without testing for any subclade, haplogroup A has been observed 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 haplogroup B or haplogroup C.

Nomenclature

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

Cruciani et al. 2011

A major shift in understanding of the Haplogroup A tree came with the publication of (Cruciani 2011). Initial sequencing of the human Y-chromosome suggested that first split in the Y-Chromosome family tree occurred with the M91 mutation that separated Haplogroup A from Haplogroup BT. However, it is now known two previously reported subclades of Haplogroup A, namely subclades A1b and A1a-T, represent a deeper split in the Y-chromosome tree than that between Haplogroup A and Haplogroup BT. The rearrangement of the Y-chromosome family tree implies that lineages classified as Haplogroup A do not necessarily form a monophyletic clade. Haplogroup A therefore refers to a collection of lineages that do not possess the markers that define Haplogroup BT, though many lineages within haplogroup A are only very distantly related.

The M91 and P97 mutations distinguish Haplogroup A from Haplogroup BT. Within Haplogroup A chromosomes, the M91 marker consists of a stretch of 8 T nucleobase units. In Haplogroup BT and chimpanzee chromosomes, this marker consists of 9 T nucleobase units. This pattern suggested that the 9T stretch of Haplogroup BT was the ancestral version and that Haplogroup A was formed by the deletion of one nucleobase.

However, according to Cruciani et al. 2011, the region surrounding the M91 marker is a mutational hotspot prone to recurrent mutations. It is therefore possible that the 8T stretch of Haplogroup A may be the ancestral state of M91 and the 9T of haplogroup BT may be the derived state that arose by an insertion of 1T. This would explain why subclades A1b and A1a-T, the deepest branches of Haplogroup A, both possess the 8T stretch. Furthermore, Cruciani et al. 2011 determined that the P97 marker, which is also used to identify haplogroup A, possessed the ancestral state in haplogroup A but the derived state in haplogroup BT.

Overview

This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) Tree, the ISOGG Y-DNA Haplogroup Tree, and subsequent published research.

Y-chromosomal Adam

Mendez et al. (2013) announced the discovery of a previously unknown haplogroup, for which they proposed the designator "A00". With an estimated age of around 270 kya, older than current estimates for the age of anatomically modern humans.

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. (Because his first known historical patrilineal ancestor was Albert Perry, the haplotype is also known as "Perry's Y.") The researchers later found the same haplogroup in genetic data of eleven Mbo males of Western Cameroon (out of a sample of 174). Further research in 2015 indicates that highest concentration of A00 is found in the Bangwa/Nweh (fr:Bangoua (peuple)) people (27 of 67 samples positive for A00 - 40,3%), and that they are in a separate sub-group to the Mbo A00 samples (Nkongho-Mbo - 9,3% (8 of 86 samples)). One individual was found who fits neither sub-group.

A0-P305

A0 or A1b-P305 is found only in Bakola Pygmies (South Cameroon) at 8.3% and Berbers from Algeria at 1.5%. Also found in Ghana.

A1a-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 Guinea-Bissau, especially among the Papel-Manjaco-Mancanha (5/64 = 7.8%). In an earlier study published in 2003, Gonçalves et al. have reported finding A1a-M31 in 5.1% (14/276) of a sample from Guinea-Bissau and in 0.5% (1/201) of a pair of samples from Cabo Verde. The authors of another study have reported finding haplogroup A1a-M31 in 5% (2/39) of a sample of Mandinka from Senegambia and 2% (1/55) of a sample of Dogon from Mali. Haplogroup A1a-M31 also has been found in 3% (2/64) of a sample of Berbers from Morocco and 2.3% (1/44) 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 (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.

A1b-M6 (A2)

The subclade A1b1a1a-M6 (formerly A2) 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, and haplogroup A2b-P28 in 17% (5/29) of a sample of Tsumkwe San, 9% (3/32) of a sample of !Kung/Sekele, 9% (1/11) of a sample of Nama, and 6% (1/18) of a sample of Dama. 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.

A1b1b-M32 (A3)

The clade A1b1b-M32 (formerly A3) contains the most populous branches of haplogroup A and is mainly found in Eastern Africa and Southern Africa.

M28

The subclade A1b1b1-M28 (formerly A3a) has only been rarely observed in the Horn of Africa. In 5% (1/20) of a mixed sample of speakers of South Semitic languages from Ethiopia, 1.1% (1/88) of a sample of Ethiopians, and 0.5% (1/201) in Somalis.

M51

The subclade A1b1b2a-M51 (formerly A3b1) occurs most frequently among Khoisan peoples (6/11 = 55% Nama, 11/39 = 28% Khoisan, 7/32 = 22% !Kung/Sekele, 6/29 = 21% Tsumkwe San, 1/18 = 6% Dama). 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.

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 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% (7/48) of a sample of Amhara and 10.3% (8/78) of a sample of Oromo. 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.

Haplogroup A-M13 also has been observed occasionally outside of Central and Eastern Africa, as in the Aegean Region of Turkey (2/30 = 6.7%), Yemenite Jews (1/20 = 5%), Egypt (4/147 = 2.7%, 3/92 = 3.3%), Palestinian Arabs (2/143 = 1.4%), Sardinia (1/77 = 1.3%, 1/22 = 4.5%), the capital of Jordan, Amman (1/101=1%), and Oman (1/121 = 0.8%).

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