Haplogroup A (Y-DNA)
|This article is outdated. (March 2013)|
|Possible time of origin||roughly 200,000 ybp|
|Possible place of origin||Africa|
|Descendants||A00, A0, A1, A2, A3, BT|
|Highest frequencies||macro-haplogroup subclades of which are found in various "Northwest-Central African" populations|
In human genetics, Haplogroup A is the a Human Y-chromosome DNA haplogroup. Unlike all other Y-DNA haplogroups, it is not defined by a specific mutation, but as the foundational clade of the patrilineal lineage of contemporary human population, by definition rooted in this population's Y-MRCA (or "Y-chromosomal Adam").
Formerly also known as "clade I", bearers of extant sub-clades of haplogroup A are entirely found in Africa (or among descendants of recently extracted African populations), in contrast with the descendant haplogroup BT ("clade II-X") 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" (also "A1a-T") and "A2-T". Haplogroup BT, ancestral to all non-African haplogroups, is a subclade of A2-T.
- 1 Origin
- 2 Distribution
- 3 Subclades
- 4 See also
- 5 References
- 6 External links
There are terminological difficulties,[clarification needed] 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 200 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) were 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. But the A lineages of Southern Africa are sub-clades of A lineages found in other parts of Africa. This suggests that A lineages 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 A 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 200 kya in a 2014 study.
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.
|||Tsumkwe San (Namibia)||66%|
|||Khwe (South Africa)||12|
|||South Semitic (Ethiopia)||10|
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.
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).
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.
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)).
The subclade A1 has been observed in Moroccan Berbers, while the subclade A3b2 has been observed in approximately 3% of Egyptian males.
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.
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.
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.
|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|
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.
But 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.
- A0 (formerly A1b) (P305, V148, V149, V154, V164, V166, V172, V173, V177, V190, V196, V223, V225, V229, V233, V239)
- A1 (A1a-T according Cruciani 2011) (L985, L989, L990, L1002, L1003, L1004, L1009, L1013, L1053, V161, V168, V171, V174, V203, V238, V241, V250, V238, V241, V250)
- A1a (M31, P82, V4, V14, V15, V25, V26, V28, V30, V40, V48, V53, V57, V58, V63, V76, V191, V201, V204, V214, V215, V236)
- A1b (A2-T according Cruciani 2011) (P108, V221)
- A1b1 (L419)
- A1b1a (V50, V82, V198, V224)
- A1b1a1 formerly A2 (M14, M23, L968/M29/P3/PN3, M71, M135, M141, M206, M276/P247, M277/P248, MEH1, P4, P5, P36.1, Page71, Page87, Page95)
- A1b1a1a (M6, M196)
- A1b1a1a1 (M212)
- A1b1a1a1a formerly A2a (M114)
- A1b1a1a1b formerly A2b (P28)
- A1b1a1a1c formerly A2c (P262)
- A1b1a1a1 (M212)
- A1b1a1a (M6, M196)
- A1b1a1 formerly A2 (M14, M23, L968/M29/P3/PN3, M71, M135, M141, M206, M276/P247, M277/P248, MEH1, P4, P5, P36.1, Page71, Page87, Page95)
- A1b1b formerly A3 (M32)
- A1b1b1 formerly A3a (M28, M59)
- A1b1b2 formerly A3b (M144, M190, M220, P289)
- A1b1b2a formerly A3b1 (M51, P100, P291)
- A1b1b2a1 formerly A3b1a (P71, P102)
- A1b1b2b formerly A3b2 (M13, M127, M202, M219, M305):
- A1b1b2b1 (M118)
- A1b1b2a formerly A3b1 (M51, P100, P291)
- A1b1a (V50, V82, V198, V224)
- BT (M42, M94, M139, M299, M60, M181/Page32, P85, P90, P97, Page65.1/SRY1532.1/SRY10831.1, V21, V29, V31, V59, V64, V102, V187, V202, V216, V235)
- A1b1 (L419)
A00 (Perry's Y-chromosome)
Mendez et al. (2013) announced the discovery of a previously unknown haplogroup, for which they proposed the designator "A00". At first 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). A 2014 follow-up publication by Elhaik et al. revised this estimate to 208 kya (95% confidence interval 163.9–260.2 kya); this is still consistent with the established 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).
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 a distinctive surname were identified as being from the A1a-M31 subgroup of haplogroup A. 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.
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.
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.
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.
The subclade A1b1b2b-M13 (formerly A3b2) that is commonly found in East Africa and northern Cameroon is different from those 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%).
- Human Y-chromosome DNA haplogroup
- Y-DNA haplogroups by populations of Sub-Saharan Africa
- Y-DNA haplogroups by ethnic groups
- Y-DNA A subclades
- equivalent to an estimate of the age of the human Y-MRCA (see there); including the A00 lineage, Elhaik et al. (2014) estimate a 95% confidence interval of 163,900 to 260,200 ybp.
- According to Cruciani et al. 2011, the most basal lineages have been detected in West, Northwest and Central Africa, suggesting plausibility for the Y-MRCA living in the general region of "Central-Northwest 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. doi:10.1016/j.ajhg.2011.05.002. PMC 3113241. 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. doi:10.1371/journal.pone.0049170. PMC 3492319. PMID 23145109.
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- Mendez, Fernando; Krahn, Thomas; Schrack, Bonnie; Krahn, Astrid-Maria; Veeramah, Krishna; Woerner, August; Fomine, Forka Leypey Mathew; Bradman, Neil; Thomas, Mark; Karafet, Tatiana M.; Hammer, Michael F. (7 March 2013). "An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree" (PDF). American Journal of Human Genetics 92 (3): 454–9. doi:10.1016/j.ajhg.2013.02.002. PMC 3591855. PMID 23453668. "Genotyping of a DNA sample that was submitted to a commercial genetic-testing facility demonstrated that the Y chromosome of this African American individual carried the ancestral state of all known Y chromosome SNPs. To further characterize this lineage, which we dubbed A00 (see Figure S1, available online, for proposed nomenclature)"; "We have renamed the basal branch in Cruciani et al.  as A0 (previously A1b) and refer to the presently reported lineage as A00. For deep branches discovered in the future, we suggest continuing the nomenclature A000, and so on."
- "The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome". EJHG 22 (9): 1111–6. 2014. doi:10.1038/ejhg.2013.303. PMID 24448544. "Our analysis indicates that the A00 lineage was derived from all the other lineages 208 300 (95% CI=163 900–260 200) years ago."
- 'Y-Chromosomal Adam Lived 208,300 Years Ago, Says New Study', Sci-News.com, 23 January 2014.
- Albert Perry, an American slave born between ca. 1819–1827 in the United States, lived in York County, South Carolina. See FamilyTreeDNA, Haplogroup A chart
- 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)".
- Gonçalves R, Rosa A, Freitas A et al. (November 2003). "Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers". Hum. Genet. 113 (6): 467–72. doi:10.1007/s00439-003-1007-4. PMID 12942365.
- 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.
- Cinnioğlu C, King R, Kivisild T et al. (January 2004). "Excavating Y-chromosome haplotype strata in Anatolia". Hum. Genet. 114 (2): 127–48. doi:10.1007/s00439-003-1031-4. PMID 14586639.
- Nebel A, Filon D, Brinkmann B, Majumder PP, Faerman M, Oppenheim A (November 2001). "The Y chromosome pool of Jews as part of the genetic landscape of the Middle East". Am. J. Hum. Genet. 69 (5): 1095–112. doi:10.1086/324070. PMC 1274378. PMID 11573163.
- Semino O, Passarino G, Oefner PJ et al. (November 2000). "The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: a Y chromosome perspective". Science 290 (5494): 1155–9. doi:10.1126/science.290.5494.1155. PMID 11073453.
- Flores C, Maca-Meyer N, Larruga JM, Cabrera VM, Karadsheh N, Gonzalez AM (2005). "Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan". J. Hum. Genet. 50 (9): 435–41. doi:10.1007/s10038-005-0274-4. PMID 16142507.
- Mendez FL, Krahn T, Schrack B et al. (March 2013). "An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree". Am. J. Hum. Genet. 92 (3): 454–9. doi:10.1016/j.ajhg.2013.02.002. PMC 3591855. PMID 23453668. as PDF
- "Y-Haplogroup A Phylogenetic Tree". March 2013. Retrieved 30 March 2013. (chart highlighting new branches added to the A phylotree in March 2013)
- Family Tree DNA — Y-Haplogroup A Project
- African Haplogroup project at FTDNA
- Spread of Haplogroup A, from National Geographic
|Evolutionary tree of human Y-chromosome DNA (Y-DNA) haplogroups [n 1] [n 2]|
|A00||A0-T [n 3]|
|L||T||MPS (K2b)||NO (K2a)||K2c||K2d||K2e [n 5]|