| Haplogroup A | |
| Time of origin | |
| Place of origin | Africa |
| Ancestor | Human Y-MRCA |
| Descendants | A1, A2, A3 |
|---|---|
| Defining mutations | M91 |
| Highest frequencies | Namibia (Tsumke San, Nama) 60-70% Sudan (Dinka,Shilluk) 50-65% |
In human genetics, Haplogroup A (A-M91) refers to a major cluster of human Y-chromosome types that represent one of the two deepest branches of the human Y chromosomal family tree. Men in the same Y-DNA haplogroup share a set of differences, or markers, on their Y chromosome, which distinguish them from men in other haplogroups. The Y chromosome is passed from father to son, and so men in M91 all descend from a shared male line ancestor.
Haplogroup A is found mainly in the Southern Nile region and Southern Africa. However at lower frequencies M91 is found in many areas of Africa, from Morocco, Egypt to Cameroon. Outside of Africa it has been detected in Caucasian males in England, and in the Eastern Mediterranean regions of Anatolia, Levant and Southern Arabia.
Haplogroup A represents one of two deep branches in the Y-chromosomal family tree, the other currently known as Haplogroup BT, therefore the lineage began evolving shortly after the time of Y-chromosomal Adam.[1].
Contents |
Origin
Within the distant past of the human species a haplotype A, the mode of haplogroup A, originated as one of two known basal lineage of the Y-chromosomal Adam, which is the patrilineal ancestor of all living males. This male had at least two sons, and one of his sons is that patrilineal ancestor of haplogroup A. This ancestor almost certainly lived in Africa before humans dispersed from Africa more than 60,000 years ago. Many estimates place the time to this ancestor about 75,000 years ago. This is approximate to the time humans some believed to have left Africa.[2]
The difficulty is describing the origins of Haplogroup A is rooted in its relatively close ties of Haplogroup A with Y-chromosomal Adam. The genetic distance to the haplogroup A node is particularly close to the Y-MRCA. For surface haplogroups, such as haplogroups R, two methods can be combined to estimate the age of the node. One is based on SNPs and the other is based on STR, however for very deep and diverse clades the STR method is not effective. The SNP based methods that are used to estimate the Y-MRCA must also be used to estimate haplogroup A, with a similar lack of confidence. Most estimates are troubled by estimates of the Chimpanzee-human last common ancestor, which is of an unknown age between 4 and 13 million years in age, and new evidence suggests Chimpanzee is evolving at a higher but unknown rate faster than humans.[3] Consequently, uncertainty in the time of Y-MRCA have also create uncertainty in the origin of Haplogroup A. with estimates of the time of the Y-MRCA have ranging from 20,000 to 200,000 years ago. Late estimates require selective sweep models, and early estimates will favor hypothesis that parallel mtDNA defined hypotheses.
Early spread proposals
Many proposals for haplogroup A's origin suggest it was associated with the genetic founding of or branching from Southern Africa's hunter-gatherers; a people that speak Khoisan click languages.[4] With these humans arose either in the region or to north and east of the Southern African deserts (Namib), and spread to the south. While studying mtDNA genomes within Khoisan group, Behar et al. (2008), found that the ancient Khoisan genomes were restricted to L0d and L0k, he estimate the younger branch L0k, to have occurred about 144,000 years ago, about 3/4ths the time of the human mitochondrial MRCA.[5] Estimates of mtEve vary widely, however the youngest estimates, based on the latest possible founding exodus of anatomically modern humans from Africa, places the time of the MtMRCA of approximately 108,000 years ago.[6] This would place this branch point approximately 80,000 years ago, however this early date suggest a very small population in Africa and conflicts with minimum population size estimates based on X-chromosome and Autosomal studies. Preferred estimates accounting for purifying selection would place this LOk branch between 120,000 and 160,000 years ago.[7][8]
| Africa | ||
| . | Study population | Freq. (in %) |
| [9] | Tsumkwe San (Namibia) | 66% |
| [9] | Nama (Namibia) | 64 |
| [10] | Dinka (Sudan) | 62 |
| [10] | Shilluk (Sudan) | 53 |
| [10] | Nuba (Sudan) | 46 |
| [11][12] | Ethiopian Jews | 41 |
| [13] | Khoisan | 44 |
| [11][9] | ǃKung/Sekele | ~40 |
| [10] | Borgu (Sudan) | 35 |
| [10] | Nuer (Sudan) | 33 |
| [10] | Fur (Sudan) | 31 |
| [9] | Maasai (Kenya) | 27 |
| [10] | Masalit (Sudan) | 19 |
| [14][9] | Amhara (Ethiopia) | ~16 |
| [13] | Ethiopians | 14 |
| [15] | Bantu (Kenya) | 14 |
| [9] | Mandara (Cameroon) | 14 |
| [10] | Hausa (Sudan) | 13 |
| [11] | Khwe (South Africa) | 12 |
| [11] | Fulbe (Cameroon) | 12 |
| [9] | Dama (Namibia) | 11 |
| [14] | Oromo (Ethiopia) | 10 |
| [9] | South Semitic (Ethiopia) | 10 |
| [15] | Arabs (Egypt) | 3 |
Y-Haplogroups A and B may have spread during this small expansion of the human population. From other studies it is estimated that the reproducing male population size is about 1/2 that of female population size, and therefore male TMRCA should be more recent than MtDNA TMRCA. Therefore the proximity of the A/BT branchpoint to haplogroup A does not necessarily need to be as great as the distance from L0k to the L0/L1 basal point.
Contiguous population hypothesis
Archeological evidence also suggests that in prehistoric times, populations ancestral to the Khoisan may have lived in areas that extended as far North as Ethiopia and Sudan. The disjointed distribution of haplogroup A may indicate that it was once frequent among hunter gatherers throughout Africa but many of its sub-clades would have been replaced by haplogroup E lineages that arrived with farmers during the Bantu migration.[9] Pockets of Haplogroups A and B would have persisted in populations, such as Ethiopians, Nilo-Saharans and Pygmies, that were isolated from migrating Bantu farmers.
Additional support for an ancient link between the Khoisan and Northeast Africans comes from mitochondrial DNA studies. As with the Y-chromosome, Ethiopians and the Khoisan share the deepest clades of the human mitochondrial phylogeny. haplogroup L0 clades are found among the Khoisan and East Africans (such as Tanzanians, Kenyans and Ethiopians) but are rare or absent in other African populations.[16]
Distribution
In a composite sample of 3551 African men, Haplogroup A had a frequency of 5.4%.[17] The highest frequencies of haplogroup A have been reported among the Khoisan of Southern Africa, Afroasiatic speakers from Ethiopia, and Nilo-Saharans from Sudan. The distribution of haplogroup A provides evidence of an ancient link between the Khoisan and Northeast African populations.
Southern Africa
One study has found haplogroup A in samples of various Khoisan tribes with frequency ranging from 10% to 70%.[9] 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.
Eastern Africa
Haplogroup A is common among the Southern Sudanese (53%),[10] especially the Dinka Sudanese (62%).[18] Haplogroup A also has been observed in another sample of a South Sudanese population at a frequency of 45% (18/40).[13] Hap-A has also been reported in 14.6% (7/48) of an Amhara sample,[14] 10.3% (8/78) of an Oromo sample,[14] 13.6% (12/88) of another sample from Ethiopia,[13] 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), Iraqw in Tanzania (3/43 = 7.0% (Luis et al. 2004) to 1/6 = 17% (Knight et al. 2003)),
Central Africa
Haplogroup A3b2-M13 has been observed in populations of northern Cameroon (2/9 = 22% Tupuri[9], 4/28 = 14% Mandara[9], 2/17 = 12% Fulbe[11]) and eastern DRC (2/9 = 22% Alur[9], 1/18 = 6% Hema[9], 1/47 = 2% Mbuti[9]).
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%).[9]
Northern Africa
The subclade A1 has been observed in North African Berbers, while the subclade A3b2 has been observed in approximately 3% of Egyptian males.
Eurasia
Haplogroup A has been observed as A1 in Caucasian men in England. In the A3 haplogroup it has been observed in Asia Minor and the Middle East it has been observed at low frequencies in Aegean Turks, Sardinians, Palestinians, Jordanians, Yemenites, and Omanis.
Subclades
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Haplogroup A family Tree
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A1-P108
In 2007, seven men from Yorkshire, England sharing a distinctive surname were identified as being from the A1 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 A-P108 subgroup is extremely rare. In addition to the seven Yorkshire men, only 25 living carriers of the A1-P108 subgroup are known, all of West African ancestry.[17] 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%).[24] 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.[9] Haplogroup A1a-M31 also has been found in 3% (2/64) of a sample of Berbers from Morocco[11] and 2.3% (1/44) of a sample of unspecified ethnic affiliation from Mali.[13]
A2-M6
This subclade of haplogroup A is typically found among Khoisan peoples. One study has reported finding haplogroup A2-M6(xA2b-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.[9]
A3-M32
This clade contains the most populous branches of haplogroup A. However, haplogroup A3-M32(xA3b1-M51, A3b2-M13) has been found only rarely, including 5% (1/20) of a mixed sample of speakers of South Semitic languages from Ethiopia.[9] The subclade A3a-M28/M59 has been reported only in 1.1% (1/88) of a sample of Ethiopians.[13]
A3b1-M51
This subclade of haplogroup A occurs most frequently among Khoisan peoples (6/11 = 55% Nama, 7/32 = 22% !Kung/Sekele, 6/29 = 21% Tsumkwe San, 1/18 = 6% Dama).[9] However, it also has been found with lower frequency among Bantu peoples of South Africa, including 2/28 = 7% Sotho-Tswana, 4/80 = 5% Xhosa, and 1/29 = 3% Zulu.[9]
A3b2-M13
The subclade of haplogroup A that is commonly found in East Africa and northern Cameroon (A3b2-M13) 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 A3b2-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 the West African migrant Hausa people, and 5/216 = 2.3% of Northern Sudanese.[25]
In Ethiopia, one study has reported finding haplogroup A3b2-M13 in 14.6% (7/48) of a sample of Amhara and 10.3% (8/78) of a sample of Oromo.[14] 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.[13]
Haplogroup A3b2 also has been observed occasionally outside of Sub-Saharan Africa, as in the Aegean Region of Turkey (2/30 = 6.7%[26]), Yemenite Jews (1/20 = 5%[12]), Egypt (4/147 = 2.7%[15], 3/92 = 3.3%[9]), Palestinian Arabs (2/143 = 1.4%[27]), Sardinia (1/77 = 1.3%[28], 1/22 = 4.5%[13]), the capital of Jordan, Amman (1/101=1%[29]), and Oman (1/121 = 0.8%[15]).
References
- ^ Wood et al
- ^ based on archaeological datings from East India, the dating of an anatomicall modern human in Liujiang China and datings of humans very similar to anatomically modern humans in the Levant at about 93,000 years ago
- ^ the estimates are based on comparisons of X-linked DNA and Autosomes over millions of years, which would give an average estimate of the rate of evolution along human Y-lineages from the CHLCA, but does not define the rate of evolution within Anatomically modern humans
- ^ Gonder et al. 2007 proposed that mtEve originated within the Tanzanian region; however more recently Tishkoff has extrapolated this origin to the Namibia/Angola border region close to the Atlantic coast
- ^ Behar, DM; Villems, R; Soodyall, H; Blue-Smith, J; Pereira, L; Metspalu, E; Scozzari, R; Makkan, H et al. (May 2008). "The dawn of human matrilineal diversity". American Journal of Human Genetics 82 (5): 1130–40. doi:. PMID 18439549. PMC 2427203. http://linkinghub.elsevier.com/retrieve/pii/S0002-9297(08)00255-3.
- ^ Endicott, P; Ho, SY; Metspalu, M; Stringer, C (September 2009), "Evaluating the mitochondrial timescale of human evolution", Trends Ecol. Evol. (Amst.) 24 (9): 515–21, doi:, PMID 19682765
- ^ Soares, P; Ermini, L; Thomson, N; Mormina, M; Rito, T; Röhl, A; Salas, A; Oppenheimer, S et al. (June 2009). "Correcting for purifying selection: an improved human mitochondrial molecular clock". American Journal of Human Genetics 84 (6): 740–59. doi:. PMID 19500773.
- ^ Gonder, MK; Mortensen, HM; Reed, FA; de Sousa, A; Tishkoff, SA (December 2007). "Whole-mtDNA genome sequence analysis of ancient African lineages". Mol. Biol. Evol 24 (3): 757–68. doi:. PMID 17194802.
- ^ a b c d e f g h i j k l m n o p q r s t u v Elizabeth T Wood, Daryn A Stover, Christopher Ehret et al., "Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes," European Journal of Human Genetics (2005) 13, 867–876. (cf. Appendix A: Y Chromosome Haplotype Frequencies)
- ^ a b c d e f g h i 28/53 (Dinka, Nuer, and Shilluk), Hassan HY, Underhill PA, Cavalli-Sforza LL, Ibrahim ME (November 2008). "Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history". Am. J. Phys. Anthropol. 137 (3): 316–23. doi:. PMID 18618658. http://dirkschweitzer.net/E3b-papers/Hassan-Sudan-2008-AJPA.pdf.
- ^ a b c d e f Fulvio Cruciani, Piero Santolamazza, Peidong Shen et al., "A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes," American Journal of Human Genetics 70:1197–1214, 2002
- ^ a b Peidong Shen, Tal Lavi, Toomas Kivisild et al., "Reconstruction of Patrilineages and Matrilineages of Samaritans and Other Israeli Populations From Y-Chromosome and Mitochondrial DNA Sequence Variation," Human Mutation 24:248-260 (2004).
- ^ a b c d e f g h Underhill PA, Shen P, Lin AA, et al. (November 2000). "Y chromosome sequence variation and the history of human populations". Nat. Genet. 26 (3): 358–61. doi:. PMID 11062480.
- ^ a b c d e Semino O, Santachiara-Benerecetti AS, Falaschi F, Cavalli-Sforza LL, Underhill PA (January 2002). "Ethiopians and Khoisan share the deepest clades of the human Y-chromosome phylogeny". Am. J. Hum. Genet. 70 (1): 265–8. doi:. PMID 11719903. PMC 384897. http://linkinghub.elsevier.com/retrieve/pii/S0002-9297(07)61301-9.
- ^ a b c d J. R. Luis, D. J. Rowold, M. Regueiro et al., "The Levant versus the Horn of Africa: Evidence for Bidirectional Corridors of Human Migrations," American Journal of Human Genetics 74:532–544, 2004.
- ^ Gonder et al. (2007). Whole-mtDNA Genome Sequence Analysis of Ancient African Lineages. http://mbe.oxfordjournals.org/cgi/content/full/24/3/757.
- ^ a b King TE, Parkin EJ, Swinfield G, et al. (March 2007). "Africans in Yorkshire? The deepest-rooting clade of the Y phylogeny within an English genealogy". Eur. J. Hum. Genet. 15 (3): 288–93. doi:. PMID 17245408.
News article: "Yorkshire clan linked to Africa". BBC News. 2007-01-24. http://news.bbc.co.uk/2/hi/uk_news/6293333.stm. Retrieved 2007-01-27. - ^ 16/26, Hassan et al. 2008
- ^ Other defining mutations are: M49, M71, M135, M141, M196, M206, M212, MEH1, P3, P4, P5, P36.1, PK1, P247, and P248
- ^ Other defining mutations are: P100, P291
- ^ Other defining mutations are: M63, M127, M202, M219, M305
- ^ Other defining mutations are: M190, M220, and P289
- ^ Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Research 18: 830–8. doi:. http://www.genome.org/cgi/content/abstract/gr.7172008v1.
- ^ Alexandra Rosa, Carolina Ornelas, Mark A Jobling et al., "Y-chromosomal diversity in the population of Guinea-Bissau: a multiethnic perspective," BMC Evolutionary Biology 2007, 7:124 doi:10.1186/1471-2148-7-124.
- ^ 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.
- ^ Cengiz Cinnioğlu, Roy King, Toomas Kivisild et al., "Excavating Y-chromosome haplotype strata in Anatolia," Human Genetics (2004) 114 : 127–148. DOI 10.1007/s00439-003-1031-4
- ^ Almut Nebel, Dvora Filon, Bernd Brinkmann et al., "The Y Chromosome Pool of Jews as Part of the Genetic Landscape of the Middle East," American Journal of Human Genetics 69:1095–1112, 2001
- ^ Ornella Semino, Giuseppe Passarino, Peter J. Oefner et al., "The Genetic Legacy of Paleolithic Homo sapiens sapiens in Extant Europeans: A Y Chromosome Perspective," Science Vol 290 (10 November 2000).
- ^ Flores et al. (2005). "Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan". J Hum Genet 50: 435–441. doi:.
See also
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Human Y-chromosome DNA (Y-DNA) haplogroups (by ethnic groups · famous haplotypes) |
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| most recent common Y-ancestor | |||||||||||||||||||||||||||||||
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| A | BT | ||||||||||||||||||||||||||||||
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| B | CT | ||||||||||||||||||||||||||||||
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| CF | DE | ||||||||||||||||||||||||||||||
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| C | F | D | E | ||||||||||||||||||||||||||||
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| G | H | IJK | |||||||||||||||||||||||||||||
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| IJ | K | ||||||||||||||||||||||||||||||
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| I | J | L | MNOPS | T | |||||||||||||||||||||||||||
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| M | NO | P | S | ||||||||||||||||||||||||||||
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| N | O | Q | R | ||||||||||||||||||||||||||||
External links
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