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Haplogroup A (Y-DNA)

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Haplogroup A
Possible time of originroughly 270,000 ybp[1]
Possible place of originAfrica[2]
AncestorHuman Y-MRCA
DescendantsA00, A0, A1, A2, A3, BT
Highest frequenciesmacro-haplogroup subclades of which are found in various "Northwest-Central African" populations

In human genetics, Haplogroup A is 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",[3] 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.

Origin

Main article: Y-MRCA

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) 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. But the A lineages of Southern Africa are sub-clades of A lineages found in other parts of Africa, suggesting that A lineages arrived in Southern Africa from elsewhere.[4] 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.[5] 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".[6]

Distribution

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,[5][7] and with the inclusion of the previously unknown "A00" haplogroup to about 270 kya in 2015 studies.[8][9]

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,[10] 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.[11][12] 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.[13][14][15]

Haplogroup A frequencies
Africa
Study population Freq.
(in %)
[14] Tsumkwe San (Namibia) 66%
[14] Nama (Namibia) 64
[16] Dinka (Sudan) 62
[16] Shilluk (Sudan) 53
[16] Nuba (Sudan) 46
[17] Khoisan 44
[18][19] Ethiopian Jews 41
[14][18] !Kung/Sekele ~40
[16] Borgu (Sudan) 35
[16] Nuer (Sudan) 33
[16] Fur (Sudan) 31
[14] Maasai (Kenya) 27
[20] Nara (Eritrea) 20
[16] Masalit (Sudan) 19
[14][21] Amhara (Ethiopia) ~16
[17] Ethiopians 14
[22] Bantu (Kenya) 14
[14] Mandara (Cameroon) 14
[16] Hausa (Sudan) 13
[18] Khwe (South Africa) 12
[18] Fulbe (Cameroon) 12
[14] Dama (Namibia) 11
[21] Oromo (Ethiopia) 10
[20] Kunama (Eritrea) 10
[14] South Semitic (Ethiopia) 10
[22] Arabs (Egypt) 3

In a composite sample of 3551 African men, Haplogroup A had a frequency of 5.4%.[23] 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,[14] 4/28 = 14% Mandara,[14] 2/17 = 12% Fulbe[18]) and eastern DRC (2/9 = 22% Alur,[14] 1/18 = 6% Hema,[14] 1/47 = 2% Mbuti[14]).

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%).[14]

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.[12]

Africa —Eastern

Haplogroup A3b2-M13 is common among the Southern Sudanese (53%),[16] especially the Dinka Sudanese (61.5%).[24] 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.[17] Haplogroup A also has been reported in 14.6% (7/48) of an Amhara sample,[21] 10.3% (8/78) of an Oromo sample,[21] 13.6% (12/88) of another sample from Ethiopia,[17] 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%.[14] 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[25] and in samples of Portuguese from southern Portugal, central Portugal, and Madeira.[26] The authors of one study have reported finding what appears to be haplogroup A in 3.1% (2/65) of a sample of Cypriots,[27] though they have not definitively excluded the possibility that either of these individuals may belong to haplogroup B or haplogroup C.

Subclades

Nomenclature

Main article: Conversion table for Y chromosome haplogroups

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
A-M31 7 I 1A 1 – H1 A A1 A1 A1 A1a A1 A1 A1a A1a A1a A1a A1a
A-M6 27 I 2 3 – H1 A A2* A2 A2 A2 A2 A2 A2 A2 A2 A2 A1b1a1a
A-M114 27 I 2 3 – H1 A A2a A2a A2a A2a A2a A2a A2a A2a A2a A2a A1b1a1a1a
A-P28 27 I 2 4 – H1 A A2b A2b A2b A2b A2b A2b A2b A2b A2b A2b A1b1a1a1b
A-M32 * * * * * * * * A3 A3 A3 A3 A3 A3 A3 A3 A3 A1b1b
A-M28 7 I 1A 1 – H1 A A3a A3a A3a A3a A3a A3a A3a A3a A3a A3a A1b1b1
A-M51 7 I 1A 1 – H1 A A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A3b1 A1b1b2a
A-M13 7 I 1A 2 Eu1 H1 A A3b2* A3b2 A3b2 A3b2 A3b2 A3b2 A3b2 A3b2 A3b2 A3b2 A1b1b2b
A-M171 7 I 1A 2 Eu1 H1 A A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a A3b2a removed
A-M118 7 I 1A 2 Eu1 H1 A A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A3b2b A1b1b2b1

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

3

Cruciani et al. 2011

The revised y-chromosome family tree by Cruciani et al. 2011 compared with the family tree from Karafet et al. 2008. A1b is now known as A0 according ISOGG.

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.[28] 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.[5] 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.[5][28]

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.[5]

Overview

This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) Tree,[29] the ISOGG Y-DNA Haplogroup Tree,[11] and subsequent published research.

Y-chromosomal Adam

  • 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)
        • 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)
      • 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)

A00 (Perry's Y-chromosome)

Mendez et al. (2013) announced the discovery of a previously unknown haplogroup, for which they proposed the designator "A00".[30] With an estimated age of around 270 kya,[8][9] older than current estimates for the age of anatomically modern humans.[31]

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."[32]) The researchers later found the same haplogroup in genetic data of eleven Mbo males of Western Cameroon (out of a sample of 174).[33] Further research in 2015 indicates that highest concentration of A00 is found in the Bangwa people (27 of 67 samples positive for A00), and that they are in a separate sub-group to the Mbo A00 samples. One individual was found who fits neither sub-group.[34]

A0-P305

A0 or A1b-P305 is found only in Bakola Pygmies (South Cameroon) at 8.3% and Berbers from Algeria at 1.5%.[5] Also found in Ghana.[6]

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%).[13] 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.[35] 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.[14] Haplogroup A1a-M31 also has been found in 3% (2/64) of a sample of Berbers from Morocco[18] and 2.3% (1/44) of a sample of unspecified ethnic affiliation from Mali.[17]

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.[23]

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.[14] 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.[17]

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,[14] 1.1% (1/88) of a sample of Ethiopians,[17] and 0.5% (1/201) in Somalis.[10]

M51

The subclade A1b1b2a-M51 (formerly A3b1) occurs most frequently among Khoisan peoples (6/11 = 55% Nama,[14] 11/39 = 28% Khoisan,[17] 7/32 = 22% !Kung/Sekele,[14] 6/29 = 21% Tsumkwe San,[14] 1/18 = 6% Dama[14]). However, it also has been found with lower frequency among Bantu peoples of Southern Africa, including 2/28 = 7% Sotho–Tswana,[14] 3/53 = 6% non-Khoisan Southern Africans,[17] 4/80 = 5% Xhosa,[14] and 1/29 = 3% Zulu.[14]

M13

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.[36]

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.[21] 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.[17]

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%[37]), Yemenite Jews (1/20 = 5%[19]), Egypt (4/147 = 2.7%,[22] 3/92 = 3.3%[14]), Palestinian Arabs (2/143 = 1.4%[38]), Sardinia (1/77 = 1.3%,[39] 1/22 = 4.5%[17]), the capital of Jordan, Amman (1/101=1%[40]), and Oman (1/121 = 0.8%[22]).

See also

Y-DNA A subclades
3

References

  1. ^ equivalent to an estimate of the age of the human Y-MRCA (see there); including the A00 lineage, Karmin et al. (2015) and Trombetta et al. (2015) estimate ages of 254,000 and 291,000 ybp, respectively.
  2. ^ 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. {{cite journal}}: Cite has empty unknown parameter: |author-separator= (help); Explicit use of et al. in: |author6= (help); Unknown parameter |displayauthors= ignored (|display-authors= suggested) (help)CS1 maint: unflagged free DOI (link)
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  11. ^ a b International Society of Genetic Genealogy. "Y-DNA Haplogroup Tree". Retrieved 2012. {{cite web}}: Check date values in: |accessdate= (help)
  12. ^ a b Berniell-Lee G, Calafell F, Bosch E, et al. (July 2009). "Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages". Mol. Biol. Evol. 26 (7): 1581–9. doi:10.1093/molbev/msp069. PMID 19369595.
  13. ^ a b Rosa A, Ornelas C, Jobling MA, Brehm A, Villems R (2007). "Y-chromosomal diversity in the population of Guinea-Bissau: a multiethnic perspective". BMC Evol. Biol. 7: 124. doi:10.1186/1471-2148-7-124. PMC 1976131. PMID 17662131.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  14. ^ a b c d e f g h i j k l m n o p q r s t u v w x y z aa Wood ET, Stover DA, Ehret C, et al. (July 2005). "Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes". Eur. J. Hum. Genet. 13 (7): 867–76. doi:10.1038/sj.ejhg.5201408. PMID 15856073.
  15. ^ Underhill PA, Passarino G, Lin AA, et al. (January 2001). "The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations". Ann. Hum. Genet. 65 (Pt 1): 43–62. doi:10.1046/j.1469-1809.2001.6510043.x. PMID 11415522.
  16. ^ 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" (PDF). Am. J. Phys. Anthropol. 137 (3): 316–23. doi:10.1002/ajpa.20876. PMID 18618658.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  17. ^ a b c d e f g h i j k 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:10.1038/81685. PMID 11062480.
  18. ^ a b c d e f Cruciani F, Santolamazza P, Shen P, et al. (May 2002). "A back migration from Asia to sub-Saharan Africa is supported by high-resolution analysis of human Y-chromosome haplotypes". Am. J. Hum. Genet. 70 (5): 1197–214. doi:10.1086/340257. PMC 447595. PMID 11910562.
  19. ^ a b Shen P, Lavi T, Kivisild T, et al. (September 2004). "Reconstruction of patrilineages and matrilineages of Samaritans and other Israeli populations from Y-chromosome and mitochondrial DNA sequence variation". Hum. Mutat. 24 (3): 248–60. doi:10.1002/humu.20077. PMID 15300852.
  20. ^ a b Cruciani F, Trombetta B, Sellitto D, et al. (July 2010). "Human Y chromosome haplogroup R-V88: a paternal genetic record of early mid Holocene trans-Saharan connections and the spread of Chadic languages". Eur. J. Hum. Genet. 18 (7): 800–7. doi:10.1038/ejhg.2009.231. PMC 2987365. PMID 20051990.
  21. ^ 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:10.1086/338306. PMC 384897. PMID 11719903.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  22. ^ a b c d Luis JR, Rowold DJ, Regueiro M, et al. (March 2004). "The Levant versus the Horn of Africa: evidence for bidirectional corridors of human migrations". Am. J. Hum. Genet. 74 (3): 532–44. doi:10.1086/382286. PMC 1182266. PMID 14973781.
  23. ^ 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:10.1038/sj.ejhg.5201771. PMC 2590664. PMID 17245408.
    News article: "Yorkshire clan linked to Africa". BBC News. 2007-01-24. Retrieved 2007-01-27.
  24. ^ 16/26, Hassan et al. 2008
  25. ^ Di Giacomo F, Luca F, Anagnou N, et al. (September 2003). "Clinal patterns of human Y chromosomal diversity in continental Italy and Greece are dominated by drift and founder effects". Mol. Phylogenet. Evol. 28 (3): 387–95. doi:10.1016/S1055-7903(03)00016-2. PMID 12927125.
  26. ^ Gonçalves R, Freitas A, Branco M, et al. (July 2005). "Y-chromosome lineages from Portugal, Madeira and Açores record elements of Sephardim and Berber ancestry". Ann. Hum. Genet. 69 (Pt 4): 443–54. doi:10.1111/j.1529-8817.2005.00161.x. PMID 15996172.
  27. ^ Capelli C, Redhead N, Romano V, et al. (March 2006). "Population structure in the Mediterranean basin: a Y chromosome perspective". Ann. Hum. Genet. 70 (Pt 2): 207–25. doi:10.1111/j.1529-8817.2005.00224.x. PMID 16626331.
  28. ^ a b 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 (5): 830–8. doi:10.1101/gr.7172008. PMC 2336805. PMID 18385274.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  29. ^ Krahn, Thomas. "YCC Tree". Houston, Texas: FTDNA. Retrieved 16 May 2011.
  30. ^ 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. [2011] 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."
  31. ^ At first (Mendez et al. 2013) 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).
  32. ^ Albert Perry, a slave born in the United States between ca. 1819–1827, lived in York County, South Carolina. See FamilyTreeDNA, Haplogroup A chart
  33. ^ 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)".
  34. ^ 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 epicenter 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.".
  35. ^ 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.
  36. ^ 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.
  37. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: numeric names: authors list (link)
  38. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  39. ^ 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.
  40. ^ 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
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