The discovery of two SNPs (V38 and V100) by Trombetta et al. (2011) significantly redefined the E-V38 phylogenetic tree. This led the authors to suggest that
E-V38 may have originated in East Africa. E-V38 joins the
West African-affiliated E-M2 and the
Northeast African-affiliated E-M329 with an earlier common ancestor who, like E-P2, may have also originated in
East Africa.[5] The downstream SNP E-M180 may have originated in the
humidSaharan savanna/grassland of
North Africa between 14,000 BP and 10,000 BP.[6][7][8][9] According to Wood et al. (2005) and Rosa et al. (2007), such population movements changed the pre-existing population Y chromosomal diversity in
Central,
Southern, and
SoutheasternAfrica, replacing the previous
haplogroup frequencies in these areas with the now dominant E1b1a1 lineages. Traces of earlier inhabitants, however, can be observed today in these regions via the presence of the Y DNA haplogroups
A1a, A1b, A2, A3, and
B-M60 that are common in certain populations, such as the
Mbuti and
Khoisan.[10][11][12] Shriner et al. (2018) similarly suggests that haplogroup E1b1a-V38 migrated across the
Green Sahara from
east to west around 19,000 years ago, where E1b1a1-M2 may have subsequently originated in
West Africa or
Central Africa. Shriner et al. (2018) also traces this migration via
sickle cell mutation, which likely originated during the Green Sahara period.[4]
Hawass et al. (2012) determined that the
ancient Egyptian mummy of an unknown man buried with Ramesses was, because of the proven genetic relationship and a
mummification process that suggested punishment, a good candidate for the pharaoh's son, Pentaweret, who was the only son to revolt against his father.[15] It was impossible to determine his cause of death.[15] Using Whit Athey's haplogroup predictor based on Y-
STR values, both mummies were predicted to share the Y chromosomal haplogroup E1b1a1-M2 and 50% of their genetic material, which pointed to a father-son relationship.[15] Gad et al. (2021) indicates that
Ramesses III and Unknown Man E, possibly
Pentawere, carried
haplogroup E1b1a.[16]
E1b1a1a1a1c2c (CTS3274) was found recently in a Middle Neolithic sample from
Noyen-sur-Seine.[20] This is the earliest example of E1b1a found anywhere in the world.
Amid the
Green Sahara, the mutation for
sickle cell originated in the
Sahara[41] or in the
northwest forest region of western Central Africa (e.g., Cameroon)[41][42] by at least 7,300 years ago,[41][42] though possibly as early as 22,000 years ago.[43][42] The ancestral sickle cell haplotype to modern haplotypes (e.g.,
Cameroon/
Central African Republic and
Benin/
Senegal haplotypes) may have first arose in the ancestors of modern West Africans, bearing haplogroups
E1b1a1-L485 and
E1b1a1-U175 or their ancestral haplogroup E1b1a1-M4732.[41] West Africans (e.g.,
Yoruba and
Esan of Nigeria), bearing the Benin sickle cell haplotype, may have migrated through the
northeastern region of Africa into the western region of
Arabia.[41] West Africans (e.g.,
Mende of Sierra Leone), bearing the Senegal sickle cell haplotype,[44][41] may have migrated into
Mauritania (77% modern rate of occurrence) and Senegal (100%); they may also have migrated across the Sahara, into
North Africa, and from North Africa, into
Southern Europe,
Turkey, and a region near northern
Iraq and southern Turkey.[44] Some may have migrated into and introduced the Senegal and Benin sickle cell haplotypes into
Basra, Iraq, where both occur equally.[44] West Africans, bearing the Benin sickle cell haplotype, may have migrated into the northern region of Iraq (69.5%),
Jordan (80%),
Lebanon (73%),
Oman (52.1%), and
Egypt (80.8%).[44]
Distribution
E-M2's frequency and diversity are highest in West Africa. Within Africa, E-M2 displays a west-to-east as well as a south-to-north clinal distribution. In other words, the frequency of the haplogroup decreases as one moves from western and southern Africa toward the eastern and northern parts of Africa.[45]
E-M2 is found at low to moderate frequencies in
North Africa, and
Northeast Africa. Some of the lineages found in these areas are possibly due to the
Bantu expansion or other migrations.[45][53] However, the discovery in 2011 of the E-M2 marker that predates E-M2 has led Trombetta et al. to suggest that E-M2 may have originated in East Africa.[5] In Eritrea and most of Ethiopia (excluding the
Anuak), E-V38 is usually found in the form of E-M329, which is autochthonous, while E-M2 generally indicates Bantu migratory origins.[54][55][56]
Outside of Africa, E-M2 has been found at low frequencies. The clade has been found at low frequencies in
West Asia. A few isolated occurrences of E-M2 have also been observed among populations in
Southern Europe, such as
Croatia,
Malta,
Spain and
Portugal.[64][65][66][67]
E1b1a1 is defined by markers DYS271/M2/SY81, M291, P1/PN1, P189, P293, V43, and V95. Whilst E1b1a reaches its highest frequency of 81% in Senegal, only 1 of the 139 Senegalese that were tested showed M191/P86.[48] In other words, as one moves to West Africa from western Central Africa, the less subclade E1b1a1f is found. Cruciani et al. (2002) states: "A possible explanation might be that haplotype 24 chromosomes [E-M2*] were already present across the Sudanese belt when the M191 mutation, which defines haplotype 22, arose in central western Africa. Only then would a later demic expansion have brought haplotype 22 chromosomes from central western to western Africa, giving rise to the opposite clinal distributions of haplotypes 22 and 24."[46]
E1b1a1a1
E1b1a1a1 is commonly defined by M180/P88. The basal subclade is quite regularly observed in M2+ samples.
E1b1a1a1a
E1b1a1a1a is defined by marker M58. 5% (2/37) of the town
Singa-Rimaïbé,
Burkina Faso tested positive for E-M58.[46] 15% (10/69) of
Hutus in
Rwanda tested positive for M58.[45] Three South Africans tested positive for this marker.[12] One
Carioca from
Rio de Janeiro,
Brazil tested positive for the M58 SNP.[83] The place of origin and age is unreported.
E1b1a1a1b
E1b1a1a1b is defined by M116.2, a private marker. A single carrier was found in
Mali.[12][d]
E1b1a1a1c
E1b1a1a1c is defined by private marker M149. This marker was found in a single South African.[12]
E1b1a1a1d
E1b1a1a1d is defined by a private marker M155. It is known from a single carrier in Mali.[12]
E1b1a1a1e
E1b1a1a1e is defined by markers M10, M66, M156 and M195. Wairak people in Tanzania tested 4.6% (2/43) positive for E-M10.[45] E-M10 was found in a single person of the Lissongo group in the
Central African Republic and two members in a "Mixed" population from the
Adamawa region.[12]
E1b1a1a1f
E1b1a1a1f is defined by L485. The basal node E-L485* appears to be somewhat uncommon but has not been sufficiently tested in large populations. The ancestral L485 SNP (along with several of its subclades) was very recently discovered. Some of these SNPs have little or no published population data and/or have yet to receive nomenclature recognition by the
YCC.
E1b1a1a1f1 is defined by marker L514. This SNP is currently without population study data outside of the
1000 Genomes Project.
E1b1a1a1f1a (YCC E1b1a7) is defined by marker M191/P86. Filippo et al. (2011) studied a number of African populations that were E-M2 positive and found the basal E-M191/P86 (without E-P252/U174) in a population of
Gur speakers in Burkina Faso.[84] Montano et al. (2011) found similar sparse distribution of E-M191* in
Nigeria,
Gabon, Cameroon and Congo.[9] M191/P86 positive samples occurred in tested populations of
Annang (38.3%),
Ibibio (45.6%),
Efik (45%), and
Igbo (54.3%) living in Nigeria, West Africa.[85] E-M191/P86 appears in varying frequencies in Central and Southern Africa but almost all are also positive for P252/U174. Bantu-speaking South Africans (89/343) tested 25.9% positive and
Khoe-San speaking South Africans tested 7.7% (14/183) positive for this SNP.[86] It also appears commonly in Africans living in the Americas. A population in Rio de Janeiro, Brazil tested 9.2% (12/130) positive.[83] 34.9% (29/83) of
African American men tested positive for M191.[75]
Veeramah et al. (2010) studies of the recombining portions of M191 positive Y chromosomes suggest that this lineage has "diffusely spread with multiple high frequency haplotypes implying a longer evolutionary period since this haplogroup arose".[85] The subclade E1b1a1a1f1a appears to express opposite clinal distributions to E1b1a1* in the West African Savanna region. Haplogroup E1b1a1a1f1a (E-M191) has a frequency of 23% in Cameroon (where it represents 42% of haplotypes carrying the DYS271 mutation or E-M2), 13% in Burkina Faso (16% of haplotypes carrying the M2/DYS271 mutation) and only 1% in
Senegal.[48] Similarly, while E1b1a reaches its highest frequency of 81% in Senegal, only 1 of the 139 Senegalese that were tested showed M191/P86.[48] In other words, as one moves to West Africa from western Central Africa, the less subclade E1b1a1f is found. "A possible explanation might be that haplotype 24 chromosomes [E-M2*] were already present across the Sudanese belt when the M191 mutation, which defines haplotype 22, arose in central western Africa. Only then would a later demic expansion have brought haplotype 22 chromosomes from central western to western Africa, giving rise to the opposite clinal distributions of haplotypes 22 and 24."[46]
E1b1a1a1f1a1 (YCC E1b1a7a) is defined by P252/U174. It appears to be the most common subclade of E-L485. It is believed to have originated near western Central Africa. It is rarely found in the most western portions of West Africa. Montano et al. (2011) found this subclade very prevalent in Nigeria and Gabon.[9] Filippo et al. (2011) estimated a tMRCA of ~4.2 kya from sample of Yoruba population positive for the SNP.[84]
E1b1a1a1f1a1b (YCC E1b1a7a2) is defined by P115. This subclade has only been observed amongst
Fang people of Central Africa.[9]
E1b1a1a1f1a1c (YCC E1b1a7a3) is defined by P116. Montano et al. (2011) observed this SNP only in Gabon and a
Bassa population from Cameroon.[9]
E1b1a1a1f1a1d is defined by Z1704. This subclade has been observed across Africa. The 1000 Genomes Project Consortium found this SNP in Yoruba Nigerian, three Kenyan
Luhyas and one African descent Puerto Rican.[87]
E1b1a1a1f1b is defined by markers L515, L516, L517, and M263.2. This subclade was found by the researchers of Y-Chromosome Genome Comparison Project using data from the commercial bioinformatics company
23andMe.[88]
E1b1a1a1g
E1b1a1a1g (YCC E1b1a8) is defined by marker U175. The basal E-U175* is extremely rare. Montano et al. (2011) only found one out of 505 tested African subjects who was U175 positive but negative for U209.[9] Brucato et al. found similarly low frequencies of basal E-U175* in subjects in the Ivory Coast and Benin. Veeramah et al. (2010) found U175 in tested Annang (45.3%), Ibibio (37%), Efik (33.3%), and Igbo (25.3%) but did not test for U209.[85]
The supposed "Bantu haplotype" found in E-U175 carriers is "present at appreciable frequencies in other
Niger–Congo languages speaking peoples as far west as
Guinea-Bissau".[85] This is the modal haplotype of STR markers that is common in carriers of E-U175.[e]
E-U175 haplotype
DYS19
DYS388
DYS390
DYS391
DYS392
DYS393
15
12
21
10
11
13
E1b1a1a1g has several subclades.
E1b1a1a1g1 (YCC E1b1a8a) is defined by U209. It is the most prominent subclade of U175. This subclade has very high frequencies of over fifty percentages in Cameroonian populations of Bassa and Bakaka, possibly indicating place of origin. However, E-U209 is widely found at lower frequencies in West and Central African countries surrounding Cameroon and Gabon.[9] Brucato et al. (2010) found the SNP in a populations of Ahizi (in
Ivory Coast) 38.8% (19/49), Yacouba (Ivory Coast) 27.5% (11/40), and Beninese 6.5% (5/77) respectively.[89]
E1b1a1a1g1a (YCC E1b1a8a1) is defined by U290. The Montano et al. (2011) study of U290 showed a lower frequency in Nigeria (11.7%) and western Central Africa than basal node U209. The highest population frequency rate in that study was 57.7% (15/26) in Ewondo in Cameroon.[9] 32.5% (27/83) of African American men tested by Sims et al. (2007) were positive for this SNP.[75]
E1b1a1a1g1a2 is defined by Z1725. This marker has been observed by The 1000 Genomes Project Consortium in Yoruba Nigerians and Luhya Kenyans.[87]
E1b1a1a1g1c (YCC E1b1a4) is defined by M154. A
Bamilike population tested 31.3% (15/48) for the marker. Bakaka speakers from Cameroon tested 8%.[46] An
Ovimbundu test population found this SNP at 14% (14/100).[90] Members of this subclade have also been found in South Africa.[91][86]
E1b1a1a1g1d is defined by V39. Trombetta et al. first published this SNP in 2011 but gave little population data about it.[5] It is only known to have been found in an African population.
E1b1a1a1h
E1b1a1a1h is defined by markers P268 and P269. It was first reported in a person from the
Gambia.[92]
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.
This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) 2008 Tree,[92] the ISOGG Y-DNA Haplogroup E Tree,[7] and subsequent published research.
^Van Oven M, Van Geystelen A, Kayser M, Decorte R, Larmuseau HD (2014). "Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome". Human Mutation. 35 (2): 187–91.
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^ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
^ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a).
^K-M2313*, which as yet has no phylogenetic name, has been documented in two living individuals, who have ethnic ties to India and South East Asia. In addition, K-Y28299, which appears to be a primary branch of K-M2313, has been found in three living individuals from India. See: Poznik op. cit.;
YFull YTree v5.08, 2017, "K-M2335", and;
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^ Haplogroup K2b1 (P397/P399) is also known as Haplogroup MS, but has a broader and more complex internal structure.
^E-M2 is approximately 7.7–7.9% of total US male population.
^The publication transposes M116.2 with M116.1 in Table 1.
^The YCAII STR marker value of 19–19 is also usually indicative of U175.
^DYS271/M2/SY81, P1/PN1, P189, P293, and M291 appear to form E1b1a1*. L576 forms a subclade immediately after the previously mentioned SNPs. L576 gave rise to a deeper subclade of M180/P88, P182, L88.3, L86, and PAGES0006. From this subclade, all the major subclades (i.e. E-U175 and E-L485) of E1b1a evolved. The exact position of V43 and V95 within these three subclades and E1b1a1a1b (M116.2), E1b1a1a1c (M149), and E1b1a1a1d (M155)
remains uncertain.
^
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^Mršić G, Gršković B, Vrdoljak A, Popović M, Valpotić I, Anđelinović Š, Stenzl V, Ehler E, Urban L, Lacković G, Underhill P, Primorac D (July 2012). "Croatian national reference Y-STR haplotype database". Molecular Biology Reports. 39 (7). Branka Grskovic, Andro Vrdoljak, Maja Popovic, Ivica Valpotic, Simun Andelinovic, Vlastimil Stenzl, Edvard Ehler, Ludvik Urban, Gordana Lackovic, Peter Underhill, Dragan Primorac: 7727–41.
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