Haplogroup E-M96

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Haplogroup E
Possible time of origin 50,000 - 55,000 years BP[1] 50,000-55,000 split between D and E[2]
Possible place of origin East Africa,[3] or possibly Asia[4]
Ancestor DE
Descendants E-P147, E-M75
Defining mutations L339, L614, M40/SRY4064/SRY8299, M96, P29, P150, P152, P154, P155, P156, P162, P168, P169, P170, P171, P172, P173, P174, P175, P176

In human genetics, Haplogroup E-M96 is a human Y-chromosome DNA haplogroup. Haplogroup E-M96 is one of the two main branches of the older Haplogroup DE, the other main branch being haplogroup D. The E-M96 clade is divided into two subclades: The more common E-P147 and the less common E-M75.

Origins

Underhill (2001) proposed that haplogroup E may have arisen in East Africa.[5] Some authors as Chandrasekar (2007), continue to accept the earlier position of Hammer (1997) that Haplogroup E may have originated in Asia,[6] given that:

  • E is a clade of Haplogroup DE, with the other major clade, haplogroup D, being Asian.
  • DE is a clade within M168 with the other two major clades, C and F, considered to have a Eurasian origin.

However, several discoveries made since the Hammer articles are thought to make an Asian origin less likely:

  1. Underhill and Kivisild (2007) demonstrated that C and F have a common ancestor meaning that DE has only one sibling which is non-African.[7]
  2. DE* is found in both Asia and Africa, meaning that not only one, but several siblings of D are found in Asia and Africa.
  3. Karafet (2008), in which Hammer is a co-author, significantly rearranged time estimates leading to "new interpretations on the geographical origin of ancient sub-clades".[1] Amongst other things this article proposed a much older age for haplogroup E-M96 than had been considered previously, giving it a similar age to Haplogroup D, and DE itself, meaning that there is no longer any strong reason to see it as an offshoot of DE which must have happened long after DE came into existence and had entered Asia.[1]

Distribution

Haplogroup E (Y-DNA)

Most members of haplogroup E-M96 belong to one of its identified subclades, and the E-M96 (xE-P147,xE-M75) lineage is rare. E1a and E-M75 are found almost exclusively in Africa. By looking at the major subclade frequencies, five broad regions of Africa can be defined: East, Central, North, Southern and West. The division can be distinguished by the prevalence of E-V38 in East, Central, Southern and West Africa, E-M78 in East Africa and E-M81 in North Africa. E-V38 is the most prevalent subclade of E in Africa. It is observed at high frequencies in all African regions except the northernmost and easternmost portions of the continent. E-M243 (especially its subclades M78 and M81) is found at high frequencies in North East Africa and North Africa and is the only subclade that is found in Europe and Asia at significant frequencies. E-M243 is common among Afro-Asiatic speakers in the Near East and North Africa as well as among some Nilo-Saharan and Niger–Congo speakers in North East Africa and Sudan. E-M243 is far less common in West, Central, and Southern Africa, though it has been observed among some Khoisan speakers[8] and among Niger–Congo speakers in Senegambia,[9] Guinea-Bissau,[10] Burkina Faso,[11] Ghana,[9] Gabon,[12] the Democratic Republic of the Congo,[9] Rwanda,[13] Namibia,[9] and South Africa.[9]

Subclades

E-M96*

The most basal lineage, paragroup E-M96*, has been reported in 2 Amharas from Ethiopia,[14] a single Bantu-speaking male from South Africa,[1] amongst pygmies and Bantus from the Cameroon/Gabon region,[12] in two individuals from Saudi Arabia[15] and in some Syrians and Lebanese individuals according to Zalloua et al. (2008), but possibly only the Arabian, Lebanese and Syrian individuals are real E-M96*, because the discovery of the V38 SNP by Trombetta et al. (2011) has, in theory, resolved the previously reported cases of E-M96* in Africa (most studies which reported E-M96* in Africa only tested for the M2 SNP but not for the recently-discovered upstream V38 SNP) and, given the paucity of the downstream M2 sub-clade in Eurasia, it is highly unlikely that the reported E-M96* is E-V38*.

E-P147

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Main article: Haplogroup E-P147

The E-P147 branch of E-M96 also contains the dominant E-P2 variant, which is not only the most frequent variant of E-M96, but also the most dominant YDNA lineage in Africa.

E-M75

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Main article: Haplogroup E-M75

E-M75 is present throughout Sub-Saharan Africa, in East Africa, Southern Africa, Central Africa, and West Africa. The highest concentration of haplogroup E-M75 has been found among South African and Kenyan Bantus, with moderate frequencies of this haplogroup being observed in samples from Burkina Faso, Cameroon, Gabon, Hutu and Tutsi from Rwanda, Malagasy from Madagascar, Fon from Benin, Iraqw from Tanzania,[16] South African Khoisan, Sudan, and Senegal, as well as small frequencies in samples obtained from Qatar, Oman, Ethiopian Oromo, and Somali immigrants to Denmark.

Phylogenetics

Phylogenetic history

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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
E-P29 21 III 3A 13 Eu3 H2 B E* E E E E E E E E E E
E-M33 21 III 3A 13 Eu3 H2 B E1* E1 E1a E1a E1 E1 E1a E1a E1a E1a E1a
E-M44 21 III 3A 13 Eu3 H2 B E1a E1a E1a1 E1a1 E1a E1a E1a1 E1a1 E1a1 E1a1 E1a1
E-M75 21 III 3A 13 Eu3 H2 B E2a E2 E2 E2 E2 E2 E2 E2 E2 E2 E2
E-M54 21 III 3A 13 Eu3 H2 B E2b E2b E2b E2b1 - - - - - - -
E-P2 25 III 4 14 Eu3 H2 B E3* E3 E1b E1b1 E3 E3 E1b1 E1b1 E1b1 E1b1 E1b1
E-M2 8 III 5 15 Eu2 H2 B E3a* E3a E1b1 E1b1a E3a E3a E1b1a E1b1a E1b1a E1b1a1 E1b1a1
E-M58 8 III 5 15 Eu2 H2 B E3a1 E3a1 E1b1a1 E1b1a1 E3a1 E3a1 E1b1a1 E1b1a1 E1b1a1 E1b1a1a1a E1b1a1a1a
E-M116.2 8 III 5 15 Eu2 H2 B E3a2 E3a2 E1b1a2 E1b1a2 E3a2 E3a2 E1b1a2 E1b1a2 E1ba12 removed removed
E-M149 8 III 5 15 Eu2 H2 B E3a3 E3a3 E1b1a3 E1b1a3 E3a3 E3a3 E1b1a3 E1b1a3 E1b1a3 E1b1a1a1c E1b1a1a1c
E-M154 8 III 5 15 Eu2 H2 B E3a4 E3a4 E1b1a4 E1b1a4 E3a4 E3a4 E1b1a4 E1b1a4 E1b1a4 E1b1a1a1g1c E1b1a1a1g1c
E-M155 8 III 5 15 Eu2 H2 B E3a5 E3a5 E1b1a5 E1b1a5 E3a5 E3a5 E1b1a5 E1b1a5 E1b1a5 E1b1a1a1d E1b1a1a1d
E-M10 8 III 5 15 Eu2 H2 B E3a6 E3a6 E1b1a6 E1b1a6 E3a6 E3a6 E1b1a6 E1b1a6 E1b1a6 E1b1a1a1e E1b1a1a1e
E-M35 25 III 4 14 Eu4 H2 B E3b* E3b E1b1b1 E1b1b1 E3b1 E3b1 E1b1b1 E1b1b1 E1b1b1 removed removed
E-M78 25 III 4 14 Eu4 H2 B E3b1* E3b1 E1b1b1a E1b1b1a1 E3b1a E3b1a E1b1b1a E1b1b1a E1b1b1a E1b1b1a1 E1b1b1a1
E-M148 25 III 4 14 Eu4 H2 B E3b1a E3b1a E1b1b1a3a E1b1b1a1c1 E3b1a3a E3b1a3a E1b1b1a3a E1b1b1a3a E1b1b1a3a E1b1b1a1c1 E1b1b1a1c1
E-M81 25 III 4 14 Eu4 H2 B E3b2* E3b2 E1b1b1b E1b1b1b1 E3b1b E3b1b E1b1b1b E1b1b1b E1b1b1b E1b1b1b1 E1b1b1b1a
E-M107 25 III 4 14 Eu4 H2 B E3b2a E3b2a E1b1b1b1 E1b1b1b1a E3b1b1 E3b1b1 E1b1b1b1 E1b1b1b1 E1b1b1b1 E1b1b1b1a E1b1b1b1a1
E-M165 25 III 4 14 Eu4 H2 B E3b2b E3b2b E1b1b1b2 E1b1b1b1b1 E3b1b2 E3b1b2 E1b1b1b2a E1b1b1b2a E1b1b1b2a E1b1b1b2a E1b1b1b1a2a
E-M123 25 III 4 14 Eu4 H2 B E3b3* E3b3 E1b1b1c E1b1b1c E3b1c E3b1c E1b1b1c E1b1b1c E1b1b1c E1b1b1c E1b1b1b2a
E-M34 25 III 4 14 Eu4 H2 B E3b3a* E3b3a E1b1b1c1 E1b1b1c1 E3b1c1 E3b1c1 E1b1b1c1 E1b1b1c1 E1b1b1c1 E1b1b1c1 E1b1b1b2a1
E-M136 25 III 4 14 Eu4 H2 B E3ba1 E3b3a1 E1b1b1c1a E1b1b1c1a1 E3b1c1a E3b1c1a E1b1b1c1a1 E1b1b1c1a1 E1b1b1c1a1 E1b1b1c1a1 E1b1b1b2a1a1

Research publications

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

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Phylogenetic trees

This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) Tree,[17] the ISOGG Y-DNA Haplogroup Tree,[18] and subsequent published research.

  • E-M96 (L339, L614, M40/SRY4064/SRY8299, M96, P29, P150, P152, P154, P155, P156, P162, P168, P169, P170, P171, P172, P173, P174, P175, P176)
    • E-P147 (P147)
      • E-M33 (M33, M132)
        • E-M44 (M44)
        • E-P110 (P110)
        • E-L94 (L94)
        • E-L133 (L133/PAGES00074)
      • E-P177 (P177)
        • E-P2 (DYS391p, P2/PN2, P179, P180, P181)
        • E-P75 (P75)
    • E-M75 (M75, P68)
      • E-M41 (M41)
      • E-M54 (M54, M90, M98)
        • E-M85 (M85)

Notes

  1. ↑ 1.0 1.1 1.2 1.3 Lua error in package.lua at line 80: module 'strict' not found.
  2. ↑ Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature 505, 87–91 (02 January 2014)
  3. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  4. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  5. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  6. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  7. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  8. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  9. ↑ 9.0 9.1 9.2 9.3 9.4 Lua error in package.lua at line 80: module 'strict' not found. (cf. Appendix A: Y Chromosome Haplotype Frequencies)
  10. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  11. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  12. ↑ 12.0 12.1 Lua error in package.lua at line 80: module 'strict' not found.
  13. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  14. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  15. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  16. ↑ Called "Wairak" and misidentified as Bantu in Luis (2004).
  17. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  18. ↑ Lua error in package.lua at line 80: module 'strict' not found.

Further reading

  • Lua error in package.lua at line 80: module 'strict' not found.
  • Lua error in package.lua at line 80: module 'strict' not found.
  • Lua error in package.lua at line 80: module 'strict' not found. Also see Supplementary Data.
  • Lua error in package.lua at line 80: module 'strict' not found.
  • Lua error in package.lua at line 80: module 'strict' not found.. Published online April 2, 2008. See also Supplementary Material.
  • Pontikos D. "Phylogeographic refinement of haplogroup E" http://dienekes.blogspot.ru/2015/07/phylogeographic-refinement-of.html
  • Lua error in package.lua at line 80: module 'strict' not found.. Published online 9 March 2005
  • Trombetta B. "Phylogeographic Refinement and Large Scale Genotyping of Human Y Chromosome Haplogroup E Provide New Insights into the Dispersal of Early Pastoralists in the African Continent" http://gbe.oxfordjournals.org/content/7/7/1940.long
  • Lua error in package.lua at line 80: module 'strict' not found.

See also

Genetics

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Y-DNA E subclades

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Y-DNA backbone tree

Evolutionary tree of human Y-chromosome DNA haplogroups [χ 1][χ 2]
"Y-chromosomal Adam"
A00 A0-T [χ 3]
A0 A1[χ 4]
A1a A1b
A1b1 BT
B CT
DE CF
D E C F
F1 F2 F3 GHIJK
G HIJK
H IJK
IJ K
I J LT [χ 5]  K2
L T NO [χ 6] K2b [χ 7]   K2c K2d K2e [χ 8]
N O K2b1 [χ 9]    P
M S [χ 10] Q R
  1. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  2. ↑ International Society of Genetic Genealogy (ISOGG; 2015), Y-DNA Haplogroup Tree 2015. (Access date: 1 February 2015.)
  3. ↑ Haplogroup A0-T is also known as A0'1'2'3'4.
  4. ↑ Haplogroup A1 is also known as A1'2'3'4.
  5. ↑ Haplogroup LT (L298/P326) is also known as Haplogroup K1.
  6. ↑ Haplogroup NO (M214) is also known as Haplogroup K2a (although the present Haplogroup K2e was also previously known as "K2a").
  7. ↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
  8. ↑ Haplogroup K2e (K-M147) was previously known as "Haplogroup X" and "K2a" (but is a sibling subclade of the present K2a, also known as Haplogroup NO).
  9. ↑ Haplogroup K2b1 (P397/P399) is similar to the former Haplogroup MS, but has a broader and more complex internal structure.
  10. ↑ Haplogroup S (S-M230) was previously known as Haplogroup K5.

External links

Phylogenetic tree and distribution maps of Y-DNA haplogroup E

Projects

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