Haplogroup E-M96

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

Haplogroup E-M96 is a human Y-chromosome DNA haplogroup. It 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 main 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:

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".[8] 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.[8]

Nonetheless, in 2015 Poznik and Underhill have claimed haplogroup E, arose outside Africa. This model of geographical segregation within the CT clade requires just one continental haplogroup exchange (E to Africa), rather than three (D, C, and F out of Africa). The timing of this putative return to Africa, between the emergence of haplogroup E and its differentiation within Africa by 58 kya, is consistent with proposals, based on non–Y chromosome data, of abundant gene flow between Africa and Arabia 50–80 kya.[9]

Distribution

Most members of haplogroup E-M96 belong to one of its identified subclades, and the E-M96(xE-P147, E-M75) 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[10] and among Niger–Congo speakers in Senegambia,[11] Guinea-Bissau,[12] Burkina Faso,[13] Ghana, Gabon,[14] the Democratic Republic of the Congo, Rwanda,[15] Namibia, and South Africa.

Subclades

E-M96*

Paragroup E-M96* refers to lineages belonging to the E clade but which cannot be classified into any known branch. E(xE1-P147, E2-M75) - that is, E which has tested negative for both P147 and M75 - has been reported in 2 Amharas from Ethiopia,[16] in 2 men from Saudi Arabia,[17] and in a single Bantu-speaking male from South Africa.[8] E(xE1a-M33, E1b1-P2, E2-M75) was reported among several Southern African populations and in an Egyptian man;[18] E(xE1a-M33, E1b1a1-M2, E1b1b-M215, E2-M75) has been observed amongst pygmies and Bantu from Cameroon and Gabon;[19] and E(xE1a-M33, E1b1a1-M2, E1b1b1-M35, E2-M75) has been found in several Lebanese,[20] in Burkina Faso,[21] and a Fulbe man from Niger.[22]

Recently it was discovered that 3 East African men previously classified only as E*-M96 could be assigned to a new branch, E-V44, which is a sister branch to E1-P147; E-P147 and E-V44 share the V3725 mutation, making E2-M75 and E-V3725 the two known primary branches of E.[23] It is not known whether or not some (or all) other E*(xE1, E2) would fall into V44 as well.

E-P147

Main article: Haplogroup E-P147

E-P147 (also known as E1) is by far the most numerous and widely distributed branch of E-M96. It has two primary branches: E-M132 (E1a) and E-P177 (E1b).

Within Haplogroup E-P177, Haplogroup E-P2 (E1b1) – a subclade of E-P177 – is not only the most frequent variant of E-M96, but is also the most common Y-DNA lineage in Africa. It is also the only subclade of E-M96 found in significant numbers in West Asia and Europe.

A prolific primary branch of E-P2, Haplogroup E-M215 (E1b1b) is distributed in high frequencies from East Africa, through North Africa into Western Asia and Southern Europe. It is also found at significant levels among populations native to Southern Africa and throughout Western Europe.

E-M75

Main article: Haplogroup E-M75

E-M75 is present throughout Subequatorial Africa, particularly in the African Great Lakes and Central Africa. The highest concentration of the haplogroup has been found among the Alur (66.67%),[18] Hema (38.89%),[18] Rimaibe (27.03%),[13] Mbuti (25.00%),[13] Daba (22.22%),[13] Eviya (20.83%),[19] Zulu (20.69%),[18] and Kenyan Bantus (17.24%).[15]

Haplogroup E-M75(xM41,M54) has been found in 6% (1/18) of Dama from Namibia,[18] 4% (1/26) of Ganda from Uganda,[18] 3% (1/39) of Mandinka from Gambia/Senegal,[18] and 2% (1/49) of Shona from Zimbabwe.[18]

Phylogenetics

Phylogenetic history

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-P2921III3A13Eu3H2BE*EEEEEEEEEE
E-M3321III3A13Eu3H2BE1*E1E1aE1aE1E1E1aE1aE1aE1aE1a
E-M4421III3A13Eu3H2BE1aE1aE1a1E1a1E1aE1aE1a1E1a1E1a1E1a1E1a1
E-M7521III3A13Eu3H2BE2aE2E2E2E2E2E2E2E2E2E2
E-M5421III3A13Eu3H2BE2bE2bE2bE2b1-------
E-P225III414Eu3H2BE3*E3E1bE1b1E3E3E1b1E1b1E1b1E1b1E1b1
E-M28III515Eu2H2BE3a*E3aE1b1E1b1aE3aE3aE1b1aE1b1aE1b1aE1b1a1E1b1a1
E-M588III515Eu2H2BE3a1E3a1E1b1a1E1b1a1E3a1E3a1E1b1a1E1b1a1E1b1a1E1b1a1a1aE1b1a1a1a
E-M116.28III515Eu2H2BE3a2E3a2E1b1a2E1b1a2E3a2E3a2E1b1a2E1b1a2E1ba12removedremoved
E-M1498III515Eu2H2BE3a3E3a3E1b1a3E1b1a3E3a3E3a3E1b1a3E1b1a3E1b1a3E1b1a1a1cE1b1a1a1c
E-M1548III515Eu2H2BE3a4E3a4E1b1a4E1b1a4E3a4E3a4E1b1a4E1b1a4E1b1a4E1b1a1a1g1cE1b1a1a1g1c
E-M1558III515Eu2H2BE3a5E3a5E1b1a5E1b1a5E3a5E3a5E1b1a5E1b1a5E1b1a5E1b1a1a1dE1b1a1a1d
E-M108III515Eu2H2BE3a6E3a6E1b1a6E1b1a6E3a6E3a6E1b1a6E1b1a6E1b1a6E1b1a1a1eE1b1a1a1e
E-M3525III414Eu4H2BE3b*E3bE1b1b1E1b1b1E3b1E3b1E1b1b1E1b1b1E1b1b1removedremoved
E-M7825III414Eu4H2BE3b1*E3b1E1b1b1aE1b1b1a1E3b1aE3b1aE1b1b1aE1b1b1aE1b1b1aE1b1b1a1E1b1b1a1
E-M14825III414Eu4H2BE3b1aE3b1aE1b1b1a3aE1b1b1a1c1E3b1a3aE3b1a3aE1b1b1a3aE1b1b1a3aE1b1b1a3aE1b1b1a1c1E1b1b1a1c1
E-M8125III414Eu4H2BE3b2*E3b2E1b1b1bE1b1b1b1E3b1bE3b1bE1b1b1bE1b1b1bE1b1b1bE1b1b1b1E1b1b1b1a
E-M10725III414Eu4H2BE3b2aE3b2aE1b1b1b1E1b1b1b1aE3b1b1E3b1b1E1b1b1b1E1b1b1b1E1b1b1b1E1b1b1b1aE1b1b1b1a1
E-M16525III414Eu4H2BE3b2bE3b2bE1b1b1b2E1b1b1b1b1E3b1b2E3b1b2E1b1b1b2aE1b1b1b2aE1b1b1b2aE1b1b1b2aE1b1b1b1a2a
E-M12325III414Eu4H2BE3b3*E3b3E1b1b1cE1b1b1cE3b1cE3b1cE1b1b1cE1b1b1cE1b1b1cE1b1b1cE1b1b1b2a
E-M3425III414Eu4H2BE3b3a*E3b3aE1b1b1c1E1b1b1c1E3b1c1E3b1c1E1b1b1c1E1b1b1c1E1b1b1c1E1b1b1c1E1b1b1b2a1
E-M13625III414Eu4H2BE3ba1E3b3a1E1b1b1c1aE1b1b1c1a1E3b1c1aE3b1c1aE1b1b1c1a1E1b1b1c1a1E1b1b1c1a1E1b1b1c1a1E1b1b1b2a1a1

Research publications

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

Phylogenetic trees

This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) Tree,[24] the ISOGG Y-DNA Haplogroup Tree,[25] and subsequent published research.

See also

Wikiquote has quotations related to: Haplogroup E-M96

Genetics

Y-DNA E subclades

Y-DNA backbone tree

Phylogenetic 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
IJK H
IJ   K
I J    LT [χ 5]  K2
L T [χ 6] NO [χ 7] K2b [χ 8]     K2c  K2d  K2e [χ 9]
N   O   K2b1 [χ 10]     P
K2b1a[χ 11]     K2b1b K2b1c      M     P1 P2
K2b1a1   K2b1a2   K2b1a3 S [χ 12] Q   R
  1. ↑ 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. doi:10.1002/humu.22468. PMID 24166809.
  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. ↑ Between 2002 and 2008, Haplogroup T (M184) was known as "Haplogroup K2" – that name has since been re-assigned to K-M526, the sibling of Haplogroup LT.
  7. ↑ Haplogroup NO (M214) is also known as Haplogroup K2a (although the present Haplogroup K2e was also previously known as "K2a").
  8. ↑ Haplogroup K2b (M1221/P331/PF5911) is also known as Haplogroup MPS.
  9. ↑ 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).
  10. ↑ Haplogroup K2b1 (P397/P399) is similar to the former Haplogroup MS, but has a broader and more complex internal structure.
  11. ↑ Haplogroup K2b1a has also been known as Haplogroup S-P405.
  12. ↑ Haplogroup S (S-M230), also known as K2b1a4, was previously known as Haplogroup K5.

Notes

  1. ↑ Karafet, T. M.; Mendez, F. L.; Meilerman, M. B.; Underhill, P. A.; Zegura, S. L.; Hammer, M. F. (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 2336805Freely accessible. PMID 18385274.
  2. ↑ Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans, Nature 505, 87–91 (02 January 2014)
  3. ↑ Semino, Ornella; Magri, Chiara; Benuzzi, Giorgia; Lin, Alice A.; Al-Zahery, Nadia; Battaglia, Vincenza; MacCioni, Liliana; Triantaphyllidis, Costas; et al. (2004). "Origin, Diffusion, and Differentiation of Y-Chromosome Haplogroups E and J: Inferences on the Neolithization of Europe and Later Migratory Events in the Mediterranean Area". The American Journal of Human Genetics. 74 (5): 1023–34. doi:10.1086/386295. PMC 1181965Freely accessible. PMID 15069642.
  4. ↑ Chiaroni, J.; Underhill, P. A.; Cavalli-Sforza, L. L. (2009). "Y chromosome diversity, human expansion, drift, and cultural evolution". Proceedings of the National Academy of Sciences. 106 (48): 20174–9. doi:10.1073/pnas.0910803106. PMC 2787129Freely accessible. PMID 19920170.
  5. ↑ Underhill, P. A.; Passarino, G.; Lin, A. A.; Shen, P.; Mirazon Lahr, M.; Foley, R. A.; Oefner, P. J.; Cavalli-Sforza, L. L. (2001). "The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations". Annals of Human Genetics. 65 (Pt 1): 43–62. doi:10.1046/j.1469-1809.2001.6510043.x. PMID 11415522.
  6. ↑ Chandrasekar; Saheb, S. Y.; Gangopadyaya, P.; Gangopadyaya, S.; Mukherjee, A.; Basu, D.; Lakshmi, G. R.; Sahani, A. K.; Das, B.; Battacharya, S.; Kumar, S.; Xaviour, D.; Sun, D.; Rao, V. R.; et al. (Sep–Oct 2007). "YAP insertion signature in South Asia". Annals of Human Biology. 34 (5): 582–6. doi:10.1080/03014460701556262. PMID 17786594.
  7. ↑ Underhill, Peter A.; Kivisild, Toomas (2007). "Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations". Annual Review of Genetics. 41: 539–64. doi:10.1146/annurev.genet.41.110306.130407. PMID 18076332.
  8. 1 2 3 Karafet (2008). "New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree". Genome Res.
  9. ↑ G David Poznik et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences, Nature Genetics (2016) doi:10.1038/ng.3559.
  10. ↑ Cruciani, Fulvio; La Fratta, Roberta; Santolamazza, Piero; Sellitto, Daniele; Pascone, Roberto; Moral, Pedro; Watson, Elizabeth; Guida, Valentina; et al. (2004). "Phylogeographic Analysis of Haplogroup E3b (E-M215) Y Chromosomes Reveals Multiple Migratory Events Within and Out of Africa". The American Journal of Human Genetics. 74 (5): 1014–22. doi:10.1086/386294. PMC 1181964Freely accessible. PMID 15042509.
  11. ↑ Wood, Elizabeth T; Stover, Daryn A; Ehret, Christopher; Destro-Bisol, Giovanni; Spedini, Gabriella; McLeod, Howard; Louie, Leslie; Bamshad, Mike; et al. (2005). "Contrasting patterns of Y chromosome and mtDNA variation in Africa: Evidence for sex-biased demographic processes". European Journal of Human Genetics. 13 (7): 867–76. doi:10.1038/sj.ejhg.5201408. PMID 15856073. (cf. Appendix A: Y Chromosome Haplotype Frequencies)
  12. ↑ Rosa, Alexandra; Ornelas, Carolina; Jobling, Mark A; Brehm, António; Villems, Richard (2007). "Y-chromosomal diversity in the population of Guinea-Bissau: A multiethnic perspective". BMC Evolutionary Biology. 7: 124. doi:10.1186/1471-2148-7-124. PMC 1976131Freely accessible. PMID 17662131.
  13. 1 2 3 4 Cruciani, Fulvio; Santolamazza, Piero; Shen, Peidong; MacAulay, Vincent; Moral, Pedro; Olckers, Antonel; Modiano, David; Holmes, Susan; et al. (2002). "A Back Migration from Asia to Sub-Saharan Africa is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes". The American Journal of Human Genetics. 70 (5): 1197–214. doi:10.1086/340257. PMC 447595Freely accessible. PMID 11910562.
  14. ↑ Berniell-Lee, G.; Calafell, F.; Bosch, E.; Heyer, E.; Sica, L.; Mouguiama-Daouda, P.; Van Der Veen, L.; Hombert, J.-M.; et al. (2009). "Genetic and Demographic Implications of the Bantu Expansion: Insights from Human Paternal Lineages". Molecular Biology and Evolution. 26 (7): 1581–9. doi:10.1093/molbev/msp069. PMID 19369595.
  15. 1 2 Luis, J; Rowold, D; Regueiro, M; Caeiro, B; Cinnioglu, C; Roseman, C; Underhill, P; Cavallisforza, L; Herrera, R (2004). "The Levant versus the Horn of Africa: Evidence for Bidirectional Corridors of Human Migrations". The American Journal of Human Genetics. 74 (3): 532–44. doi:10.1086/382286. PMC 1182266Freely accessible. PMID 14973781.
  16. ↑ Abu-Amero, Khaled K; Hellani, Ali; González, Ana M; Larruga, Jose M; Cabrera, Vicente M; Underhill, Peter A (2011). "Variation in Y chromosome, mitochondrial DNA and labels of identity on Ethiopia". UCL Discovery. 10: 59. doi:10.1186/1471-2156-10-59. PMC 2759955Freely accessible. PMID 19772609.
  17. ↑ Abu-Amero, Khaled K; Hellani, Ali; González, Ana M; Larruga, Jose M; Cabrera, Vicente M; Underhill, Peter A (2009). "Saudi Arabian Y-Chromosome diversity and its relationship with nearby regions". BMC Genetics. 10: 59. doi:10.1186/1471-2156-10-59. PMC 2759955Freely accessible. PMID 19772609.
  18. 1 2 3 4 5 6 7 8 Wood (2005). "Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes". Eur J Hum Genet.
  19. 1 2 Berniell-Lee (2009). "Genetic and demographic implications of the Bantu Expansion: insights from human paternal lineages". Mol Biol Evol.
  20. ↑ Zalloua (2008). "Y-chromosomal diversity in Lebanon is structured by recent historical events". Am J Hum Genet.
  21. ↑ de Filippo (2011). "Y-chromosomal variation in Sub-Saharan Africa: insights into the history of Niger-Congo groups". Mol Biol Evol.
  22. ↑ Bučkova (2013). "Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel". Am J Phys Anthropol.
  23. ↑ Trombetta (2015). "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". Genome Biol Evol.
  24. ↑ Krahn, Thomas. "YCC Tree". Houston, Texas: FTDNA. Retrieved 16 May 2011.
  25. ↑ International Society of Genetic Genealogy. "Y-DNA Haplogroup Tree". Retrieved 2012. Check date values in: |access-date= (help)

Further reading

Phylogenetic tree and distribution maps of Y-DNA haplogroup E

Projects

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