Haplogroup E-M96

Haplogroup E-M96 is a human Y-chromosome DNA haplogroup. It is one of the two main branches of the older and ancestral 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.

This article is about the human Y-DNA haplogroup. For the human mtDNA haplogroup, see Haplogroup E (mtDNA).
Haplogroup E
Possible time of origin65 ka,[1] 69 ka,[2] or about 73 ka[3]
Possible place of originEast Africa[4][5][6][3] or West Asia[7][8]
AncestorDE
DescendantsE-P147, E-M75
Defining mutationsL339, L614, M40/SRY4064/SRY8299, M96, P29, P150, P152, P154, P155, P156, P162, P168, P169, P170, P171, P172, P173, P174, P175, P176

Origins

Underhill (2001) proposed that haplogroup E may have arisen in East Africa.[9] Some authors as Chandrasekar (2007), accept the earlier position of Hammer (1997) that Haplogroup E may have originated in Asia,[10] given that:

  • E is a clade of Haplogroup DE, with the other major clade, haplogroup D, being exclusively distributed in Asia.
  • 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.[11]
  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".[12] 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.[12]

In 2015 Poznik and Underhill have claimed haplogroup E, arose outside Africa, arguing that, "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."[7]

In 2015 Trobetta et al. suggested an East African origin for haplogroup E, stating: "our phylogeographic analysis, based on thousands of samples worldwide, suggests that the radiation of haplogroup E started about 58 ka, somewhere in sub-Saharan Africa, with a higher posterior probability (0.73) for an eastern African origin."[6]

A Eurasian center of origin and dispersal for haplogroup E has also been hypothesized by Cabrera et al. (2018) based on the similar age of the clade's parent haplogroup DE and the mtDNA haplogroup L3. According to this hypothesis, after an initial Out-of-Africa migration of early anatomically modern humans around 125 kya, E-carrying males are thus proposed to have back-migrated from the paternal haplogroup's place of origin in Eurasia around 70 kya along with females bearing the maternal haplogroup L3, which the study also hypothesizes to have originated in Eurasia. These new Eurasian lineages were then suggested to have largely replaced the old autochthonous male and female African lineages.[8]

A 2019 study by Haber et al. supports an African origin for haplogroup E (based on an analysis of the Y-chromosomal phylogenetic structure, haplogroup divergence times, and the recently discovered haplogroup D0 found in three Nigerians, an additional branch of the DE lineage diverging early from the D branch). The authors support an African origin for DE (parent haplogroup of E) with E and D0 also originating in Africa, along with the migration out of Africa of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes. The early divergence dates found in the study for DE, E, and D0 (all dated from about 71-76 kya), which are determined to predate the migration out-of-Africa of the ancestors of Eurasians (dated to ca. 50-60 kya), are also considered by the authors to support an African origin for those haplogroups.[3]

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-M2 in East, Central, Southern and West Africa, E-M78 in East Africa and E-M81 in North Africa. E-M2 is the most prevalent subclade of E in Africa. It is observed at high frequencies in all African regions from moderate to high. 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[13] and among Niger–Congo speakers in Senegambia,[14] Guinea-Bissau,[15] Burkina Faso,[16] Ghana, Gabon,[17] the Democratic Republic of the Congo, Rwanda,[18] Namibia, and South Africa.

One of various Pre-Pottery Neolithic B fossils that were analysed for ancient DNA was found to carry the paternal haplogroup E(xE2,E1a,E1b1a1a1c2c3b1,E1b1b1b1a1,E1b1b1b2b) (1/7; ~14%).[19]

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,[20] in 2 men from Saudi Arabia,[21] and in a single Bantu-speaking male from South Africa.[12] E(xE1a-M33, E1b1-P2, E2-M75) was reported among several Southern African populations and in an Egyptian man;[22] E(xE1a-M33, E1b1a1-M2, E1b1b-M215, E2-M75) has been observed amongst pygmies and Bantu from Cameroon and Gabon;[17] and E(xE1a-M33, E1b1a1-M2, E1b1b1-M35, E2-M75) has been found in several Lebanese,[23] in Burkina Faso,[24] and a Fulbe man from Niger.[25]

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.[26] 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%),[22] Hema (38.89%),[22] Rimaibe (27.03%),[16] Mbuti (25.00%),[16] Daba (22.22%),[16] Eviya (20.83%),[17] Zulu (20.69%),[22] and Kenyan Bantus (17.24%).[18]

Haplogroup E-M75(xM41,M54) has been found in 6% (1/18) of Dama from Namibia,[22] 4% (1/26) of Ganda from Uganda,[22] 3% (1/39) of Mandinka from Gambia/Senegal,[22] and 2% (1/49) of Shona from Zimbabwe.[22]

Phylogenetics

Phylogenetic history
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-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.

  • α Jobling and Tyler-Smith 2000 and Kaladjieva 2001
  • β Underhill 2000
  • γ Hammer 2001
  • δ Karafet 2001
  • ε Semino 2000
  • ζ Su 1999
  • η Capelli 2001

Phylogenetic trees

This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) Tree,[27] the ISOGG Y-DNA Haplogroup Tree,[28] 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)

See also

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 [χ 6]
L     T    K2a [χ 7]        K2b [χ 8]     K2c     K2d K2e [χ 9]  
K-M2313 [χ 10]     K2b1 [χ 11] P [χ 12]
NO   S [χ 13]  M [χ 14]    P1     P2
N O Q R

Notes
  1. formed: 68.3–62.1 ka (CI 95%), TMRCA: 55.3–49.5 ybp (CI 95%) YFull YTree v6.02
  2. Kamin M, Saag L, Vincente M, et al. (April 2015). "A recent bottleneck of Y chromosome diversity coincides with a global change in culture". Genome Research. 25 (4): 459–466. doi:10.1101/gr.186684.114. PMC 4381518. PMID 25770088.
  3. Haber M, Jones AL, Connel BA, Asan, Arciero E, Huanming Y, Thomas MG, Xue Y, Tyler-Smith C (June 2019). "A Rare Deep-Rooting D0 African Y-chromosomal Haplogroup and its Implications for the Expansion of Modern Humans Out of Africa". Genetics. 212 (4): 1421–1428. doi:10.1534/genetics.119.302368. PMC 6707464. PMID 31196864.
  4. 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 1181965. PMID 15069642.
  5. 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. Bibcode:2009PNAS..10620174C. doi:10.1073/pnas.0910803106. PMC 2787129. PMID 19920170.
  6. Trombetta et al. 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
  7. Poznik, G David; et al. (2016). "Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences". Nature Genetics. 48 (6): 593–599. doi:10.1038/ng.3559. PMC 4884158. PMID 27111036.
  8. Cabrera VM (2017). "Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago". bioRxiv 10.1101/233502.
  9. 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. S2CID 9441236.
  10. 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. S2CID 11860142.
  11. 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.
  12. 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 2336805. PMID 18385274.
  13. 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 1181964. PMID 15042509.
  14. 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)
  15. 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 1976131. PMID 17662131.
  16. 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 447595. PMID 11910562.
  17. 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.
  18. 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 1182266. PMID 14973781.
  19. Lazaridis, Iosif; et al. (17 June 2016). "The genetic structure of the world's first farmers". bioRxiv 10.1101/059311. -- Table S6.1 - Y-chromosome haplogroups
  20. 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 2759955. PMID 19772609.
  21. 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 2759955. PMID 19772609.
  22. Wood (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.
  23. Zalloua (2008). "Y-chromosomal diversity in Lebanon is structured by recent historical events". Am J Hum Genet. 82 (4): 873–82. doi:10.1016/j.ajhg.2008.01.020. PMC 2427286. PMID 18374297.
  24. de Filippo (2011). "Y-chromosomal variation in Sub-Saharan Africa: insights into the history of Niger-Congo groups". Mol Biol Evol. 28 (3): 1255–1269. doi:10.1093/molbev/msq312. PMC 3561512. PMID 21109585.
  25. Bučkova (2013). "Multiple and differentiated contributions to the male gene pool of pastoral and farmer populations of the African Sahel". Am J Phys Anthropol. 151 (1): 10–21. doi:10.1002/ajpa.22236. PMID 23460272.
  26. 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. 7 (7): 1940–50. doi:10.1093/gbe/evv118. PMC 4524485. PMID 26108492.
  27. Krahn, Thomas. "YCC Tree". Houston, Texas: FTDNA. Archived from the original on 26 July 2011. Retrieved 16 May 2011.
  28. 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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