Haplogroup E-V38

Haplogroup E-V38/ E3a/ E1b1a
Possible time of origin approx 25,000-30,000 years BP[1]
Possible place of origin East Africa [2]
Ancestor E-P2
Descendants E-M2, E-M329
Defining mutations L222.1, V38, V100

In human genetics, Haplogroup E-V38 is a human Y-chromosome DNA haplogroup. It is the phylogenetic term for the series of unique sequence variants on the human Y-chromosome. It is often found in African males and their descendants and is heritably passed in lineage from father to son. Geneticists study these variants in populations to find the evolutionary lineage to a common male human ancestor. It can also be referred to in phylogenetic nomenclature by names such as E1b1a (although the exact definition of phylogenetic names can vary over time).

E-V38 has two basal branches, E-M329 (formerly E1b1c) and E-M2 (formerly E1b1a), the former is almost exclusively found in Ethiopia. The E-M2 branches are the predominant lineage in Western Africa, Central Africa, Southern Africa, and the southern parts of Eastern Africa. E-M2 has several subclades, however many members are included in either E-L485 or E-U175.

Origins

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. V38 joins the West African-affiliated E-M2 and the northern East African-affiliated E-M329 with an earlier common ancestor who, like E-P2, may have also originated in East Africa.[2] It is possible that soon after the evolution of E-V38, trans-Saharan migrants carried the E-V38 marker to North and Central Africa and/or West Africa where the more common E-M2 marker later arose and became prolific within the last 20,000-30,000 years.[1][3]

The downstreams SNP E-M180 possibly originated on the moist south-central Saharan savannah/grassland of northern West Africa during the early Holocene period. Much of the population that carried E-M2 retreated to southern West Africa with the drying of the Sahara. These later people migrated from Igboland and Cameroon ~8.0 kya to Central Africa, East Africa, and Southern Africa causing or following the Bantu expansion.[4][5][6] According to Wood et al. (2005) and Rosa et al. (2007), such population movements from West Africa changed the pre-existing population Y chromosomal diversity in Western, Central, Southern and southern East Africa, replacing the previous haplogroups 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.[1][7][8]

Distribution

E-V38 reaches frequencies of over 80% in many parts of West Africa, Central Africa, East Africa as well as Southern Africa.[9] This haplogroup's frequency and diversity are highest in the West Africa region. Within Africa, E-V38 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 the continent.[10]

Incidence of E-V38
Population group frequency References
Bamileke 96%-100% [10][11]
Ewe 97%[7]
Ga 97%[7]
Yoruba 93.1%[12]
Tutsi 85%[10]
Fante 84%[7]
Mandinka 79%-87%[1][7]
Ovambo 82%[7]
Senegalese 81%[13]
Ganda 77%[7]
Bijagós 76%[1]
Balanta 73%[1]
Fula 73%[1]
Herero 71%[7]
Nalú 71%[1]

Populations on the northern fringes of West Africa, central Eastern Africa and Madagascar have tested at more moderate frequencies.

Incidence of E-V38
Population group frequency References
Tuareg from Tânout, Niger 44.4% (8/18 subjects)[14]
Tuareg from Gorom, Burkina Faso 16.6% (3/18)[14]
Tuareg from Gossi, Mali 9.1% (1/9)[14]
Cape Verdeans 15.9% (32/201)[15]
Maasai 15.4% (4/26)[7]
Luo 66% (6/9)[7]
Iraqw 11.11% (1/9)[7]
Comoros 23.46% (69/294)[16]
Merina people (also called Highlanders) 44% (4/9)[17]
Antandroy 69.6% (32/46)[17]
Antanosy 48.9% (23/47)[17]
Antaisaka 37.5% (3/8)[17]

E-V38 is found at low to moderate frequencies in North Africa, and northern East Africa. The some of the lineages found in these areas are possibly due to the Bantu expansion or other migrations.[10][18] The E-M2 marker that appeared in North African samples may stem from recent acquisitions.[10] However, the discovery in 2011 of the E-V38 marker that predates E-M2 has led Trombetta et al. to suggest that E-V38 may have originated in East Africa (please refer to the Origins section for the details).

Incidence of E-V38
Population group frequency References
Tuareg from Al Awaynat and Tahala, Libya 46.5% (20/43) [Note 1] [19]
Oran, Algeria 8.6% (8/93)[20]
Berbers, southern and north-central Morocco 9.5% (6/63)[21][Note 2]
Moroccan Arabs6.8% (3/44)[21]
Saharawis3.5% (1/29)[21]
Egyptians 8.33% (3/36), 1.4% (2/147), and (0/73)[10][22][23]
Tunisians 1.4% (2/148)[23]
Sudanese Hausa12.5% (4/32)[24]
Somalis 1.5% (3/201)[18]
Ethiopians 3.4% (3/88)[25]
Oromo 2.6% (2/78)[13]
Amhara 0% (0/48)[Note 3][13]

Outside of Africa, E-V38 has been found at low frequencies. In Eurasia, the clade has primarily been found in West Asia. There have also been reported a few isolated incidents of E-V38 in Southern European populations in Croatia, Malta, Spain and Portugal.[26] [27][28][29]

Incidence of E-V38 in Eurasia
Population group frequency References
Saudi Arabians 7.6% (12/157)

[30]

Omanis 6.6% (8/121)[10]
Emiratis 5.5% (9/164)[31]
Yemenis 4.8% (3/62)[31]
Majorcans 3.2% (2/62) [29]
Qataris 4.2% (3/72)[31]
Southern Iranians 1.7% (2/117)[32]
Iraqis 1.4% (2/139)[33]
Pakistanis 1.4% (9/638)[34]
Istanbul, Turkey 1.2% (1/81)[35]

The Trans-Atlantic slave trade brought people to North America, Central America and South America including the Caribbean. Consequently, the haplogroup is often observed in the United States populations in men who self-identify as African Americans.[9] It has also been observed in a number of populations in Mexico, the Caribbean, Central America, and South America among people of African descent.

Incidence of E-V38 in populations of the Americas
Population group frequency References
U.S. Americans 7.7-7.9% [Note 4][9]
Cubans 9.8% (13/132)[36]
Dominicans 7.69% (2/26)[37]
Puerto Ricans19.23% (5/26)[37]
Nicaraguans5.5% (9/165)[38]
Several populations of Colombians6.18% (69/1116)[39]
Alagoas, Brazil 4.45% (11/247)[40]
Bahia, Brazil 19% (19/100)[41]

Subclades

E1b1a1

African spatial distribution of haplogroup E3a-M2. Rosa et al. (2007)

All Africans carry E1B1A which was present in the Pharaoh Ramesses III of ancient Egypt. E1b1a1 is defined by markers DYS271/M2/SY81, M291, P1/PN1, P189, P293, V43, and V95.

E1b1a1a1

E1b1a1a1 is commonly defined by M180/P88. The basal subclade is quite regularly observed in V38+ samples.

E1b1a1a1a

E1b1a1a1a is defined by marker M58. 5% (2/37) of the town Singa-Rimaïbé, Burkina Faso tested positive for E-M58.[11] 15% (10/69) of Hutus in Rwanda tested positive for M58.[10] Three South Africans tested positive for this marker.[8] One Carioca from Rio de Janeiro, Brazil tested positive for the M58 SNP.[42] 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.[8] [Note 5]

E1b1a1a1c

E1b1a1a1c is defined by private marker M149. This marker was found in a single South African.[8]

E1b1a1a1d

E1b1a1a1d is defined by a private marker M155. It is known from a single carrier in Mali.[8]

E1b1a1a1e

E1b1a1a1e is defined by markers M10, M66, M156 and M195. Wairak people in Tanzania tested 4.6% (2/43) positive for E-M10.[10] 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.[8]

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.

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".[44] 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.[13] Similarly, while E1b1a reaches its highest frequency of 81% in Senegal, only 1 of the 139 Senegalese that were tested showed M191/P86.[13] 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."[11]

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.[6] 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.[44]

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".[44] This is the modal haplotype of STR markers that is common in carriers of E-U175.[Note 6]

E-U175 haplotype DYS19 DYS388 DYS390 DYS391 DYS392 DYS393
151221101113

E1b1a1a1g has several subclades.

E1b1a1a1h

E1b1a1a1h is defined by markers P268 and P269. It was first reported in a person from the Gambia.[50]

E1b1a2

E1b1a2 is defined by the SNP mutation M329.[Note 7] The majority of the few cases so far observed have been found in East Africa. Semino et al. (2004) found 2 Ethiopian Oromo in a study of >2400 individuals, including 78 Oromo.[51] Cadenas et al. (2007) found 1 case in Qatar, out of 72 people tested there in that study.[31]

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.

Tree

This phylogenetic tree of haplogroup subclades is based on the Y-Chromosome Consortium (YCC) 2008 Tree,[50] the ISOGG Y-DNA Haplogroup E Tree,[4] and subsequent published research.

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. 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. 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.

See also

Wikiquote has quotations related to: Haplogroup E-V38

Ancient Genetics

According to a genetic study in December 2012, Egyptian Monarch Ramesses III belonged to Y-DNA haplogroup E1b1a, a YDNA haplogroup mainly found in Africa with a possible source of origin in East Africa.[52]

Genetics

Y-DNA E subclades

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. 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. 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.

Notes

  1. All were positive for U175.
  2. The publication refers to E-V38 as H22.
  3. Five of the 48 Amhara tested positive for P2 but were negative for M215,M2 and M329. They were not tested for V38 or L222.
  4. E-V38 is approximately 7.7-7.9% of total US male population.
  5. The publication transposes M116.2 with M116.1 in Table 1.
  6. The YCAII STR marker value of 19-19 is also usually indicative of U175.
  7. It was formerly known as E1b1c.
  8. 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.

References

  1. 1 2 3 4 5 6 7 8 Rosa, Alexandra; Carolina Ornelas; Mark A Jobling; António Brehm; Richard Villems (27 July 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.
  2. 1 2 3 Trombetta, Beniamino; Fulvio Cruciani; Daniele Sellitto; Rosaria Scozzari (6 January 2011). MacAulay, Vincent, ed. "A New Topology of the Human Y Chromosome Haplogroup E1b1 (E-P2) Revealed through the Use of Newly Characterized Binary Polymorphisms". PLoS ONE 6 (1): e16073. doi:10.1371/journal.pone.0016073. PMC 3017091. PMID 21253605. Retrieved 7 January 2010.
  3. Semino, Ornella; Chiara Magri, Giorgia Benuzzi, Alice A. Lin, Nadia Al-Zahery, Vincenza Battaglia, Liliana Maccioni, Costas Triantaphyllidis, Peidong Shen, Peter J. Oefner, Lev A. Zhivotovsky, Roy King, Antonio Torroni, L. Luca Cavalli-Sforza, Peter A. Underhill, and A. Silvana Santachiara-Benerecetti (1 May 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". American Journal of Human Genetics 74 (5): 1023–1034. doi:10.1086/386295. PMC 1181965. PMID 15069642.
  4. 1 2 International Society of Genetic Genealogy (3 February 2010). "Y-DNA Haplogroup E and its Subclades - 2010". Retrieved 17 December 2010.
  5. Adams, Jonathan. "Africa During the Last 150,000 Years". Retrieved 26 January 2011.
  6. 1 2 3 4 5 6 7 8 Montano, Valeria; Gianmarco Ferri; Veronica Marcari; Chiara Batini; Okorie Anyaele; Giovanni Destro-Bisol; David Comas (1 July 2011). "The Bantu expansion revisited a new analysis of Y chromosome variation in Central Western Africa". Molecular Ecology 20 (13): 2693–2708. doi:10.1111/j.1365-294X.2011.05130.x. PMID 21627702.
  7. 1 2 3 4 5 6 7 8 9 10 11 Wood, Elizabeth T; Daryn A Stover, Christopher Ehret, Giovanni Destro-Bisol, Gabriella Spedini, Howard McLeod, Leslie Louie, Mike Bamshad, Beverly I Strassmann, Himla Soodyall and Michael F Hammer (27 Apr 2005). "Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes". European Journal of Human Genetics 13 (7): 867–876. doi:10.1038/sj.ejhg.5201408. PMID 15856073. Retrieved 2010-10-20.
  8. 1 2 3 4 5 6 7 Underhill, P.A; Passarino G, Lin AA, Shen P, Mirazón Lahr M, Foley RA, Oefner PJ, Cavalli-Sforza LL. (Jan 2001). "The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations". Annals of Human Genetics 65 (1): 43–62. doi:10.1046/j.1469-1809.2001.6510043.x. PMID 11415522.
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