Haplogroup DE

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Haplogroup DE
Possible time of origin59,100–68,300[1] or 50,000-55,000 years split between D and E and 70,000-75,000 or already 141,000 years split between CF and DE[2], ca. 73,000 years ago
Possible place of originUnknown, Eastern Africa[3][4] or Eurasia[5]
AncestorCT
DescendantsD, E
Defining mutationsM1/YAP, M145 = P205, M203, P144, P153, P165, P167, P183

Haplogroup DE is a human Y-chromosome DNA haplogroup. It is defined by the single nucleotide polymorphism (SNP) mutations, or UEPs, M1(YAP), M145(P205), M203, P144, P153, P165, P167, P183.[6] DE is unique because it is distributed in several geographically distinct clusters. An immediate subclade, haplogroup D, is normally found only in eastern Asia, parts of Central Asia and the Andaman Islands, and the other immediate subclade, haplogroup E, is common in Africa, Europe and the Middle East.

The most well-known unique event polymorphism (UEP) that defines DE is the Y-chromosome Alu Polymorphism "YAP". The mutation was caused when a strand of DNA, known as Alu, inserted a copy of itself into the Y chromosome. Hence, all Y chromosomes belonging to DE, D, E and their subclades are YAP-positive (YAP+). All Y chromosomes that belong to other haplogroups and subclades are YAP-negative (YAP-).

The age of haplogroup DE is generally estimated between 65,000 and 71,000 years.[1]

Distribution[edit]

The subclades of DE continue to confound investigators trying to reconstruct the migration of humans because, while they are common in Africa and East Asia, they are also largely absent between these two regions. As the paragroup DE* is extremely rare, the majority of DE male lines fall into subclades of either D-M174 or E-M96. While D-M174 likely originated in Asia – the only place where it is now found,[1] E-M96 is more likely to have originated in East Africa.[7][8] However, a West Asian origin for E-M96 is considered possible by some scholars.[9] Some researchers have suggested that the exceptional rarity of DE lineages in India – a region considered important in the dispersal of modern humans – may be meaningful, because D-M174 and E-M96 have remained common in neighbouring areas.[3]

DE* has been found in five separate studies, at very low frequencies, among males from widely separated locations: West Africa and East Asia. A 2003 study by Weale et al., of the DNA of over 8,000 males worldwide, found that five out of 1,247 Nigerian males belonged to DE*. The DE* found possessed by these five Nigerians, according to the study's authors, was "the least derived of all YAP chromosomes according to currently known binary markers" – to such an extent that it suggested that DE had originated in West Africa and expanded from there. However, Weale et al., cautioned that such inferences may well be incorrect. In addition, the seemingly "paraphyletic" (basal) status of the Nigerian examples of DE-YAP may be "illusory" because the "branching order, and hence the origin, of YAP-derived haplogroups remains uncertain". It was "easy to misinterpret apparently paraphyletic groups", and subsequent research might show that the Nigerian examples of DE were as divergent from DE*, D* and E*. "[T]he only genealogically meaningful definition of the age of a clade is the time to its most recent common ancestor, but only if DE* is [truly] paraphyletic does it ... become automatically older than D or E..." The relationship between DE*, according to Weale et al., "can be viewed as a missing-data problem..." In 2007, another West African example of DE* was reported – carried by a speaker of the Nalu language who was among 17 Y-DNA samples taken in Guinea Bissau. The sequence of this individual differed by one mutation from those of the Nigerian individuals, indicating common ancestry, although the relationship between the two lineages has not been determined. But according to the authors, the sampled individuals (including the former five samples) likely share common paternal ancestors because of the highly similar microsatellite haplotype sizes.[10][11]

In 2004, haplogroup DE was found in tribal populations of Karnataka in India at a frequency of about 6.1% of the total group tested.[12] More recent studies did not find any further DE* outside of Karnataka in India.[13]

In 2008, a basal paternal marker belonging to DE* was identified in two individuals from Tibet (two out of 594), belonging to the Tibeto-Burman group.[14]

In 2012, haplogroup DE* was found in one Caribbean sample.[15]

A 2019 study by Haber et al., suggested that three of the Nigerians analysed by Weale et al. belong, not to DE*, but to D0, a proposed haplogroup thought to represent a deep-rooting DE lineage branching close to the DE bifurcation (near the split of D and E) but on the D branch as an outgroup to all other known D chromosomes.[16] Another found carrier of D0 (the D-FT75 branch) is an individual named Ruslan bin Makin Al-Bitar from Syria.[17] Recently two other D0 samples were found in Western Asia (in Saudi Arabia).[18]

Origins[edit]

Most parsimonious phylogeny of YAP based on Underhill and Kivisild 2007[3]

Discovery[edit]

The YAP insertion was discovered by scientists led by Michael Hammer of the University of Arizona.[19] Between 1997 and 1998 Hammer published three articles relating to the origins of haplogroup DE.[20][21][22] These articles state that YAP insertion originated in Asia. As recently as 2007, some studies such as Chandrasekar et al. 2007, cite the publications by Hammer when arguing for an Asian origin of the YAP insertion.[9]

The scenarios outlined by Hammer include an out of Africa migration over 100,000 years ago, the YAP+ insertion on an Asian Y-chromosome 55,000 years ago and a back migration of YAP+ from Asia to Africa 31,000 years ago by its subclade haplogroup E.[22] This analysis was based on the fact that older African lineages, such as haplogroups A and B, were YAP negative whereas the younger lineage, haplogroup E was YAP positive. Haplogroup D, which is YAP positive, was clearly an Asian lineage, being found only in East Asia with high frequencies in Andaman Islands, Japan and Tibet. Because the mutations that define haplogroup E were observed to be in the ancestral state in haplogroup D, and haplogroup D at 55kya, was considerably older than haplogroup E at 31kya, Hammer concluded that haplogroup E was a subclade of haplogroup D and migrated back to Africa.[22]

A 2000 study concerning the origin of the YAP+ mutation analyzed 841 Y-chromosomes representing 36 human populations of wide geographical distribution for the presence of a Y-specific Alu insert (YAP+ chromosomes). They also analyzed the Out-of-Africa and out-of-Asia models for the YAP mutations. According to the authors, the most ancient YAP+ mutation is found in the Asian lineage of Tibetans and in northern India, but curiously not in Japanese lineages. More recent YAP+ lineages are distributed almost equally in Asians and Africans, with a smaller distribution in Europe. The scientists concluded that the information available does not allow one to decide between the out-of-Asia or out-of-Africa models. They further suggest that the YAP+ mutation had already originated 141,000 years ago.[23]

Contemporary studies[edit]

Since 2000, some scientists, including Underhill et al., had started to reassess the hypothesis of an Asian origin of the YAP insertion and to suggest an African origin.[7]

Underhill et al. 2001 identified the D-M174 mutation that defines haplogroup D. The M174 allele is found in the ancestral state in all African lineages including haplogroup E. The discovery of M174 mutation meant that haplogroup E could not be a subclade of haplogroup D. These findings effectively neutralized the argument of an Asian origin of the YAP+ based on the character state of the M40 and M96 mutations that define haplogroup E. According to Underhill et al. 2001, the M174 data alone would support an African origin of the YAP insertion.[24]

In Altheide and Hammer 1997, the authors argue that haplogroup E arose in Asia on an ancestral YAP+ allele before migrating back to Africa.[21] However some studies, such as Semino et al., indicate that the highest frequency and diversity of haplogroup E is in Africa, and East Africa is the most likely place of origin of the haplogroup.[25]

The models supporting an African origin or an Asian origin of the YAP+ insertion both required the extinction of the ancestral YAP chromosome to explain the current distribution of the YAP+ polymorphism. Paragroup DE* possesses neither the mutations that define haplogroup D or haplogroup E. If paragroup DE* was found in one location but not the other, it would boost one theory over the other.[26] Haplogroup DE* has recently been found in Nigeria,[10] Guinea-Bissau[11] and also in Tibet.[14] The phylogenetic relationship of three DE* sequences has yet to be determined, but it is known that the Guinea Bissau sequences differ from the Nigerian sequences by at least one mutation.[11] Weale et al. state that the discovery of DE* among Nigerians pushes back the date for the most recent common ancestor (MRCA) of African YAP chromosomes. This, in his view, has the effect of reducing the time window through which a possible back migration from Asia to Africa could occur.[10]

Chandrasekhar et al. 2007[27], have argued for an Asian origin of the YAP+. They state:

The presence of the YAP insertion in Northeast Indian tribes and Andaman Islanders with haplogroup D suggests that some of the M168 chromosomes gave rise to the YAP insertion and M174 mutation in South Asia

They also argue that YAP+ migrated back to Africa with other Eurasian haplogroups, such as Haplogroup R1b1* (18-23kya), which has been observed with especially high frequency among the members of some peoples in northern Cameroon, and Haplogroup T (39-45 kya), which has been observed in low frequencies in Africa. Haplogroup E at 50kya is considerably older than these haplogroups and has been observed at frequencies of 80-92% in Africa.

Peter Underhill stated in 2007 again that there will always be uncertainty regarding the precise origins of DNA sequence variants such as YAP because of a lack of knowledge concerning prehistoric demographics and population movements. However Underhill contends that with all the available information, the African origin of the YAP+ polymorphism is more parsimonious and more plausible than the Asian origin hypothesis.[3]

In a press release concerning a study by Karafet et al. 2008, Michael Hammer, revised the dates for the origin Haplogroup DE from 55,000 years ago to 65,000 years ago. For haplogroup E, Hammer revised the dates from 31,000 years ago to 50,000 years ago. Hammer is also quoted as saying “The age of haplogroup DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old”.[28]

A molecular genetic study in 2018, based on analyzing both maternal and paternal haploid markers, the current distribution of uni-parental lineages, and inferences from the DNA of the Altai Neanderthals, supports an Asian origin of paternal haplogroup DE and maternal haplogroup L3. The study suggests a back migration into Africa and a following admixture of the native Africans with immigrating peoples from Asia. The scientists said that this is further supported by autosomal DNA analyses. It is suggested that DE originated about 70,000 years ago somewhere near Tibet and Central Asia. Additionally, a basal marker of DE was found in Tibet, which the authors argue supports the origin of DE* and DE in this region. Similarly, Tibet shows the greatest genetic diversity concerning haplogroup D and D*. The ancestral lineage E* was found in both the Arabian peninsula and the Levant which is considered to suggest that haplogroup E split from DE in the middle East. It is further argued that Haploid diversity of haplogroup E supports a strong Eurasian male gene flow. The authors conclude that this supports an Asian origin and also explain signals of small percentages of Neanderthal and Eurasian DNA found in northern and some western Africans.[29]

A 2019 study by Haber et al. supports an African origin for haplogroup DE* (based partially on the proposed discovery of haplogroup D0 found in three Nigerians, according to the authors a branch of the DE lineage near the DE split but on the D branch, as well as on y-dna phylogeny, hapogroup divergence dates, and evidence for ancestral Eurasians outside Africa). The authors consider the possibility that D0 and E are part of a back-migration from Asia about 71 kya for D0 and about 59 kya for E, but conclude that an African origin for haplogroups DE*, D0, and E is more supported by their study. They explain: "Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE* lineage within Africa with D0 and E remaining there, and the migration out of the three lineages (C, D and FT) that now form the vast majority of non-African Y chromosomes." The authors find divergence times for DE*, E, and D0, likely within a period of about 76,000-71,000 years ago, and a likely date for the exit of the ancestors of modern Eurasians out of Africa (and ensuing Neanderthal admixture) later around 49,900-59,400 years ago, which they argue, also supports an African origin for those haplogroups.[4]

Recently ftdna (2019) found other D0 samples in Western Asia: one found in a Syrian (the most basal sample of D0 found to date), and two samples of D0 in Saudi Arabians. According to Runfeldt and Sager, D0 is a divergent branch of D and should not be considered as more deeply rooted than D itself. According to their schematics, D0 can be grouped into an Asian cluster (West Asia) and African cluster (Nigeria). Two deeply-rooted D0 branches were confirmed: D-FT75 found in West Asia and D-FT76 found in West Asia and West Africa. The research team says they will continue to analyze additional samples.[30]

Both theories (Out-of-Africa and Out-of-Asia) regarding the origin of haplogroup DE are discussed and more studies are needed to conclude about a proposed origin.

Tree[edit]

This phylogenetic tree of para-haplogroup DE is based on the YCC 2008 tree[1] and subsequent published research.

  • DE (M1/YAP, M145 [P205], M203, P144, P153, P165, P167, P183)
    • D (M174, (021355))
    • E (SRY4064, M96, P29, P150, P152, P154, P155, P156, P162)
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

See also[edit]

References[edit]

  1. ^ a b c d Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (May 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.
  2. ^ Raghavan, Maanasa; Skoglund, Pontus; Graf, Kelly E.; Metspalu, Mait; Albrechtsen, Anders; Moltke, Ida; Rasmussen, Simon; Stafford Jr, Thomas W.; Orlando, Ludovic; Metspalu, Ene; Karmin, Monika; Tambets, Kristiina; Rootsi, Siiri; Mägi, Reedik; Campos, Paula F.; Balanovska, Elena; Balanovsky, Oleg; Khusnutdinova, Elza; Litvinov, Sergey; Osipova, Ludmila P.; Fedorova, Sardana A.; Voevoda, Mikhail I.; Degiorgio, Michael; Sicheritz-Ponten, Thomas; Brunak, Søren; Demeshchenko, Svetlana; Kivisild, Toomas; Villems, Richard; Nielsen, Rasmus; Jakobsson, Mattias; Willerslev, Eske (2014). "Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans". Nature. 505 (7481): 87–91. Bibcode:2014Natur.505...87R. doi:10.1038/nature12736. PMC 4105016. PMID 24256729.
  3. ^ a b c d Underhill PA, Kivisild T (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.
  4. ^ a b 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: genetics.302368.2019. doi:10.1534/genetics.119.302368. PMID 31196864.
  5. ^ Cabrera VM (2017). "Carriers of mitochondrial DNA macrohaplogroup L3 basic lineages migrated back to Africa from Asia around 70,000 years ago". bioRxiv 233502.
  6. ^ ISOGG reference webpage.
  7. ^ a b Underhill (2001). "The case for an African rather than an Asian origin of the human Y-chromosome YAP insertion". Genetic, Linguistic and Archaeological Perspectives on Human Diversity in Southeast Asia. New Jersey: World Scientific. ISBN 981-02-4784-2.
  8. ^ Cruciani F, La Fratta R, Santolamazza P, Sellitto D, Pascone R, Moral P, Watson E, Guida V, Colomb EB, Zaharova B, Lavinha J, Vona G, Aman R, Cali F, Akar N, Richards M, Torroni A, Novelletto A, Scozzari R (May 2004). "Phylogeographic analysis of haplogroup E3b (E-M215) y chromosomes reveals multiple migratory events within and out of Africa". American Journal of Human Genetics. 74 (5): 1014–22. doi:10.1086/386294. PMC 1181964. PMID 15042509.
  9. ^ a b Chandrasekar A, Saheb SY, Gangopadyaya P, Gangopadyaya S, Mukherjee A, Basu D, Lakshmi GR, Sahani AK, Das B, Battacharya S, Kumar S, Xaviour D, Sun D, Rao VR (2007). "YAP insertion signature in South Asia". Annals of Human Biology. 34 (5): 582–6. doi:10.1080/03014460701556262. PMID 17786594.
  10. ^ a b c Weale ME, Shah T, Jones AL, Greenhalgh J, Wilson JF, Nymadawa P, Zeitlin D, Connell BA, Bradman N, Thomas MG (September 2003). "Rare deep-rooting Y chromosome lineages in humans: lessons for phylogeography". Genetics. 165 (1): 229–34. PMC 1462739. PMID 14504230.
  11. ^ a b c Rosa A, Ornelas C, Jobling MA, Brehm A, Villems R (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.
  12. ^ Independent origins of Indian caste and tribal paternal lineages. - Cordaux R, et al. Curr Biol. 2004
  13. ^ A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations. - Singh M et al. Nature. 2018.
  14. ^ a b Shi H, Zhong H, Peng Y, Dong YL, Qi XB, Zhang F, Liu LF, Tan SJ, Ma RZ, Xiao CJ, Wells RS, Jin L, Su B (October 2008). "Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations". BMC Biology. 6: 45. doi:10.1186/1741-7007-6-45. PMC 2605740. PMID 18959782.
  15. ^ Simms TM, Wright MR, Hernandez M, Perez OA, Ramirez EC, Martinez E, Herrera RJ (2012). "Y-chromosomal diversity in Haiti and Jamaica: Contrasting levels of sex-biased gene flow". American Journal of Physical Anthropology: 618–31. doi:10.1002/ajpa.22090. PMID 22576450.
  16. ^ https://www.genetics.org/content/early/2019/06/13/genetics.119.302368
  17. ^ https://www.familytreedna.com/public/sidoroff/default.aspx?section=yresults
  18. ^ Estes, Roberta (2019-06-21). "Exciting New Y DNA Haplogroup D Discoveries!". DNAeXplained - Genetic Genealogy. Retrieved 2019-07-06.
  19. ^ Hammer MF (September 1994). "A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies". Molecular Biology and Evolution. 11 (5): 749–61. doi:10.1093/oxfordjournals.molbev.a040155. PMID 7968488.
  20. ^ Hammer MF, Karafet T, Rasanayagam A, Wood ET, Altheide TK, Jenkins T, Griffiths RC, Templeton AR, Zegura SL (April 1998). "Out of Africa and back again: nested cladistic analysis of human Y chromosome variation". Molecular Biology and Evolution. 15 (4): 427–41. doi:10.1093/oxfordjournals.molbev.a025939. PMID 9549093.
  21. ^ a b Altheide TK, Hammer MF (August 1997). "Evidence for a possible Asian origin of YAP+ Y chromosomes". American Journal of Human Genetics. 61 (2): 462–6. doi:10.1016/S0002-9297(07)64077-4. PMC 1715891. PMID 9311756.
  22. ^ a b c Hammer MF, Spurdle AB, Karafet T, Bonner MR, Wood ET, Novelletto A, Malaspina P, Mitchell RJ, Horai S, Jenkins T, Zegura SL (March 1997). "The geographic distribution of human Y chromosome variation". Genetics. 145 (3): 787–805. PMC 1207863. PMID 9055088.
  23. ^ Origin of YAP+ lineages of the human Y‐chromosome - M. Bravi et al.[full citation needed]
  24. ^ Underhill PA, Passarino G, Lin AA, Shen P, Mirazón Lahr M, Foley RA, Oefner PJ, Cavalli-Sforza LL (January 2001). "The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations" (PDF). Annals of Human Genetics. 65 (Pt 1): 43–62. doi:10.1046/j.1469-1809.2001.6510043.x. PMID 11415522. Archived from the original (PDF) on 2009-08-15.
  25. ^ Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, Battaglia V, Maccioni L, Triantaphyllidis C, Shen P, Oefner PJ, Zhivotovsky LA, King R, Torroni A, Cavalli-Sforza LL, Underhill PA, Santachiara-Benerecetti AS (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): 1023–34. doi:10.1086/386295. PMC 1181965. PMID 15069642.
  26. ^ Wells RS, Yuldasheva N, Ruzibakiev R, Underhill PA, Evseeva I, Blue-Smith J, Jin L, Su B, Pitchappan R, Shanmugalakshmi S, Balakrishnan K, Read M, Pearson NM, Zerjal T, Webster MT, Zholoshvili I, Jamarjashvili E, Gambarov S, Nikbin B, Dostiev A, Aknazarov O, Zalloua P, Tsoy I, Kitaev M, Mirrakhimov M, Chariev A, Bodmer WF (August 2001). "The Eurasian heartland: a continental perspective on Y-chromosome diversity". Proceedings of the National Academy of Sciences of the United States of America. 98 (18): 10244–9. doi:10.1073/pnas.171305098. PMC 56946. PMID 11526236.
  27. ^ YAP insertion signature in South Asia - Chandrasekar 2007 (https://www.researchgate.net/publication/6053145_YAP_insertion_signature_in_South_Asia)
  28. ^ Scientists reshape Y chromosome haplogroup tree gaining new insights into human ancestry
  29. ^ Cabrera VM, Marrero P, Abu-Amero KK, Larruga JM (June 2018). "Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago". BMC Evolutionary Biology. 18 (1): 98. doi:10.1186/s12862-018-1211-4. PMC 6009813. PMID 29921229.
  30. ^ Estes, Roberta (2019-06-21). "Exciting New Y DNA Haplogroup D Discoveries!". DNAeXplained - Genetic Genealogy. Retrieved 2019-07-06.

External links[edit]