Haplogroup DE

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Haplogroup DE
Possible time of origin 65,000 (59,100–68,300) BP[1] 50,000-55,000 split between D and E, 70,000-75,000 split between CF and DE [2]
Possible place of origin Africa or Asia
Ancestor CT
Descendants D, E
Defining mutations M1/YAP, M145 = P205, M203, P144, P153, P165, P167, P183

In human genetics, 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.[3]

Haplogroup DE is often referred to by the most well-known unique event polymorphism (UEP) which defines it, the Y-chromosome Alu Polymorphism (YAP). The YAP mutation was caused when a strand of DNA called Alu, which copies itself, inserted a copy into the Y chromosome. A Y chromosome that has the YAP mutation is called YAP-positive (YAP+), and a Y chromosome that does not have the YAP mutation is labeled YAP-negative (YAP-).

Haplogroup DE is an estimated 65,000 years old.[1]

Distribution

The majority of DE male lines can be categorized as being in either Haplogroup D (Y-DNA), which likely originated in Asia, the only place where it has been found,[1] or haplogroup E, which is believed to have originated in East Africa[4][5] or the Near East.[6] The remainder are said to be in the paragroup DE*, confirmed cases of which are extremely rare.

DE* has been most frequently observed amongst Nigerians, albeit at a low frequency. In a study of over 8,000 men worldwide, five out of 1,247 Nigerian males were so classified. However, the study's authors have cautioned that "the apparently paraphyletic status of this haplogroup, and hence the conclusions of nested cladistic analysis, are also likely to be illusory" and that "the only genealogically meaningful definition of the age of a clade is the time to its most recent common ancestor, but only if DE* is paraphyletic does it also become automatically older than D or E in this sense."[7] More recently, one example of DE* was possibly found among speakers of the Nalu language in Guinea Bissau (1/17). The DE* sequence of this individual differs by one mutation from the DE* sequence of the Nigerian individuals. This indicates common ancestry, though the phylogenetic relationship between the two lineages was not determined in this particular study.[8] A 2008 study detected DE* in two individuals from Tibet (2/594).[9] The paragroup DE* in Africa is probably a divergent form of E while the paragroup DE in Tibet probably is a more divergent form of D, or (possibly but not likely) this DE* may simply be a subclade of E or D with a back mutation. This has happened before for example the F* in India is really H some of the K* in Timor Melanesia is really P the NO* in China is really N and the R* in Northern pakistan is really R2 [10]

Haplogroup DE is found in Africa (Haplogroups E and DE*) and East Asia (Haplogroups D and DE* and E*) but is largely absent in between these two regions. The presence of DE across widely separated regions has confounded investigators trying to reconstruct the migration of humans from Africa to Asia. At some time, there was an extinction of DE lineages in West, South and Central Asia. Autochthonous DE lineages are absent in India, an important region in the dispersal of humans in Asia. However DE lineages have been detected in relict populations of the Andaman Islands. Underhill et al. 2007, suggest the possibility that deleterious mutations in some DE carriers may explain the extinction of DE lineages in India.[11]

Origins

Most parsimonious phylogeny of YAP based on Underhill and Kivisild 2007[11]

Discovery

The YAP insertion was discovered by scientists led by Michael Hammer of the University of Arizona.[12] Between 1997 and 1998 Hammer published three articles relating to the origins of haplogroup DE.[13][14][15] These articles state that YAP insertion occurred 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.[6]

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.[15] 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 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.[15]

Contemporary studies

In 2000 a number of scientists had started to reassess the hypothesis of an Asian origin of the YAP insertion. Underhill et al. 2000 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. 2000, the M174 data alone would support an African origin of the YAP insertion.[16]

Further arguments were made supporting and African origin of the YAP in Underhill et al. 2001. The arguments for an African origin include.[4]

  1. Africa has the highest frequency of YAP(>80%). Whereas the YAP+ in Asia has a fairly restricted geographic distribution, mainly at low to moderate frequencies (average 9.6%) in East Asia.[9]
  2. It was claimed that there was no archaeological evidence of a back-migration to Africa, and at the time of writing that there was no unequivocal Y DNA, mitochondrial DNA or autosomal DNA evidence of a back migration to Africa.[4]
  3. Although Haplogroup C seems to have originated in Asia at a similar time to Haplogroup DE's origin, Haplogroup C shows no sign of back migration to Africa.

The African origin of the YAP+ is also supported by studies concerning haplogroup E. In Altheide and Hammer 1997, the authors argue that haplogroup E arose in Asia on an ancestral YAP+ allele before migrating back to Africa.[14] However some studies, such as Semino et al., indicate that the highest frequency and diversity of haplogroup E is in Africa, and Africa is the most likely place of origin of the haplogroup.[9][17]

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 of the other.[18] Haplogroup DE* has recently been found in Nigeria,[7] Guinea-Bissau[8] and also in Tibet.[9] 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.[8] 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.[7]

Chandrasekhar et al. 2007, have argued for the 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. These include Haplogroup R1b1* (18-23kya), which has been observed with especially high frequency among the members of some peoples in northern Cameroon, and Haplogroup T (25-30kya), 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.

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,” in which he implies that haplogroup DE left Africa along with Haplogroup CF.[19]

Peter Underhill states 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.[11] Other authors who have published or co-published works in support of an African origin of the YAP+ include Luigi Luca Cavalli-Sforza,[16] Toomas Kivisild,[11] Spencer Wells,[18] Linda Stone and Paul F. Lurquin.[20]

Tree

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)


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.

See also

References

  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. ↑ ISOGG reference webpage.
  4. ↑ 4.0 4.1 4.2 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. ↑ 6.0 6.1 Lua error in package.lua at line 80: module 'strict' not found.
  7. ↑ 7.0 7.1 7.2 Lua error in package.lua at line 80: module 'strict' not found.
  8. ↑ 8.0 8.1 8.2 Lua error in package.lua at line 80: module 'strict' not found.
  9. ↑ 9.0 9.1 9.2 9.3 Lua error in package.lua at line 80: module 'strict' not found.
  10. ↑ http://biorxiv.org/content/early/2013/11/22/000802.1
  11. ↑ 11.0 11.1 11.2 11.3 Lua error in package.lua at line 80: module 'strict' not found.
  12. ↑ 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. ↑ 14.0 14.1 Lua error in package.lua at line 80: module 'strict' not found.
  15. ↑ 15.0 15.1 15.2 Lua error in package.lua at line 80: module 'strict' not found.
  16. ↑ 16.0 16.1 Lua error in package.lua at line 80: module 'strict' not found.
  17. ↑ Lua error in package.lua at line 80: module 'strict' not found.
  18. ↑ 18.0 18.1 Lua error in package.lua at line 80: module 'strict' not found.
  19. ↑ Scientists reshape Y chromosome haplogroup tree gaining new insights into human ancestry
  20. ↑ Lua error in package.lua at line 80: module 'strict' not found.

External links

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