Haplogroup U (mtDNA)


Haplogroup U (mtDNA)
Haplogroup U
Possible time of origin 55,000 BP
Possible place of origin Western Asia
Ancestor R
Descendants U1, U5, U6, U2'3'4'7'8'9
Defining mutations 11467, 12308, 12372[1]

In human mitochondrial genetics, Haplogroup U is a human mitochondrial DNA (mtDNA) haplogroup.

Contents

Origins

Haplogroup U descends from a woman in the Haplogroup R (mtDNA) branch of the phylogenetic tree, who lived around 55,000 years ago. Her descendants gave birth to several different subgroups, some of which exhibit specific geographic homelands.

Distribution

Haplogroup U is subdivided into Haplogroups U1-U8. Haplogroup K is a subclade of U8.[2] The old age has led to a wide distribution of the descendant subgroups that harbor specific European, Berber, Indian, African, Arab, northern Caucasus Mountains and the Near East clades.[3]

Subclades

Haplogroup U1

Haplogroup U1 (named 'Una' by Bryan Sykes) seems to appear mostly in the Middle East, however low frequency results appear scattered throughout Europe particularly in the Mediterranean. U1a in particular is found from India to Europe, but is extremely rare among the northern and Atlantic fringes of Europe including the British Isles and Scandinavia. Several examples in Tuscany have been noted. In India U1a has been found in the Kerala region. U1b has a similar spread but is rarer than U1a. Some examples of U1b have been found among Jewish diaspora. U1a and U1b appear in equal frequency in eastern Europe.[4]

Haplogroup U2

Haplogroup U2 (named 'Uta' by Bryan Sykes) is most common in South Asia[5] but also found in low frequency in Central and West Asia, as well as in Europe as U2e.[6]

This haplogroup has been found in the remains of a 30,000-year-old hunter-gatherer in South European Russia (Kostenki).[7]

Haplogroup U3

Haplogroup U3 (named 'Uma' by Bryan Sykes) is defined by the HVR1 transition A16343G. It is found at low levels throughout Europe (about 1% of the population), the Near East (about 2.5% of the population), and Central Asia (1%). U3 is present at higher levels among populations in the Caucasus (about 6%) and among Lithuanian Romani, Polish Romani, and Spanish Romani populations (36-56%).[8][9][10]

Haplogroup U4

Haplogroup U4 (named 'Ulrike' by Bryan Sykes) has its origin in the Upper Palaeolithic, dating to approximately 25,000 years ago. It is widely distributed in Europe, and has been implicated in the expansion of modern humans into Europe occurring before the Last Glacial Maximum.

Haplogroup U5

Among the oldest mtDNA haplogroups found in European remains of Homo sapiens is U5. The age of U5 is estimated at 50,000 but could be as old as 60,500 years. Approximately 11% of total Europeans and 10% of European-Americans are in haplogroup U5.

The presence of haplogroup U5 in Europe pre-dates the expansion of agriculture in Europe. Bryan Sykes' popular book The Seven Daughters of Eve calculated that it arose 45,000-50,000 years ago in the area of Delphi, Greece and named the originator of haplogroup U5 Ursula. However the details related to location and age are speculative. Barbujani and Bertorelle estimate the age of haplogroup U5 as about 52,000 years ago, being the oldest subclade of haplogroup U.[11] Thus, the name 'Ursula' could be applied to the entirety of haplogroup U, as well as U5.

U5 has been found in human remains dating from the Mesolithic in England, Germany, Lithuania, Poland, Portugal, Russia [12], Sweden [13], and France [14] .

Haplogroup U5 and its subclades U5a and U5b form the highest population concentrations in the far north, in Sami, Finns, and Estonians, but it is spread widely at lower levels throughout Europe. This distribution, and the age of the haplogroup, indicate individuals from this haplogroup were part of the initial expansion tracking the retreat of ice sheets from Europe ~10kya.

Haplogroup U5 is found also in small frequencies and at much lower diversity in the Near East and parts of Africa, suggesting back-migration of people from northern Europe to the south.[3]

Mitochondrial haplogroup U5a has also been associated with HIV infected individuals displaying accelerated progression to AIDS and death.[15]

  • U5 has polymorphisms in the locations of 3197 9477 13617 16192 16270
    • U5a arose around 20000 years ago and has polymorphisms in 14793 16256 ( + U5 polymorphisms).[10]
      • U5a1 arose around 16000 years ago and has polymorphisms in 15218 16399( + U5a polymorphisms).
        • U5a1a arose around 15000 years ago and has polymorphisms in 1700 16192( + U5a1 polymorphisms).
          • U5a1a1 arose around 12000 years ago and has polymorphisms in 5495 15924( + U5a1a polymorphisms).
            • U5a1a1a has polymorphisms in 152 3816( + U5a1a1 polymorphisms).
          • U5a1a2 has polymorphisms in 573.1C (deletion) 12346( + U5a1a polymorphisms).
            • U5a1a2a has polymorphisms in 5319 6629 6719( + U5a1a2 polymorphisms).
        • U5a1b arose around 11000 years ago and has polymorphisms in 9667 (A9667G) ( + U5a1 polymorphisms).
          • U5a1b1 arose around 10000 years ago and has polymorphisms in 16291 (C16291T) ( + U5a1b polymorphisms).
            • U5a1b1a has polymorphisms in 356.1C (deletion) 4553 ( + U5a1b1 polymorphisms).
            • U5a1b1b has polymorphisms in 8119 (T8119C)( + U5a1b1 polymorphisms).
            • U5a1b1c has polymorphisms in 9055 (G9055A)( + U5a1b1 polymorphisms).
            • U5a1b1c1 has polymorphisms in 1187 (T1187C)( + U5a1b1c polymorphisms).
            • U5a1b1d has polymorphisms in 12358 16093 ( + U5a1b1 polymorphisms).
            • U5a1b1e has polymorphisms in 12582 16192 16294 ( + U5a1b1 polymorphisms).
          • U5a1b2 has polymorphisms in 9632 ( + U5a1b polymorphisms).
          • U5a1b3 has polymorphisms in 16362 16428 ( + U5a1b polymorphisms).
        • U5a1c arose around 13000 years ago and has polymorphisms in 16320 ( + U5a1 polymorphisms).
          • U5a1c1 has polymorphisms in 195 13802 ( + U5a1c polymorphisms).
          • U5a1c2 has polymorphisms in 961 965.1C (deletion)( + U5a1c polymorphisms).
        • U5a1d arose around 19000 years ago and has polymorphisms in 3027 ( + U5a1 polymorphisms).
          • U5a1d1 has polymorphisms in 5263 13002 (to adenosine)( + U5a1d polymorphisms).
          • U5a1d2 has polymorphisms in 573.1C (deletion) 3552 (+ U5a1d polymorphisms).
            • U5a1d2a has polymorphisms in 195 4823 5583 16145 16189 (+ U5a1d2 polymorphisms).
        • U5a1e has polymorphisms in 3564 8610 ( + U5a1 polymorphisms).
        • U5a1f has polymorphisms in 6023 ( + U5a1 polymorphisms).
      • U5a2 arose around 14000 years ago and has polymorphisms in 16526( + U5a polymorphisms).
        • U5a2a arose around 6000 years ago and has polymorphisms in 13827 13928C 16114 16294 ( + U5a2 polymorphisms).
        • U5a2b arose around 8000 years ago and has polymorphisms in 9548 ( + U5a2 polymorphisms).
        • U5a2c arose around 13000 years ago and has polymorphisms in 10619( + U5a2 polymorphisms).
        • U5a2d and has polymorphisms in 7843 7978 8104 11107 16192! (backmutated in 16192 to the original Cambridge sequence) ( + U5a2 polymorphisms).
        • U5a2e and has polymorphisms in 151 152 3768 15289 16189 16311 16362 ( + U5a2 polymorphisms).
    • U5b arose around 24000 years ago and has polymorphisms in 150 7768 14182( + U5 polymorphisms).
      • U5b1 arose around 18000 years ago and has polymorphisms in 5656( + U5b polymorphisms).
        • U5b1a has polymorphisms in 5656 15097, 16189 and has lost its polymorphism in 7028 (backmutation)( + U5b1 polymorphisms).
        • U5b1b: has been found in Fulbe and Papel people in Guinea-Bissau and Yakuts people of northeastern Siberia. [16][17] It arose around 11000 years ago and has polymorphisms in 12618 16189 ( + U5b1 polymorphisms).
        • U5b1c has polymorphisms in 5656 15191, 16189, 16311 + U5b1 polymorphisms) and arose about 13000 years ago.
        • U5b1d has polymorphisms in 5437 5656 and has lost its polymorphism in 16192 (backmutation)( + U5b1 polymorphisms).
        • U5b1e has polymorphisms in 152 2757 10283 12616 16189 and has lost its polymorphism in 16192 (backmutation)( + U5b1 polymorphisms) and arose about 6600 years ago.U5b1e is mainly seen in central Europe among Czechs, Slovaks, Hungarians and southern Russians..[18]
        • U5b1g has polymorphisms in 151 228 573.1C 5656 10654 13759 14577 ( + U5b1 polymorphisms).
      • U5b2 arose around 24000 years ago and has polymorphisms in 1721 13637( + U5b polymorphisms).
      • U5b3: The subclade is found primary on the island of Sardinia.[19]

Haplogroup U6

Haplogroup U6 was named 'Ulla' by Bryan Sykes. It is common (around 10% of the people) [3] in North Africa (with a maximum of 29% in an Algerian Berber people[20]) and the Canary Islands (18%). It is also found in the Iberian peninsula, where it has the highest diversity (10 out of 19 sublineages are only found in this region and not in Africa),[20] Eastern Africa and occasionally in other locations.

U6 is thought to have entered North Africa around 30,000 years ago from the Near-East. In spite of the highest diversity of Iberian U6, Maca-Meyer argues for an Iberian origin of this clade based on the highest diversity of subclade U6a in that region,[20] where it would have arrived from West Asia. She estimates the age of U6 between 25,000 and 66,000 years BP. However U6 has its highest frequencies in North Africa and seems to be a specific haplogroup of that region.

U6 has three main subclades:[20]

Subgroup U6a reflects the first African expansion from the Maghrib returning to the east in Paleolithic times. Derivative clade U6a1 signals a posterior movement from East Africa back to the Maghrib and the Near East. This migration coincides with the probable Afroasiatic linguistic expansion. U6b and U6c clades, restricted to West Africa, had more localized expansions. U6b probably reached the Iberian Peninsula during the Capsian diffusion in North Africa. Two autochthonous derivatives of these clades (U6b1 and U6c1) indicate the arrival of North African settlers to the Canarian Archipelago in prehistoric times, most probably due to the Saharan desiccation. The absence of these Canarian lineages nowadays in Africa suggests important demographic movements in the western area of this Continent.
—Maca-Meyer 2003
  • U6a: it is the most widespread (from Canary Islands and Iberian Peninsula to Syria, Ethiopia and Kenya) and has highest diversity in Eastern Africa. Estimated age: 24-27,500 BP. It has one major subclade:
    • U6a1: with similar distribution to U6a. Estimated age: 15-20,000 BP. Found in Brittany (France) at 4.5% frequency.[21] Also found among the Akan people at 4.5% frequency.[22]
  • U6b: shows a more patched and western distribution. In the Iberian peninsula U6b is more frequent in the North (while U6a is in the South). It has also been found in low amounts in Morocco, Algeria, Senegal and Nigeria. Estimated age: 8,500-24,500 BP. It has one subclade:
    • U6b1: found only in the Canary Islands and in the Iberian peninsula. Estimated age: c. 6000 BP.
  • U6c: only found in Morocco and Canary Islands. Estimated age: 6,000-17,500 BP.

U6a and U6b share a common basal mutation (16219) that is not present in U6c.

Haplogroup U7

Many European populations lack Haplogroup U7 (named 'Ulaana' by Bryan Sykes), but its frequency climbs over 4% in the Near East and up to 5% in Pakistan, reaching nearly 10% level in Iranians. In India, haplogroup U7 frequency peaks at over 12% in Gujarat, the westernmost state of India, while for the whole of India its frequency stays around 2%. Expansion times and haplotype diversities for the Indian and Near and Middle Eastern U7 mtDNAs are strikingly similar. The possible homeland of this haplogroup spans Indian Gujarat and Iran because from there its frequency declines steeply both to the east and to the west. If the origin were in Iran rather than in India, then its equally high frequency as well as diversity in Gujarat favors a scenario whereby U7 has been introduced to the coastal western India either very early, or by multiple founders.[5]

Haplogroup U8

  • U8a: The Basques have the most ancestral phylogeny in Europe for the mitochondrial haplogroup U8a, a rare subgroup of U8, placing the Basque origin of this lineage in the Upper Palaeolithic. The lack of U8a lineages in Africa suggests that their ancestors may have originated from West Asia.[2]
  • U8b: This clade has been found in Italy and Jordan.[2]

Haplogroup K

Haplogroup K (named 'Katrine' by Bryan Sykes) makes up a sizeable fraction of European and West Asian mtDNA lineages. It is now known it is actually a subclade of haplogroup U8b'K,[2] and is believed to have first arisen in northeastern Italy. Haplogroup UK shows some evidence of being highly protective against AIDS progression.[15]

Tree

This phylogenetic tree of haplogroup U subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation[1] and subsequent published research.

See also

Evolutionary tree of Human mitochondrial DNA (mtDNA) haplogroups

  Mitochondrial Eve (L)    
L0 L1-6
L1 L2 L3   L4 L5 L6
  M N  
CZ D E G Q   A S   R   I W X Y
C Z B F R0   pre-JT P  U
HV JT K
H V J T

References

  1. ^ a b van Oven M, Kayser M (February 2009). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation 30 (2): E386–94. doi:10.1002/humu.20921. PMID 18853457. 
  2. ^ a b c d González AM, García O, Larruga JM, Cabrera VM (2006). "The mitochondrial lineage U8a reveals a Paleolithic settlement in the Basque country". BMC Genomics 7: 124. doi:10.1186/1471-2164-7-124. PMC 1523212. PMID 16719915. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1523212. 
  3. ^ a b c The Genographic Project at National Geographic
  4. ^ mtDNA Haplogroup U1a page at cagetti.com
  5. ^ a b Metspalu M, Kivisild T, Metspalu E, et al. (August 2004). "Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans". BMC Genetics 5: 26. doi:10.1186/1471-2156-5-26. PMC 516768. PMID 15339343. http://evolutsioon.ut.ee/publications/Metspalu2004.pdf. 
  6. ^ FTDNA mtDNA U2 Haplogroup project.
  7. ^ "DNA analysed from early European". BBC News. 2010-01-01. http://news.bbc.co.uk/2/hi/science/nature/8435317.stm. Retrieved 2010-05-04. 
  8. ^ Richards M, Macaulay V, Hickey E, et al. (November 2000). "Tracing European founder lineages in the Near Eastern mtDNA pool". American Journal of Human Genetics 67 (5): 1251–76. doi:10.1016/S0002-9297(07)62954-1. PMC 1288566. PMID 11032788. http://evolutsioon.ut.ee/publications/Richards2000.pdf. 
  9. ^ Quintana-Murci L, Chaix R, Wells RS, et al. (May 2004). "Where west meets east: the complex mtDNA landscape of the southwest and Central Asian corridor". American Journal of Human Genetics 74 (5): 827–45. doi:10.1086/383236. PMC 1181978. PMID 15077202. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1181978. 
  10. ^ a b Malyarchuk BA, Grzybowski T, Derenko MV, Czarny J, Miścicka-Sliwka D (March 2006). "Mitochondrial DNA diversity in the Polish Roma". Annals of Human Genetics 70 (2): 195–206. doi:10.1111/j.1529-8817.2005.00222.x. PMID 16626330. 
  11. ^ Barbujani G, Bertorelle G (January 2001). "Genetics and the population history of Europe". Proceedings of the National Academy of Sciences of the United States of America 98 (1): 22–5. doi:10.1073/pnas.98.1.22. PMC 33353. PMID 11136246. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=33353. 
  12. ^ Bramanti B, Thomas MG, Haak W, et al. (October 2009). "Genetic discontinuity between local hunter-gatherers and central Europe's first farmers". Science 326 (5949): 137–40. doi:10.1126/science.1176869. PMID 19729620. 
  13. ^ Malmstrom, H.et al. (November 2009). "Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians". Current Biology 1: 1–5. 
  14. ^ Deguilloux, M-F.,et al. (January 2011). "News from the west: Ancient DNA from a French megalithic burial chamber". American Journal of Physical Anthropology 144 (1): 108–18. doi:10.1002/ajpa.21376. 
  15. ^ a b Hendrickson SL, Hutcheson HB, Ruiz-Pesini E, et al. (November 2008). "Mitochondrial DNA haplogroups influence AIDS progression". AIDS 22 (18): 2429–39. doi:10.1097/QAD.0b013e32831940bb. PMC 2699618. PMID 19005266. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2699618. 
  16. ^ Rosa A, Ornelas C, Jobling MA, Brehm A, Villems R (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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1976131. 
  17. ^ Achilli A, Rengo C, Battaglia V, et al. (May 2005). "Saami and Berbers--an unexpected mitochondrial DNA link". American Journal of Human Genetics 76 (5): 883–6. doi:10.1086/430073. PMC 1199377. PMID 15791543. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1199377. 
  18. ^ Malyarchuk B, Derenko M, Grzybowski T, Perkowa M, Rogalla U, Vanecek T, Tsybovsky I (November 2010). "The Peopling of Europe from the Mitochondrial Haplogroup U5 Perspective". PLoS ONE 5 (4): e10285. doi:10.1371/journal.pone.0010285. PMC 2858207. PMID 20422015. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2858207. 
  19. ^ Pala M, Achilli A, Olivieri A, et al. (June 2009). "Mitochondrial haplogroup U5b3: a distant echo of the epipaleolithic in Italy and the legacy of the early Sardinians". American Journal of Human Genetics 84 (6): 814–21. doi:10.1016/j.ajhg.2009.05.004. PMC 2694970. PMID 19500771. http://www.moebiusonline.eu/fuorionda/doc/art_postglac2009.pdf. 
  20. ^ a b c d Maca-Meyer N, González AM, Pestano J, Flores C, Larruga JM, Cabrera VM (October 2003). "Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography". BMC Genetics 4: 15. doi:10.1186/1471-2156-4-15. PMC 270091. PMID 14563219. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=270091. 
  21. ^ http://www.nature.com/ejhg/journal/v12/n4/fig_tab/5201145t2.html#figure-title
  22. ^ Liane Fendt et al., MtDNA diversity of Ghana: a forensic and phylogeographic view, 2011

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