Haplogroup U Explained

U
Origin-Date:46,500 ± 3,300 years ago[1]
Origin-Place:West Asia,[2]
Ancestor:R
Descendants:U1, U5, U6, U2'3'4'7'8'9
Mutations:11467, 12308, 12372

Haplogroup U is a human mitochondrial DNA haplogroup (mtDNA). The clade arose from haplogroup R, likely during the early Upper Paleolithic. Its various subclades (labelled U1 - U9, diverging over the course of the Upper Paleolithic) are found widely distributed across Northern and Eastern Europe, Central, Western and South Asia, as well as North Africa, the Horn of Africa, and the Canary Islands.

Origins

Haplogroup U descends from the haplogroup R mtDNA branch of the phylogenetic tree. The defining mutations (A11467G, A12308G, G12372A) are estimated to have arisen between 43,000 and 50,000 years ago, in the early Upper Paleolithic (around 46,530 ± 3,290 years before present, with a 95% confidence interval per Behar et al., 2012).

Ancient DNA classified as belonging to the U* mitochondrial haplogroup has been recovered from human skeletal remains found in Western Siberia, which have been dated to c. 45,000 years ago.[3] The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) has been identified as the basal haplogroup U6* not previously found in any ancient or present-day humans.[4]

Haplogroup U has been found among Iberomaurusian specimens dating from the Epipaleolithic at the Taforalt and Afalou prehistoric sites.[5] Among the Taforalt individuals, around 13% of the observed haplotypes belonged to various U subclades, including U4a2b (1/24; 4%), U4c1 (1/24; 4%), and U6d3 (1/24; 4%). A further 41% of the analysed haplotypes could be assigned to either haplogroup U or haplogroup H. Among the Afalou individuals, 44% of the analysed haplotypes could be assigned to either haplogroup U or haplogroup H (3/9; 33%).[6]

Haplogroup U has also been observed among ancient Egyptian mummies excavated at the Abusir el-Meleq archaeological site in Middle Egypt, dated to the 1st millennium BC, 13 of the 90 mummies bearing haplgroup U (U carriers all of the late period) and various subclades of it, U, U1,U3,U5,U6,U7 and U8.[7] and in a separate study, DNA extracted from a tooth the mummified head of a much older mummy of about 4,000 years ago Djehutynakht of the very end of the 11th or early 12th Dynasty who belonged to belonged to mtDNA haplogroup U5b2b5 (with no exact matches found in a modern population of U5 carriers) from a 2018 article by Odile Loreille et al.[8]

Additionally, haplogroup U has been observed in ancient Guanche fossils excavated in Gran Canaria and Tenerife on the Canary Islands, which have been radiocarbon-dated to between the 7th and 11th centuries CE. All of the clade-bearing individuals were inhumed at the Tenerife site, with these specimens found to belong to the U6b1a (4/7; 57%) and U6b (1/7; 14%) subclades.[9]

Distribution

Haplogroup U is found in 15% of Indian caste and 8% of Indian tribal populations.[10] Haplogroup U is found in approximately 11% of native Europeans and is held as the oldest maternal haplogroup found in that region.[11] [12] In a 2013 study, all but one of the ancient modern human sequences from Europe belonged to maternal haplogroup U, thus confirming previous findings that haplogroup U was the dominant type of Mitochondrial DNA (mtDNA) in Europe before the spread of agriculture into Europe from the Near East.[13]

Haplogroup U has various subclades numbered U1 to U9. Haplogroup K is a subclade of U8.[14] The old age has led to a wide distribution of the descendant subgroups across Western Eurasia, North Africa, and South Asia. Some subclades of haplogroup U have a more specific geographic range.

Subclades

Subclades are labelled U1 - U9; Haplogroup K is a subclade of U8.

Van Oven and Kayser (2009) proposed subclades "U2'3'4'7'8" and "U4'9".[15] Behar et al. (2012) amended this by grouping "U4'9" as subordinate to "U2'3'4'7'8" for a new intermediate subclade "U2'3'4'7'8'9".

Haplogroup U

Basal U was found in the 26,000 years old remains of Ancient North Eurasian, Mal'ta boy (MA1).

Haplogroup U1

The U1 subclades are: U1a (with deep-subclades U1a1, U1a1a, U1a1a1, U1a1b)[16] and U1b.[16]

Haplogroup U1 estimated to have arisen between 26,000 and 37,000 years ago. It is found at very low frequency throughout Europe. It is more often observed in eastern Europe, Anatolia and the Near East. It is also found at low frequencies in India. U1 is found in the Svanetia region of Georgia at 4.2%. Subclade U1a is found from India to Europe, but is extremely rare among the northern and Atlantic fringes of Europe including the British Isles and Scandinavia. In India, U1a has been found in the Kerala region. U1b has a similar spread but is rarer than U1a. A variety of subclade U1b1 with the mutations G14070A! and A3426G is found in Ashkenazi Jews.[17] Subclades U1a and U1b appear in equal frequency in eastern Europe.[18]

The rare U1 clade is also found among Algerians in Oran (0.83%-1.08%) and the Reguibat tribe of the Sahrawi (0.93%).[19]

The U1a1a subclade has been observed in an ancient individual excavated at the Kellis 2 cemetery in the Dakleh Oasis, located in the southwestern desert of Egypt. 21 of the Kellis burials have been radiocarbon-dated to around 80-445 AD, a timeframe within the Romano-Christian period.[20] Haplogroup U1 has also been found among specimens at the mainland cemetery in Kulubnarti, Sudan, which date from the Early Christian period (AD 550-800).[21]

DNA analysis of excavated remains now located at ruins of the Church of St. Augustine in Goa, India have also revealed the unique mtDNA subclade U1b. This sublineage is absent in India, but present in Georgia and surrounding regions.[22] Since the genetic analysis corroborates archaeological and literary evidence, it is believed that the excavated remains belong to Ketevan the Martyr, queen of Georgia.[22]

Haplogroup U5

The age of U5 is estimated at between 25,000 and 35,000 years old,[23] roughly corresponding to the Gravettian culture. Approximately 11% of Europeans (10% of European-Americans) have some variant of haplogroup U5. The haplogroup most likely originated in Europe.[24] [25]

U5 was the predominant mtDNA of mesolithic Western Hunter Gatherers (WHG).

U5 has been found in human remains dating from the Mesolithic in England, Germany, Lithuania, Poland, Portugal, Russia,[26] Sweden,[27] France[28] and Spain.[29] Neolithic skeletons (~7,000 years old) that were excavated from the Avellaner cave in Catalonia, northeastern Spain included a specimen carrying haplogroup U5.[30]

Haplogroup U5 and its subclades U5a and U5b today form the highest population concentrations in the far north, among Sami, Finns, and Estonians. However, it is spread widely at lower levels throughout Europe. This distribution, and the age of the haplogroup, indicate individuals belonging to this clade were part of the initial expansion tracking the retreat of ice sheets from Europe around 10,000 years ago.

The modern Basques and Cantabrians possess almost exclusively U5b lineages (U5b1f, U5b1c1, U5b2).[31] [32]

Additionally, haplogroup U5 is found in small frequencies and at much lower diversity in the Near East and parts of northern Africa (areas with sizable U6 concentrations), suggesting back-migration of people from Europe toward the south.[33]

Mitochondrial haplogroup U5a has also been associated with HIV infected individuals displaying accelerated progression to AIDS and death.[34]

U5 was the main haplogroup of mesolithic European hunter gatherers. U haplogroups were present at 83% in European hunter gatherers before influx of Middle Eastern farmer and steppe Indo-European ancestry decreased its frequency to less than 21%.[20]

Haplogroup U6

Haplogroup U6 was dated to between 31,000 and 43,000 years ago by Behar et al. (2012). Basal U6* was found in a Romanian specimen of ancient DNA (Peștera Muierilor) dated to 35,000 years ago.[56] Hervella et al. (2016) take this find as evidence for Paleolithic back-migration of Homo sapiens from Eurasia into Africa. The discovery of basal U6* in ancient DNA contributed to setting back the estimated age of U6 to around 46,000 years ago.[57]

Usually U6 genetic history is envisioned as a migration from southwest Asia through North Africa. This hypothesis is based on the general origin of haplogroup U sub-clades in Southwest Asia, which is also the center of the geographical distribution of U sub-clades: Europe, India, Central Asia, East Africa and North Africa. Two possible scenarios for the first U6 haplotype (bearing mutations 3348 and 16172) can be advanced: i) these mutations aroused in the founder region but did not leave any genetic legacy in current human populations there; ii) they originated probably somewhere in North Africa, after the arrival of the U6 founder haplotype. Within North Africa U6 is only significantly frequent at its western edge (as well as in South-western Europe). More importantly, all the most basal branches are virtually restricted to that region (U6b, U6c and U6d), what could indicate its western origin. Nevertheless, it cannot be excluded the major sub-clade U6a, which shows a richness of sub-clades in Northwest Africa although a few of derivative branches also include sequences from East African and the Middle Eastern populations (e.g. U6a2).

Haplogroup U6 is common (with a prevalence of around 10%)[33] in Northwest Africa (with a maximum of 29% in an Algerian Mozabites[58]) and the Canary Islands (18% on average with a peak frequency of 50.1% in La Gomera). 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),[59] Northeast Africa and occasionally in other locations. U6 is also found at low frequencies in the Chad Basin, including the rare Canarian branch. This suggests that the ancient U6 clade bearers may have inhabited or passed through the Chad Basin on their way westward toward the Canary Islands.[60]

U6 is thought to have entered North Africa from the Near East around 30,000 years ago. It has been found among Iberomaurusian specimens dating from the Epipaleolithic at the Taforalt prehistoric site.[61] In spite of the highest diversity of Iberian U6, Maca-Meyer argues for a Near East origin of this clade based on the highest diversity of subclade U6a in that region,[59] where it would have arrived from West Asia, with the Iberian incidence primarily representing migration from the Maghreb and not persistence of a European root population.

According to Hernández et al. 2015 "the estimated entrance of the North African U6 lineages into Iberia at 10 ky correlates well with other L African clades, indicating that U6 and some L lineages moved together from Africa to Iberia in the Early Holocene."[62]

U6 has four main subclades:[59]

U6a, U6b and U6d share a common basal mutation (16219) that is not present in U6c, whereas U6c has 11 unique mutations. U6b and U6d share a mutation (16311) not shared by U6a, which has three unique mutations.

U2'3'4'7'8'9

Subclades U2, U3, U4, U7, U8 and U9 are now thought to be monophyletic, their common ancestor"U2'3'4'7'8'9" defined by mutation A1811G, arising between about 42,000 and 48,000 years ago (Behar et al., 2012).Within U2'3'4'7'8'9, U4 and U9 may be monophyletic, as "U4'9" (mutations T195C!, G499A, T5999C) arising between 31,000 and 43,000 years ago (Behar et al., 2012).

U2'3'4'7'8'9 was found in the remains of two 32,000 years old Ancient North Siberians (ANS) from the Yana RHS Site on river Yana.[66]

Haplogroup U2

Haplogroup U2 is most common in South Asia[67] but is also found in low frequency in Central and West Asia, as well as in Europe as U2e (the European variety of U2 is named U2e).[68] The overall frequency of U2 in South Asia is largely accounted for by the group U2i in India whereas haplogroup U2e, common in Europe, is rare; given that these lineages diverged approximately 50,000-years-ago, these data have been interpreted as indicating very low maternal-line gene-flow between South Asia and Europe throughout this period.[67] Approximately one half of the U mtDNAs in India belong to the Indian-specific branches of haplogroup U2 (U2i: U2a, U2b and U2c). Haplogroup U2b2 has been found in the remains of a 4500 year old female excavated from the Rakhigarhi site of Indus Valley civilisation, in present day state of Haryana, India.[69] While U2 is typically found in India,[67] it is also present in the Nogais, descendants of various Mongolic and Turkic tribes, who formed the Nogai Horde.[70] Both U2 and U4 are found in the Ket and Nganasan peoples, the indigenous inhabitants of the Yenisei River basin and the Taymyr Peninsula.[71]

The U2 subclades are: U2a,[72] U2b,[73] U2c,[74] U2d,[75] and U2e.[76] With the India-specific subclades U2a, U2b, and U2c collectively referred to as U2i, the Eurasian haplogroup U2d appears to be a sister clade with the Indian haplogroup U2c,[77] while U2e is considered a European-specific subclade but also found in South India.

Haplogroup U2 has been found in the remains of a 37,000[78] and 30,000-year-old hunter-gatherer from the Kostyonki, Voronezh Oblast in Central-South European Russia.,[79] in 4800 to 4000-year-old human remains from a Beaker culture site of the Late Neolithic in Kromsdorf Germany,[80] and in 2,000-year-old human remains from Bøgebjerggård in Southern Denmark. However, haplogroup U2 is rare in present-day Scandinavians.[81] The remains of a 2,000-year-old West Eurasian male of haplogroup U2e1 was found in the Xiongnu Cemetery of Northeast Mongolia.[82]

Haplogroup U3

Haplogroup U3 falls into two subclades:: U3a[83] and U3b.[83]

Coalescence age for U3a is estimated as 18,000 to 26,000-years-ago while the coalescence age for U3b is estimated as 18,000 to 24,000-years-ago. U3a is found in Europe, the Near East, the Caucasus and North Africa. The almost-entirely European distributed subclade, U3a1, dated at 4000 to 7000-years-ago, suggests a relatively recent (late Holocene or later) expansion of these lineages in Europe. There is a minor U3c subclade (derived from U3a), represented by a single Azeri mtDNA from the Caucasus. U3b is widespread across the Middle East and the Caucasus, and it is found especially in Iran, Iraq and Yemen, with a minor European subclade, U3b1b, dated at 2000 to 3000-years-ago.[84] Haplogroup U3 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 (about 1% of the population). U3 is present in the Svan population from the Svaneti region (about 4.2% of the population) and among Lithuanian Romani, Polish Romani, and Spanish Romani populations (36-56%)[85] [86] [87] [88]

The U3 clade is also found among Mozabite Berbers (10.59%),[19] as well as Egyptians in the El-Hayez (2.9%)[89] and Gurna oases (2.9%),[90] and Algerians in Oran (1.08%-1.25%).[19] The rare U3a subclade occurs among the Tuareg inhabiting Niger (3.23%)[91] and among Somalis (1.6%).[92]

Haplogroup U3 has been found in some of the 6400-year-old remains (U3a) discovered in the caves at Wadi El-Makkukh near Jericho associated with the Chalcolithic period.[93] Haplogroup U3 was already present in the West Eurasian gene pool around 6,000-years-ago and probably also its subclade U3a as well.[93]

Haplogroup U4

Haplogroup U4 has its origin between 21,000 and 14,000 years ago. Its distribution is associated with the population bottleneck due to the Last Glacial Maximum.

U4 has been found in ancient DNA,[94] and it is relatively rare in modern populations, although it is found in substantial ratios in certain indigenous populations of Northern Asia and Northern Europe, being associated with the remnants of ancient European hunting-gatherers preserved in the indigenous populations of Siberia.[95] [96] [97] U4 is found in the endangered Nganasan people of the Taymyr Peninsula,[71] [98] in the Mansi (16.3%),[97] and in the Ket people (28.9%) of the Yenisei River.[97] It is found in Europe with highest concentrations in Scandinavia and the Baltic states.[99] and is found in the Sami population of the Scandinavian peninsula (although, U5b has a higher representation).[100] U4 is also preserved in the Kalash people (current population size 3,700)[101] a unique tribe among the Indo-Aryan peoples of Pakistan where U4 (subclade U4a1[102]) attains its highest frequency of 34%.[103]

The U4 subclades are: U4a,[104] U4b,[105] U4c,[106] and U4d.[107]

Haplogroup U4 is associated with ancient European hunter-gatherers and has been found in 7,200 to 6,000-year-old remains of the Pitted Ware culture in Gotland Sweden and in 4,400 to 3,800-year-old remains from the Damsbo site of the Danish Beaker culture.[108] [109] Remains identified as subclade U4a2 are associated with the Corded Ware culture, which flourished 5200 to 4300 years ago in Eastern and Central Europe and encompassed most of continental northern Europe from the Volga River in the east to the Rhine in the west.[110] Mitochondrial DNA recovered from 3,500 to 3,300-year-old remains at the Bredtoftegård site in Denmark associated with the Nordic Bronze Age include haplogroup U4 with 16179T in its HVR1 indicative of subclade U4c1.[111] [112] 2 out of 9 1700-year-old remains in the extreme southwest of Ivanovo Region were U4c1.[113]

Haplogroup U7

Haplogroup U7 is considered a West Eurasian–specific mtDNA haplogroup, believed to have originated in the Black Sea area approximately 30,000 years ago.[114] [115] In modern populations, U7 occurs at low frequency in the Caucasus,[115] the western Siberian tribes,[116] West Asia (about 4% in the Near East, while peaking with 10% in Iranians),[67] South Asia (about 12% in Gujarat, the westernmost state of India, while for the whole of India its frequency stays around 2%, and 5% in Pakistan),[67] and the Vedda people of Sri Lanka where it reaches it highest frequency of 13.33% (subclade U7a).[117] One third of the West Eurasian-specific mtDNAs found in India are in haplogroups U7, R2 and W. It is speculated that large-scale immigration carried these mitochondrial haplogroups into India.[67]

The U7 subclades are U7a (with deep-subclades U7a1, U7a2, U7a2a, U7a2b)[118] and U7b.[118]

Genetic analysis of individuals associated with the Late Hallstatt culture from Baden-Württemberg Germany considered to be examples of Iron Age "princely burials" included haplogroup U7.[119] Haplogroup U7 was reported to have been found in 1200-year-old human remains (dating to around 834), in a woman believed to be from a royal clan who was buried with the Viking Oseberg Ship in Norway.[120] Haplogroup U7 was found in 1000-year-old human remains (dating to around AD 1000-1250) in a Christian cemetery is Kongemarken Denmark. However, U7 is rare among present-day ethnic Scandinavians.[116]

The U7a subclade is especially common among Saudis, constituting around 30% of maternal lineages in the Eastern Province.[121]

Haplogroup U8

See also: Haplogroup K (mtDNA). The haplogroup U8b's most common subclade is haplogroup K, which is estimated to date to between 30,000 and 22,000 years ago. Haplogroup K 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,[14] and is believed to have first arisen in northeastern Italy. Haplogroup UK shows some evidence of being highly protective against AIDS progression.[34]

Haplogroup U9

Haplogroup U9 is a rare clade in mtDNA phylogeny, characterized only recently in a few populations of Pakistan (Quintana-Murci et al. 2004). Its presence in Ethiopia and Yemen, together with some Indian-specific M lineages in the Yemeni sample, points to gene flow along the coast of the Arabian Sea. Haplogroups U9 and U4 share two common mutations at the root of their phylogeny. It is interesting that, in Pakistan, U9 occurs frequently only among the so-called Makrani population. In this particular population, lineages specific to parts of Eastern Africa occur as frequently as 39%, which suggests that U9 lineages in Pakistan may have an African origin (Quintana-Murci et al. 2004). Regardless of which coast of the Arabian Sea may have been the origin of U9, its Ethiopian–southern Arabian–Indus Basin distribution hints that the subclade's diversification from U4 may have occurred in regions far away from the current area of the highest diversity and frequency of haplogroup U4—East Europe and western Siberia.[122]

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Further reading

External links

Notes and References

  1. Behar et al. (2012), note the revised estimate of 42–58 key based on ancient DNA by Hervella et al. (2016).
  2. Hervella et al. (2016) "Individuals carrying haplogroup U possibly spread westward from Western Asia around 39–52 ky, reaching Europe as signaled by haplogroup U5, and North Africa signaled by haplogroup U6"
  3. Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM . Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area . BMC Evolutionary Biology . 17 . 1 . 115 . May 2017 . 28535779 . 5442693 . 10.1186/s12862-017-0964-5 . free . 2017BMCEE..17..115L . Marrero P, Abu-Amero KK, Larruga JM, Cabrera VM . Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia . BMC Evolutionary Biology . 16 . 1 . 246 . November 2016 . 27832758 . 5105315 . 10.1186/s12862-016-0816-8 . free . 2016BMCEE..16..246M .
  4. Hervella M, Svensson EM, Alberdi A, Günther T, Izagirre N, Munters AR, Alonso S, Ioana M, Ridiche F, Soficaru A, Jakobsson M, Netea MG, de-la-Rua C . 6 . The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa . Scientific Reports . 6 . 25501 . May 2016 . 27195518 . 4872530 . 10.1038/srep25501 . 2016NatSR...625501H . .
  5. Secher B, Fregel R, Larruga JM, Cabrera VM, Endicott P, Pestano JJ, González AM . The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents . BMC Evolutionary Biology . 14 . 109 . May 2014 . 1 . 24885141 . 4062890 . 10.1186/1471-2148-14-109 . free . 2014BMCEE..14..109S .
  6. Kefi R, Hechmi M, Naouali C, Jmel H, Hsouna S, Bouzaid E, Abdelhak S, Beraud-Colomb E, Stevanovitch A . 6 . On the origin of Iberomaurusians: new data based on ancient mitochondrial DNA and phylogenetic analysis of Afalou and Taforalt populations . Mitochondrial DNA Part A . 29 . 1 . 147–157 . January 2018 . 28034339 . 10.1080/24701394.2016.1258406 . 4490910 .
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  12. Web site: Maternal Ancestry. Oxford Ancestors. 7 February 2013. https://web.archive.org/web/20170715205636/http://www.oxfordancestors.com/content/view/35/55/. 15 July 2017.
  13. Fu Q, Mittnik A, Johnson PL, Bos K, Lari M, Bollongino R, Sun C, Giemsch L, Schmitz R, Burger J, Ronchitelli AM, Martini F, Cremonesi RG, Svoboda J, Bauer P, Caramelli D, Castellano S, Reich D, Pääbo S, Krause J . 6 . A revised timescale for human evolution based on ancient mitochondrial genomes . Current Biology . 23 . 7 . 553–559 . April 2013 . 23523248 . 5036973 . 10.1016/j.cub.2013.02.044 . 2013CBio...23..553F .
  14. González AM, García O, Larruga JM, Cabrera VM . The mitochondrial lineage U8a reveals a Paleolithic settlement in the Basque country . BMC Genomics . 7 . 1 . 124 . May 2006 . 16719915 . 1523212 . 10.1186/1471-2164-7-124 . free .
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  19. Bekada A, Arauna LR, Deba T, Calafell F, Benhamamouch S, Comas D . Genetic Heterogeneity in Algerian Human Populations . PLOS ONE . 10 . 9 . e0138453 . September 24, 2015 . 26402429 . 4581715 . 10.1371/journal.pone.0138453 . 2015PLoSO..1038453B . free .
  20. Molto JE, Loreille O, Mallott EK, Malhi RS, Fast S, Daniels-Higginbotham J, Marshall C, Parr R . 6 . Complete Mitochondrial Genome Sequencing of a Burial from a Romano-Christian Cemetery in the Dakhleh Oasis, Egypt: Preliminary Indications . Genes . 8 . 10 . 262 . October 2017 . 28984839 . 5664112 . 10.3390/genes8100262 . free .
  21. Sirak K, Frenandes D, Novak M, Van Gerven D, Pinhasi R . Abstract Book of the IUAES Inter-Congress 2016 - A community divided? Revealing the community genome(s) of Medieval Kulubnarti using next- generation sequencing . Abstract Book of the Iuaes Inter-Congress 2016 . 2016 . 115 . IUAES .
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