Haplogroup R (mtDNA)

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Haplogroup R
Haplogroup R (mtDNA) & subclades.PNG
Possible time of origin66.8±14.2 kya [1]
Possible place of origin Southeast Asia [2]
Ancestor N
Descendants R0, R1, R1b, R2'JT, R3, R5, R6'7, R8, R9, R11'B, R12'21, R14, R22, R23, R30, R31, P, U
Defining mutations12705, 16223 [3]

Haplogroup R is a widely distributed human mitochondrial DNA (mtDNA) haplogroup. Haplogroup R is associated with the peopling of Eurasia after about 70,000 years ago, and is distributed in modern populations throughout the world outside of sub-Saharan Africa. [4]

Contents

Haplogroup R is a descendant of the macro-haplogroup N. Among the R clade's descendant haplogroups are B, U (and thus K), F, R0 (and thus HV, H, and V), and JT (the ancestral haplogroup of J and T).

Origin

Soares et al. (2009) estimate the age of haplogroup R at roughly 50,000 to 70,000 years ago. [1]

This is consistent with an emergence in the course of the Southern Dispersal out of East Africa to West, South and Southeast Asia. [5] It has been suggested that the early lineage of haplogroups M, N and R along the coastal route during the period of roughly 70,000 to 60,000 years ago. [6] The northern route out of Africa is another possibility, where the expansion of haplogroup R may originate from Southeast Asia. [7]

Haplogroup R has wide diversity and antiquity in the indigenous population of South Asia. Tribes and castes of Western and Southern India show higher diversity than the other regions, possibly suggesting their autochthonous status. [8] Larruga et al. (2017) found mtDNA R spread to Eurasia and Australia from a core area along the Southeast Asian coast. [4]

Archaeogenetics

The Ust'-Ishim man of Siberia, dated ca. 45,000 years old, belongs to haplogroup R* (formerly classified as U*). [9] [10]

Haplogroup R has also been observed among Egyptian mummies excavated at the Abusir archaeological site in Lower Egypt, which date from the late New Kingdom of Egypt, the Ptolemaic Kingdom, and Roman Egypt. [11]

Subclade R2 was observed in the remains of a Neolithic human from western Iran in Tepe Abdul Hosein. [12]

Distribution

Haplogroup R and its descendants are distributed all over Australasia, Americas, Southeast Asia, South Asia, Central Asia, West Asia, East Asia, Europe, North Africa and Horn of Africa.

The basal R* clade is found among the Soqotri (1.2%), as well as in Northeast Africa (1.5%), the Middle East (0.8%), the Near East (0.8%), and the Arabian Peninsula (0.3%). [13]

Subclades

Tree

This phylogenetic tree of haplogroup R subclades is based on the paper by Mannis van Oven and Manfred Kayser Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation [3] and subsequent published research.

References

  1. 1 2 Soares, Pedro; Ermini, Luca; Thomson, Noel; Mormina, Maru; Rito, Teresa; Röhl, Arne; Salas, Antonio; Oppenheimer, Stephen; MacAulay, Vincent (2009). "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". The American Journal of Human Genetics. 84 (6): 740–59. doi:10.1016/j.ajhg.2009.05.001. PMC   2694979 . PMID   19500773.
  2. ↑ Larruga, Jose M (23 May 2017). "Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area". BMC Evolutionary Biology. 17 (1): 115. Bibcode:2017BMCEE..17..115L. doi: 10.1186/s12862-017-0964-5 . PMC   5442693 . PMID   28535779.
  3. 1 2 Van Oven, Mannis; Kayser, Manfred (2009). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation. 30 (2): E386–94. doi: 10.1002/humu.20921 . PMID   18853457. S2CID   27566749.
  4. 1 2 Larruga, Jose M (23 May 2017). "Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area". BMC Evolutionary Biology. 17 (1): 115. Bibcode:2017BMCEE..17..115L. doi: 10.1186/s12862-017-0964-5 . PMC   5442693 . PMID   28535779.
  5. 1 2 3 4 Karmin, Monika (2005). Human mitochondrial DNA haplogroup R in India: dissecting the phylogenetic tree of South Asian-specific lineages (M.Sc. Thesis). University of Tartu. hdl:10062/567. OCLC   692161090.[ page needed ]
  6. 1 2 3 4 Palanichamy, Malliya Gounder; Sun, Chang; Agrawal, Suraksha; Bandelt, Hans-Jürgen; Kong, Qing-Peng; Khan, Faisal; Wang, Cheng-Ye; Chaudhuri, Tapas Kumar; Palla, Venkatramana (2004). "Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia". The American Journal of Human Genetics. 75 (6): 966–78. doi:10.1086/425871. PMC   1182158 . PMID   15467980.
  7. ↑ Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM (2017). "Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area". BMC Evolutionary Biology. 17 (1): 115. Bibcode:2017BMCEE..17..115L. doi: 10.1186/s12862-017-0964-5 . PMC   5442693 . PMID   28535779.
  8. ↑ Maji, Suvendu; Krithika, S.; Vasul, T.S. (2008). "Distribution of Mitochondrial DNA Macrohaplogroup N in India with Special Reference to Haplogroup R and its Sub-Haplogroup U" (PDF). International Journal of Human Genetics. 8 (1–2): 85–96. doi:10.1080/09723757.2008.11886022. S2CID   14231815.
  9. ↑ Marrero, Patricia; Abu-Amero, Khaled K; Larruga, Jose M; Cabrera, Vicente M (2016). "Carriers of human mitochondrial DNA macrohaplogroup M colonized India from southeastern Asia". BMC Evolutionary Biology. 16 (1): 246. Bibcode:2016BMCEE..16..246M. doi: 10.1186/s12862-016-0816-8 . PMC   5105315 . PMID   27832758.
  10. ↑ Larruga, Jose M; Marrero, Patricia; Abu-Amero, Khaled K; Golubenko, Maria V; Cabrera, Vicente M (2017). "Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area". BMC Evolutionary Biology. 17 (1): 115. Bibcode:2017BMCEE..17..115L. doi: 10.1186/s12862-017-0964-5 . PMC   5442693 . PMID   28535779.
  11. ↑ Schuenemann, Verena J.; et al. (2017). "Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods". Nature Communications. 8: 15694. Bibcode:2017NatCo...815694S. doi:10.1038/ncomms15694. PMC   5459999 . PMID   28556824.
  12. ↑ Broushaki, Farnaz; Thomas, Mark G.; Link, Vivian; López, Saioa; van Dorp, Lucy; Kirsanow, Karola; Hofmanová, Zuzana; Diekmann, Yoan; Cassidy, Lara M.; Díez-del-Molino, David; Kousathanas, Athanasios; Sell, Christian; Robson, Harry K.; Martiniano, Rui; Blöcher, Jens; Scheu, Amelie; Kreutzer, Susanne; Bollongino, Ruth; Bobo, Dean; Davoudi, Hossein; Munoz, Olivia; Currat, Mathias; Abdi, Kamyar; Biglari, Fereidoun; Craig, Oliver E.; Bradley, Daniel G.; Shennan, Stephen; Veeramah, Krishna R.; Mashkour, Marjan; Wegmann, Daniel; Hellenthal, Garrett; Burger, Joachim (29 July 2016). "Early Neolithic genomes from the eastern Fertile Crescent". Science. 353 (6298): 499–503. Bibcode:2016Sci...353..499B. doi:10.1126/science.aaf7943. PMC   5113750 . PMID   27417496.
  13. ↑ Černý, Viktor; et al. (2009). "Out of Arabia—the settlement of island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity" (PDF). American Journal of Physical Anthropology. 138 (4): 439–447. doi:10.1002/ajpa.20960. PMID   19012329. Archived from the original (PDF) on 6 October 2016. Retrieved 13 June 2016.
  14. ↑ Non, Amy. "ANALYSES OF GENETIC DATA WITHIN AN INTERDISCIPLINARY FRAMEWORK TO INVESTIGATE RECENT HUMAN EVOLUTIONARY HISTORY AND COMPLEX DISEASE" (PDF). University of Florida. Archived from the original (PDF) on 13 October 2020. Retrieved 22 April 2016.
  15. 1 2 3 4 Quintana-Murci, Lluís; Chaix, Raphaëlle; Wells, R. Spencer; Behar, Doron M.; Sayar, Hamid; Scozzari, Rosaria; Rengo, Chiara; Al-Zahery, Nadia; Semino, Ornella (2004). "Where West Meets East: The Complex mtDNA Landscape of the Southwest and Central Asian Corridor". The American Journal of Human Genetics. 74 (5): 827–45. doi:10.1086/383236. PMC   1181978 . PMID   15077202.
  16. 1 2 Helgason, Agnar; Hickey, Eileen; Goodacre, Sara; Bosnes, Vidar; Stefánsson, Kári; Ward, Ryk; Sykes, Bryan (2001). "MtDNA and the Islands of the North Atlantic: Estimating the Proportions of Norse and Gaelic Ancestry". The American Journal of Human Genetics. 68 (3): 723–37. doi:10.1086/318785. PMC   1274484 . PMID   11179019.
  17. 1 2 Abu-Amero, Khaled K; Larruga, José M; Cabrera, Vicente M; González, Ana M (2008). "Mitochondrial DNA structure in the Arabian Peninsula". BMC Evolutionary Biology. 8 (1): 45. Bibcode:2008BMCEE...8...45A. doi: 10.1186/1471-2148-8-45 . PMC   2268671 . PMID   18269758.
  18. 1 2 Malyarchuk, B.; Grzybowski, T.; Derenko, M.; Perkova, M.; Vanecek, T.; Lazur, J.; Gomolcak, P.; Tsybovsky, I. (2008). "Mitochondrial DNA Phylogeny in Eastern and Western Slavs". Molecular Biology and Evolution. 25 (8): 1651–8. doi: 10.1093/molbev/msn114 . PMID   18477584.
  19. ↑ Mittnik, Alissa; Wang, Chuan-Chao; Pfrengle, Saskia; Daubaras, Mantas; Zariņa, Gunita; Hallgren, Fredrik; Allmäe, Raili; Khartanovich, Valery; Moiseyev, Vyacheslav; Tõrv, Mari; Furtwängler, Anja (2018-01-30). "The genetic prehistory of the Baltic Sea region". Nature Communications. 9 (1): 442. Bibcode:2018NatCo...9..442M. doi:10.1038/s41467-018-02825-9. ISSN   2041-1723. PMC   5789860 . PMID   29382937.
  20. ↑ Serk, Piia (2004). Human Mitochondrial DNA Haplogroup J in Europe and Near East (M.Sc. Thesis). Estonia: University of Tartu. hdl:10062/777. OCLC   692161303.[ page needed ]
  21. ↑ oxfordancestors.com Maternal Ancestry [ usurped ]
  22. ↑ Mannis van Oven's PhyloTree.org – mtDNA subtree R Archived 2009-06-13 at the Wayback Machine
  23. ↑ Fu, Qiaomei; Posth, Cosimo; Hajdinjak, Mateja; Petr, Martin; Mallick, Swapan; Fernandes, Daniel; Furtwängler, Anja; Haak, Wolfgang; Meyer, Matthias; Mittnik, Alissa; Nickel, Birgit (June 2016). "The genetic history of Ice Age Europe". Nature. 534 (7606): 200–205. Bibcode:2016Natur.534..200F. doi:10.1038/nature17993. hdl:10211.3/198594. ISSN   1476-4687. PMC   4943878 . PMID   27135931.
  24. 1 2 3 Metspalu, Mait; Kivisild, Toomas; Metspalu, Ene; Parik, Jüri; Hudjashov, Georgi; Kaldma, Katrin; Serk, Piia; Karmin, Monika; Behar, Doron M; Gilbert, M Thomas P; Endicott, Phillip; Mastana, Sarabjit; Papiha, Surinder S; Skorecki, Karl; Torroni, Antonio; Villems, Richard (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.
  25. 1 2 3 4 5 6 7 Chaubey, Gyaneshwer; Karmin, Monika; Metspalu, Ene; Metspalu, Mait; Selvi-Rani, Deepa; Singh, Vijay; Parik, Jüri; Solnik, Anu; Naidu, B Prathap; Kumar, Ajay; Adarsh, Niharika; Mallick, Chandana; Trivedi, Bhargav; Prakash, Swami; Reddy, Ramesh; Shukla, Parul; Bhagat, Sanjana; Verma, Swati; Vasnik, Samiksha; Khan, Imran; Barwa, Anshu; Sahoo, Dipti; Sharma, Archana; Rashid, Mamoon; Chandra, Vishal; Reddy, Alla G; Torroni, Antonio; Foley, Robert A; Thangaraj, Kumarasamy; Singh, Lalji (2008). "Phylogeography of mtDNA haplogroup R7 in the Indian peninsula". BMC Evolutionary Biology. 8 (1): 227. Bibcode:2008BMCEE...8..227C. doi: 10.1186/1471-2148-8-227 . PMC   2529308 . PMID   18680585.
  26. ↑ Ahmad, Farah; Afzal, Muhammad; Shahzad, Muhammad Saqib (2023-11-04). "GENETIC CHARACTERIZATION OF MITOCHONDRIAL DNA CONTROL REGION OF ARAIN ETHNIC GROUP IN PAKISTAN". Journal of Population Therapeutics and Clinical Pharmacology. 30 (18): 1577–1591. doi: 10.53555/jptcp.v30i18.3311 . ISSN   2561-8741.
  27. 1 2 3 Chaubey, Gyaneshwer; et al. (4 August 2008). "Figure 4. The frequency distribution of R7a and R7b clades in Indian subcontinent". BMC Evolutionary Biology. 8 (1): 227. Bibcode:2008BMCEE...8..227C. doi: 10.1186/1471-2148-8-227 . PMC   2529308 . PMID   18680585. in Chaubey, Gyaneshwer; Karmin, Monika; Metspalu, Ene; Metspalu, Mait; Selvi-Rani, Deepa; Singh, Vijay; Parik, Jüri; Solnik, Anu; Naidu, B Prathap; Kumar, Ajay; Adarsh, Niharika; Mallick, Chandana; Trivedi, Bhargav; Prakash, Swami; Reddy, Ramesh; Shukla, Parul; Bhagat, Sanjana; Verma, Swati; Vasnik, Samiksha; Khan, Imran; Barwa, Anshu; Sahoo, Dipti; Sharma, Archana; Rashid, Mamoon; Chandra, Vishal; Reddy, Alla G; Torroni, Antonio; Foley, Robert A; Thangaraj, Kumarasamy; Singh, Lalji (2008). "Phylogeography of mtDNA haplogroup R7 in the Indian peninsula". BMC Evolutionary Biology. 8 (1): 227. Bibcode:2008BMCEE...8..227C. doi: 10.1186/1471-2148-8-227 . PMC   2529308 . PMID   18680585.
  28. ↑ Figure 4 in Thangaraj, Kumarasamy; Nandan, Amrita; Sharma, Vishwas; Sharma, Varun Kumar; Eaaswarkhanth, Muthukrishnan; Patra, Pradeep Kumar; Singh, Sandhya; Rekha, Sashi; Dua, Monika; et al. (2009). Ahmed, Niyaz (ed.). "Deep Rooting In-Situ Expansion of mtDNA Haplogroup R8 in South Asia". PLOS ONE. 4 (8): e6545. Bibcode:2009PLoSO...4.6545T. doi: 10.1371/journal.pone.0006545 . PMC   2718812 . PMID   19662095.
  29. ↑ Ian Logan 2009, Haplogrupo R9b, Mitochondrial DNA Site
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  31. ↑ Scholes, Clarissa; Siddle, Katherine; Ducourneau, Axel; Crivellaro, Federica; Järve, Mari; Rootsi, Siiri; Bellatti, Maggie; Tabbada, Kristina; Mormina, Maru (2011). "Genetic diversity and evidence for population admixture in Batak Negritos from Palawan". American Journal of Physical Anthropology. 146 (1): 62–72. doi:10.1002/ajpa.21544. PMID   21796613.
  32. ↑ Albert Min-Shan Ko, Chung-Yu Chen, Qiaomei Fu, et al. (2014), "Early Austronesians: Into and Out Of Taiwan." The American Journal of Human Genetics 94, 426–436, March 6, 2014.
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  34. ↑ Derenko, Miroslava; Malyarchuk, Boris; Grzybowski, Tomasz; Denisova, Galina; Dambueva, Irina; Perkova, Maria; Dorzhu, Choduraa; Luzina, Faina; Lee, Hong Kyu (2007). "Phylogeographic Analysis of Mitochondrial DNA in Northern Asian Populations". The American Journal of Human Genetics. 81 (5): 1025–41. doi:10.1086/522933. PMC   2265662 . PMID   17924343.
  35. ↑ Tanaka, M.; Cabrera, VM; González, AM; Larruga, JM; Takeyasu, T; Fuku, N; Guo, LJ; Hirose, R; Fujita, Y (2004). "Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan". Genome Research. 14 (10a): 1832–50. doi:10.1101/gr.2286304. PMC   524407 . PMID   15466285.
  36. ↑ Hwan Young Lee, Ji-Eun Yoo, Myung Jin Park, Ukhee Chung, Chong-Youl Kim, and Kyoung-Jin Shin, "East Asian mtDNA haplogroup determination in Koreans: Haplogroup-level coding region SNP analysis and subhaplogroup-level control region sequence analysis." Electrophoresis (2006). DOI 10.1002/elps.200600151.
  37. ↑ He, J-D; Peng, M-S; Quang, HH; Dang, KP; Trieu, AV; et al. (2012). "Patrilineal Perspective on the Austronesian Diffusion in Mainland Southeast Asia". PLOS ONE. 7 (5): e36437. Bibcode:2012PLoSO...736437H. doi: 10.1371/journal.pone.0036437 . PMC   3346718 . PMID   22586471.
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  39. ↑ Pierson, M. J.; Martinez-Arias, R; Holland, BR; Gemmell, NJ; Hurles, ME; Penny, D (2006). "Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes". Molecular Biology and Evolution. 23 (10): 1966–75. doi:10.1093/molbev/msl063. PMC   2674580 . PMID   16855009.
  40. ↑ Kutanan, Wibhu; Kampuansai, Jatupol; Changmai, Piya; et al. (2018). "Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand". Scientific Reports. 8 (1): 1536. Bibcode:2018NatSR...8.1536K. doi:10.1038/s41598-018-20020-0. PMC   5784115 . PMID   29367746.
  41. ↑ Haplogroup R14, Ian Logan's Mitochondrial DNA Site
  42. ↑ Mona, S.; Grunz, K. E.; Brauer, S.; Pakendorf, B.; Castri, L.; Sudoyo, H.; Marzuki, S.; Barnes, R. H.; Schmidtke, J. (2009). "Genetic Admixture History of Eastern Indonesia as Revealed by Y-Chromosome and Mitochondrial DNA Analysis". Molecular Biology and Evolution. 26 (8): 1865–77. doi: 10.1093/molbev/msp097 . PMID   19414523.
  43. ↑ Trivedi, Rajni; Sitalaximi, T.; Banerjee, Jheelam; et al. (2006). "Molecular insights into the origins of the Shompen, a declining population of the Nicobar archipelago". J Hum Genet. 51 (3): 217–226. doi: 10.1007/s10038-005-0349-2 . PMID   16453062.
  44. ↑ Peng, Min-Sheng; Ho Quang, Huy; Pham Dang, Khoa; et al. (2010). "Tracing the Austronesian Footprint in Mainland Southeast Asia: A Perspective from Mitochondrial DNA". Mol. Biol. Evol. 27 (10): 2417–2430. doi: 10.1093/molbev/msq131 . PMID   20513740.
  45. 1 2 Fornarino, Simona; Pala, Maria; Battaglia, Vincenza; Maranta, Ramona; Achilli, Alessandro; Modiano, Guido; Torroni, Antonio; Semino, Ornella; Santachiara-Benerecetti, Silvana A (2009). "Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): A reservoir of genetic variation". BMC Evolutionary Biology. 9 (1): 154. Bibcode:2009BMCEE...9..154F. doi: 10.1186/1471-2148-9-154 . PMC   2720951 . PMID   19573232.
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  47. ↑ Kayser, M.; Brauer, S; Cordaux, R; Casto, A; Lao, O; Zhivotovsky, LA; Moyse-Faurie, C; Rutledge, RB; Schiefenhoevel, W (2006). "Melanesian and Asian Origins of Polynesians: MtDNA and Y Chromosome Gradients Across the Pacific". Molecular Biology and Evolution. 23 (11): 2234–44. doi: 10.1093/molbev/msl093 . hdl: 11858/00-001M-0000-0010-0145-0 . PMID   16923821.
  48. ↑ Harding, Rosalind 2006, Gene tree analyses of Aboriginal Australians. Archived 2009-09-20 at the Wayback Machine University of Oxford
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  50. ↑ mtDNA Haplogroup U1a page at cagetti.com
  51. ↑ Karima Fadhlaoui-Zid; Laura Rodríguez-Botigué; Nejib Naoui; Amel Benammar-Elgaaied; Francesc Calafell; David Comas (May 2011). "Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley" (PDF). American Journal of Physical Anthropology. 145 (1): 107–117. doi:10.1002/ajpa.21472. hdl: 10261/42802 . PMID   21312180 . Retrieved 22 April 2016.
  52. ↑ Maca-Meyer, Nicole; González, Ana M; Pestano, José; Flores, Carlos; Larruga, José M; Cabrera, Vicente M (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.
  53. ↑ Mohamed, Hisham Yousif Hassan. "Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan". University of Khartoum. Archived from the original (PDF) on 10 November 2020. Retrieved 22 April 2016.
  54. ↑ Bernard Secher; Rosa Fregel; José M Larruga; Vicente M Cabrera; Phillip Endicott; José J Pestano; Ana M González (2014). "The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents". BMC Evolutionary Biology. 14 (1): 109. Bibcode:2014BMCEE..14..109S. doi: 10.1186/1471-2148-14-109 . PMC   4062890 . PMID   24885141.
  55. 1 2 3 Kutanan, Wibhu; Kampuansai, Jatupol; Srikummool, Metawee; Kangwanpong, Daoroong; Ghirotto, Silvia; Brunelli, Andrea; Stoneking, Mark (2016). "Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai–Kadai languages". Hum Genet. 136 (1): 85–98. doi: 10.1007/s00439-016-1742-y . PMC   5214972 . PMID   27837350.

Phylogenetic 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   O A S R   I W X Y
C Z B F R0   pre-JT   P   U
HV JT K
H V J T
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