Haplogroup R (mtDNA)

From Wikipedia, the free encyclopedia
Jump to: navigation, search
For the Y-chromosome haplogroup, see Haplogroup R (Y-DNA).
Haplogroup R
Haplogroup R (mtDNA) & subclades.PNG
Possible time of origin 66,000 YBP [1]
Possible place of origin Near East
Ancestor N
Descendants R0, R1, R2'JT, R3, R5, R6'7, R8, R9, R11'B, R12'21, R14, R22, R23, R30, R31, P, U
Defining mutations 12705, 16223[2]

Haplogroup R is a widely distributed human mitochondrial DNA (mtDNA) haplogroup. It is the most common macro-haplogroup in West Eurasia.

Haplogroup R is a descendant of macro-haplogroup N. Among its 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[edit]

As of June 2009, the most recent study dates the origin of haplogroup R to 66.8kya (thousand years ago) with a 95% confidence interval of 52.6-81kya.[1]

South Asia lies on the way of earliest dispersals from Africa and is therefore a valuable well of knowledge on early human migrations.[3] The analysis of the indigenous haplogroup R lineages in India points to a common first spread of the root haplotypes of M, N, and R along the southern route some 60–70 kya.[4]

Haplogroup R has wide diversity and antiquity among varied ethnic status and different language families in South Asia. In Indian western region among the castes and southern region among the Adivasi show higher haplogroup diversity than the other regions, possibly suggesting their autochthonous status.[5]

Distribution[edit]

Haplogroup R and its descendants are distributed all over Europe, North Africa, the Horn of Africa, the Near East, the Indian Subcontinent, Oceania and the Americas.

The basal R* clade is found among the Socotri (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%).[6]

Subclades[edit]

Tree[edit]

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[2] and subsequent published research.

  • R
    • R0 (formerly pre-HV)
      • R0a
        • R0a1
        • R0a2
      • HV
        • HV0 (formerly pre-V)
          • HV0a
        • H
    • R1
      • R1a
        • R1a1
          • R1a1a
    • R2'JT
    • R5
      • R5a
        • R5a1
          • R5a1a
        • R5a2
          • R5a2a
          • R5a2b
            • R5a2b1
            • R5a2b2
            • R5a2b3
            • R5a2b4
    • R6'7
      • R6
        • R6a
          • R6a1
            • R6a1a
      • R7
        • R7a
          • R7a1
            • R7a1a
            • R7a1b
              • R7a1b1
              • R7a1b2
        • R7b
          • R7b1
            • R7b1a
    • R8
      • R8a
        • R8a1
          • R8a1a
            • R8a1a1
            • R8a1a2
            • R8a1a3
          • R8a1b
        • R8a2
      • R8b
        • R8b1
        • R8b2
    • (16304)
      • R9
        • R9b
          • R9b1
          • R9b2
        • R9c
        • F
        • R22
    • R11'B (16189)
      • R11
        • R11a
      • B
      • R24
    • R12'21
      • R12
      • R21
    • R14
    • R23
    • R30
      • R30a
      • R30b
        • R30b1
    • R31
      • R31a
        • R31a1
      • R31b
    • P
    • U

References[edit]

  1. ^ a b 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 2694979free to read. PMID 19500773. 
  2. ^ a b 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. 
  3. ^ a b 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. OCLC 692161090. hdl:10062/567. [page needed]
  4. ^ a b c d 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 1182158free to read. PMID 15467980. 
  5. ^ 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. 
  6. ^ 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. Retrieved 13 June 2016. 
  7. ^ Non, Amy. "ANALYSES OF GENETIC DATA WITHIN AN INTERDISCIPLINARY FRAMEWORK TO INVESTIGATE RECENT HUMAN EVOLUTIONARY HISTORY AND COMPLEX DISEASE" (PDF). University of Florida. Retrieved 22 April 2016. 
  8. ^ a b c d e 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 1181978free to read. PMID 15077202. 
  9. ^ a b 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 1274484free to read. PMID 11179019. 
  10. ^ a b 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: 45. doi:10.1186/1471-2148-8-45. PMC 2268671free to read. PMID 18269758. 
  11. ^ a b 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. 
  12. ^ Serk, Piia (2004). Human Mitochondrial DNA Haplogroup J in Europe and Near East (M.Sc. Thesis). Estonia: University of Tartu. OCLC 692161303. hdl:10062/777. [page needed]
  13. ^ oxfordancestors.com Maternal Ancestry
  14. ^ Mannis van Oven's PhyloTree.org – mtDNA subtree R
  15. ^ a b c 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 516768free to read. PMID 15339343. 
  16. ^ a b c d e f g 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: 227. doi:10.1186/1471-2148-8-227. PMC 2529308free to read. PMID 18680585. 
  17. ^ a b c "Figure 4. The frequency distribution of R7a and R7b clades in Indian subcontinent".  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: 227. doi:10.1186/1471-2148-8-227. PMC 2529308free to read. PMID 18680585. 
  18. ^ Figure 4. Isofrequency map of mtDNA haplogroup R8 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 2718812free to read. PMID 19662095. 
  19. ^ Ian Logan 2009, Haplogrupo R9b, Mitochondrial DNA Site
  20. ^ a b Hill, C.; Soares, P.; Mormina, M.; MacAulay, V.; Meehan, W.; Blackburn, J.; Clarke, D.; Raja, J. M.; Ismail, P. (2006). "Phylogeography and Ethnogenesis of Aboriginal Southeast Asians". Molecular Biology and Evolution. 23 (12): 2480–91. doi:10.1093/molbev/msl124. PMID 16982817. 
  21. ^ 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. 
  22. ^ a b c Hill, Catherine; Soares, Pedro; Mormina, Maru; MacAulay, Vincent; Clarke, Dougie; Blumbach, Petya B.; Vizuete-Forster, Matthieu; Forster, Peter; Bulbeck, David; Oppenheimer, Stephen; Richards, Martin (2007). "A Mitochondrial Stratigraphy for Island Southeast Asia". The American Journal of Human Genetics. 80: 29–43. doi:10.1086/510412. PMC 1876738free to read. PMID 17160892. 
  23. ^ 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 2265662free to read. PMID 17924343. 
  24. ^ 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 524407free to read. PMID 15466285. 
  25. ^ a b Tabbada, K. A.; Trejaut, J.; Loo, J.-H.; Chen, Y.-M.; Lin, M.; Mirazon-Lahr, M.; Kivisild, T.; De Ungria, M. C. A. (2009). "Philippine Mitochondrial DNA Diversity: A Populated Viaduct between Taiwan and Indonesia?". Molecular Biology and Evolution. 27 (1): 21–31. doi:10.1093/molbev/msp215. PMID 19755666. 
  26. ^ 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 2674580free to read. PMID 16855009. 
  27. ^ Haplogroup R14, Ian Logan's Mitochondrial DNA Site
  28. ^ 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. 
  29. ^ 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. 
  30. ^ 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. 
  31. ^ a b 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: 154. doi:10.1186/1471-2148-9-154. PMC 2720951free to read. PMID 19573232. 
  32. ^ a b c Friedlaender, J.; Schurr, T; Gentz, F; Koki, G; Friedlaender, F; Horvat, G; Babb, P; Cerchio, S; Kaestle, F (2005). "Expanding Southwest Pacific Mitochondrial Haplogroups P and Q". Molecular Biology and Evolution. 22 (6): 1506–17. doi:10.1093/molbev/msi142. PMID 15814828. 
  33. ^ 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. PMID 16923821. 
  34. ^ Harding, Rosalind 2006, Gene tree analyses of Aboriginal Australians. University of Oxford
  35. ^ Hudjashov, G.; Kivisild, T.; Underhill, P. A.; Endicott, P.; Sanchez, J. J.; Lin, A. A.; Shen, P.; Oefner, P.; Renfrew, C.; et al. (2007). "Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis". Proceedings of the National Academy of Sciences. 104 (21): 8726–30. Bibcode:2007pnas..104.8726h. doi:10.1073/pnas.0702928104. JSTOR 25427741. PMC 1885570free to read. PMID 17496137. 
  36. ^ mtDNA Haplogroup U1a page at cagetti.com[unreliable source?]
  37. ^ 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. Retrieved 22 April 2016. 
  38. ^ 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 270091free to read. PMID 14563219. 
  39. ^ Mohamed, Hisham Yousif Hassan. "Genetic Patterns of Y-chromosome and Mitochondrial DNA Variation, with Implications to the Peopling of the Sudan" (PDF). University of Khartoum. Retrieved 22 April 2016. 
  40. ^ Bernard Secher; Rosa Fregel; José M Larruga; Vicente M Cabrera; Phillip Endicott; José J Pestano; Ana M González. "The history of the North African mitochondrial DNA haplogroup U6 gene flow into the African, Eurasian and American continents". BMC Evolutionary Biology. Retrieved 22 April 2016. 

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

External links[edit]