Haplogroup R (mtDNA)

For the Y-chromosome haplogroup, see Haplogroup R (Y-DNA).

Haplogroup R

Possible time of origin	66,000 YBP ^[1]
Possible place of origin	Indian subcontinent^[2]
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^[3]

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

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.^[4] 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.^[5]

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.^[2]

Distribution

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

Haplogroup R
- R0 or pre-HV
  - R0a or (preHV)1: Occurs commonly in the Arabian peninsula, with its highest frequency observed among the Socotri.^[7] Moderate frequencies found in North Africa, the Horn of Africa, and Central Asia.
  - HV: It is a west Eurasian haplogroup mainly found throughout the Middle East, including Iran.^[8] It is also found in North Africa, Central Asia and South Asia.
    - - V: Found at moderately low frequencies around Europe; the highest frequency is in the Sami people 40%.^[9]
    - HV1: Mainly in the Middle East.^[10]
    - HV2: Mainly in South Asia.^[8]
    - HV3: Mainly in Eastern Europe.^[11]
    - H: In West Eurasia. It is the most common mtDNA haplogroup in Europe.
- R1
  - R1* (16278): In Kurdish from Turkmenistan (9%).^[8]
  - R1a
    - R1a* (3337): Found in Brahmins from Uttar Pradesh (India).^[5] Also in Adygei people (Caucasus).
    - R1a1: Found in Northwest Caucasian people like Kabardins and Adygei people. Observed in eastern European populations like northwestern Russians and Poles.^[11]
- pre-JT or R2'JT
  - R2: Found mainly in Balochistan (Pakistan).^[8]
    - (13500): Found in Rajasthan and Uttar Pradesh (India).^[4]
    - (150, 303+1C): In Iran, Georgia and Turkey.
  - JT
    - J: The highest frequency is in the Near East (12%), 21% in Saudi Arabia.^[10] J declines towards Europe at 11%, Caucasus 8%, North Africa 6% and becomes practically missing in East Asia.^[12]
    - T: The highest frequency is in the Caspian region (Caucasus, Northern Iran, Turkmenistan).^[8] It is important in Europe (almost 10%),^[13] Middle East, Central Asia, Pakistan and North Africa. Small frequency in the Horn of Africa and India.
- R3: Found in Armenia.^[14]
- R5: Widely spread in the Indian subcontinent. Specially in Madhya Pradesh (India) at 17%.^[15]
  - R5a
    - R5a1: Found within the Indo-European speaking populations of India.^[16]
    - R5a2: Specially among Dravidic groups of India and Sri Lanka.^[16]
- R6'7 (16362) The most important presence is among Austroasiatic language-speakers from India (10%).^[16]
  - R6: Small frequencies in India and Pakistan.^[15]
  - R7: In the Indian subcontinent .^[16]^[17]
    - R7a: Mainly in East India, specially in Santals from Bihar and Jharkhand.^[17]
    - R7b: Specially in Dravidian tribes of East India.^[17]
- R8: The highest frequency occurs towards East India, especially within Orissa (12%), and it is found among the Austroasiatic tribes (Munda speakers). It is also present in low frequency among the Dravidian and Indo-European speaking family ^[18]
  - R8a: Found mainly in Orissa and Andhra Pradesh (India).
  - R8b: In Orissa, Gujarat, Andhra Pradesh (India).
- R9 (16304)
  - R9b: It appears mostly in Southeast Asia.^[19] Found all over Indonesia, in Indochina, Malaysia, in Aboriginal Malays like Semelai at 28% and Temuan 21%.^[20]
  - (249d)
    - R9c: All over the Malay Archipelago and Taiwan. Mainly in Batak (Palawan) at 58% ^[21] and Alor (Indonesia) at 11%.^[22]
    - F: Fairly common in East Asia and Southeast Asia. Higher frequencies occur in some areas like Nicobar at 50% and Arunachal Pradesh 31% (India),^[15] and Shors people from Siberia at 44%.^[23] There is also an important frequency in Taiwanese aborigines, Guangdong (China), Maluku (Indonesia), Thailand and Vietnam.
- R11'B (16189)
  - R11: Found in China, mainly in Lahu people from Yunnan at 12.5%.^[24] Also in Japan and Rajasthan (India).
  - B
    - B4: It is found often in East Asia, Southeast Asia, Polynesia, Melanesia, Micronesia, Madagascar and Indigenous peoples of the Americas.
    - B5: Spread in East Asia and Southeast Asia.
  - R24: Found in Philippines.^[25]
- R12'21
  - R12: Found in Australia.^[26]
  - R21: In indigenous peoples of Malaysia like Jahai Negritos at 63%^[20] and Senoi 37%.
- R14: Found in Papua New Guinea^[27] and in Austronesian speakers of East Timor and Lembata.^[28]
- R22 or R12: Very frequent in the Shompen (10/29 = 34.5%).^[29] Elsewhere found mainly in south-central Indonesia (11.4% Mataram, 8.0% Waingapu, 7.3% Bali, 1.9% Borneo) and in Cham of Bình Thuận, Vietnam (7/168 = 4.2%),^[30] with singleton or sporadic occurrences in Thailand, Sumatra, Java, Sulawesi, and Alor.^[22]
- R23: Small clade found in Bali and Sumba (Indonesia).^[22]
- R30
  - R30a: Found in Andhra Pradesh, Uttar Pradesh (India), in the Tharu people from Nepal^[31] and Sinhalese people from Sri Lanka.^[16]
  - R30b: Found in Punjab.^[16]
  - R30* (1598, 16189): Found in Punjab, Nepal and Japan.^[31]
- R31
  - R31a: In Brahmins from Uttar Pradesh^[5] and Rajputs from Rajasthan (India).^[16]
  - R31b: In Reddys from Andhra Pradesh (India).^[5]
- P: It is characteristic of Sahul. Found in Philippines and East Indonesia.
  - (16176)
    - P1: Widespread in Melanesia. Higher frequencies occur in Papua New Guinea.^[32] Also found in Maluku, Nusa Tenggara and Polynesia.^[33]
    - P2'10
      - P2: In Melanesia,^[32] specially in New Guinea and New Caledonia.
      - P10: Found in Philippines.^[25]
    - P9 (or AuE): In Aboriginal Australians from the central region.^[34]
  - P3: In Australia and Melanesia.^[32]
  - P4: In Australia and Melanesia.^[35]
- U
  - U1: It appears mostly in the Middle East and Caucasus. Found from India to the Mediterranean and to the rest of Europe.^[36]
  - U5: Approximately 11% of total Europeans and 10% of European-Americans. The highest frequency is in the Sami people.^[9]
  - U6: It is common in North Africa and the Horn of Africa, especially in the Maghreb.^[37] Highest frequencies of the subclade occur among Algerian Berbers (29%)^[38] and Egyptian Copts (27.6%).^[39] U6 has also been found among Iberomaurusian specimens dating from the Epipaleolithic at the Taforalt prehistoric site.^[40]
  - U2'3'4'7'8'9 (1811): Widely spread in West Eurasia and the Indian subcontinent.
    - U8
      - K

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.

R
- R0 (formerly pre-HV)
  - R0a
    - R0a1
    - R0a2
  - HV
    - HV0 (formerly pre-V)
      - HV0a
        V
    - H
- R1
  - R1a
    - R1a1
      - R1a1a
- R2'JT
  - R2
  - JT
    - J
    - T
- 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

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1 2 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.
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.
1 2 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.
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.
↑ 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.
↑ 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.
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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: 45. doi:10.1186/1471-2148-8-45. PMC 2268671. PMID 18269758.
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.
↑ 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.
↑ oxfordancestors.com Maternal Ancestry
↑ Mannis van Oven's PhyloTree.org – mtDNA subtree R
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.
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: 227. doi:10.1186/1471-2148-8-227. PMC 2529308. PMID 18680585.
1 2 3 "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 2529308. PMID 18680585.
↑ 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 2718812. PMID 19662095.
↑ Ian Logan 2009, Haplogrupo R9b, Mitochondrial DNA Site
1 2 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.
↑ 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.
1 2 3 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 1876738. PMID 17160892.
↑ 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.
↑ 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.
1 2 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.
↑ 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.
↑ Haplogroup R14, Ian Logan's Mitochondrial DNA Site
↑ 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.
↑ 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.
↑ 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.
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: 154. doi:10.1186/1471-2148-9-154. PMC 2720951. PMID 19573232.
1 2 3 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.
↑ 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.
↑ Harding, Rosalind 2006, Gene tree analyses of Aboriginal Australians. University of Oxford
↑ 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 1885570. PMID 17496137.
↑ mtDNA Haplogroup U1a page at cagetti.com
↑ 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.
↑ 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.
↑ 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.
↑ 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.

Phylogenetic tree of human mitochondrial DNA (mtDNA) haplogroups

Mitochondrial Eve (L)

L1–6

pre-JT

External links

Mannis van Oven's PhyloTree.org – mtDNA subtree R
Ian Logan's Mitochondrial DNA Site

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