Haplogroup R (mtDNA)

In human mitochondrial genetics, haplogroup R is a very extended mitochondrial DNA (mtDNA) haplogroup and 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 the ancestral haplogroup of J and T.

Origin [edit]

As of June 2009, the most recent study dates the origin of haplogroup R to 66.6kya with a 95% confidence interval of 52.6-81kya.^[1][3]

South Asia lies on the way of earliest dispersals from Africa and is therefore a valuable well of knowledge on early human migration.^[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 tribes show higher haplogroup diversity than the other regions, possibly suggesting their autochthonous status.^[6]

Distribution [edit]

R and its descendants are spread all over Eurasia, Oceania and the Americas. These descendants are specially prevailing in Western Eurasia. About 89% of Europeans are of mtDNA macro-haplogroup R.^[7]

Subclades [edit]

• Haplogroup R
  • R0 or pre-HV
    • R0a or (preHV)1: Higher frequencies occur in Southwest Asia, specially in the Arabian Plate.^[8] Smaller frequencies in North Africa, the Horn of Africa, South Asia & Europe.
    • HV: It is a west Eurasian haplogroup mainly found throughout the Middle East, including Iran.^[9] It is also found in North Africa, Central Asia and South Asia.
      • HV0 or Pre*V: Mainly in Western Europe.^[10]
        • V: Found at moderately low frequencies around Europe; the highest frequency is in the Sami people 40%.^[11]
      • HV1: Mainly in the Middle East.^[8]
      • HV2: Mainly in South Asia.^[9]
      • HV3: Mainly in Eastern Europe.^[12]
      • H: In West Eurasia. It is the most common mtDNA haplogroup in Europe.
  • R1
    • R1* (16278): In Kurdish from Turkmenistan (9%).^[9]
    • 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.^[12]
  • pre-JT or R2'JT
    • R2: Found mainly in Balochistan (Pakistan).^[9]
      • (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.^[8] J declines towards Europe at 11%, Caucasus 8%, North Africa 6% and becomes practically missing in East Asia.^[13]
      • T: The highest frequency is in the Caspian region (Caucasus, Northern Iran, Turkmenistan).^[9] It is important in Europe (almost 10%),^[14] Middle East, Central Asia, Pakistan and North Africa. Small frequency in the Horn of Africa and India.
  • R3: Found in Armenia.^[15]
  • R5: Widely spread in the Indian subcontinent. Specially in Madhya Pradesh (India) at 17%.^[16]
    • R5a
      • R5a1: Found within the Indo-European speaking populations of India.^[17]
      • R5a2: Specially among Dravidic groups of India and Sri Lanka.^[17]
  • R6'7 (16362) The most important presence is among Austroasiatic language-speakers from India (10%).^[17]
    • R6: Small frequencies in India and Pakistan.^[16]
    • R7: In the Indian subcontinent (see map).^[17]
      • R7a: Mainly in East India, specially in Santals from Bihar and Jharkhand. (map)
      • R7b: Specially in Dravidian tribes of East India. (map)
  • 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 (see map).^[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),^[16] 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] Nicobar Islands^[6] and Lesser Sunda Islands.^[28] Also known as R12.
  • R22 or R12: Typical for Eastern Indonesia, specially in Lesser Sunda Islands (8%).^[22] Low in Thailand.
  • 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^[29] and Sinhalese people from Sri Lanka.^[17]
    • R30b: Found in Punjab.^[17]
    • R30* (1598, 16189): Found in Punjab, Nepal and Japan.^[29]
  • R31
    • R31a: In Brahmins from Uttar Pradesh^[5] and Rajputs from Rajasthan (India).^[17]
    • 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.^[30] Also found in Maluku, Nusa Tenggara and Polynesia.^[31]
      • P2'10
        • P2: In Melanesia,^[30] specially in New Guinea and New Caledonia.
        • P10: Found in Philippines.^[25]
      • P9 (or AuE): In Aboriginal Australians from the central region.^[32]
    • P3: In Australia and Melanesia.^[30]
    • P4: In Australia and Melanesia.^[33]
  • U
    • U1: It appears mostly in the Middle East and Caucasus. Found from India to the Mediterranean and to the rest of Europe.^[34]
    • U5: Approximately 11% of total Europeans and 10% of European-Americans. The highest frequency is in the Sami people.^[11]
    • U6: It is common in North Africa (around 10% of the people) ^[35] with a maximum of 29% in Algerian Berbers^[36]
    • U2'3'4'7'8'9 (1811): Widely spread in West Eurasia and the Indian subcontinent.
      • U8
        • K

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
          • 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 [edit]

1. ^ ^{a b} Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary material. pp. page89. 2009. 
2. ^ ^{a b} van Oven, Mannis; Manfred Kayser (13 Oct 2008). "Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation". Human Mutation 30 (2): E386–E394. doi:10.1002/humu.20921. PMID 18853457. Retrieved 2009-05-20. 
3. ^ Soares, P; Ermini, L; Thomson, N; Mormina, M; Rito, T; Röhl, A; Salas, A; Oppenheimer, S et al. (2009). "Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock". American Journal of Human Genetics 84 (6): 740–59. doi:10.1016/j.ajhg.2009.05.001. PMC 2694979. PMID 19500773.  |displayauthors= suggested (help)
4. ^ ^{a b} Karmin, Monika 2005, Human mitochondrial DNA haplogroup R in India Thesis, University of Tartu
5. ^ ^{a b c d} Palanichamy, M. et al. 2004. Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia.
6. ^ ^{a b} Maji, S. et al. 2008, Distribution of Mitochondrial DNA Macrohaplogroup N in India with Special Reference to Haplogroup R and its Sub-Haplogroup U. Int J Hum Genet, 8(1-2): 85-96 (2008)
7. ^ Eupedia.com. Distribution of European mitochondrial DNA (mtDNA) haplogroups by region in percentage
8. ^ ^{a b c} Abu-Amero, Khaled K, Larruga, José M, Cabrera, Vicente M, Gonz�lez, Ana M (2008). "Mitochondrial DNA structure in the Arabian Peninsula". BMC Evolutionary Biology 8 (45): 52. doi:10.1186/1471-2148-8-45. PMC 2268671. PMID 18269758. 
9. ^ ^{a b c d e} Quintana-Murci, Lluís et al. (2004). "Where West Meets East: The Complex mtDNA Landscape of the Southwest and Central Asian Corridor". Am J. Hum. Genet 74: 2004. 
10. ^ Haplogroups V & pre*V.
11. ^ ^{a b} Helgason, Agnar; Hickey, E; Goodacre, S; Bosnes, V; Stefánsson, K; Ward, R; Sykes, B (2001). "mtDNA and the Islands of the North Atlantic: Estimating the Proportions of Norse and Gaelic Ancestry". Am J. Hum. Genet 68 (3): 723–737. doi:10.1086/318785. PMC 1274484. PMID 11179019. 
12. ^ ^{a b} Malyarchuk, B. et al. 2008a Mitochondrial DNA Phylogeny in Eastern and Western Slavs.
13. ^ Serk, Piia. 2004. Human Mitochondrial DNA Haplogroup J in Europe and Near East. Thesis University of Tartu, Estonia
14. ^ oxfordancestors.com Maternal Ancestry
15. ^ Mannis van Oven's PhyloTree.org – mtDNA subtree R
16. ^ ^{a b c} Metspalu, M. et al. 2005, 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 2004, 5:26
17. ^ ^{a b c d e f g} Chaubey G. et al. 2008a Phylogeography of mtDNA haplogroup R7 in the Indian peninsula
18. ^ Thangaraj, K. et al. 2009, Deep Rooting In-Situ Expansion of mtDNA Haplogroup R8 in South Asia.
19. ^ Ian Logan 2009, Haplogrupo R9b, Mitochondrial DNA Site
20. ^ ^{a b} Hill, Catherine et al. 2006, Phylogeography and Ethnogenesis of Aboriginal Southeast Asians Mol. Biol. Evol. 23(12):2480–2491. 2006
21. ^ Clarissa Scholes et al. Genetic Diversity and Evidence for Population Admixture in Batak Negritos from Palawan, AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY. 000:000–000 (2011)
22. ^ ^{a b c} Hill, C. et al. 2007, A Mitochondrial Stratigraphy for Island Southeast Asia. Am J Hum Genet. 2007 January; 80(1): 29–43.
23. ^ Derenko, Miroslava 2007 Phylogeographic Analysis of Mitochondrial DNA in Northern Asian Populations The American Journal of Human Genetics 81, 5, Nov 07, 1025–1041
24. ^ Tanaka, Masashi et al. 2004, Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan. Genome Res. 2004. 14: 1832–1850
25. ^ ^{a b} Tabbada, Kristina. et al. 2009, Philippine mitochondrial DNA diversity: a populated viaduct between Taiwan and Indonesia? Molecular Biology and Evolution, doi:10.1093/molbev/msp215
26. ^ Pierson, Melanie et al. 2006, Deciphering Past Human Population Movements in Oceania: Provably Optimal Trees of 127 mtDNA Genomes. MBE Advance Access published July 19, 2006
27. ^ Haplogroup R14, Ian Logan's Mitochondrial DNA Site
28. ^ Mona, Stefano et al 2009, Genetic admixture history of eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis Mol Biol Evol (2009) doi:10.1093/molbev/msp097
29. ^ ^{a b} Fornarino, Simona et al. 2009, Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evolutionary Biology 2009, 9:154 doi:10.1186/1471-2148-9-154
30. ^ ^{a b c} Friedlaender, Jonathan et al 2005, Expanding Southwest Pacific mitochondrial haplogroups P and Q. MBE Advance Access published April 6, 2005
31. ^ Kayser, Manfred tl 2006, Melanesian and Asian Origins of Polynesians: mtDNA and Y Chromosome Gradients Across the Pacific
32. ^ Harding, Rosalind 2006, Gene tree analyses of Aboriginal Australians. University of Oxford
33. ^ Hudjashov, Georgi et al. 2007. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. PNAS May 22, 2007 vol. 104 no. 21 8726-8730
34. ^ mtDNA Haplogroup U1a page at cagetti.com
35. ^ The Genographic Project at National Geographic
36. ^ N. Maca-Mayer, Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genetics, 2003

External links [edit]

• Haplogroup R
  • Mannis van Oven's PhyloTree.org – mtDNA subtree R
  • Spread of Haplogroup R, from National Geographic
  • Haplogroup R project at Family Tree DNA
• General
  • Ian Logan's Mitochondrial DNA Site