Haplogroup R (mtDNA)

Haplogroup R
Time of origin	66,000 YBP ^[1]
Place of origin	South Asia
Ancestor	N
Descendants	R0, R1, R2'JT, R5, R6'7, R8, 16304, R11'B, R12'21, R14, R23, R30, R31, P, U
Defining mutations	12705, 16223^[2]

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.

1 Origin
2 Distribution
- 2.1 Subclades
3 Tree
4 References
5 External links

Origin

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 linguistic 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

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

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: The highest frequency is in 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.
- 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 Austro-Asiatic languages speakers from India (10%).^[16]
  - R6: Small frequencies in India and Pakistan.^[15]
  - R7: In the Indian subcontinent (see map).^[16]
    - R7a: Mainly in East India, specially in Santals from Bihar. (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 Austro-Asiatic tribes (Munda speakers). It is also present in low frequency among the Dravidian and Indo-European speaking family (see map).^[17]
  - R8a: Found mainly in Orissa and Andhra Pradesh (India).
  - R8b: In Orissa, Gujarat, Andhra Pradesh (India).
- (16304)
  - R9
    - R9b: It appears mostly in Southeast Asia.^[18] Found all over Indonesia, in Indochina, Malaysia, in Aboriginal Malays like Semelai at 28% and Temuan 21%.^[19]
    - R9c: All over East Asia and Southeast Asia. Mainly in Alor (Indonesia) at 11%.^[20]
    - 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%.^[21] There is also an important frequency in Taiwanese aborigines, Guangdong (China), Maluku (Indonesia), Thailand and Vietnam.
  - R22 or R12: Typical for Indonesia, specially in Lesser Sunda Islands (8%).^[20] Low in Thailand.
- R11'B (16189)
  - R11: Found in China, mainly in Lahu people from Yunnan at 12.5%.^[22] 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.^[23]
- R12'21
  - R12: Found in Australia.^[24]
  - R21: In indigenous peoples of Malaysia like Jahai Negritos at 63%^[19] and Senoi 37%.
- R14: Found in Papua New Guinea^[25] and Nicobar Islands.^[6] Also known as R12.
- R23: Small clade found in Bali and Sumba (Indonesia).^[20]
- R30
  - R30a: Found in Andhra Pradesh, Uttar Pradesh (India), in the Tharu people from Nepal^[26] and Sinhalese people from Sri Lanka.^[16]
  - R30b: Found in Punjab.^[16]
  - R30* (1598, 16189): Found in Punjab, Nepal and Japan.^[26]
- 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.
  - (16176)
    - P1: Wide spread in Melanesia. Higher frequencies occur in Papua New Guinea.^[27]
    - P2'10
      - P2: In Melanesia,^[27] speciallly in New Guinea and New Caledonia.
      - P10: Found in Philippines.^[23]
    - P9 (or AuE): In Aboriginal Australians from the central region.^[28]
  - P3: In Australia and Melanesia.^[27]
  - P4: In Australia and Melanesia.^[29]
- U
  - U1: It appears mostly in the Middle East and Caucasus. Found from India to the Mediterranean and to the rest of Europe.^[30]
  - 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) ^[31] with a maximum of 29% in Algerian Berbers^[32]
  - 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^[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

^ ^a ^b Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock Supplementary material. 2009. pp. page89. http://download.cell.com/AJHG/mmcs/journals/0002-9297/PIIS0002929709001633.mmc1.pdf.
^ ^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. PMID 18853457 doi:10.1002/humu.20921. http://www3.interscience.wiley.com/journal/121449735/abstract?CRETRY=1&SRETRY=0. Retrieved 2009-05-20.
^ Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock. 2009. doi:10.1016/j.ajhg.2009.05.001. http://www.cell.com/AJHG/abstract/S0002-9297(09)00163-3.
^ ^a ^b Karmin, Monika 2005, Human mitochondrial DNA haplogroup R in India Thesis, University of Tartu
^ ^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.
^ ^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)
^ Eupedia.com. Distribution of European mitochondrial DNA (mtDNA) haplogroups by region in percentage
^ ^a ^b ^c Abu-Amero et al. 2008 February. "Mitochondrial DNA structure in the Arabian Peninsula", BMC Evolutionary Biology. 8(45): 52.
^ ^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. 74:000–000, 2004
^ Haplogroups V & pre*V.
^ ^a ^b Helgason, Agnar et al. 2001, mtDNA and the Islands of the North Atlantic: Estimating the Proportions of Norse and Gaelic Ancestry Am. J. Hum. Genet. 68:723–737
^ ^a ^b Malyarchuk, B. et al. 2008a Mitochondrial DNA Phylogeny in Eastern and Western Slavs.
^ Serk, Piia. 2004. Human Mitochondrial DNA Haplogroup J in Europe and Near East. Thesis University of Tartu, Estonia
^ oxfordancestors.com Maternal Ancestry
^ ^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
^ ^a ^b ^c ^d ^e ^f ^g Chaubey G. et al. 2008a Phylogeography of mtDNA haplogroup R7 in the Indian peninsula
^ Thangaraj, K. et al. 2009, Deep Rooting In-Situ Expansion of mtDNA Haplogroup R8 in South Asia.
^ Ian Logan 2009, Haplogrupo R9b, Mitochondrial DNA Site
^ ^a ^b Hill, Catherine et al. 2006, Phylogeography and Ethnogenesis of Aboriginal Southeast Asians Mol. Biol. Evol. 23(12):2480–2491. 2006
^ ^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.
^ Derenko, Miroslava 2007 Phylogeographic Analysis of Mitochondrial DNA in Northern Asian Populations The American Journal of Human Genetics 81, 5, Nov 07, 1025-1041
^ Tanaka, Masashi et al. 2004, Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan. Genome Res. 2004. 14: 1832-1850
^ ^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
^ 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
^ Haplogroup R14, Ian Logan's Mitochondrial DNA Site
^ ^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
^ ^a ^b ^c Friedlaender, Jonathan et al 2005, Expanding Southwest Pacific mitochondrial haplogroups P and Q. MBE Advance Access published April 6, 2005
^ Harding, Rosalind 2006, Gene tree analyses of Aboriginal Australians. University of Oxford
^ 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
^ mtDNA Haplogroup U1a page at cagetti.com
^ The Genographic Project at National Geographic
^ N. Maca-Mayer, Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genetics, 2003

Human mitochondrial DNA (mtDNA) haplogroups

Mitochondrial Eve (L)

pre-JT

Former Clusters IWX

External links

Haplogroup R
- Mannis van Oven's PhyloTree.org - mtDNA subtree R
- Spread of Haplogroup R, from National Geographic
General
- Ian Logan's Mitochondrial DNA Site

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