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In human mitochondrial genetics, haplogroup E is a human mitochondrial DNA (mtDNA) haplogroup typical for the Malay Archipelago. It is a subgroup of haplogroup M9.

Haplogroup E
Possible time of origin8,000[1] to 39,000[2] YBP
Possible place of originIndonesia[2] or Fujian coast[1]
DescendantsE1, E2
Defining mutations3027, 3705, 7598, 13626, 16390[3]



Two contrasting proposals have been made for the location and time of the origin of Haplogroup E. One view is that the clade was formed over 30,000 years ago, around the time of the Last Glacial Maximum, on the northeast coast of Sundaland (near modern Borneo). In this model, the haplogroup was dispersed by rising sea levels during the Late Glacial period.[2][4]

In 2014, the mitochondrial DNA of an 8,000-year-old skeleton found on Liang Island, one of the Matsu Islands off the southeast China coast, was found to belong to Haplogroup E, with two of the four mutations characteristic of the E1 subgroup. From this, Ko et al infer that Haplogroup E arose 8,000 to 11,000 years ago on the north Fujian coast, travelled to Taiwan with Neolithic settlers 6,000 years ago, and from there spread to Maritime Southeast Asia with the Austronesian language dispersal.[1] Soares et al caution against over-emphasizing a single sample, and maintain that a constant molecular clock implies the earlier date (and more southerly origin) remains more likely.[5]


Haplogroup E is found throughout Maritime Southeast Asia.[4] It is nearly absent from mainland East Asia, where its sister group M9a (also found in Japan) is common.[4][6] In particular, it is found among speakers of Austronesian languages, and it is rare even in Southeast Asia among members of other language families. It has been detected in populations of Taiwan, the Philippines, Indonesia, Malaysia (including Sabah of Borneo, but not the Orang Asli of peninsular Malaysia), coastal Papua New Guinea, and especially in the Chamorros of the Mariana Islands.[4][7][8][9][10][11] Of the four subclades, only E1a and E2b are found in Taiwan.[2]

Frequencies of MtDNA Haplogroup E
Population Frequency Count Source Subtypes
Chamorro (85 Guam, 14 Saipan, & 6 Rota) 0.924 105 Vilar 2013 E2a=68, E1a2=29
East Indonesian (Sulawesi, incl. 89 Manado, 64 Toraja, 46 Ujung Padang, & 38 Palu) 0.266 237 Hill 2007 E1a=42, E1b=9, E2=7, E1(xE1a, E1b)=5
Filipino (Mindanao) 0.214 70 Tabbada 2010 E1a1a=10, E2(xE2b)=4, E1b=1
Filipino (Visayas) 0.214 112 Tabbada 2010 E1a1a=18, E2(xE2b)=5, E1(xE1a1a, E1a2, E1b)=1
East Indonesian (Ambon) 0.163 43 Hill 2007 E1(xE1a, E1b)=3, E1a=2, E2=2
East Indonesian (Waingapu, Sumba) 0.160 50 Hill 2007 E1b=6, E1a=1, E2=1
Indonesian (Bangka) 0.147 34 Hill 2006 E=5
Borneo (89 Banjarmasin & 68 Kota Kinabalu) 0.146 157 Hill 2007 E1a=14, E2=5, E1b=3, E1(xE1a, E1b)=1
Filipino 0.125 64 Tabbada 2010 E1a1a=5, E2(xE2b)=2, E1a2=1
Filipino (Luzon) 0.124 177 Tabbada 2010 E1a1a=14, E1b=5, E2(xE2b)=2, E2b=1
Taiwan (aborigine) 0.120 640 Peng 2011 E=77
East Indonesian (Alor) 0.111 45 Hill 2007 E1a=3, E1b=2
East Indonesian (Mataram, Lombok) 0.091 44 Hill 2007 E1b=3, E1a=1
Indonesian (Padang, Sumatra) 0.083 24 Hill 2006 E=2
Indonesian (Medan, Sumatra) 0.071 42 Hill 2006 E=3
Indonesian (Pekanbaru, Medan, Bangka, Palembang, & Padang) 0.067 180 Hill 2007 E1a=6, E1b=4, E1(xE1a, E1b)=1, E2=1
Indonesian (Bali) 0.061 82 Hill 2007 E1a=3, E1b=1, E1(xE1a, E1b)=1
Filipino (Palawan) 0.050 20 Scholes 2011 E1a=1
Indonesian (Palembang, Sumatra) 0.036 28 Hill 2006 E=1
Tujia (Yanhe County, Guizhou) 0.034 29 Li 2007 E=1
Gelao (Daozhen County, Guizhou) 0.032 31 Li 2007 E=1
Indonesian (Java, incl. 36 from Tengger) 0.022 46 Hill 2007 E1b=1
Indonesian (Pekanbaru, Sumatra) 0.019 52 Hill 2006 E=1
Cham (Bình Thuận, Vietnam) 0.012 168 Peng 2010 E1a1a=1, E2a=1
Carolinian (Saipan) 0.000 17 Vilar 2013 -
Yi (Hezhang County, Guizhou) 0.000 20 Li 2007 -
Dong (Tianzhu County, Guizhou) 0.000 28 Li 2007 -
Batek (Malaysia) 0.000 29 Hill 2006 -
Cun (Hainan) 0.000 30 Peng 2011 -
Batak (Palawan) 0.000 31 Scholes 2011 -
Lingao (Hainan) 0.000 31 Peng 2011 -
Mendriq (Malaysia) 0.000 32 Hill 2006 -
Temuan (Malaysia) 0.000 33 Hill 2006 -
Danga (Hainan) 0.000 40 Peng 2011 -
Jahai (Malaysia) 0.000 51 Hill 2006 -
Senoi (Malaysia) 0.000 52 Hill 2006 -
Semelai (Malaysia) 0.000 61 Hill 2006 -
Gelao (Daozhen County, Guizhou) 0.000 102 Liu 2011 -
Li (Hainan) 0.000 346 Peng 2011 -


This phylogenetic tree of haplogroup E 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.

  • E
    • E1
      • E1a
        • E1a1
          • E1a1a
            • E1a1a1
        • E1a2
      • E1b
        • E1b1
    • E2
      • E2a
      • E2b
        • E2b1
        • E2b2

See alsoEdit


  1. ^ a b c Ko, Albert Min-Shan; Chen, Chung-Yu; Fu, Qiaomei; Delfin, Frederick; Li, Mingkun; Chiu, Hung-Lin; Stoneking, Mark; Ko, Ying-Chin (2014). "Early Austronesians: into and out of Taiwan". The American Journal of Human Genetics. 94 (3): 426–436. doi:10.1016/j.ajhg.2014.02.003. PMC 3951936. PMID 24607387.
  2. ^ a b c d Soares, Pedro; Trejaut, Jean Alain; Loo, Jun-Hun; Hill, Catherine; Mormina, Maru; Lee, Chien-Liang; Chen, Yao-Ming; Hudjashov, Georgi; Forster, Peter; Macaulay, Vincent; Bulbeck, David; Oppenheimer, Stephen; Lin, Marie; Richards, Martin B. (2008). "Climate Change and Postglacial Human Dispersals in Southeast Asia". Molecular Biology and Evolution. 25 (6): 1209–1218. doi:10.1093/molbev/msn068. PMID 18359946.
  3. ^ 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. Archived from the original on 4 December 2012. Retrieved 2009-05-20. Cite uses deprecated parameter |dead-url= (help)
  4. ^ a b c d 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". American Journal of Human Genetics. 80 (1): 29–43. doi:10.1086/510412. PMC 1876738. PMID 17160892.
  5. ^ Soares, Pedro A.; Trejaut, Jean A.; Rito, Teresa; Cavadas, Bruno; Hill, Catherine; Eng, Ken Khong; Mormina, Maru; Brandão, Andreia; Fraser, Ross M.; Wang, Tse-Yi; Loo, Jun-Hun; Snell, Christopher; Ko, Tsang-Ming; Amorim, António; Pala, Maria; Macaulay, Vincent; Bulbeck, David; Wilson, James F.; Gusmão, Leonor; Pereira, Luísa; Oppenheimer, Stephen; Lin, Marie; Richards, Martin B. (2016). "Resolving the ancestry of Austronesian-speaking populations". Human Genetics. 135 (3): 309–326. doi:10.1007/s00439-015-1620-z. PMC 4757630. PMID 26781090.
  6. ^ Trejaut, Jean A.; Kivisild, Toomas; Loo, Jun Hun; Lee, Chien Liang; He, Chun Lin; Hsu, Chia Jung; Li, Zheng Yuan; Lin, Marie (2005). "Traces of Archaic Mitochondrial Lineages Persist in Austronesian-Speaking Formosan Populations". PLoS Biology. 3 (8). e247. doi:10.1371/journal.pbio.0030247. PMC 1166350. PMID 15984912.
  7. ^ Kristina A. Tabbada, Jean Trejaut, Jun-Hun Loo et al., "Philippine Mitochondrial DNA Diversity: A Populated Viaduct between Taiwan and Indonesia?", Mol. Biol. Evol. 27(1):21–31. (2010) doi:10.1093/molbev/msp215
  8. ^ Min-Sheng Peng, Huy Ho Quang, Khoa Pham Dang et al., "Tracing the Austronesian Footprint in Mainland Southeast Asia: A Perspective from Mitochondrial DNA", Mol. Biol. Evol. 27(10):2417–2430. (2010) doi:10.1093/molbev/msq131
  9. ^ Catherine Hill, Pedro Soares, Maru Mormina et al., "Phylogeography and Ethnogenesis of Aboriginal Southeast Asians", Mol. Biol. Evol. 23(12):2480–2491. (2006) doi:10.1093/molbev/msl124
  10. ^ Miguel G. Vilar, Chim W. Chan, Dana R. Santos et al., "The Origins and Genetic Distinctiveness of the Chamorros of the Marianas Islands: An mtDNA Perspective", American Journal of Human Biology, Volume 25, Issue 1, pages 116–122, January/February 2013. DOI: 10.1002/ajhb.22349
  11. ^ Min-Sheng Peng, Jun-Dong He, Hai-Xin Liu, and Ya-Ping Zhang, "Tracing the legacy of the early Hainan Islanders - a perspective from mitochondrial DNA", BMC Evolutionary Biology 2011, 11:46.

External linksEdit