Haplogroup E (mtDNA)

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.

This article is about the human mtDNA haplogroup. For the human Y-DNA haplogroup, see Haplogroup E-M96.
Haplogroup E
Possible time of origin35,000[1] to 8,000[2] YBP
Possible place of origineast Sundaland[1] or Fujian coast[2]
AncestorM9
DescendantsE1, E2
Defining mutations3027, 3705, 7598, 13626, 16390[3]

Origin

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.[1][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 and colleagues argue that Haplogroup E arose 8,000 to 11,000 years ago near 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.[2] 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]

Distribution

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 principal subclades, E1b and E2a are found mainly in Maritime Southeast Asia, while only E1a and E2b are also found in Taiwan.[12] E2b has low diversity within Taiwan, suggesting that it arrived there about 5,000 years ago.[12] The most common E subclade, E1a1a, has highest diversity in Taiwan, followed by the Philippines and Sulawesi. Moreover, other branches of E1a1 are largely confined to Taiwan.[13]

Frequencies of MtDNA Haplogroup E
Population Frequency Count Source Subtypes
Chamorro (85 Guam, 14 Saipan, & 6 Rota)0.924105Vilar et al 2013E2a=68, E1a2=29
East Indonesian (Sulawesi, incl. 89 Manado, 64 Toraja, 46 Ujung Padang, & 38 Palu)0.266237Hill et al 2007E1a=42, E1b=9, E2=7, E1(xE1a, E1b)=5
Filipino (Mindanao)0.21470Tabbada et al 2010, p. 24E1a1a=10, E2(xE2b)=4, E1b=1
Filipino (Visayas)0.214112Tabbada et al 2010, p. 24E1a1a=18, E2(xE2b)=5, E1(xE1a1a, E1a2, E1b)=1
East Indonesian (Ambon)0.16343Hill et al 2007E1(xE1a, E1b)=3, E1a=2, E2=2
East Indonesian (Waingapu, Sumba)0.16050Hill et al 2007E1b=6, E1a=1, E2=1
Indonesian (Bangka)0.14734Hill et al 2006E=5
Borneo (89 Banjarmasin & 68 Kota Kinabalu)0.146157Hill et al 2007E1a=14, E2=5, E1b=3, E1(xE1a, E1b)=1
Filipino0.12564Tabbada et al 2010, p. 24E1a1a=5, E2(xE2b)=2, E1a2=1
Filipino (Luzon)0.124177Tabbada et al 2010, p. 24E1a1a=14, E1b=5, E2(xE2b)=2, E2b=1
Taiwan (aborigine)0.120640Peng et al 2011E=77
East Indonesian (Alor)0.11145Hill et al 2007E1a=3, E1b=2
East Indonesian (Mataram, Lombok)0.09144Hill et al 2007E1b=3, E1a=1
Indonesian (Padang, Sumatra)0.08324Hill et al 2006E=2
Indonesian (Medan, Sumatra)0.07142Hill et al 2006E=3
Indonesian (Pekanbaru, Medan, Bangka, Palembang, & Padang)0.067180Hill et al 2007E1a=6, E1b=4, E1(xE1a, E1b)=1, E2=1
Indonesian (Bali)0.06182Hill et al 2007E1a=3, E1b=1, E1(xE1a, E1b)=1
Filipino (Palawan)0.05020Scholes et al 2011E1a=1
Indonesian (Palembang, Sumatra)0.03628Hill et al 2006E=1
Tujia (Yanhe County, Guizhou)0.03429Li et al 2007E=1
Gelao (Daozhen County, Guizhou)0.03231Li et al 2007E=1
Indonesian (Java, incl. 36 from Tengger)0.02246Hill et al 2007E1b=1
Indonesian (Pekanbaru, Sumatra)0.01952Hill et al 2006E=1
Cham (Bình Thuận, Vietnam)0.012168Peng et al 2010E1a1a=1, E2a=1
Carolinian (Saipan)0.00017Vilar et al 2013-
Yi (Hezhang County, Guizhou)0.00020Li et al 2007-
Dong (Tianzhu County, Guizhou)0.00028Li et al 2007-
Batek (Malaysia)0.00029Hill et al 2006-
Cun (Hainan)0.00030Peng et al 2011-
Batak (Palawan)0.00031Scholes et al 2011-
Lingao (Hainan)0.00031Peng et al 2011-
Mendriq (Malaysia)0.00032Hill et al 2006-
Temuan (Malaysia)0.00033Hill et al 2006-
Danga (Hainan)0.00040Peng et al 2011-
Jahai (Malaysia)0.00051Hill et al 2006-
Senoi (Malaysia)0.00052Hill et al 2006-
Semelai (Malaysia)0.00061Hill et al 2006-
Gelao (Daozhen County, Guizhou)0.000102Liu et al 2011-
Li (Hainan)0.000346Peng et al 2011-

Subclades

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
gollark: It... shouldn't.
gollark: ```python#!/usr/bin/env python3from PIL import Imageimport mathimport sysdef chunks(l, n): for i in range(0, len(l), n): yield l[i:i + n]def from_bit_list(bl): i = 0 for ix, v in enumerate(bl): i |= v * (2 ** (7 - ix)) return iim = Image.open("out.png")id = im.load()(w, h) = im.sizebits = []for x in range(w): for y in range(h): bits.append(id[x, y])bits = [1 if x >= 1 else 0 for x in bits]byts = [from_bit_list(bytegroup) for bytegroup in chunks(bits, 8)]sys.stdout.buffer.write(bytes(byts))```Here it is. It's really rather awful.
gollark: With the companion program.
gollark: You can decode it with the companion program, which I can send an image of.
gollark: This is not potatOS. This is some random text.

See also

Phylogenetic 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

References
  1. Soares et al 2008, p. 1215.
  2. Ko et al 2014.
  3. van Oven & Kayser 2008.
  4. Hill et al 2007.
  5. Soares et al 2016.
  6. Trejaut et al 2005.
  7. Tabbada et al 2010, pp. 24, 28.
  8. Peng et al 2010.
  9. Hill et al 2006.
  10. Vilar et al 2013.
  11. Peng et al 2011.
  12. Soares et al 2008, p. 1213.
  13. Tabbada et al 2010, p. 29.
  • Hill, Catherine; Soares, Pedro; Mormina, Maru; Macaulay, Vincent; Meehan, William; Blackburn, James; Clarke, Douglas; Raja, Joseph Maripa; Ismail, Patimah; Bulbeck, David; Oppenheimer, Stephen; Richards, Martin (2006). "Phylogeography and Ethnogenesis of Aboriginal Southeast Asians". Molecular Biology and Evolution. 23 (12): 2480–2491. doi:10.1093/molbev/msl124. PMID 16982817.
  • 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.
  • 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.
  • Li, Binbin; Zhong, Fuguang; Yi, Hongsheng; Wang, Xianran; Li, Liangfang; Wang, Lilan; Qi, Xiaolan; Wu, Lifu (2007). "Genetic Polymorphism of Mitochondrial DNA in Dong, Gelao, Tujia, and Yi Ethnic Populations from Guizhou, China". Journal of Genetics and Genomics. 34 (9): 800–811. doi:10.1016/S1673-8527(07)60091-5. PMID 17884690.
  • Liu, Chang; Wang, Sha-Yan; Zhao, Mian; Xu, Zhi-Yong; Hu, Yu-Hua; Chen, Feng; Zhang, Ruan-Zhang; Gao, Guo-Feng; Yu, Yue-Sheng; Kong, Qing-Peng (2011). "Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China". Forensic Science International Genetics. 5 (1): PE4–E10. doi:10.1016/j.fsigen.2010.04.007. PMID 20494640.
  • Peng, Min-Sheng; Quang, Huy Ho; Dang, Khoa Pham; Trieu, An Vu; Wang, Hua-Wei; Yao, Yong-Gang; Kong, Qing-Peng; Zhang, Ya-Ping (2010). "Tracing the Austronesian Footprint in Mainland Southeast Asia: A Perspective from Mitochondrial DNA". Molecular Biology and Evolution. 27 (10): 2417–2430. doi:10.1093/molbev/msq131. PMID 20513740.
  • Peng, Min-Sheng; He, Jun-Dong; Liu, Hai-Xin; Zhang, Ya-Ping (2011). "Tracing the legacy of the early Hainan Islanders – a perspective from mitochondrial DNA". BMC Evolutionary Biology. 11 (46). doi:10.1186/1471-2148-11-46. PMC 3048540. PMID 21324107.
  • Scholes, Clarissa; Siddle, Katherine; Ducourneau, Axel; Crivellaro, Federica; Järve, Mari; Rootsi, Siiri; Bellatti, Maggie; Tabbada, Kristina; Mormina, Maru; Reidla, Maere; Villems, Richard; Kivisild, Toomas; Lahr, Marta Mirazon; Migliano, Andrea Bamberg (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.
  • 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.
  • 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.
  • Tabbada, Kristina A.; Trejaut, Jean; Loo, Jun-Hun; Chen, Yao-Ming; Lin, Marie; Mirazón-Lahr, Marta; Kivisild, Toomas; De Ungria, Maria Corazon A. (2010). "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.
  • Trejaut, Jean A.; Kivisild, Toomas; Loo, Jun Hun; Lee, Chien Liang; He, Chun Lin; Hsu, Chia Jung; Lee, 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.
  • van Oven, Mannis; Kayser, Manfred (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.CS1 maint: ref=harv (link)
  • Vilar, Miguel G.; Chan, Chim W.; Santos, Dana R.; Lynch, Daniel; Spathis, Rita; Garruto, Ralph M.; Lum, J. Koji (2013). "The Origins and Genetic Distinctiveness of the Chamorros of the Marianas Islands: An mtDNA Perspective". American Journal of Human Biology. 25 (1): 116–122. doi:10.1002/ajhb.22349. PMC 4335639. PMID 23180676.
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