Haplogroup E (mtDNA)

This article is about the human mtDNA haplogroup. For the human Y-DNA haplogroup, see Haplogroup E-M96.

Haplogroup E
Possible time of origin	35,000[1] to 8,000[2] YBP
Possible place of origin	east Sundaland[1] or Fujian coast[2]
Ancestor	M9
Descendants	E1, E2
Defining mutations	3027, 3705, 7598, 13626, 16390[3]

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.

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

See also

• Genealogical DNA test
• Genetic genealogy
• Human mitochondrial genetics
• Population genetics
• Human mitochondrial DNA haplogroups

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. hdl:1885/23220. 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): 46. Bibcode:2011BMCEE..11...46P. 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. S2CID 27566749.
• 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.

External links

• General
  • Mannis van Oven's Phylotree
• Haplogroup E
  • Ian Logan's Haplogroup E
  • Ian Logan's Haplogroup E1
  • Ian Logan's Haplogroup E1a1b
  • Ian Logan's Haplogroup E1a2
  • Ian Logan's Haplogroup E2
  • YFull MTree's Haplogroup E
  • MITOMAP's Haplogroup E
  • FamilyTreeDNA's mtDNA Haplotree: Haplogroup E
  • Ballinger, S.W.; Schurr, T.G.; Torroni, A.; Gan, Y.Y.; Hodge, J.A.; Hassan, K.; Chen, K.H.; Wallace, D.C. (1992). "Southeast Asian Mitochondrial DNA Analysis Reveals Genetic Continuity of Ancient Mongoloid Migrations". Genetics. 130 (1): 139–152. doi:10.1093/genetics/130.1.139. PMC 1204787. PMID 1346259.
  • Herrnstadt, C.; Elson, J.L.; Fahy, E.; et al. (2002). "Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups". American Journal of Human Genetics. 70 (5): 1152–1171. doi:10.1086/339933. PMC 447592. PMID 11938495.
  • Ingman, M.; Kaessmann, H.; Pääbo, S.; Gyllensten, U. (2000). "Mitochondrial genome variation and the origin of modern humans". Nature. 408 (6813): 708–713. Bibcode:2000Natur.408..708I. doi:10.1038/35047064. PMID 11130070. S2CID 52850476.
  • Stoneking, M.; Jorde, L.B.; Bhatia, K.; Wilson, A.C. (1990). "Geographic Variation in Human Mitochondrial DNA from Papua New Guinea". Genetics. 124 (3): 717–733. doi:10.1093/genetics/124.3.717. PMC 1203963. PMID 1968873.