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 origin35,000[1] to 8,000[2] YBP
Possible place of origineast Sundaland[1] or Fujian coast[2]
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.[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]



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 -



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


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