# 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.

## 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.
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. 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.

## Distribution

Haplogroup E is found throughout Maritime Southeast Asia. It is nearly absent from mainland East Asia, where its sister group M9a (also found in Japan) is common. 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.
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. E2b has low diversity within Taiwan, suggesting that it arrived there about 5,000 years ago. 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.
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 and subsequent published research.
* E
** E1
*** E1a
**** E1a1
***** E1a1a
****** E1a1a1
**** E1a2
*** E1b
**** E1b1
** E2
*** E2a
*** E2b
**** E2b1
**** E2b2