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]

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

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

• 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.