"[8] In 2015, Trobetta et al. suggested an East African origin for haplogroup E, stating: "our phylogeographic analysis, based on thousands of samples worldwide, suggests that the radiation of haplogroup E started about 58 ka, somewhere in sub-Saharan Africa, with a higher posterior probability (0.73) for an eastern African origin.

According to this hypothesis, after an initial Out-of-Africa migration of early anatomically modern humans around 125 kya, haplogroup DE diversified around the Himalayas and in or westward of the Tibet, after which E-carrying males are proposed to have back-migrated from the paternal haplogroup's place of origin in Eurasia around 70 kya along with females bearing the maternal haplogroup L3, which the study also hypothesizes to have originated in Eurasia, into Africa.

Haplogroup E1a is split into two main branches: E1a1 (E-M44) which has been mostly found in Europe, West Asia and among Ashkenazi Jews; and E1a2 (E-Z958) which has been exclusively identified in Sub-Saharan Africa.

[17] Haplogroup E-M2 is the most prevalent subclade of E in Sub-Saharan Africa and is strongly associated with expansion of Bantu speakers.

E-M215 is far less common in West, Central, and Southern Africa, though it has been observed among some Khoisan speakers[18] and among Niger–Congo speakers in Senegambia,[19] Guinea-Bissau,[20] Burkina Faso,[21] Ghana, Gabon,[22] the Democratic Republic of the Congo, Rwanda,[23] Namibia, and South Africa.

Haplogroup E1a is split into two branches: E1a1 (E-M44) which has been mostly found in Europe, West Asia and among Ashkenazi Jews; and E1a2 (E-Z958) which has been exclusively identified in Sub-Saharan Africa.

[33] Haplogroup E-P2 (E1b1) is the most frequent variant of E-M96 and the most common Y-DNA lineage in Africa with two main descendants: E-V38 (E1b1a) and E-M215 (E1b1b).

Another descendant of E-V38, E-M329 (E1b1a2), has been observed in an Ethiopian hunter-gatherer from 4,200 ybp, and is mostly found in males from the Horn of Africa and Arabian Peninsula.

The highest concentration of the haplogroup has been found among the Alur (66.67%),[28] Hema (38.89%),[28] Rimaibe (27.03%),[21] Mbuti (25.00%),[21] Daba (22.22%),[21] Eviya (20.83%),[22] Zulu (20.69%),[28] and Kenyan Bantus (17.24%).

[23] Haplogroup E-M75(xM41,M54) has been found in 6% (1/18) of Dama from Namibia,[28] 4% (1/26) of Ganda from Uganda,[28] 3% (1/39) of Mandinka from Gambia/Senegal,[28] and 2% (1/49) of Sena from Mozambique .

[28] Private commercial DNA testing at Family Tree DNA shows numerous E-M75 males originating from the Arabian Peninsula (Saudi Arabia, Bahrain, Kuwait, Yemen, and the United Arab Emirates), and among Ashkenazi Jews.