The discovery of two SNPs (V38 and V100) by Trombetta et al. (2011) significantly redefined the E-V38 phylogenetic tree.

[6][7][8][9] According to Wood et al. (2005) and Rosa et al. (2007), such population movements changed the pre-existing population Y chromosomal diversity in Central, Southern, and Southeastern Africa, replacing the previous haplogroup frequencies in these areas with the now dominant E1b1a1 lineages.

Traces of earlier inhabitants, however, can be observed today in these regions via the presence of the Y DNA haplogroups A1a, A1b, A2, A3, and B-M60 that are common in certain populations, such as the Mbuti and Khoisan.

Shriner et al. (2018) also traces this movement via sickle cell mutation, which likely originated during the Green Sahara period.

[13][14] At Taukome, in Botswana, an individual, dated to the Early Iron Age (1100 BP), carried haplogroups E1b1a1 (E-M2, E-Z1123) and L0d3b1.

[13][14] Hawass et al. (2012) determined that the ancient Egyptian mummy of an unknown man buried with Ramesses III was, because of the proven genetic relationship and a mummification process that suggested punishment, a good candidate for the pharaoh's son, Pentaweret, who was the only son to revolt against his father.

[15] Gad et al. (2021) indicates that Ramesses III and Unknown Man E, possibly Pentawere, carried haplogroup E1b1a.

[19] At Pont-sur-Seine, in France, a male individual, dated to the Middle Neolithic, carried haplogroups E1b1a1a1a1c2c and U5b1-16189-@16192.

[21] Human leukocyte antigen alleles further confirm that the individuals were of Sub-Saharan African origin.

[22] At Cabeço da Amoreira, in Portugal, an enslaved West African man, who may have been from the Senegambian coastal region of Gambia, Mauritania, or Senegal, and carried haplogroups E1b1a and L3b1a, was buried among shell middens between the 16th century CE and the 18th century CE.

[28] An enslaved African American man and woman, from the 18th century CE Anson Street burial site in Charleston, South Carolina, who carried haplogroup L3e1e, shared this haplogroup with freed Africans in Saint Helena.

[29] Based on those who were present among enlaved Africans, the ratio of males-to-females supports the conclusion of there being a strong selection bias for males in the latter period of the Trans-Atlantic Slave Trade.

[39] At an Anson Street burial site, in Charleston, South Carolina, there were 18 African Americans found who were dated to the 18th century CE.

[40] Amid the Green Sahara, the mutation for sickle cell originated in the Sahara[41] or in the northwest forest region of western Central Africa (e.g., Cameroon)[41][42] by at least 7,300 years ago,[41][42] though possibly as early as 22,000 years ago.

[41] West Africans (e.g., Yoruba and Esan of Nigeria), bearing the Benin sickle cell haplotype, may have migrated through the Northeast Africa into the western Arabia.

[41] West Africans (e.g., Mende of Sierra Leone), bearing the Senegal sickle cell haplotype,[44][41] may have migrated into Mauritania (77% modern rate of occurrence) and Senegal (100%); they may also have migrated across the Sahara, into North Africa, and from North Africa, into Southern Europe, Turkey, and a region near northern Iraq and southern Turkey.

[44] Some may have migrated into and introduced the Senegal and Benin sickle cell haplotypes into Basra, Iraq, where both occur equally.

[44] West Africans bearing the Benin sickle cell haplotype, may have migrated into the northern region of Iraq (69.5%), Jordan (80%), Lebanon (73%), Oman (52.1%), and Egypt (80.8%).

Some of the lineages found in these areas are possibly due to the Bantu expansion or other migrations.

[45][53] However, the discovery in 2011 of the E-M2 marker that predates E-M2 has led Trombetta et al. to suggest that E-M2 may have originated in East Africa.

[5] In Eritrea and most of Ethiopia (excluding the Anuak), E-V38 is usually found in the form of E-M329, which is autochthonous, while E-M2 generally indicates Bantu migratory origins.

A few isolated occurrences of E-M2 have also been observed among populations in Southern Europe, such as Croatia, Malta, Spain and Portugal.

Consequently, the haplogroup is often observed in the United States populations in men who self-identify as African Americans.

Whilst E1b1a reaches its highest frequency of 81% in Senegal, only 1 of the 139 Senegalese that were tested showed M191/P86.

[12] One Carioca from Rio de Janeiro, Brazil tested positive for the M58 SNP.

[45] E-M10 was found in a single person of the Lissongo group in the Central African Republic and two members in a "Mixed" population from the Adamawa region.

The basal node E-L485* appears to be somewhat uncommon but has not been sufficiently tested in large populations.

[9] Brucato et al. found similarly low frequencies of basal E-U175* in subjects in the Ivory Coast and Benin.

[85] The supposed "Bantu haplotype" found in E-U175 carriers is "present at appreciable frequencies in other Niger–Congo languages speaking peoples as far west as Guinea-Bissau".

[92] Prior to 2002, there were in academic literature at least seven naming systems for the Y-Chromosome Phylogenetic tree.