The other immediate subclade, haplogroup E, is common in Africa, and to a lesser extent the Middle East and southern Europe.

As recently as 2007, some studies such as Chandrasekar et al. 2007, cite the publications by Hammer when arguing for an Asian origin of the YAP insertion.

Haplogroup D, which is YAP positive, was clearly an Asian lineage, being found only in East Asia with high frequencies in the Andaman Islands, Japan and Tibet.

[12] A 2000 study concerning the origin of the YAP+ mutation analyzed 841 Y-chromosomes representing 36 human populations of wide geographical distribution for the presence of a Y-specific Alu insert (YAP+ chromosomes).

[16] In Altheide and Hammer 1997, the authors argue that haplogroup E arose in Asia on an ancestral YAP+ allele before migrating back to Africa.

[20] Weale et al. state that the discovery of DE* among Nigerians pushes back the date for the most recent common ancestor (MRCA) of African YAP chromosomes.

This, in his view, has the effect of reducing the time window through which a possible back migration from Asia to Africa could occur.

In a 2007 study, Peter Underhill and Toomas Kivisild stated that there will always be uncertainty regarding the precise origins of DNA sequence variants such as YAP because of a lack of knowledge concerning prehistoric demographics and population movements.

The study suggests a back migration into Africa and a following admixture of the native Africans with immigrating peoples from Asia.

The authors conclude that this supports an Asian origin and may also explain signals of small percentages of Neanderthal DNA found in northern and some western Africans.

[4] FTDNA, in 2019, found three other D0 samples: one in a man from Russia of paternal Syrian descent and two in Al Wajh on the west coast of Saudi Arabia.

[26] According to Runfeldt and Sager of FTDNA (as also found by Haber et al.), D0 is a very divergent offshoot on the D branch, splitting off around 71,000 years ago, and lacking the M174 mutation that defines other D chromosomes.

[28][29] The subclades of DE continue to confound investigators trying to reconstruct the migration of humans because, while they are common in Africa and East Asia, they are also largely absent between these two regions.

Given that D-M174 is dominant in Japan, the Andaman Islands, and Tibet, whereas E-M96 is relatively common in Africa and the Middle East, some researchers have suggested that the rarity of DE lineages in India – a region considered important in the dispersal of modern humans – may be meaningful.

Basal DE* is extremely unusual in that it is found, at very low frequencies, among males from three widely separated regions: West Africa, the Caribbean, and East Asia.

In addition, the seemingly "paraphyletic" (basal) status of the Nigerian examples of DE-YAP may be "illusory" because the "branching order, and hence the origin, of YAP-derived haplogroups remains uncertain".

[36] A 2021 study by Mengge Wang et al. found one sample of Y-chromosome DE-M145 in a group of 679 Mongolians, but stated that it was uncertain whether it was (undifferentiated) DE* or a sub lineage, stating that they "could not confirm the detailed sublineages of the individuals belonging to DE-M145 due to the lack of subhaplogroups of E."[37] Haplogroup E-M96 is a subclade of haplogroup DE.