My attempt at an Initial Upper Palaeolithic and a Middle Palaeolithic breakdown. The IUP model shows the deep ancestral composition of our SSA component! Check the description for my analysis of the images.
The images present two models, one being a two way between proto-Eurasian/ANEA and SAHG + AEA, and the other being a three way between Eurasian, ANEA, and SAHG + AEA.
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Since it’s quite a long post I wrote a TLDR. Read beyond the following “•••” for the rest of the post.
TLDR; our indigenous African component seems to be an almost 50/50 mix between the remainders of the proto-OoA population and a coalition of Ancestral East African (Y-DNA B and mtDNA L1 & L2) and South African hunter gatherer (Y-DNA A-M32 and mtDNA L0). I believe that from the 50% coalition, pure SAHG would make up a smaller part of it and AEA make up the larger part of this 50%.
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To get some terminologies straight:
Proto-Eurasian and ANEA (Ancestral Northeast African) = the population which the main Eurasians/Out-of-Africans split away from just before they left Africa.
AEA (Ancestral East African) = Ancestral to the foragers of East Africa.
SAHG = South African hunter gatherers.
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Regarding my models:
Eurasian’s proxy is Dzudzuana
ANEA’s proxy is Zlaty Kun
SAHG+AEA’s proxy is South Africa 2000 BCE
Despite being 100% Eurasian, Zlaty Kun seems to perfectly capture the proto-OOA/proto-Eurasian/ANEA component due to it having the least drift to the original Out of African population.
Dzudzuana is able to capture our Eurasian in its complete form (however, there seems to be a 5% margin error for Somalis and PN samples) due to it having little drift to the Eurasian groups which we directly descend from.
South African HG is also capturing some AEA since AEA has much more drift from Zlaty Kun than SAHG, which is why the latter captures it.
Additionally, since modern Nilo-Saharans have Niger-Congo admix (South Sudanese Nilotes) or SAHG-shifted Mota admix (Surmics like the Mursi), there is a very slight increase in the SAHG/AEA component carried by modern Nilo-Saharans. u/some_professional_76 ‘s “Pre-Nilotic” sim seemingly captures our indigenous African component quite well, but his sim doesn’t score higher ANEA than the Zaghawa and the Nuba who have small amounts of Niger-Congo admix.
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Looking at the phylogenetic Y-DNA tree, South African HGs under A-M32 spread this clade northwards, leading to A-M28 and A-M13 among East Africans. The MRCA of the SAHG and East Africans under A-M32 appears to have lived approximately 49–57 kya. This founder-effect outweighed the local E1b1 and E2 variants particularly along the Middle and Upper Nile.
Regarding mtDNA, the splits seem to be less clear to me. Looking at the MRCA of the East African L0f2 clade, SAHGs seem to have spread L0f northwards some time between 53–77 kya (95% CI), which could fit within the same timeframe as A-M32’s contribution. However, I can’t recognise the same pattern with L0a due to its younger MRCAs shared with modern South Africans (which could possibly just be back-migrations into Southern Africa? Someone chime in here).
Regardless, what can be said for sure is that this ANEA/AEA/SAHG-admixed group had fully formed during the Upper Palaeolithic era. The skull of the Nazlet Khater 2 individual, which was found in Egypt and dates back to around 35 kya, shows signs of minor SAHG ancestry through his shared dental morphologies with the Khoisan.
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I’m not a geneticist, so don’t take everything that I’m saying as the inevitable truth. I just want to give us an idea of what to expect if DNA was recovered from the Palaeolithic and Mesolithic foragers of Northeastern and eastern Africa.