Ancient Egyptian Old Kingdom DNA (2500-3000 BCE): 10% Sub-Saharan and no Iran-Chalcolithic

I have larger, more expansive posts in the works but I had to share this as yet another piece of quick, interesting findings that seemed to have not popped up on a lot of people's radars. Credit should go to a Somalispot poster by the username of Xareen for bringing it to my attention on there. We now have a Bronze-Age Egyptian sample thanks to the thesis of one Adeline Morez from Liverpool John Moores University.[1]

In her thesis she goes over a sample dated to ~2,868-2,492 BCE from the Nuerat cemetery just south of Beni Hasan in the Minya governorate of Upper Egypt and they found that this sample is about ~10% Dinka-like in its ancestry

NUE001 also carries ~10% ancestry similar to the one found in the 4,500-year-old Ethiopian genome, derived from the eastern sub-Saharan African component

That component has gone by many names over the years in the anthropology sphere. East-African (EA), Ancestral East African (AEA), "Nilo-Saharan", or simply "Dinka-like" as it makes up the vast majority of the ancestry of Nilo-Saharan groups such as Dinkas and the Gumuz above, as well as the Mota Hunter-Gatherer of Southern Ethiopia. It further makes up the vast majority of the Sub-Saharan African ancestry in modern Horn-Africans such as Somalis, Amharas, Oromos, Tigrinyas, Aris and Wolaytas who are mostly genetically intermediate populations between Middle-Easterners and groups such as the Dinka (see here).

It appears this Egyptian, unlike the Iron-Age Egyptians from 8 years ago [2], has a bit of this ancestry much like modern Copts do:

They also seem to lack or have very little Iran-Chalcolithic-related ancestry, unlike the later Egyptians of the Iron Age, with the author in my opinion correctly speculating that this is due to the later period Egyptians having significant admixture from Asiatic (Semitic-speaking) groups such as the Hyksos:

The Nuerat sample did not carry the Caucasus Hunter-Gatherer genetic component that started to spread across West Asia ~4,000 years ago and is widely spread in present-day populations. The presence of this component in Egypt is likely associated with admixture between local Egyptian populations and Bronze Age-related populations from West Asia. This admixture pattern might result from the dominance of Lower Egypt by Canaanite (Levantine) rulers during the Second Intermediate Period (ca. 1,650-1,550 BCE).

A group of West Asiatic foreigners, possibly Canaanites, labelled as Aamu (ꜥꜣmw), including the leading man with a Nubian ibex labelled as Abisha the Hyksos (𓋾𓈎𓈉 ḥqꜣ-ḫꜣsw, Heqa-kasut for "Hyksos"). Tomb of 12th-dynasty official Khnumhotep II, at Beni Hasan (c. 1890 BC).

So, it seems many of us who assumed Ancient and Pre-historic Egypt may have not had any Dinka-like ancestry were being premature in going off those Iron-Age genomes we got several years ago, if indeed this sample is representative and I see no reason to believe it is not. It appears that when the West-Asian migrants came in they brought with them not just significant Iran-Neolithic/Caucasus-Hunter-Gatherer type ancestry but they also diluted out the previously present Sub-Saharan ancestry.

This sample, if we can get it into David Wesolowski's Eurogenes Global 25 PCA should be extremely interesting to run for many populations including my own Horn-Africans as I strongly suspect it will prove quite representative of our non-Arabian MENA ancestors who consistently appear very similar to Natufians—with a slight Iberomaurusian shift—in G25 based runs:

I reckon this individual will essentially be that with ~10% Dinka-like ancestry. We'll see, and here's to seeing more ancient genomes from Egypt from around this period and earlier. 

References

1. Morez A. Reconstructing past human genetic variation with ancient DNA: case studies from ancient Egypt and medieval Europe [doctoral thesis]. Liverpool: Liverpool John Moores University; 2023. Available from: 

https://researchonline.ljmu.ac.uk/id/eprint/18979/

2. Schuenemann VJ, Peltzer A, Welte B, van Pelt WP, Molak M, Wang CC, et al. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat Commun. 2017 May 30;8:15694. doi: 10.1038/ncomms15694. Available from: https://www.nature.com/articles/ncomms15694

3. Wikimedia Commons. Drawing of the procession of the Aamu group tomb of Khnumhotep II at Beni Hassan [Internet]. Available from: https://commons.wikimedia.org/wiki/File:Drawing_of_the_procession_of_the_Aamu_group_tomb_of_Khnumhotep_II_at_Beni_Hassan.jpg.

Simplified for total laymen:

About eight years ago, Iron-Age Egyptian genomes were analyzed, showing no detectable "Black" African ancestry, unlike modern Egyptians—both Muslim and Christian—who have such ancestry at usually a range of 10-20%. This led to the assumption that such ancestry was a later addition and largely absent in Ancient Egypt.

Media headlines sensationalized the findings, with some even falsely and absurdly claiming that Ancient Egyptians were "closer to Europeans" than to modern Egyptians, their direct descendants. This is misleading because mostly non-Eurasian admixed Africans are genetically quite distinct from Eurasians. Even if two populations share 90% of their ancestry, a small (~10%) amount of Sub-Saharan ("Black") ancestry can inflate genetic distance, making them appear more distant from a closely related group than other Eurasians are, even when those Eurasians (such as Europeans) share no ancestry from within the last 5,000 to 10,000 years or more with the group that lacks Sub-Saharan ancestry unlike the group that's 10% Sub-Saharan. To be fair, the researchers didn't necessarily sensationalize the findings like that—the media did.

However, this new data discussed above regarding an Old Kingdom sample suggests that migrations from the Levant (Palestine-Israel region)—possibly during the Middle Kingdom—introduced new Eurasian ancestry, temporarily diluting the earlier Sub-Saharan African component. 

So, Egypt seems to for now have had some minor but not negligible Black-African ancestry (~10%), lost it for a time due to migrations from Asia, then got it back through a mixture of intermixing with Nubians (likely what happened with Copts) and the Trans-Saharan Slave Trade (mostly what seems to have happened with the Muslims), the latter case of which brought some completely new Black-African elements such as West-African ancestry. The rest is nerdy stuff about the other strains of ancestry from the Middle-East the average person probably won't be that interested in but I'll be discussing in future posts so feel free to stick around if you're intrigued.