Old Kingdom Egyptian aDNA

[The alchemist]

Thanks for the random drop.

Quick takes:

Ghaba is a Cushitic population.

Pretty much the picture is, that agro-pastoralist Cushites settled in the Nile Valley from southern Western Egypt over 7000 years ago. Ghaba was one of the earliest settlements of several, the other being El Barga which had similar overall osteological features. Kadruka was close to EBK_N geographically and subsequently temporally (4200-4000 BC), so the morphological overlap makes total sense, it being the descendants of people related to El-Barga, if not directly. All in all, these were generally coherent people and I would be extremely shocked if they were not Cushites.

Those exotic haplogroups are the result of contamination with more recent European and East Eurasian DNA.

I think only the L3e2b+152 and R0 might be real; one seems very West African but is in truth western Saharan, mediated by people heavy with ANA. R0 is common among MENA groups.

These are much later samples, mainly from terminal Meoritic, and one Napatan (TARP9B_oslo). To give you the gist, besides the H2a which is likely Egyptian, they fall in with the typical mtDNA of Somalis, i.e., Cushitic:

The Egyptian samples are part regional, part Levant. But I don't think this is a complete snapshot of, let's say, the first pharaohs.

That paper was low quality. I'm not sure why they give the rare samples to people with little experience. Why not outsource it to Harvard or Max Plank instead of a student?

 

[NidarNidar]

Thanks for the random drop.

Quick takes:

Ghaba is a Cushitic population.
View attachment 354538

Pretty much the picture is, that agro-pastoralist Cushites settled in the Nile Valley from southern Western Egypt over 7000 years ago. Ghaba was one of the earliest settlements of several, the other being El Barga which had similar overall osteological features. Kadruka was close to EBK_N geographically and subsequently temporally (4200-4000 BC), so the morphological overlap makes total sense, it being the descendants of people related to El-Barga, if not directly. All in all, these were generally coherent people and I would be extremely shocked if they were not Cushites.
View attachment 354541
View attachment 354542

Those exotic haplogroups are the result of contamination with more recent European and East Eurasian DNA.

I think only the L3e2b+152 and R0 might be real; one seems very West African but is in truth western Saharan, mediated by people heavy with ANA. R0 is common among MENA groups.

These are much later samples, mainly from terminal Meoritic, and one Napatan (TARP9B_oslo). To give you the gist, besides the H2a which is likely Egyptian, they fall in with the typical mtDNA of Somalis, i.e., Cushitic:
View attachment 354540

The Egyptian samples are part regional, part Levant. But I don't think this is a complete snapshot of, let's say, the first pharaohs.

That paper was low quality. I'm not sure why they give the rare samples to people with little experience. Why not outsource it to Harvard or Max Plank instead of a student?

Dropping some good stuff bruddah.

 

[Xareen]

Thanks for the random drop.

Quick takes:

Ghaba is a Cushitic population.
View attachment 354538

Pretty much the picture is, that agro-pastoralist Cushites settled in the Nile Valley from southern Western Egypt over 7000 years ago. Ghaba was one of the earliest settlements of several, the other being El Barga which had similar overall osteological features. Kadruka was close to EBK_N geographically and subsequently temporally (4200-4000 BC), so the morphological overlap makes total sense, it being the descendants of people related to El-Barga, if not directly. All in all, these were generally coherent people and I would be extremely shocked if they were not Cushites.
View attachment 354541
View attachment 354542

Those exotic haplogroups are the result of contamination with more recent European and East Eurasian DNA.

I think only the L3e2b+152 and R0 might be real; one seems very West African but is in truth western Saharan, mediated by people heavy with ANA. R0 is common among MENA groups.

These are much later samples, mainly from terminal Meoritic, and one Napatan (TARP9B_oslo). To give you the gist, besides the H2a which is likely Egyptian, they fall in with the typical mtDNA of Somalis, i.e., Cushitic:
View attachment 354540

The Egyptian samples are part regional, part Levant. But I don't think this is a complete snapshot of, let's say, the first pharaohs.

That paper was low quality. I'm not sure why they give the rare samples to people with little experience. Why not outsource it to Harvard or Max Plank instead of a student?

Interesting! On contamination, I'm convinced it's the case after coming across this tweet:

Spoiler: for alchy walchy only

You don't have permission to view the spoiler content. Log in or register now.

 

[Nilotic]

Thanks for the random drop.

Quick takes:

Ghaba is a Cushitic population.
View attachment 354538

Pretty much the picture is, that agro-pastoralist Cushites settled in the Nile Valley from southern Western Egypt over 7000 years ago. Ghaba was one of the earliest settlements of several, the other being El Barga which had similar overall osteological features. Kadruka was close to EBK_N geographically and subsequently temporally (4200-4000 BC), so the morphological overlap makes total sense, it being the descendants of people related to El-Barga, if not directly. All in all, these were generally coherent people and I would be extremely shocked if they were not Cushites.
View attachment 354541
View attachment 354542

Those exotic haplogroups are the result of contamination with more recent European and East Eurasian DNA.

I think only the L3e2b+152 and R0 might be real; one seems very West African but is in truth western Saharan, mediated by people heavy with ANA. R0 is common among MENA groups.

These are much later samples, mainly from terminal Meoritic, and one Napatan (TARP9B_oslo). To give you the gist, besides the H2a which is likely Egyptian, they fall in with the typical mtDNA of Somalis, i.e., Cushitic:
View attachment 354540

The Egyptian samples are part regional, part Levant. But I don't think this is a complete snapshot of, let's say, the first pharaohs.

So what component is missing or should be more prominent in the first Pharaohs?

 

[puntDNALKing]

I don't take qpAdm output too seriously—it produces some of the dumbest results I’ve ever seen, like Somalis being Kura-Araxes on their MENA side. Absolute garbage. It’s easily skewed by the exact reference populations used. Honestly, I trust PCA and ADMIXTURE more.

And if PCAs, ADMIX and I bet you even some other methods like the ALDER methodology used by Pickrell et al. 2013 all fine something opposite to what qpAdm is saying and their results make more historical sense, then it's obvious it's wrong. No methodology is statistical magic and leagues better than the others. They all have their pitfalls and for me I like to see several of them lining up and intuitively making sense coupled with understanding why the one that doesn't fit is probably wrong like I said with the reference pops.

qpAdm is overused and most people who use it do not follow the proper rules, such as never use a source population younger than the target population, never use outgroups that are related to or have recent gene flow to target population, use wide source of genetic range when it comes to outgroups to delineate and make the genetic map larger, etc...
Sheika, its punt, I hope you are doing well, we need to talk and catch up. I recently came back into it and the new studies we have now is amazing. Let me know if you get your hands on the Neurat sample, I was able to download and run the Takarkori sample from Libya (TKH001), she turns out to be 60-70 percent SSA. If you want the sample, I have it. We will talk Inshallah

 

[The alchemist]

@Cognitive

It was a very surprising result.

Previously I've made the assertion that these samples were a northern peripheral peoples of a central Saharan population. Conveniently, the interpretation of the genetic substructure by these Takarkori early Middle Neolithic individuals allows for such inference of a southern regional confluence that defined such an entanglement.

The West African comes from the western Sahara. The Iberomaurusian had a wider southern expanse toward the Saharan central beyond the Maghrebi temperate geography. Then you had the Nilo-Saharan expansion westward that brought the pottery and harpoons during the pre-pastoral days.

This was said with the pottery that spread from the Nile Valley or the southern Western Desert:

"The motifs are similar in the esthetic pattern but difer in the technique and general arrangement, perhaps implying a mechanism of “imitation” rather than direct cultural transmission and suggesting distinct social boundaries within a broader, fairly uniform “cultural horizon” (Gosselain, 2011; WallaertPêtre, 2001). This, together with the widespread dissemination of other decorative types like RPD and DWL, may corroborate the existence of an extensive network of contacts and connections over the vast Sahara-Sahel area facilitated by eco-geographical features and active throughout the Holocene though with diferent routes and timings (Brass et al., 2018; Caneva, 1987; Mohammed-Ali & Khabir, 2003). The result is regionalization within a common cultural tradition, as exemplifed in the re-interpretation of some decorative patterns which, though similar, are never identical (Garcea, 2013; Jesse, 2010)."

This is evidence of such a network:

The Gobero cemetery in Niger could be one of these places for these distinct peoples to come and exchange genetics, technology, and living ways, specifically for the Takarkori people that have an entirely 3-way mixture. Interestingly, tooth sharpening and removal of lower incisors were observed among those Gobero individuals. The people I know who remove their two lower teeth, are Nilo-Saharan. In this case, those Gobero individuals (I think 7000 BP date) could already have been mixed with Nilo-Sahara types.

My simulation goes like this:

Early Niger-Congo speakers that were situated somewhere in the western Sahara river systems (these used to be well furnaced with wetlands and greenery) moved East toward oases (refugia) during drying conditions, with another more successfull western movement, forming the early Niger-Congo speakers in West Africa. You had Iberomaurusans and ANA existing in the central Sahara long before this period. Then we have evidence of the Nilo-Saharan expansion towards the Sahara during this period. Pottery and harpoons existed among the earliest Tenerians before pastoralism shows traces in the Gobero occupational site. This means Iberomaurusian individuals came in contact with Nilo-Saharan peoples during the Mesolithic. Now we know that there were different water systems around the area, and as such, the Iberomarusian-like people had pottery and harpoons I suggest a hypothesis that the pre-agricultural Nilo-Saharans passed on such technology through the hunter-fisher regime, probably pushing westward through the lake Mega Chad river systems.

There they found the hunter-gatherers with Iberomaurusian ancestry, through the western periphery of the lake environmental plain. Later they went more westward via the watershed and various lacustrine ecosystems, in the central region. Subsequently, the West African expansion eastward occurred, mixing with these peoples, somewhere south of the Takarkori but around Gobero.

Were there two types of pastoralist expansions that defined the pastoral Neolithic in the Central and Northern Saharan regions? The one that touched ground in the southern border regions in Algeria and Libya represented by the Takarkori:

And one later that expanded from the Levant into Morocco:

By the way, similar to the ancient Tunisian samples recently published, these samples got WHG. I noticed that from way back and found it weird no one mentioned it. But that is beside the point. My focus here is that these pastoralists came from the Levant, passed through Egypt, and then migrated through the Magrheb to Morocco. These people are clear in their origin in the Levant. (I have a separate and maybe more coherent explanation down below).

I'm not sure Takarkori has anything to do with that (Levant) expansion. However, the Tunisian Neolithic individuals got Sudanic and Yoruba-like DNA.

Are we looking at the convergence of two separate pastoralist systems?

We have these mtDNAs among the Tunisians overlapping the process I highlight with the central Saharan process:

Then you have the Y-DNA, which, no matter if it is from east or west, reveals hunter-gatherers moved across the Sahara before people were pastoralists.

What I'm trying to get at, is that, despite those Levantine-heavy Tunisian and Moroccan samples not expressing an elevation in the eastern and western African DNA, their uniparental associations reveal a more complex migratory picture. Furthermore, this is underscored by how the Neolithic Tunisian individuals show minor West African and Sudanic sub-structure that explains that those people had contact with pastoralists with heavy Nilo-Saharan and West African DNA. I think this West African Iberomarusian parity was more prevalent in the Central Sahara because you see groups like Zagawa, Toubou, and such with West African and Iberomaurusian proportions that seem similar in size in specific model-based conditions in G25 runs.

So what does this mean? A West African expansion, an East African expansion, and a central African contraction for a northward pull during drying times, post mixture. That seems reasonable to me.

Desiccation is a major factor. Usually, people become mobile pastoralists when it becomes too dry for anything sedentary but not unlivable. So my theory is, that high mobility surged during oscillating climatic periods. Northward contraction explains the northern movements of Iberomaursian people who now carried equal amounts of ancestry from east and west. There was a migration from the central Sahara towards the West north and East after as well due to complete desertification. Many haplogroups show this result, however, that is another topic.

We have those pottery types all the way in Mali during the hunter-gatherer days. I think those people had Sudanic admixture, then got overrun by Yoruba-like people (genetically) while adopting the living traditions of Sudanics. As their lifeways aligned with those of Sudan in wetlands that when they mixed during the eastern expansion, they were not far off subsistence-wise with the Nilo-Saharans (as the Niger-Congo peoples were Sudanic influenced already). Also, I think those West Africans brought plant culture. Not necessarily farming, but some type of proto-farming where they use grains and whatnot since you had technology in Mali for such use. It makes sense that Takarkori had some type of grain emphasis which they probably got from the West African side. However, this is not completely necessary since even in the broader Westen Desert, the early pastoralists heavily dabbled in wild grains.

 

[The alchemist]

@Cognitive

It was a very surprising result.

The question is, where did pastoralism come from?

I propose a new hypothesis. I think that pastoralism could have come from the Western Desert, i.e., where Cushites sourced their ancestry. That doesn't mean they were Cushitic at all. This could have taken place before such ancestry mixed. However, it could have been in a differentiated form. So in the Western Desert of Egypt, pastoralism spread not only to the Nile Valley but also to the west.

This coincides with other types of movements, namely Chadic and even Berber expansion. Also, I think the L3f has something to do with this complex. The fact that Chadic loaned the word of sheep to people like Kanuri tells us that they were pastoralists.

The Egyptian Western Desert became dry, Afro-Asiatic groups like Cushites moved east toward the Nile, and proto-Chadic moved West toward Lake Chad but subsequently experienced a period of intense drying so they moved further south with the recessing lacustrine environment. There they encountered the West Africans who once expanded and farmed, and so they took up farming.

"At the Proto-Chadic period, on the order of about 7,000 years ago, a much vaster Lake Mega-Chad occupied the heart of the basin. e initial period of Chadic divergence into either three or four daughter societies would have spread Chadic communities all across the areas immediately west and south of that lake, from the plains north of the Jos Plateau on the west, to the Mandara Mountains in the middle, to as far east as the Guerra Mountains."

It seems to me that these Takarkori peoples were the early Afro-Asiatic speakers in that region and that Afro-Asiatics brought pastoralism. The Levantine phenomenon might have been a north expansion of Afro-Asiatic speakers to the Egyptian Delta, mixed with newly arrived Levantines, then a western expansion towards the Maghreb encountering the Takarkori, also initially starting in the Western Desert of Egypt. Those people could have been proto-Berbers.

It could have been that Chadics from the get-go were more AEA instead of resembling the heavy Eurasian Cushitic mixture. Western Egypt had some type of diversity. I believe this pastoral picture is complex. I have said before that Nilo-Saharan people from the Saharan region have a Cushitic AEA side to them and this is probably caused by the Chadic expansion.

All in all, Somalis are probably a genetic intermediate between heavy AEA proto-Chadian and what is maximized by pre-dynastic Egyptians, minus the later Levant influence that we see in the simulated Old Kingdom from Giza. That does not mean Cushitic is a mixture of both, but that this component existed heterogeneously in various spots in that western region while mixing with each other and forming a coherent pastoral culture before migrating due to the drying of oases.

There was also a group of Epipaleolithic peoples in Elkab that seem to have association with the early Western Desert pastoralists. Another hunter-fisher people were found in the Qarunian or as they call the Fayum B. The archeology fits with Elkab and similarly got connections with the early Pastoral traditions of the Western Desert, however, a fossil was revealed from that context, a 40-year-old woman in a flexed position that had phenotype similar to someone you'd imagine had a lot of Eurasian ancestry.

I believe if we ever get a transect of the Western Desert of Egypt, we will uncover much of the key genetic Afro-Asiatic history.

Their dental morphology always seemed complex between that of North Africans and AEA/SSA:

"In previous studies (Irish 1993; 1994; 1997; 1998a,b,c,d; Irish and Turner 1990), up to 36 noncorrelated (per Kendall's tau-b and Spearman's rho) ASU traits were recorded in 30 samples of Late Pleistocene through recent Sub-Saharan and North Africans. Of these 36 traits, it was determined (Irish 1993) that 23 differ significantly (p ~ 0.05 using Pearson's X2) between pooled samples! from the two geographic regions. Thus, it was decided to use as many of these diagnostic traits as possible to get a cursory indication of whether the E-97- 17, E-OO-1, and E-91-1 individuals are phenetic ally more akin to Sub-Saharan or North Africans. As Henneberg et al. (1980) note, there is uncertainty about the identity of Neolithic Nabta Playa inhabitants. Their provenience places them at a crossroads between the north and south, and their semi-nomadic way of life (Wendorf and Schild 1980; 1984; 1995-96; and elsewhere in this volume) may have brought them into contact with peoples from both regions."

The dentition of three individuals showed African characteristics with one possibly leaning more toward West Eurasians.

"Despite an ostensible resemblance to Sub-Saharan Africans in 26 out of 30 observations, the worn, largely incomplete dentitions are only from three individuals who mayor may not be representative of the general Nabta Playa population. A proper biological affinity estimate based on dental morphological data requires a larger sample, using more traits from both the mandible and maxilla (Turner 1985; Irish 1993; 1997, 1998a, b, c, d for examples). Furthermore, in the case of E-97-17, the small teeth with fine roots, interpreted here as female indicators, could be suggestive of a North African linkage; North Africans often exhibit reduced, morphologically simple teeth (Irish 1993; 1996; 1998a, b, c, d). Thus, these initial results should be viewed with caution."

Other studies have described the Gebel Ramalah peoples as more heterogenous, holding North African and "sub-Saharan African" characteristics, with most holding mosaic features between both.

Also for the people who doubt when I say that C-Group are the direct ancestors of Somalis:

"The MMD data (Tables 6.17, 6.19, 6.21, and 6.23) reveal that Lower Nubians share a closer affinity to sub-Saharan groups on average than do Upper Nubians. The earlier Lower Nubian samples, especially C-Group, are mainly responsible. These data reveal that both C-Group samples share close affinities to all sub-Saharan groups (i.e., Ethiopia, Somalia, Tanzania, Chad, and Kenya). Figures 6.8-6.13 reveal that the C-Group samples may have a stronger relationship with the samples from the east (Somali, Ethiopia, and sub-Saharan East), over other areas of the subcontinent. Gebel Ramlah shares some similarities with sub-Saharan African groups but is still significantly different from the C-Group. These affinities suggest that both cultures have something of a relationship with sub-Saharan Africans, though with potentially different origins."

I forgot about it, but I already have lightly mentioned some of these earlier points.

The Somali With Saharan Haplogroup, Theory

New Somali sample from NW Africa https://www.yfull.com/tree/E-PF2438/ No relatives for 9200 years Responding to this highly interesting post by @Reformed J, I will have to post what I think about it: That Somali could have a direct Chado-Berber node ancestry. My assumption is movement...

www.somalispot.com

 

[The alchemist]

Interesting! On contamination, I'm convinced it's the case after coming across this tweet:
View attachment 354553

Spoiler: for alchy walchy only

You don't have permission to view the spoiler content. Log in or register now.

Spoiler

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[Step a side]

@The alchemist great work. Had to read it 3x just to try and visualise and get a good understanding of it all. The L2a1 Yfull graph made your theory even more compelling.

I haven’t been keeping up to date with these new studies lately. From what I could gather so far is that

1) The Takarkori (a 3 way IBM-Nilo Saharan-West African group) represents an afroasiatic speaking group (proto-Chadic?) while the heavy LNF group represents the Proto Berber group that came some time after to the Maghreb from the direction of Egypt?

2) Also where is the EEF ancestry that was known to have been present in Neolithic Maghreb in large quantities? It’s possible this type of ancestry hasn’t reached the SW Libyan corner yet at the time of the Takaroki but surely they should have shown up with the Tunisian and Moroccan Neolithic samples?


3) Could the WHG ancestry found in some of these samples be the group that brought R-V88 to Africa from Iberia?

 

[The alchemist]

So what component is missing or should be more prominent in the first Pharaohs?

I believe Cushitic ancestry is going to be prominent among rulers in the predynastic era of Hierakonpolis/Nekhen and pre/dynastic Abydos up to maybe a couple of first dynasties. What we call Ancient Egyptians was uniquely a mix of wealthy Cushitic elite rulers that were partly acculturated by the Naqadan, reigning over a majority Naqadan population (with a majority genetic Badarian descent), and this unique peripheral charge set off the dynastic period, the civilizational foundations for Ancient Egypt.

 

[The alchemist]

@The alchemist great work. Had to read it 3x just to try and visualise and get a good understanding of it all. The L2a1 Yfull graph made your theory even more compelling.

I haven’t been keeping up to date with these new studies lately. From what I could gather so far is that

1) The Takarkori (a 3 way IBM-Nilo Saharan-West African group) represents an afroasiatic speaking group (proto-Chadic?) while the heavy LNF group represents the Proto Berber group that came some time after to the Maghreb from the direction of Egypt?

2) Also where is the EEF ancestry that was known to have been present in Neolithic Maghreb in large quantities? It’s possible this type of ancestry hasn’t reached the SW Libyan corner yet at the time of the Takaroki but surely they should have shown up with the Tunisian and Moroccan Neolithic samples?


3) Could the WHG ancestry found in some of these samples be the group that brought R-V88 to Africa from Iberia?

That one seemed to come from West Asia, strangely. I think it came via the Levant and not the Western Mediterranean.

If you look at R-Y8451, that seems to be on the Eastern Mediterranean. Then you have a noteworthy presence of old Egyptian clades as well. It is clear this sample came via northeast Africa. Egypt experienced several Levant waves. That could be one of the early Bronze Age movements. The fact that this clade does not age beyond the Bronze Age makes it seem it had nothing to do with Chadic or Berber... Which is interesting. Perhaps we're looking at a rapid movement of Bronze Age people from the Fertile Crescent that went past Egypt directly into the Sahara.

With the Iberian question; that ancestry was farming-related and only first penetrated the northwestern Maghreb. The Takarkori had a different process relating to the central Sahara as its genetic mixing point. The pastoralists that entered that region of Morocco certainly mixed with Iberian ancestry.

I wouldn't define the LNF as the Berber. Merely the ones that came and mixed with them far north as the ones that came with Berber. They would hold Levant Neolithic ancestry that seems to be non-existent among the Takarkori.