GENETICS Old Kingdom Egyptian is Neolithic Moroccan?

[Xareen]

ENA Browser

ENA Browser

www.ebi.ac.uk

Egypt_Nuerat_Old_Kingdom:NUE001__BC_2680_Cov_87.67%,0.011382,0.129988,-0.043746,-0.122095,0.008925,-0.05271,-0.029141,-0.006,0.078128,-0.005832,0.008607,-0.017984,0.044152,0,0.00665,0.009546,-0.00326,-0.007348,-0.010559,0.023761,0.002496,-0.002844,0.00986,0.012532,-0.003832

Y-DNA: https://www.yfull.com/tree/E-Y222180/
mtDNA: I

I have a lot to say, but don't have the time to make a fleshed-out post. much more to this. and good things.

until then, have fun playing with it. our best proxy in 2-way run.

 

[Garaad Awal]

 

[NidarNidar]

 

[Garaad Awal]

View attachment 359570
View attachment 359571

What is the AEA Nilotic?

 

[NidarNidar]

What is the AEA Nilotic?

Got it off a guy on Reddit.

Sudan_AEA_Nilotic,-0.56272837,0.04715103,0.00844811,-0.01816994,-0.00767743,-0.01277314,-0.01311748,0.00252006,0.130011,-0.15324418,-0.02188116,0.01151451,-0.05030099,-0.00063816,0.02455798,-0.04415771,0.03729095,-0.00435367,0.03069317,-0.01649585,0.01409658,0.02152539,-0.00447418,-0.00153823,-0.00535147

 

[Garaad Awal]

Got it off a guy on Reddit.

Sudan_AEA_Nilotic,-0.56272837,0.04715103,0.00844811,-0.01816994,-0.00767743,-0.01277314,-0.01311748,0.00252006,0.130011,-0.15324418,-0.02188116,0.01151451,-0.05030099,-0.00063816,0.02455798,-0.04415771,0.03729095,-0.00435367,0.03069317,-0.01649585,0.01409658,0.02152539,-0.00447418,-0.00153823,-0.00535147

I guess it’s Dinka without their Ancient West African ancestry

 

[NidarNidar]

I guess it’s Dinka without their Ancient West African ancestry

Yeah looks like it.

 

[Xareen]

I guess it’s Dinka without their Ancient West African ancestry

Sourced by getting rid of South African ancestry in Mota using Genoplot's thingy thing

 

[Shimbiris]

View attachment 359570
View attachment 359571

Did you guys include Northwestern Yemenis in these models like Jawf, Ma'rib and Bayda?

 

[Garaad Awal]

Did you guys include Northwestern Yemenis in these models like Jawf, Ma'rib and Bayda?

Used the Early Islamic Arabs (lack the minor Cushitic in Yemenis) for a Cushitic (Pastoral N & IA), Arab & AE model.Some individuals prefer the Arabs while others prefer the Old Kingdom sample, same goes for the Northern Horners.

Seems like it would be better to use qpadm as both are very similar to each other as heavily Natufian-like pops.

With an ancient basic breakdown run most Horners generally have an even split between AE & Natufians.

 

[Shimbiris]

Used the Early Islamic Arabs (lack the minor Cushitic in Yemenis) for a Cushitic (Pastoral N & IA), Arab & AE model.Some individuals prefer the Arabs while others prefer the Old Kingdom sample, same goes for the Northern Horners.

Seems like it would be better to use qpadm as both are very similar to each other as heavily Natufian-like pops.

With an ancient basic breakdown run most Horners generally have an even split between AE & Natufians.

I don't think those Yemenis really have any actual Cushitic. Especially from that area of Yemen to the north. In straight forward models (just using Natufian, Mota etc) they don't really show even a hint of Mota. So idk, the "Cushitic" doesn't seem legit to me and even if it is, it's clearly not strong enough to show elements like Mota so the affinity is seemingly more on our side than theirs.

And qpAdm sadly probably wouldn't help too much. As you say, these groups are awfully similar with lots of shared ancient which would further complicate how to select the right outgroups. But good models. I'll noodle when I get the chance and report back sometime.

 

[Garaad Awal]

I don't think those Yemenis really have any actual Cushitic. Especially from that area of Yemen to the north. In straight forward models (just using Natufian, Mota etc) they don't really show even a hint of Mota. So idk, the "Cushitic" doesn't seem legit to me

They have minor Cushitic in qpadm. Even the Yemenite Jews have it as well. But this is a topic for another thread

 

[Garaad Awal]

Ancient Nubians & modern copts

 

[Xareen]

Ancient Nubians & modern copts

View attachment 359594
View attachment 359595

They only scored 20% Cushitic on qpAdm. Think G25 elevates Cushitic ancestry as it does ANF

 

[The alchemist]

The sample is northern Old Kingdom Egyptian with Levantine influence. It has about ~10% Cushitic ancestry.

This is a mixed individual. As we know, closely after the unification of Egypt, a demographically dense agrarian population of Levantine origin living in Lower Egypt mixed with the people that dominated them from Upper Egypt, expanding the culture south-north, with rapid diffusion. This person's half-ancestry is non-ancient Egyptian.

The Cushitic ancestry was mostly concentrated in the south, with a rapid decline because of how it was mostly maximized in the elites that brought the Egyptian political dynastic paradigm. They, too, would also mix and water down their Cushitic ancestry rapidly after the Early Dynastic Period. However, the fact that it is still at 10% in such a northern region, among a people that are this highly mixed with foreign influence, amidst non-elites, tells me how enduring it was.

 

[The alchemist]

Yeah looks like it.

It is Mota minus South African HG-related ancestry and Eurasian.

 

[The alchemist]

They only scored 20% Cushitic on qpAdm. Think G25 elevates Cushitic ancestry as it does ANF

No offence, sxb, But that is nonsense. The results undercuts Cushitic ancestry.

I know how to roughly control for this. It is, Nilo-Saharan DNA has exessive enriched Shum-Laka type signal.

I figured that the Iron Age Pastoral sample average had ~40% Dinka-like DNA on top of a Somali-like profile. It had 8.2% West-central African hunter-gatherer ancestry, something I ascertained through a model I devised.

Then, by the assumption that Nilo-Saharan ancestry from Wadi Howar would essentially have the same signal, that could reflect a proxy for a relative measure. So I needed to test this. 8.2% represents 40% Dinka-like ancestry. Right? So I went to check how much Shum Laka appeared for the Danagla sample. It gave me, 5.2%.

What is 5.2 of 8.2? It is 63.4%. What is 63.4% of 40? It is 25.

Thus we should expect around 25% Nilo-Saharan to be the result for the Danagla sample.

Well, it checks. Lets do the same for Mahas.

skipping the stuff, it is 21.4%.

Yet again, it checks.

The third one, Halfawi.

4.2%.

It should be at 20%.

Yet it gets 16%....

Why is this the case? I suspect it is because it got minor West African admixture or because the NS has a HG skew, probably sourcing the NS from Saharans from further West.


By the way, the AEA Somalis have 0% of that signal. That is why this is a near-perfect benchmark to delineate NS ancestry from the Cushitic AEA link.

We're supposedly 60% AEA but have zero of the HG signal.

Now, to the conversation, the Christian Nubians were less NS than modern Nubians.

They on average score less than modern Nubians, and they have less than 20% on average:

The average from R cemetery.

This is 14.6% NS.

Checks again.

Then the S Cemetery:

11.68% NS.

Initially, it gave a high number, 18%. And this is a discrepancy. Then I wondered again, similar to the Halfwai, maybe it prefers something different with a stronger shift. I picked the samples from a Nilotic girl who shared her results, and she fit the bill:

I say this to say, the tool the guy used to infer that NS should be more enriched and Cushitic reduced does not hold water. I know this tool fairly well and one can figure out if something is an overfit or disproportionate skew.

Nubians are actually substantially Cushitic. The Christian period averages are lower than the modern averages we have. Most of the time, I can replicate results from qpAdm if it is sound. Many times it simply is not. You will not get the correct results if one does not model right, no matter if you use qpAdm or G25.

 

[Xareen]

The sample is northern Old Kingdom Egyptian with Levantine influence. It has about ~10% Cushitic ancestry.

View attachment 359560

This is a mixed individual. As we know, closely after the unification of Egypt, a demographically dense agrarian population of Levantine origin living in Lower Egypt mixed with the people that dominated them from Upper Egypt, expanding the culture south-north, with rapid diffusion. This person's half-ancestry is non-ancient Egyptian.

The Cushitic ancestry was mostly concentrated in the south, with a rapid decline because of how it was mostly maximized in the elites that brought the Egyptian political dynastic paradigm. They, too, would also mix and water down their Cushitic ancestry rapidly after the Early Dynastic Period. However, the fact that it is still at 10% in such a northern region, among a people that are this highly mixed with foreign influence, amidst non-elites, tells me how enduring it was.

I'm starting to come around to this but how do we know it's Cushitic and not Dinka + Eurasian, especially with NS loanwords in Egyptian for important subsistence-related terminology (cattlepen, iirc)? Does Somali work better than, say, Agaw or Amhara? Our best proxies on qpAdm include Jordan_EBA only when paired with LN_Moroccan too, and that profile (Skhirat-esque) is essentially what this Egyptian is with additional Iranian (20% on qpAdm.

I think he's foreign too, but what could that mean for contemporary Upper Egyptian genomes? A cool 20% in Lower Egypt, 30% in Upper Egypt, 60% after first cataract (pre-Noba-admixed Kulubnarti - contemporaries of Meroitic state - were probably about 40% Nile Cushitic), and almost 100% nearing the 4th (Kadruka). A believable cline if one were to take a look at the osteology.

 

[Xareen]

No offence, sxb, But that is nonsense. The results undercuts Cushitic ancestry.

Absolutely none taken bro. Glad you responded. I also realise how I erred, being overexcited by my ability to finally get the software up and running.

For Cushitic proxy, I used Elmenteitan, whose Mota ancestry probably does the same thing the HG signal does, obfuscating Cushitic ancestry. Fairs. 20% Elmenteitan could mean up to 30%-40%. I'll run some more stuff later.

I know how to roughly control for this. It is, Nilo-Saharan DNA has exessive enriched Shum-Laka type signal.

I figured that the Iron Age Pastoral sample average had ~40% Dinka-like DNA on top of a Somali-like profile. It had 8.2% West-central African hunter-gatherer ancestry, something I ascertained through a model I devised.

Then, by the assumption that Nilo-Saharan ancestry from Wadi Howar would essentially have the same signal, that could reflect a proxy for a relative measure. So I needed to test this. 8.2% represents 40% Dinka-like ancestry. Right? So I went to check how much Shum Laka appeared for the Danagla sample. It gave me, 5.2%.
View attachment 359628

What is 5.2 of 8.2? It is 63.4%. What is 63.4% of 40? It is 25.

Thus we should expect around 25% Nilo-Saharan to be the result for the Danagla sample.

View attachment 359631

My Dongolawi friend is closer to 50%. Interesting nonetheless.

Well, it checks. Lets do the same for Mahas.

View attachment 359632

skipping the stuff, it is 21.4%.

View attachment 359633

Yet again, it checks.

The third one, Halfawi.

4.2%.

It should be at 20%.

Yet it gets 16%....

Why is this the case? I suspect it is because it got minor West African admixture or because the NS has a HG skew, probably sourcing the NS from Saharans from further West.


By the way, the AEA Somalis have 0% of that signal. That is why this is a near-perfect benchmark to delineate NS ancestry from the Cushitic AEA link.
View attachment 359634

We're supposedly 60% AEA but have zero of the HG signal.

Now, to the conversation, the Christian Nubians were less NS than modern Nubians.

They on average score less than modern Nubians, and they have less than 20% on average:

The average from R cemetery.

View attachment 359635

This is 14.6% NS.
View attachment 359636

Checks again.

Then the S Cemetery:

View attachment 359637

11.68% NS.

Initially, it gave a high number, 18%. And this is a discrepancy. Then I wondered again, similar to the Halfwai, maybe it prefers something different with a stronger shift. I picked the samples from a Nilotic girl who shared her results, and she fit the bill:
View attachment 359638

I say this to say, the tool the guy used to infer that NS should be more enriched and Cushitic reduced does not hold water. I know this tool fairly well and one can figure out if something is an overfit or disproportionate skew.

Nubians are actually substantially Cushitic. The Christian period averages are lower than the modern averages we have. Most of the time, I can replicate results from qpAdm if it is sound. Many times it simply is not. You will not get the correct results if one does not model right, no matter if you use qpAdm or G25.

Thanks. I actually done the exact same runs a while ago but figured it was a PCA issue. I'll use the Roman Serbian dude as a Cushitic proxy instead and I'll see what qp gives me. That's if I figure out how.

 

[Midas]

Eygptian migration history is so weird. You've got the naqda culture 1 in Upper eygpt then by the naqada 2 phase they seem to have migrated upto lower eygpt. Then they were somehow back in Upper eygpt for phase 3.

I wonder when exactly upper eygpt became more culutrally simikar to loeer eygpt compared to lower nubia. Since it seems already by the old kingdom nubians were considered a culturally distinct pouplation from (upper + lower eygpt)