GENETICS Old Kingdom Egyptian aDNA

[Xareen]

Whole genome data from a town near Giza dated to when the pyramids were being built.

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

Seems like it would make a decent proxy?

What really caught my eye was the 64 f***ing samples from Ghaba (South Upper Nubia) that we don't get much of any comment on. They all had some super exotic mtDNA which isnt uncommon for Nubia but I didn't expect even the Neolithic samples to be entirely non-L.

@Shimbiris @The alchemist

 

[New World]

What does this mean?

 

[Abdirazaq]

Hopefully this should be the debate ender as to “who the ancient Egyptians were”.

This is gonna be a long read.

 

[Shimbiris]

Wow, looks like this individual is about ~10% @Nilotic-like and that's without counting the ANA ancestry they probably have hidden within their MENA ADMIXTURE component:

At K=12 (Fig 4.3, S4.8-S4.10), the ADMIXTURE component analysis shows that NUE001 shares the same main ancestry as present-day populations from the Arabian Peninsula as well as BedouinB, which ultimately derived from Levantine Epipaleolithic Natufians (Fig 4.3, in yellow, Lazaridis et al., 2016), consistent with the PCA. 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 (Fig 4.3, in red).

You can see it clearly in their ADMIXTURE run:

They show Nilotic ancestry whereas the other ancient MENAs like the Levantines do not. The rest of their ancestry, to me, possibly seems mostly like Anatolian-Neolithic/Natufians and is probably pretty much just an ANA and Anatolian-HG mix like Natufians and would cluster I reckon somewhere around here:

Hopefully this should be the debate ender as to “who the ancient Egyptians were”.

This is gonna be a long read.

What this does, for now, is that the Ancient Egyptians from the early periods, if this sample is representative, were definitely part SSA. Part Nilotic and part "ANA". Yes, I consider ANA an SSA cluster as it clearly clusters as such and just has a Eurasian-pull because it's probably closely related to the Proto-Eurasians and may very well be descended from the early hold-overs who kept Y-DNA E in Africa.

In my opinion, this simulated ANA sample is showing the same sort of affinity the 40-50kya Ust-Ishim sample is in having a strange "SSA" pull. They're both representing very ancient affinities that are from a time when SSAs and Eurasians weren't as differentiated and developed in their drift as now:

E may have started out as early "Eurasian" but it clearly re-entered or stayed in Africa very early and now all of its upstream brothers are SSA, one being the clade of Mota, and the other being the clade of West-Africans while M35 seems to originate with ANAs, themselves an "SSA" group.

And from looking at modern Egyptians, Natufians, Horners and ancient Maghrebis like the IBM, it's clear Early AEs' Y-DNA will be mostly E-M35 which most likely comes from the IBM's ANA ancestry whereas their Anatolian-HG-related ancestry is represented by their Eurasian mtDNA meaning AE Y-DNA is overwhelmingly SSA as well but they will probably have mostly Eurasian mtDNA and of course a shit ton of Anatolian-HG ancestry like Neolithic Levantines and Natufians do.

I hope I can get this sample from the academic, get David to G25 it and see how much Iran-Chalcolithic it has. I suspect very little compared to the later Iron-Age Egyptians. This is probably a pre-Semitic admixture individual. If so, this will hopefully be a brilliant proxy for Horners' Natufian/IBM ancestry in G25. And the author's findings seem to track with that:

Nuerat sequenced to 0.22X coverage, dated to 2,868-2,492 cal BCE (95.4% probability) - consistent with the 3rd-4th Dynasties of the Old Kingdom. Allele frequency-based analyses (PCA, ADMIXTURE, f-statistics, qpAdm) show a strong genetic affinity of this sample to Levantine Natufians. Compared with genomes dated from the end of the Dynastic period (Third Intermediate Period) and present-day Egyptians, 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 presentday 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).

@Xareen you are a BOQOR for this finding!

@Idilinaa

 

[Aseer]

Wow, looks like this individual is about ~10% @Nilotic-like and that's without counting the ANA ancestry they probably have hidden within their MENA ADMIXTURE component:



You can see it clearly in their ADMIXTURE run:

They show Nilotic ancestry whereas the other ancient MENAs like the Levantines do not. The rest of their ancestry, to me, possibly seems mostly like Anatolian-Neolithic/Natufians and is probably pretty much just an ANA and Anatolian-HG mix like Natufians and would cluster I reckon somewhere around here:

What this does, for now, is that the Ancient Egyptians from the early periods, if this sample is representative, were definitely part SSA. Part Nilotic and part "ANA". Yes, I consider ANA an SSA cluster as it clearly clusters as such and just has a Eurasian-pull because it's probably closely related to the Proto-Eurasians and may very well be descended from the early hold-overs who kept Y-DNA E in Africa.

In my opinion, this simulated ANA sample is showing the same sort of affinity the 40-50kya Ust-Ishim sample is in having a strange "SSA" pull. They're both representing very ancient affinities that are from a time when SSAs and Eurasians weren't as differentiated and developed in their drift as now:

E may have started out as early "Eurasian" but it clearly re-entered or stayed in Africa very early and now all of its upstream brothers are SSA, one being the clade of Mota, and the other being the clade of West-Africans while M35 seems to originate with ANAs, themselves an "SSA" group.

And from looking at modern Egyptians, Natufians, Horners and ancient Maghrebis like the IBM, it's clear Early AEs' Y-DNA will be mostly E-M35 which most likely comes from the IBM's ANA ancestry whereas their Anatolian-HG-related ancestry is represented by their Eurasian mtDNA meaning AE Y-DNA is overwhelmingly SSA as well but they will probably have mostly Eurasian mtDNA and of course a shit ton of Anatolian-HG ancestry like Neolithic Levantines and Natufians do.

I hope I can get this sample from the academic, get David to G25 it and see how much Iran-Chalcolithic it has. I suspect very little compared to the later Iron-Age Egyptians. This is probably a pre-Semitic admixture individual. If so, this will hopefully be a brilliant proxy for Horners' Natufian/IBM ancestry in G25. And the author's findings seem to track with that:



@Xareen you are a BOQOR for this finding!

@Idilinaa

Does this better connect somalis to anciemt egypt?

 

[Abdirazaq]

Wow, looks like this individual is about ~10% @Nilotic-like and that's without counting the ANA ancestry they probably have hidden within their MENA ADMIXTURE component:



You can see it clearly in their ADMIXTURE run:

They show Nilotic ancestry whereas the other ancient MENAs like the Levantines do not. The rest of their ancestry, to me, possibly seems mostly like Anatolian-Neolithic/Natufians and is probably pretty much just an ANA and Anatolian-HG mix like Natufians and would cluster I reckon somewhere around here:

What this does, for now, is that the Ancient Egyptians from the early periods, if this sample is representative, were definitely part SSA. Part Nilotic and part "ANA". Yes, I consider ANA an SSA cluster as it clearly clusters as such and just has a Eurasian-pull because it's probably closely related to the Proto-Eurasians and may very well be descended from the early hold-overs who kept Y-DNA E in Africa.

In my opinion, this simulated ANA sample is showing the same sort of affinity the 40-50kya Ust-Ishim sample is in having a strange "SSA" pull. They're both representing very ancient affinities that are from a time when SSAs and Eurasians weren't as differentiated and developed in their drift as now:

E may have started out as early "Eurasian" but it clearly re-entered or stayed in Africa very early and now all of its upstream brothers are SSA, one being the clade of Mota, and the other being the clade of West-Africans while M35 seems to originate with ANAs, themselves an "SSA" group.

And from looking at modern Egyptians, Natufians, Horners and ancient Maghrebis like the IBM, it's clear Early AEs' Y-DNA will be mostly E-M35 which most likely comes from the IBM's ANA ancestry whereas their Anatolian-HG-related ancestry is represented by their Eurasian mtDNA meaning AE Y-DNA is overwhelmingly SSA as well but they will probably have mostly Eurasian mtDNA and of course a shit ton of Anatolian-HG ancestry like Neolithic Levantines and Natufians do.

I hope I can get this sample from the academic, get David to G25 it and see how much Iran-Chalcolithic it has. I suspect very little compared to the later Iron-Age Egyptians. This is probably a pre-Semitic admixture individual. If so, this will hopefully be a brilliant proxy for Horners' Natufian/IBM ancestry in G25. And the author's findings seem to track with that:



@Xareen you are a BOQOR for this finding!

@Idilinaa

Walaalo, its clear that they were extremely closely related to West Asian populations at their respective times, the slight pull towards SSA populations isn't surprising considering the geographic proximity to SSA populations, overall they're basically Natufian.

If these people existed today they would be considered typical arabs, brown people etc. Looking at the results you could make the argument that these ancient samples have even less SSA ancestry than a considerable amount of modern North Africans.

Its a shame there's not much on the Nubian samples they picked up.

 

[Shimbiris]

Walaalo, its clear that they were extremely closely related to West Asian populations at their respective times, the slight pull towards SSA populations isn't surprising considering the geographic proximity to SSA populations, overall they're basically Natufian.

If these people exesited today they would be considered typical arabs, brown people etc.

Once you count ANA these guys are at least about 20% SSA. That's not a joke and is about 1/4th of their ancestry. Not to mention like 10% of that 1/4th would be Dinka-like people.

So, I wouldn't undersell how much this shifts the pendulum from what it was a few years ago when those Iron-Age Egyptian genomes hit. Back then people were claiming Dinka-like ancestry was new to Egypt and only came with Copts who might have mixed a bit with Nubians but that seems not true and the migration of West-Asian Semites like the Hyksos (Amorites) not only brought Iran-Chalcolithic but pretty much diluted out Dinka-like ancestry.

The Hyksos

But you are correct that overall, today, these would be brown MENA people. Absolutely. But it can't be undersold that their dominant Y-DNA is of ultimately African origins and they themselves appear about 1/4th African.

Does this better connect somalis to anciemt egypt?

People like this sample would be very close to our pre-historic and possibly also early historic Egyptian ancestors. I hope I can get the sample off the academic and start running it through models.

 

[Abdirazaq]

Once you count ANA these guys are at least about 20% SSA. That's not a joke and is about 1/4th of their ancestry. Not to mention like 10% of that 1/4th would be Dinka-like people.

So, I wouldn't undersell how much this shifts the pendulum from what it was a few years ago when those Iron-Age Egyptian genomes hit. Back then people were claiming Dinka-like ancestry was new to Egypt and only came with Copts who might have mixed a bit with Nubians but that seems not true and the migration of West-Asian Semites like the Hyksos (Amorites) not only brought Iran-Chalcolithic but pretty much diluted out Dinka-like ancestry.

The Hyksos

But you are correct that overall, today, these would be brown MENA people. Absolutely. But it can't be undersold that their dominant Y-DNA is of ultimately African origins and they themselves appear about 1/4th African.



People like this sample would be very close to our pre-historic and possibly also early historic Egyptian ancestors. I hope I can get the sample off the academic and start running it through models.

Even if they were 20% which is about 1/5th, that would put them equal to a lot of modern Egyptians anyway as well as a lot populations considered arab without much question, unlike modern sudani populations who are still considered black, even though they're basically arab culturally and linguisticsly for the most part.

I'm more disappointed they didn't dig deeper into the Nubian samples.

 

[Shimbiris]

Even if they were 20% which is about 1/5th, that would put them equal to a lot of modern Egyptians anyway as well as a lot populations considered arab without much question, unlike modern sudani populations who are still considered black, even though they're basically arab culturally and linguisticsly for the most part.

It might be as high as 25%. I'd need to run them through G25 and see how much ANA they have. If it's 15-20% like Natufians on-top of the Dinka-like then yeah, quite a lot. But you're right. It's funny to think what essentially happened is that Egypt was 1/4-1/5th SSA then became very diluted then became the same again thanks to the slave-trade.

I'm not remotely arguing these people were madow, saaxiib. Idk why you're fixating on that like I'm some Hotep. I'm just pointing out that they clearly had SSA ancestry (even Y-DNA wise) and that racist types who were celebrating a few years ago like SSA ancestry had ABSOLUTELY NOTHING to do with Ancient Egypt were clearly dead wrong.

And ditto on the Nubians. Sad stuff...

 

[Abdirazaq]

It might be as high as 25%. I'd need to run them through G25 and see how much ANA they have. If it's 15-20% like Natufians on-top of the Dinka-like then yeah, quite a lot. But you're right. It's funny to think what essentially happened is that Egypt was 1/4-1/5th SSA then became very diluted then became the same again thanks to the slave-trade.

I'm not remotely arguing these people were madow, saaxiib. Idk why you're fixating on that like I'm some Hotep. I'm just pointing out that they clearly had SSA ancestry (even Y-DNA wise) and that racist types who were celebrating a few years ago like SSA ancestry had ABSOLUTELY NOTHING to do with Ancient Egypt were clearly dead wrong.

And ditto on the Nubians. Sad stuff...

No, I don't think you're Hoteping but instead correcting the narrative set post-2017 (when that study came out) when people went as far as to claim that Europeans were closer related to ancient Egyptians than modern Egyptians, which was wild, I understand were you're coming from and you're giving a more nuanced take.

I was just thinking about the bigger picture and how the layman should interpret these results. I feel like guys like you (no offence) get lost in all the higher-end conversations on these types of topics that they forget to give a more coherent/easier-to-understand take about issues like this that explains what the truth about the situation is.

I apologize if you took offence.

 

[Garaad Awal]

E-M35 supremacy

 

[Shimbiris]

No, I don't think you're Hoteping but instead correcting the narrative set post-2017 (when that study came out) when people went as far as to claim that Europeans were closer related to ancient Egyptians than modern Egyptians, which was wild, I understand were you're coming from and you're giving a more nuanced take.

I was just thinking about the bigger picture and how the layman should interpret these results. I feel like guys like you (no offence) get lost in all the higher-end conversations on these types of topics that they forget to give a more coherent/easier-to-understand take about issues like this that explains what the truth about the situation is.

I apologize if you took offence.

Yeah, I think you're correct that we nerdy types kinda forget to simplify things for the average person and get lost in the details. Tbh, part of why I fell for this site and having anthro discussions here is that the formality somewhat dies down here and I sometimes find myself speaking about these concepts in simple terms for complete laymen who aren't as familiar. It's refreshing and I think I'm gonna experiment with having a "tl;dr for total laymen" section at the end of Anthromadness posts.

 

[Step a side]

Few months ago I saw these Egyptian DNA samples being discussed on Reddit. 1 from the Old Kingdom, 1 from between the Old Kingdom and Middle Kingdom, 1 from the Middle Kingdom.

@Shimbiris I believe there was a pre-dynastic J1 sample in Egypt if I am not mistaken as well as Middle Kingdom priest Nakht-Ankh with IranN/CHG. This component must have arrived with Levantine migrants starting from the Old Kingdom onwards and increasing by the Middle Kingdom.

 

[Shimbiris]

Made a post and credited you, huuno:

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 ...

anthromadness.blogspot.com

 

[Apostle]

Wow, looks like this individual is about ~10% @Nilotic-like and that's without counting the ANA ancestry they probably have hidden within their MENA ADMIXTURE component:



You can see it clearly in their ADMIXTURE run:

They show Nilotic ancestry whereas the other ancient MENAs like the Levantines do not. The rest of their ancestry, to me, possibly seems mostly like Anatolian-Neolithic/Natufians and is probably pretty much just an ANA and Anatolian-HG mix like Natufians and would cluster I reckon somewhere around here:

What this does, for now, is that the Ancient Egyptians from the early periods, if this sample is representative, were definitely part SSA. Part Nilotic and part "ANA". Yes, I consider ANA an SSA cluster as it clearly clusters as such and just has a Eurasian-pull because it's probably closely related to the Proto-Eurasians and may very well be descended from the early hold-overs who kept Y-DNA E in Africa.

In my opinion, this simulated ANA sample is showing the same sort of affinity the 40-50kya Ust-Ishim sample is in having a strange "SSA" pull. They're both representing very ancient affinities that are from a time when SSAs and Eurasians weren't as differentiated and developed in their drift as now:

E may have started out as early "Eurasian" but it clearly re-entered or stayed in Africa very early and now all of its upstream brothers are SSA, one being the clade of Mota, and the other being the clade of West-Africans while M35 seems to originate with ANAs, themselves an "SSA" group.

And from looking at modern Egyptians, Natufians, Horners and ancient Maghrebis like the IBM, it's clear Early AEs' Y-DNA will be mostly E-M35 which most likely comes from the IBM's ANA ancestry whereas their Anatolian-HG-related ancestry is represented by their Eurasian mtDNA meaning AE Y-DNA is overwhelmingly SSA as well but they will probably have mostly Eurasian mtDNA and of course a shit ton of Anatolian-HG ancestry like Neolithic Levantines and Natufians do.

I hope I can get this sample from the academic, get David to G25 it and see how much Iran-Chalcolithic it has. I suspect very little compared to the later Iron-Age Egyptians. This is probably a pre-Semitic admixture individual. If so, this will hopefully be a brilliant proxy for Horners' Natufian/IBM ancestry in G25. And the author's findings seem to track with that:



@Xareen you are a BOQOR for this finding!

@Idilinaa

What do you make of this:

However, qpAdm ancestry modelling confirmed that NUE001 could not be modelled as a mixture of Levant Natufian and East Africa Late Stone Age ancestries, same for the two Third Intermediate Period Egyptians (JK2911 and JK2134) (Fig 4.4C). The low ancestry component estimate with ADMIXTURE could result from background noise (Fig 4.3), making it unlikely that NUE001 carried East African-related ancestry.

 

[Shimbiris]

What do you make of this:

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.

 

[Zak12]

@Shimbiris Did the ancient Egyptians or at least any early Egyptian population shared Y-DNA with Somalis and other Cushitic populations?

 

[NidarNidar]

Garreh carry a non-basal version(which means a lineage is not at the root of its branch but has additional mutations that place it further down the evolutionary tree) of E-V12 and E-V32 is a subclade of E-V12(meaning it is a branch that descends from E-V12. E-V32 has additional genetic mutations that differentiate it from its parent clade, E-V12. In other words, E-V32 is a more specific and recent subgroup within the E-V12 lineage.), 74% of Egyptian males still carry E-V12 in Upper Egypt.

Data Used:​

The studies included are:

1. Fadhloui-Zid et al. (2013)
2. Bekada et al. (2013)
3. Luis et al. (2004)
4. Kujanová et al. (2009) - El-Hayez Oasis Egyptians
5. Pagani et al. (2015)
6. Arredi et al. (2004) - Northern and Southern Egyptians

---

Average Breakdown of Egyptians per Haplogroup:​

Haplogroup	Average Frequency
A/B	1.05%
E1b1a	2.48%
E1b1b1 (M35)	3.35%
E1b1b1a (M78)	25.63%
E1b1b1b1 (M81)	9.14%
E1b1b1b2 (M123, M34)	4.99%
F	0.15%
K	0.04%
G	3.34%
I	1.82%
J1	20.74%
J2	6.92%
R1a	2.24%
R1b	6.31%
Other	4.73%

Key Observations:​

1. E1b1b1a (M78) is the most dominant haplogroup among Egyptians, with an average frequency of 25.63%. This haplogroup is strongly associated with North African populations.
2. J1 is the second most common haplogroup, with an average frequency of 20.74%, reflecting significant Middle Eastern influence.
3. E1b1b1b1 (M81) and R1b also show notable frequencies, likely due to historical migrations and interactions with Berber and European populations.
4. Other haplogroups (e.g., A/B, E1b1a, G, I, R1a) are present at lower frequencies, indicating diverse genetic influences over time.

This breakdown provides a general overview of the genetic makeup of Egyptians based on Y-chromosome haplogroups.

 

[Xareen]

Not sure if it's worth making a separate thread but the BAM files for Takakori ANA samples have been released on ENA. Signs the study shouldn't be too far behind (I'd hold my breath even still cos Kadruka lagged by a year and a half).

ENA Browser

ENA Browser

www.ebi.ac.uk

@Shimbiris not sure who else is any good at admixtools but do let them know

 

[Cognitive]

Someone call the Alchemist too.
@Shimbiris, what are your thoughts on the recently "published" genome from Takarkori?
Could it potentially account for the 10% in Nuerat?

x.com

x.com

Human genomes from the Green Sahara reveal ancestral North African lineage