4000-year-old sample from the Middle Nile a potential source of early eastern Africa pastoralists

I heard that those early Cushitic nomads were even more Eurasian shifted than modern Horn African populations.
Its hard to say because they don't specify which samples it was identical too, either way, the early samples had a ton of Mota ancestry which i don't expect to find in Sudan, so I doubt its identical like the authors said.
 
the Eurasian component is undoubtedly Levantine in origin.
Not true, 14,000 year old remains in Sudan (Al Khiday) cluster with lower Nubians who cluster with ancient upper Egyptians and Afro-Asiatic Horners, the so-called "Eurasian" or "Levantine" affinity is already present in NE Africa during the Mesolithic, these people undoubtedly had little to no Natufian ancestry given their age.

Think about the phylogeny of the most important lineages on our Cushitic component (E-M215 and all of its subclades and its ancestors), its phylogeny is nearly entirely NE African, not Levantine.
 
Its hard to say because they don't specify which samples it was identical too, either way, the early samples had a ton of Mota ancestry which i don't expect to find in Sudan, so I doubt its identical like the authors said.
I think they're talking about it from the lens of the Kerman sample being the "source". As in, remove the Mota, and they're indistinguishable.
 
Not true, 14,000 year old remains in Sudan (Al Khiday) cluster with lower Nubians who cluster with ancient upper Egyptians and Afro-Asiatic Horners, the so-called "Eurasian" or "Levantine" affinity is already present in NE Africa during the Mesolithic, these people undoubtedly had little to no Natufian ancestry given their age.
You need to put me on, broski. Where are these anthropometric studies on Ancient Sudan found?
Think about the phylogeny of the most important lineages on our Cushitic component (E-M215 and all of its subclades and its ancestors), its phylogeny is nearly entirely NE African, not Levantine.
The same can't be said for the South Cushites, though, can it? It'd make sense if we were Levantine in lineage (E-M293 and whatnot) until like 4000-5000 years ago, wouldn't it?

Edit: I mean to say E-Z827 subclades and their presence in Natufians.
 
You need to put me on, broski. Where are these anthropometric studies on Ancient Sudan found?
1657195094825.png

JSA is Jebel Sahaba, this is a very Sub-Saharan like remain which doesn't cluster very closely with Lower Nubians and ancient Egyptians.

AKH is Al Khiday, its like 13-14,000 years old, so it couldn't have had Neolithic Levantine ancestry, and theres nothing indicating Natufians settling in Africa, esp at this time, so this is a native people that shows affinities to Nubians such as Kerma, A group, Christian Period Nubians etc... all of these groups have a lot of Natufian-like ancestry but its presence in NE Africa predates the existence of the Natufians IMO.
 
The same can't be said for the South Cushites, though, can it? It'd make sense if we were Levantine in lineage (E-M293 and whatnot) until like 4000-5000 years ago, wouldn't it?

Edit: I mean to say E-Z827 subclades and their presence in Natufians.
I don't get what you mean, the E lineages found in Natufians were either African in origin or their parent clade was African, North East African to be specific. The phylogeny of much of those E lineages are completely NE African.
 
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JSA is Jebel Sahaba, this is a very Sub-Saharan like remain which doesn't cluster very closely with Lower Nubians and ancient Egyptians.
Is there a Nilotic reference point to compare with these pre and Meso-Neolithic samples? How are you sure it's SSA shifted and not something else?
AKH is Al Khiday, its like 13-14,000 years old, so it couldn't have had Neolithic Levantine ancestry, and theres nothing indicating Natufians settling in Africa, esp at this time, so this is a native people that shows affinities to Nubians such as Kerma, A group, Christian Period Nubians etc... all of these groups have a lot of Natufian-like ancestry but its presence in NE Africa predates the existence of the Natufians IMO.
And the Al-Khiday sample is likely ancestral to us, making us not Levantine, but North African in origin. I see. I wonder, though, why they show such genetic affinities with proceeding Levantine populations and why we aren't better modelled by, say, Dinka + Egyptian than Dinka + Levantine.
 
Is there a Nilotic reference point to compare with these pre and Meso-Neolithic samples? How are you sure it's SSA shifted and not something else?
We know its SSA-like because Jebel Sahaba was most similar to SSA groups and shows little affinities to Afro-Asiatic speakers in North Africa and the HOA.
Idk if there was a Nilotic ref, they used some SE Africans who would have tons of Nilotic so yh, close enough imo
Read this

And the Al-Khiday sample is likely ancestral to us, making us not Levantine, but North African in origin.
Well maybe not this exact sample but something very similar to it yes.
The way i see it, there would have been a metapopulation in Paleolithic/Mesolithic North Africa, Arabia and the Levant with all of these regions being rich Basal Eurasian-like + Common West Eurasian-like + MSA SSA-like.
Those 3 ancestries account for pretty much all of the genomes of Natufians and Taforalt/IBM, just in different proportions, Al Khiday and some of Egyptian/Sudanese remains would have been a part of this metapopulation IMO.

You can kinda see this in the fact that Natufian/Taf work as sources of ancesty for North Africans and East Africans, despite the fact there is no strong evidence for a movement of Iberomaurisians or Natufians into NE Africa, but something related to both of those groups clearly existed in NE Africa given how much Natufian/Taf we all score, and the existence of 14,000 year old Sudanis showing strong affinities with Natufian/Taf rich populations. So we don't have much literal Natufian ancestry, just something closely related to it that was in Egypt/North Sudan. I doubt Natufians are ancestral to anyone outside of the Neolithic Levantines and anyone descended from them, this includes Arabians, Lazaradis has a tree where he shows Arabian HG(this is believed to be the source of the direct Natufian-like input) as being descended from whatever Natufians are descended from, even though they can be modelled as Natufian, so not literally Natufians.

I wonder, though, why they show such genetic affinities with proceeding Levantine populations
See above. We also have some Neolithic Levantine and maybe Chalcolithic Levantine, but the Natufian we score on top of the other stuff I just mentioned is largely Egyptian in origin, just closely related to Natufians, if you want me to say why/how i think this happened feel free to ask.
why we aren't better modelled by, say, Dinka + Egyptian than Dinka + Levantine.
Well modern Egyptians have never been used as a source of ancestry for Horners in any study AFAIK but they likely have too much Iranian and Anatolian Farmer ancestry too work for us, the Egyptians I'm talking about are 10,000+ years old btw, not 200 lol, so we'd need early Egyptian DNA. The late period Egyptian samples worked as a source of ancestry for Horners, better than Arabians, they didn't compare with a Levantine source, but Egyptians CAN work as a source for us.
 
were the proto somalis living kerma?
I wouldn't call them proto-Somalis, much more like distant cousins. Still, we'll have to wait for the full study to be published.

We know its SSA-like because Jebel Sahaba was most similar to SSA groups and shows little affinities to Afro-Asiatic speakers in North Africa and the HOA.
Idk if there was a Nilotic ref, they used some SE Africans who would have tons of Nilotic so yh, close enough imo
Read this
Thanks for clearing this up, mate. I was looking for something exactly like the article you linked.
Well maybe not this exact sample but something very similar to it yes.
The way i see it, there would have been a metapopulation in Paleolithic/Mesolithic North Africa, Arabia and the Levant with all of these regions being rich Basal Eurasian-like + Common West Eurasian-like + MSA SSA-like.
Those 3 ancestries account for pretty much all of the genomes of Natufians and Taforalt/IBM, just in different proportions, Al Khiday and some of Egyptian/Sudanese remains would have been a part of this metapopulation IMO.

You can kinda see this in the fact that Natufian/Taf work as sources of ancesty for North Africans and East Africans, despite the fact there is no strong evidence for a movement of Iberomaurisians or Natufians into NE Africa, but something related to both of those groups clearly existed in NE Africa given how much Natufian/Taf we all score, and the existence of 14,000 year old Sudanis showing strong affinities with Natufian/Taf rich populations. So we don't have much literal Natufian ancestry, just something closely related to it that was in Egypt/North Sudan. I doubt Natufians are ancestral to anyone outside of the Neolithic Levantines and anyone descended from them, this includes Arabians, Lazaradis has a tree where he shows Arabian HG(this is believed to be the source of the direct Natufian-like input) as being descended from whatever Natufians are descended from, even though they can be modelled as Natufian, so not literally Natufians.
Makes sense. I think this, on top of the publication of the 105CE sample, should really clear things up.

There's also an excavation ongoing on Kushitic tombs from near the end of the Meroitic period, and I heard through Twitter that DNA would also be extracted. Though I doubt it'll aid in helping us discover anything about ourselves, it'll be interesting to see.
See above. We also have some Neolithic Levantine and maybe Chalcolithic Levantine, but the Natufian we score on top of the other stuff I just mentioned is largely Egyptian in origin, just closely related to Natufians, if you want me to say why/how i think this happened feel free to ask.
There was no doubt in my mind that they were Egyptian as the admixture event did happen in that area, but I thought they were very recent immigrants and entirely Natufian lol. Please elaborate if you can, bro.
Well modern Egyptians have never been used as a source of ancestry for Horners in any study AFAIK but they likely have too much Iranian and Anatolian Farmer ancestry too work for us, the Egyptians I'm talking about are 10,000+ years old btw, not 200 lol, so we'd need early Egyptian DNA. The late period Egyptian samples worked as a source of ancestry for Horners, better than Arabians, they didn't compare with a Levantine source, but Egyptians CAN work as a source for us.
There is this Middle Kingdom Egyptian K13+K36 reconstruction sample, and he wasn't the best fit either, I think. I'll check rn:
BoringFit:
1657214825611.png

WeWuzFit:
1657214770566.png

A better fit than Levant_PPNB for sure. Probably should've used Natufian but yh.
 
It says the DNA they managed to extract is extremely damaged and degraded. So interpret the data with a bit of skepticism.

If replicate-able i think, it lends evidence to theory of dispersal point of Cushitic speakers
 
There was no doubt in my mind that they were Egyptian as the admixture event did happen in that area, but I thought they were very recent immigrants and entirely Natufian lol. Please elaborate if you can, bro.
Think of Natufian as a stand-in, we don't have Paleolithic or Mesolithic DNA from Egypt, so the Natufians are the next best thing. The genetic relationship between populations across North Africa and the Levant would have been similar modern Afro Asiatic speakers in the Horn of Africa, purely in the sense that they would have largely been made up of the same stuff just in different proportions, just varying amounts of Cushitic, Yemeni/Sabean and Omotic. Focusing on the lions share of the ancestry in Horners, Eritreans and Somalis aren't differentiated by the presence of different components but mostly due to variance in proportions, with Eritreans having the most Yemeni and Somalis the most Cushitic but both groups still have all of those ancestries. I think Mesolithic NA would have been the same.
Those ancestries that they would have shared would have been Basal Eurasian + Common West Eurasian + MSA(Middle Stone Age) SSA-like, this is literally what the Natufians and IBM/Taf is, just varying proportions, Natufians were like 6-8% SSA-like, and Taf was 35-45% SSA-like, wildly different amounts but its shared between them, same with their West Eurasian and Basal Eurasian ancestry.

A typical model for Natufians = Dzudzuana + IBM + Mota

A typical model for Taf = Dzudzuana + ANA

These are examples of commonly cited models for those groups, Dzudzuana is an important source (again, probably not literally) of ancestry for both the Natufians and IBM, so we can already see this is one layer of ancestry they share. The original model for IBM was Natufian + recent SSA groups, so we can see both groups can be modelled using each other aswell as common sources (Dzudzuana + Mota). I think this shows that most of their ancestries will be shared but in differing amounts. I think Paleo/Meso Egypt would have been a part of the aforementioned metapopulation which allows Natufians to be used as a source of our ancestry because they are also members of that metapopulation.

There is this Middle Kingdom Egyptian K13+K36 reconstruction sample, and he wasn't the best fit either, I think. I'll check rn:
If your talking about the M1a1 carrier be careful with that sample, from what i remember its fits were terrible and distances very high with modern and late period Egyptians, i don't think its possible to "reconstruct" ancient DNA using just mtDNA data alone.
 
Think of Natufian as a stand-in, we don't have Paleolithic or Mesolithic DNA from Egypt, so the Natufians are the next best thing. The genetic relationship between populations across North Africa and the Levant would have been similar modern Afro Asiatic speakers in the Horn of Africa, purely in the sense that they would have largely been made up of the same stuff just in different proportions, just varying amounts of Cushitic, Yemeni/Sabean and Omotic. Focusing on the lions share of the ancestry in Horners, Eritreans and Somalis aren't differentiated by the presence of different components but mostly due to variance in proportions, with Eritreans having the most Yemeni and Somalis the most Cushitic but both groups still have all of those ancestries. I think Mesolithic NA would have been the same.
Those ancestries that they would have shared would have been Basal Eurasian + Common West Eurasian + MSA(Middle Stone Age) SSA-like, this is literally what the Natufians and IBM/Taf is, just varying proportions, Natufians were like 6-8% SSA-like, and Taf was 35-45% SSA-like, wildly different amounts but its shared between them, same with their West Eurasian and Basal Eurasian ancestry.

A typical model for Natufians = Dzudzuana + IBM + Mota

A typical model for Taf = Dzudzuana + ANA

These are examples of commonly cited models for those groups, Dzudzuana is an important source (again, probably not literally) of ancestry for both the Natufians and IBM, so we can already see this is one layer of ancestry they share. The original model for IBM was Natufian + recent SSA groups, so we can see both groups can be modelled using each other aswell as common sources (Dzudzuana + Mota). I think this shows that most of their ancestries will be shared but in differing amounts. I think Paleo/Meso Egypt would have been a part of the aforementioned metapopulation which allows Natufians to be used as a source of our ancestry because they are also members of that metapopulation.
Okay, that makes everything so much clearer. Drawing parallels with modern Horn African populations was smart lol, idk why I struggled to see it that way beforehand. I'll read up more on these components. Thanks a lot.
If your talking about the M1a1 carrier be careful with that sample, from what i remember its fits were terrible and distances very high with modern and late period Egyptians, i don't think its possible to "reconstruct" ancient DNA using just mtDNA data alone.
Wow lol. I should really check where I get my samples from. I had no idea whatsoever of the progress, but trusted it was scientifically sound blindly. I'll go ahead and delete that sample from my files.



One last thing I want to ask is whether you know anything about the Old Kingdom study supposedly ongoing. I think I heard of it through here, but can't be sure.
 
Okay, that makes everything so much clearer. Drawing parallels with modern Horn African populations was smart lol, idk why I struggled to see it that way beforehand. I'll read up more on these components. Thanks a lot.
No problem, feel free to ask away.
Wow lol. I should really check where I get my samples from. I had no idea whatsoever of the progress, but trusted it was scientifically sound blindly. I'll go ahead and delete that sample from my files.
I'm not saying its useless, don't delete it just be cautious is all, I don't expect MK ancient Egyptians to be radically different from those samples but our Egyptian-like ancestry won't be represented well by Dynastic Egyptians simply because it would have spread from Lower Nubia and would have retained its Mesolithic profile better than Dynastic Egyptians who would have had a lot more Neolithic, Chalcolithic and Bronze Age Levantine. When i say we have Egyptian ancestry instead of Levantine, I mean moreso Mesolithic/Paleolithic Egyptian, we might have some Dynastic Egyptian ancestry but i doubt its appreciable tbh, so MK samples aren't ideal for us.
We need something with the perfect proportion of Mesolithic Egyptian(Al Khiday-like) to Levantine Farmer to model our Nile Valley ancestry. We don't even really know what those proportions look like in modern Horners and Neolithic Pastoralists, some models will tell you our Nile Valley ancestry is Mesolithic Egyptian + Dinka, some will show its Chalcolithic Israeli + Dinka, so a lot of this stuff is still in the air.
 
Not true, 14,000 year old remains in Sudan (Al Khiday) cluster with lower Nubians who cluster with ancient upper Egyptians and Afro-Asiatic Horners, the so-called "Eurasian" or "Levantine" affinity is already present in NE Africa during the Mesolithic, these people undoubtedly had little to no Natufian ancestry given their age.

Think about the phylogeny of the most important lineages on our Cushitic component (E-M215 and all of its subclades and its ancestors), its phylogeny is nearly entirely NE African, not Levantine.
Al-Khiday was likely a semi-sedentary hunter-gatherer that was Natufian-like elevated Iberomaursian individual by the samples' unique craniofacial morphology within the edge of the Neolithic metric agglomeration highlighting external factors of in-situ endemic region-specific genetic profile (an understated crucial cultural/traditional and social precursor to the cultural undercurrent horizon in pre-history into historical age of Nile-Valley). Still, comparatively very drifted from Jebel Sahaba contemporaries in Lower Nubia that seem very distinct from all the Neolithic Lower Nubians of later times. I'm certain it was once the dominant Northeast African Eurasian rich in the terminal Pleistocene with strong autosomal continuity into the early Neolithic days of the broader region. But there was a clear Neolithic diffusion of technology and subsistence strategy markers that indicate demic geneflow from the Levant, and for the most part, this Al-Khiday-type took a secondary stage in autosomal ratio at some point down the line of thousands of years. You can see the Holecence food-producing samples from Nubia and Egypt forming a tighter morphological cluster shifting away from the Upper Nubia positioned hunter-gatherer in slight relative respect. This can mean a homogenizing introduction of Neolithic farmers with gracile, less robust phenotypic characteristics influenced a strong selection of common trait potentiality irrespective of the variation of Sub-Saharan African ancestry contained in those samples. We can further infer a good backed statement that one can draw a base of continuity from a Northeast African source toward early Egyptian population, and other groups such as the Cushitic, without needing a complete population replacement to represent a West Asian genetic frequency distribution/radiation.

A caveat has to be stated, even though this does provide some insight quantifying the inter-sample affinity of the earliest time-slices relevant to this discussion measuring morphometric changes, overall the analytical framework is not the strongest of evidence. We need to humble ourselves to some extent by remembering that a lot of people believed that Natufians were African peoples based on their shown characteristics in fossil records. Surely we now know that hunter-gatherers were more robust in general, but I still believe the sudden changes in phenotype in the Nile-Valley onset of Neolithic was not a local evolution of Lower Nubian hunter-gatherers (Jebel Sahaba/Tushka and Wadi Halfa) but movements of peoples and mixing, and the existence of distinct groups in the region pre-agricultural introduction.

Good reading material:
 
What do you make of this ES reconstruction a friend of mine made? What limitations would reconstructing the ES component strictly from the DNA of modern Somalis have?
How did he go about doing this?
Ethio Somali is supposed to be 23ka, whether its real or not its either Paleolithic or Mesolithic, so it can't carry Iranian ancestry, but yh I think Ethio Somali could be modelled loosely as the rest of that stuff. IMO Ethio Somali and Maghrebi are part of the same Paleolithic-Mesolithic NA metapopulation i spoke about before.


Edit: To your last question, I don't think it would matter that much, I think Somalis are a good enough proxy to get a decent picture of what ES looks like.
 

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