First Genomes from Ancient Egypt

I wish someone has finally made a calculator, strictly based on these ancient samples of 3 farmer groups (or better the h-gs they came from) and 3 h-gs groups. Sort of gold standard, based on samples from 10 kya.
Relly?! Could you link me to this fact as I don't seem to remember it. One impossible thing to overcome is that genesis of Natufians starts at the same time as genesis of WHG about 14 kya, and they plot way away on PCA. THis is the first that I hear that WHG was an ancestor of Natufian, and in 50% level. There is some degree of "immediate" common ancestry, but not 50% and not directly WHG!
Sure they are on the same cline, as I said that they have big degree of same ancestry, but you wouldn't ever say that Iberia Copper is the same as Levant Neolithic. At least half of their genome is different from each other and drifted 5 thousand years apart, so even having closely related genes they developed different alleles, mutations.

Exactly so.
 
so the Palestinians are not the Filistines, the Sea People that settled in Gaza

maybe the Jews and the Phoenicians have common ancestors, but that is then from before they entered in history
Phoenicians are from the Lebanese coast, often a place for refugees from inland, trying to escape from the domination of the Hittites or the Egyptians
and the origin of the Jews are marginal herders in the hills in the interface between the Southern Levant and the Negev desert who expanded into the vacuum created by the Egyptians when they abandonned the Levant

That's true Bicicleur, but didn't the Canaanite paper make the point that the Sidon sample and the Levant Bronze Age sample from further inland were very much alike? I think they made the specific point that coastal and inland people were basically the same even if they had different modes of subsistence.
 
Since he talks about various dynasties, how much SSA did the Nubian dynasty had?

Sorry, I just saw this while going through the thread. Somehow I missed it the first time. When we get some Nubian dynasty era genomes, and perhaps some from Nubian era mummy we'll know. Right now, based on representations, I think they had quite a lot.

This is the Pharaoh Taharqa
Egypt_Nubian_Taharqa.jpg


Shebitku:
889cafba9d202d70bcf7797c2ab7df36.jpg

It just goes to show that some short lived invasions can come and go without having a profound effect on the total gene pool of the "native" people.

There are also a few Pharaohs from prior periods who have a bit of an SSA look to them, but rulers are notorious for taking wives and concubines from foreign lands. How "English" is the House of Windsor after all? It also doesn't change the composition of the people.

Then we have Ramses III, who carried an African y, yet doesn't look at all SSA to me. The y can so easily and quickly become decoupled from autosomal dna.

hqdefault.jpg


ramesses3-8.jpg
 
Relly?! Could you link me to this fact as I don't seem to remember it. One impossible thing to overcome is that genesis of Natufians starts at the same time as genesis of WHG about 14 kya, and they plot way away on PCA. THis is the first that I hear that WHG was an ancestor of Natufian, and in 50% level. There is some degree of "immediate" common ancestry, but not 50% and not directly WHG!

Well they plot away because Basal Eurasian is highly divergent. It started differentiating prior to the East and West Eurasian split.
Also there's no evidence WHG or WHG-related ancestry wasn't around before 14kya.

Here are few quotes from the paper "Genomic insights into the origin of farming in the ancient Near East":

(from the abstract)
We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other.

We used qpAdm to estimate Basal Eurasian ancestry in each Test population. We obtain the highest estimates in the earliest populations from both Iran (66±13% in the likely Mesolithic sample, 48±6% in Neolithic samples), and the Levant (44±8% in Epipaleolithic Natufians) (Fig. 2) showing that Basal Eurasian ancestry was widespread across the ancient Near East.

MA1, EHG, SHG, Switzerland_HG are consistent with having no Basal Eurasian ancestry, while at least some such ancestry is inferred for the remaining populations. Neolithic Iran and Natufians could be derived from the same Basal Eurasian population but are genetically closer to EHG and WHG respectively We take the model of Fig. S4.9 and attempt to fit Natufians as a mixture of the same Basal Eurasian population that contributes to Iran_N and any other population of the tree. Several solutions are feasible, and we show the best one (lowest ADMIXTUREGRAPH score) in Fig. S4.10.
We can add both EHG and MA1 as simple branches to the model structure of Fig. S4.10 and show the results in Fig. S4.11. An interesting aspect of this model is that it derives both Natufians and Iran_N from Basal Eurasians but Natufians have ancestry from a population related to WHG, while Iran_N has ancestry related to EHG. Natufians and Iran_N may themselves reside on clines of WHG-related/EHG-related admixture.

http://www.nature.com/nature/journal/v536/n7617/full/nature19310.html#extended-data

Sure they are on the same cline, as I said that they have big degree of same ancestry, but you wouldn't ever say that Iberia Copper is the same as Levant Neolithic. At least half of their genome is different from each other and drifted 5 thousand years apart, so even having closely related genes they developed different alleles, mutations.

It's less than half even for Iberia Copper, more like 40%. Just look at the PCA, Levant Neolithic and Anatolia Neolithic (which maybe has some 20% extra WHG) are relatively similar and for the most part same stock. You can think of them as Bell Beaker vs Corder Ware if you like, they are not particularly drifted:

PCAtest.jpg
 
We have no analyzed Mesolithic samples from the Near East. Who knows what hunter-gatherers were present?

Iran Neolithic is heavily CHG and is also heavily Basal Eurasian, as is CHG, and yet David Reich just got through explaining that the western and eastern farmers were initially as different from one another as East Asians and Europeans are today, despite sharing high levels of Basal Eurasian.

Obviously as admixture occurs, various different groups who carry similar percentages of these ancient groups will cluster together.

I don't see the point of this whole line of argumentation.
 
We have no analyzed Mesolithic samples from the Near East. Who knows what hunter-gatherers were present?

Iran Neolithic is heavily CHG and is also heavily Basal Eurasian, as is CHG, and yet David Reich just got through explaining that the western and eastern farmers were initially as different from one another as East Asians and Europeans are today, despite sharing high levels of Basal Eurasian.

Obviously as admixture occurs, various different groups who carry similar percentages of these ancient groups will cluster together.

I don't see the point of this whole line of argumentation.

Wasn't there a rumour or statement in a study that they found a mesolithic Anatolian sample which looked like a WHG individual? I for sure remember something like that. So indeed as I have proposed it seems there was a fluent cline from WHG to ANE from Anatolia to Caucasus/North Iran. And than a Basal Eurasian like group moved further North (possibly from the Persian Gulf/Mesopotamia or even Arabia) and merged with WHG like group in the West (Anatolia/Levant) and ANE like group in the East.
 
Sorry, I just saw this while going through the thread. Somehow I missed it the first time. When we get some Nubian dynasty era genomes, and perhaps some from Nubian era mummy we'll know. Right now, based on representations, I think they had quite a lot.

[..]

The point is there might have been dynasties with 0% SSA or with 50+% etc. I don't believe we can consider those samples representative of 'Ancient Egyptians', since they could have acquired non-native admixture at that point.
 
The point is there might have been dynasties with 0% SSA or with 50+% etc. I don't believe we can consider those samples representative of 'Ancient Egyptians', since they could have acquired non-native admixture at that point.

I am sure the admixture varied by dynasty, but you specifically asked about the Nubian dynasty.

Plus, these samples weren't royal samples. Ruling dynasties can carry certain dna in proportions that aren't at all representative of the majority of the people. That's something that I think we all have to keep in mind when we make broad generalizations based on usually elite graves.

If you're thinking that the SSA present in the samples analyzed came from the time of the Nubian dynasty because perhaps there was a somewhat substantial folk migration during their rule I don't know.

The Nubian pharaohs ruled from 760 BC to 656 BC.
https://en.wikipedia.org/wiki/Twenty-fifth_Dynasty_of_Egypt

Does anyone know the date for the three samples for which they were able to get the y and the autosomal admixture?

If it's after the date of the Nubian reign, it's certainly possible that this affected the population.

On the other hand, there has been contact with Nubia throughout Egypt's history. Ramses III and his y are before this Nubian dynasty period.

From the authors:

"By comparing ancient individuals from Abusir el-Meleq with modern Egyptian reference populations, we found an influx of sub-Saharan African ancestry after the Roman Period, which corroborates the findings by Henn and colleagues16. Further investigation would be needed to link this influx to particular historic processes. Possible causal factors include increased mobility down the Nile and increased long-distance commerce between sub-Saharan Africa and Egypt49. Trans-Saharan slave trade may have been particularly important as it moved between 6 and 7 million sub-Saharan slaves to Northern Africa over a span of some 1,250 years, reaching its high point in the nineteenth century50. However, we note that all our genetic data were obtained from a single site in Middle Egypt and may not be representative for all of ancient Egypt. It is possible that populations in the south of Egypt were more closely related to those of Nubia and had a higher sub-Saharan genetic component, in which case the argument for an influx of sub-Saharan ancestries after the Roman Period might only be partially valid and have to be nuanced. Throughout Pharaonic history there was intense interaction between Egypt and Nubia, ranging from trade to conquest and colonialism, and there is compelling evidence for ethnic complexity within households with Egyptian men marrying Nubian women and vice versa51,52,53. Clearly, more genetic studies on ancient human remains from southern Egypt and Sudan are needed before apodictic statements can be made."

There is also this:
"The ancient DNA data revealed a high level of affinity between the ancient inhabitants of Abusir el-Meleq and modern populations from the Near East and the Levant. This finding is pertinent in the light of the hypotheses advanced by Pagani and colleagues, who estimated that the average proportion of non-African ancestry in Egyptians was 80% and dated the midpoint of this admixture event to around 750 years ago17. Our data seem to indicate close admixture and affinity at a much earlier date, which is unsurprising given the long and complex connections between Egypt and the Middle East. These connections date back to Prehistory and occurred at a variety of scales, including overland and maritime commerce, diplomacy, immigration, invasion and deportation54. Especially from the second millennium BCE onwards, there were intense, historically- and archaeologically documented contacts, including the large-scale immigration of Canaanite populations, known as the Hyksos, into Lower Egypt, whose origins lie in the Middle Bronze Age Levant54.
Our genetic time transect suggests genetic continuity between the Pre-Ptolemaic, Ptolemaic and Roman populations of Abusir el-Meleq, indicating that foreign rule impacted the town’s population only to a very limited degree at the genetic level. It is possible that the genetic impact of Greek and Roman immigration was more pronounced in the north-western Delta and the Fayum, where most Greek and Roman settlement concentrated43,55, or among the higher classes of Egyptian society55. Under Ptolemaic and Roman rule, ethnic descent was crucial to belonging to an elite group and afforded a privileged position in society55. Especially in the Roman Period there may have been significant legal and social incentives to marry within one’s ethnic group, as individuals with Roman citizenship had to marry other Roman citizens to pass on their citizenship. Such policies are likely to have affected the intermarriage of Romans and non-Romans to a degree55. Additional genetic studies on ancient human remains from Egypt are needed with extensive geographical, social and chronological spread in order to expand our current picture in variety, accuracy and detail."

People are making claims based on this paper which the authors themselves don't make, but then the authors either know a bit of history or are working with historians. Typical.

I find it particularly interesting to look at the vast difference between the undoubted findings of this paper and the ridiculous findings of the authors relying on Alder and other flawed methods, and so collapse thousands of years of gene flow into the latest and most recent episode.
 
The point is there might have been dynasties with 0% SSA or with 50+% etc. I don't believe we can consider those samples representative of 'Ancient Egyptians', since they could have acquired non-native admixture at that point.

If the samples are homogenous over a timespan of 1000 years and more, I guarantee you we are not dealing here with foreign admixture. South Egyptians might had more SSA admixture (around 15% like modern Egyptians) but I doubt that North and Middle Egyptians differed much from these samples at hand.
 
Wasn't there a rumour or statement in a study that they found a mesolithic Anatolian sample which looked like a WHG individual? I for sure remember something like that.

Can anyone verify this? The closest thing I can think of is that one Anatolian from the Neolithic period had y-dna I and another had y-dna I2c, but of course this is something very different.
 
Can anyone verify this? The closest thing I can think of is that one Anatolian from the Neolithic period had y-dna I and another had y-dna I2c, but of course this is something very different.
Yes there was a statement of a sample from very early Neolithic in Central Anatolia who was significantly higher in the WHG like component compared to the later Anatolian_Farmers.
 
Well they plot away because Basal Eurasian is highly divergent. It started differentiating prior to the East and West Eurasian split.
Also there's no evidence WHG or WHG-related ancestry wasn't around before 14kya.
That's what I said, that they are related by some common ancestry. Not by 50% of WHG mixed into Natufian, as you mentioned in post before. They never met directly or indirectly, just related by some common ancestry thousands of years before.
Look at the distance between WHG and Natufians on PCA chart. It is even bigger than Natufians to Iranian Farmers.


It's less than half even for Iberia Copper, more like 40%. Just look at the PCA, Levant Neolithic and Anatolia Neolithic (which maybe has some 20% extra WHG) are relatively similar and for the most part same stock. You can think of them as Bell Beaker vs Corder Ware if you like, they are not particularly drifted:
I'm not sure where you going with this "close relation". Let's put it this way. They were divergent and distinct enough to warrant their own admixture colour, as a different source population. CW and BB overlap on PCA plot, where there is a substantial gap between LN and AF.
 
I don't know if it was female or male driven. Does it change the fact that the gene flow occurred? Does it somehow not count if it was female driven? I think not.

I don't have an agenda or a paper or a book or thousands of prior posts to defend. I'm just following the data. It's possible there was bride exchange at the edges into a very lightly populated steppe. However, a lot, if not most, of the mtdna looks standard northern. How could that amount of "southern" mtdna have led to people who were roughly half "southern"? Maybe a modified version of Maciamo's theory is correct. I always thought it was a possibility. I'm content to wait and see what the dna shows.

As for the mixing agent being "Caucasus", color me skeptical that this population survived in unadmixed form thousands of years after those ancient samples. Plus, as Marko pointed out, the Reich Lab has modeled the mixing agent as something resembling Iran Chl. As Lazaridis intelligently pointed out, they may find a population which fits better, and it may not have actually come from Iran.

Honestly, it's as if there's a phobia with connecting anything with Iran. I suppose I don't completely get the subtext.

You get the subtext perfectly! The simple answer is that Iranians aren't Nordic. The rule set in stone by the majority of anthro sites is that you're either nordic or a loser. You aren't blessed unless you've been stamped with odin's seal of approval.

Yeah, Kiss Me, I'm Norwegian.

Seriously, the idiots who are afraid of connecting anything with Iran are bigots who can't amount to much else so they try to see themselves as members of the "winning team" to build up their self esteem.

I bet that quite a few of them are sick to their stomachs over this study which strengthens the common sense idea that Egypt wasn't Norway on the Nile.
Lol.
 
I am sure the admixture varied by dynasty, but you specifically asked about the Nubian dynasty.

Plus, these samples weren't royal samples. Ruling dynasties can carry certain dna in proportions that aren't at all representative of the majority of the people. That's something that I think we all have to keep in mind when we make broad generalizations based on usually elite graves.

If you're thinking that the SSA present in the samples analyzed came from the time of the Nubian dynasty because perhaps there was a somewhat substantial folk migration during their rule I don't know.

The Nubian pharaohs ruled from 760 BC to 656 BC.
https://en.wikipedia.org/wiki/Twenty-fifth_Dynasty_of_Egypt

Does anyone know the date for the three samples for which they were able to get the y and the autosomal admixture?

If it's after the date of the Nubian reign, it's certainly possible that this affected the population.

On the other hand, there has been contact with Nubia throughout Egypt's history. Ramses III and his y are before this Nubian dynasty period.

From the authors:
[...]

People are making claims based on this paper which the authors themselves don't make, but then the authors either know a bit of history or are working with historians. Typical.

I find it particularly interesting to look at the vast difference between the undoubted findings of this paper and the ridiculous findings of the authors relying on Alder and other flawed methods, and so collapse thousands of years of gene flow into the latest and most recent episode.

I actually think that these samples may have acquired admixture from outside Africa. What they found is important but actually that is 'Genetic continuity between the Pre-Ptolemaic, Ptolemaic and Roman populations of Abusir el-Meleq' and the title of their study should have stated just that, because now they make a statement that their data do not allow them to make, irrespective of if it is likely or not.

Those are the samples (3,4,6). I copied them from
ancestraljourneys.org

RoyalEgyptDeir el Bahari [Ramses III]1155 BCE1b1aHawass 2012
RoyalEgyptDeir el Bahari [Unknown man E - Pentawere?]1155 BC?E1b1aHawass 2012
Tomb mummyEgyptAbusir el-Meleq [JK2134]776-569 cal BCJJ1dSchuenemann 2017
Tomb mummyEgyptAbusir el-Meleq [JK2911]769-560 cal BCJM1a1Schuenemann 2017
Tomb mummyEgypt[DMG5]402-385 BCI273G, 152C, 199C, 204C, 207A, 250C, 263G, 750G, 1438G, 1719A, 2706G, 4529T, 4769G, 7028T, 8251A, 8860G, 10034C, 10238C, 10398G, 11719A, 12501G*, 12705T, 13780G, 14766T, 15043A, 15326G, 15758G, 15924G, 16129A, 16223T, 16391A, 16519C**= excluded by HaploGrep in analysisKhairat 2013
Tomb mummyEgyptAbusir el-Meleq [JK2888]97-2 cal BCE1b1b1a1b2 [V22]U6a2Schuenemann 2017
 
That's what I said, that they are related by some common ancestry. Not by 50% of WHG mixed into Natufian, as you mentioned in post before. They never met directly or indirectly, just related by some common ancestry thousands of years before.


It's not "some" common ancestry. It's over 50% WHG-related (as per figure S4.10) and Natufians clearly sit halfway on a Basal-WHG cline, not Basal-SHG or Basal-EHG, what do you think that means? Or did you perhaps miss the Iron Gates_HG and Varna HG genomes from the Balkans which are overwhelmingly WHG? It's not a huge leap from there to Anatolia/Levant, you know.

Look at the distance between WHG and Natufians on PCA chart. It is even bigger than Natufians to Iranian Farmers.

And? Of course they would be more distant. It's Basal that is highly divergent from European HG, not European HG from each other.

I'm not sure where you going with this "close relation". Let's put it this way. They were divergent and distinct enough to warrant their own admixture colour, as a different source population. CW and BB overlap on PCA plot, where there is a substantial gap between LN and AF.

As a matter of fact they are more or less equidistant. CW and BB do not overlap, only few outliers do; we already know few in Central Europe interacted and intermingled. Check again:

pcacwbbs.jpg
 
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It's not "some" common ancestry. It's over 50% WHG-related (as per figure S4.10) and Natufians clearly sit halfway on a Basal-WHG cline, not Basal-SHG or Basal-EHG, what do you think that means? Or did you perhaps miss the Iron Gates_HG and Varna HG genomes from the Balkans which are overwhelmingly WHG? It's not a huge leap from there to Anatolia/Levant, you know.
What is your argument about? Let me repeat myself. I don't have problem with them sharing common ancestry. I had problem with you describing this sharing ancestry as a relation of Natufians with WHG, which is false. In case you forgot what you said, here it is:
IIRC Lazaridis modeled Natufians roughly as 50% Basal Eurasian and 50% WHG;
And this is what experts say:
Natufians have ancestry from a population related to WHG
We still don't know where your 50% is coming from. And let's stress that relationship between ancestral groups is very distant in time. Perhaps peak of LGM or even before.

And? Of course they would be more distant. It's Basal that is highly divergent from European HG, not European HG from each other.



As a matter of fact they are more or less equidistant. CW and BB do not overlap, only few outliers do; we already know few in Central Europe interacted and intermingled. Check again:
Obviously perceiving distances is like seeing beauty. In eye of beholder.
 
I actually think that these samples may have acquired admixture from outside Africa. What they found is important but actually that is 'Genetic continuity between the Pre-Ptolemaic, Ptolemaic and Roman populations of Abusir el-Meleq' and the title of their study should have stated just that, because now they make a statement that their data do not allow them to make, irrespective of if it is likely or not.

Those are the samples (3,4,6). I copied them from
ancestraljourneys.org

RoyalEgyptDeir el Bahari [Ramses III]1155 BCE1b1aHawass 2012
RoyalEgyptDeir el Bahari [Unknown man E - Pentawere?]1155 BC?E1b1aHawass 2012
Tomb mummyEgyptAbusir el-Meleq [JK2134]776-569 cal BCJJ1dSchuenemann 2017
Tomb mummyEgyptAbusir el-Meleq [JK2911]769-560 cal BCJM1a1Schuenemann 2017
Tomb mummyEgypt[DMG5]402-385 BCI273G, 152C, 199C, 204C, 207A, 250C, 263G, 750G, 1438G, 1719A, 2706G, 4529T, 4769G, 7028T, 8251A, 8860G, 10034C, 10238C, 10398G, 11719A, 12501G*, 12705T, 13780G, 14766T, 15043A, 15326G, 15758G, 15924G, 16129A, 16223T, 16391A, 16519C**= excluded by HaploGrep in analysisKhairat 2013
Tomb mummyEgyptAbusir el-Meleq [JK2888]97-2 cal BCE1b1b1a1b2 [V22]U6a2Schuenemann 2017

So, yes, these three for which we have autosomal material are after the reign of the Nubian Pharaohs and the last one is also after the arrival of the Greeks. I can see where an argument could be made for some relatively recent Nubian introgression at that period, but are you saying there was also Greek introgression? On the last sample? You don't think that the authors would have been able to pick it up?

I'm sorry, but I'm not getting your point here. Are you talking about the Hyksos? The authors already talk about their possible impact.

No "ethnic" group is totally static. The Europeans pre-Bronze Age were very different from the Europeans post-Bronze Age. The same thing seems to have happened in Egypt.
 
What is your argument about? Let me repeat myself. I don't have problem with them sharing common ancestry. I had problem with you describing this sharing ancestry as a relation of Natufians with WHG, which is false. In case you forgot what you said, here it is:

And this is what experts say:

We still don't know where your 50% is coming from. And let's stress that relationship between ancestral groups is very distant in time. Perhaps peak of LGM or even before.

Obviously perceiving distances is like seeing beauty. In eye of beholder.

I don't get it either. After thousands of years of drift, all these populations, despite some common ancestry in the far distant past, were as far apart from one another as East Asians from West Eurasians. It was the migration of the Anatolian farmers and later that of the people from around the Caucasus who drew the populations of West Eurasia together.
 
I read a pretty good book "Egypt, Canaan, and Israel in Ancient Times"

It sited some pretty compelling evidence that the dynasties originated only after what appears to be strong influence from Mesopotamia. I don't really know how to apply this to the genetics that we have right now, but it's some good food for thought.

Remember we already have a bunch of genomes from West Asia that span from the Neolithic (mesolithic-ish in some cases) to the bronze age, and the Old Kingdom dynasties don't even begin until the Bronze Age well after when we see the mixing of these different farming populations just to the North East around the fertile crescent. I guess my point is that once Egypt starting acting like Egypt they probably looked much like Bronze Age Levant, for the most part with of course some Nubian here and there.

The interesting conundrum with Egypt is that all the resources (lots of gold) seem to be flowing from up river in Nubia, yet the dynasties themselves appear to be oriented closer to the delta with the evidence of influence from across the Sinai as I mentioned. So I think there's still some puzzles that enough genetic data could help us solve. The obvious model is that the dynastic powers emerged with a strong influence from the fertile crescent as a means to tap these resources from up river. I know that before the emergence of the Old Kingdom dynasties we see gold and other stuff from Nubia in the already developed Mesopotamian urban powers.
 
The paper has already made its way onto youtube.
https://www.youtube.com/watch?v=IiPLOK59CFk

Unfortunately, from the first few comments it has brought out all the white supremacist nut jobs too.

Predictably, their take away is that "the ancient Egyptians were European". No, they weren't. The Egyptians of this era were closest to Arabians and Levant people, who, the last time I checked, were not Europeans. What they were like in the time of Pharaohs like Ramses III with his African y we don't know, although the mtdna, of which they have a lot more, doesn't seem to change very much over a much longer period.

When that is pointed out the claim is then made that all the people from Europe through the Middle East were "white" and so all those accomplishments coming from the Near East were by "white" people. Well, that's certainly interesting. Now all of a sudden the Saudis and Palestinians and Syrians are white. Bedouin too, I guess.

And so the madness continues.

Oh, and for those racists who mimic ghetto slang to make fun of the claim that SSA or SSA admixed people were ever Kings of Egypt, get out your history books and read about the 25th NUBIAN DYNASTY. If you can read and actually comprehend what you read, that is.
 

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