First Genomes from Ancient Egypt

[harena]

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.

You would know had you actually taken the time to read the paper, particularly figure S4.10; there's a big arrow from the WHG tree going straight into the Natufian tree with a 55% estimate upon it.

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

LOL.

 

[davef]

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.

It's so predictable. And what's amazing is that a simple peak at the charts should reveal that those Ancient Egyptians were very Bedouin like (subtract SSA admixture in Bedouins). It's shocking that in spite of clear, easy to grasp evidence that Ancient Egypt wasn't "European", these morons still cling to their silly versions of ancient history/genetics.

"Well, that's certainly interesting. Now all of a sudden the Saudis and Palestinians and Syrians are white. Bedouin too, I guess"

Using that argument, they would respond saying that these groups used to be white until they began mixing heavily with slaves. lol.

 

[Angela]

You would know had you actually taken the time to read the paper, particularly figure S4.10; there's a big arrow from the WHG tree going straight into the Natufian tree with a 55% estimate upon it.



LOL.

What in heaven's name is your point? The Iranian Neolithic farmers and the western farmers shared the same amount of Basal Eurasian. It didn't stop all the scientific papers from stating that they were distinct populations, as distant from one another as East Asians and Europeans are today.

Just spit it out. What are you trying to prove? Is it a round about way of trying to say that Natufians are really "white" or "European" because they have a lot of something WHG like? Are you aware of how bizarre that is? There were no "Europeans" in those days, and the WHG were probably as dark as South Asians.

If that isn't it, then explain why this is so important and why it belongs on a thread about ancient Egyptians.

Otherwise, drop it and get back on topic.

 

[Alan]

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.

These white supremacists nut jobs are as bad as Afro_Centrics. I have been commenting on some of these articles from various News websites. The headers of many of these articles are so misleading. For example Russia Todays headline is "Ancient Egyptians have ancestry from Europe and the Middle East", from Europe what?

 

[Alan]

It's so predictable. And what's amazing is that a simple peak at the charts should reveal that those Ancient Egyptians were very Bedouin like (subtract SSA admixture in Bedouins). It's shocking that in spite of clear, easy to grasp evidence that Ancient Egypt wasn't "European", these morons still cling to their silly versions of ancient history/genetics.

"Well, that's certainly interesting. Now all of a sudden the Saudis and Palestinians and Syrians are white. Bedouin too, I guess"

Using that argument, they would respond saying that these groups used to be white until they began mixing heavily with slaves. lol.

I have a problem with this claim too. Many people come to the conclusion they were Bedouin like because they cluster on 2 dimensional PCAs just next to them. But this is merely projection bias. When I run ancient Levant Neolithic samples through calculators and compare them with Bedouin samples. One thing get's obvious. modern Bedouins have allot more Iran_Neolithic like admixture while in older calculators Levant_neolithics more of the Eastmed and even significant Westmed admixture in combination with the Southwest Asian component. While Bedouins are almost exclusively of the Southwest Asian variant.
The Southwest Asian itself is a component made up on Bedouins as proxy and combines Levant_Neo and Iran_Neo ancestry with possibly little SSA admixture.
So with other words Bdouins main components are actually allot more Eastern shifted (towards Iran_Neolithic) but the ~6-8% SSA admixture in them pushes them further towards Southwest on the PCA which makes them appear to be very close to Levant_Neolithic. While in reality Bedouins are like predominantly Levant_Neolithic + allot of Iran_Neolithic + some SSA.

With other words we basically don't have any modern population that fits ancient Levantine samples. The best fit would still be modern Lebanese minus the Iran_CHL admixture or Palestinians minus Iran_CHL and the little SSA admixture

 

[Alan]

What in heaven's name is your point? The Iranian Neolithic farmers and the western farmers shared the same amount of Basal Eurasian. It didn't stop all the scientific papers from stating that they were distinct populations, as distant from one another as East Asians and Europeans are today.

I criticized that statement already back than. THey probably made this statement to make clear how different they were. But looking at the genetic data or any PCA. that statement is obviously wrong. The difference between Iran_Neolithic and Levant_Neolithic is not comparable to that of West and East Eurasians, not even in the slightest.

 

[davef]

I have a problem with this claim too. Many people come to the conclusion they were Bedouin like because they cluster on 2 dimensional PCAs just next to them. But this is merely projection bias. When I run ancient Levant Neolithic samples through calculators and compare them with Bedouin samples. One thing get's obvious. modern Bedouins have allot more Iran_Neolithic like admixture while in older calculators Levant_neolithics more of the Eastmed and even significant Westmed admixture in combination with the Southwest Asian component. While Bedouins are almost exclusively of the Southwest Asian variant.

So with other words Bdouins main components are actually allot more Eastern shifted (towards Iran_Neolithic) but the ~6-8% SSA admixture in them pushes them further towards Southwest on the PCA which makes them appear to be very close to Levant_Neolithic. While in reality Bedouins are like predominantly Levant_Neolithic + allot of Iran_Neolithic + some SSA.

With other words we basically don't have any modern population that fits ancient Levantine samples. The best fit would still be modern Lebanese minus the Iran_CHL admixture or Palestinians minus Iran_CHL and the little SSA admixture

You're right. My faulty memory is to blame, I've been under the weather lately. And it's interesting how modern Levantine populations are different from ancients, that iranian_chl shook the Levantine gene pool into something new. The closest to those ancient egyptian samples is Bronze Age levant by a landslide. Maybe perhaps the ancient Levantine gene pool was much more Egyptian like. I'd safely bet on that assumption.

 

[LeBrok]

You would know had you actually taken the time to read the paper, particularly figure S4.10; there's a big arrow from the WHG tree going straight into the Natufian tree with a 55% estimate upon it.

This one?
No Natufians, no levant Neolithic, not even Anatolian neolithic. Instead it shows connection of West Eurasian to EEF, though we know now that there was a direct gene donation from WHG to EEF, or even Anatolian Farmer. Quite outdated chart anyway.

Or this one? Again, no direct connection of WHG to Natufians! Doesn't even show ancestral connections through Basal Eurasian. There is known, indirect connection of WHG to Levant Neolithic mediated through Anatolian Neolithic, time in which Natufians didn't exist anymore.

Let's remember how it started, and what you said:

IIRC Lazaridis modeled Natufians roughly as 50% Basal Eurasian and 50% WHG;

Well, you didn't Remembered Correctly. One could have only hopped that you would notice it in time and corrected your statement. We would have avoided all of this unnecessary argumentation.

I'm going to explain to you what S4.10 actually says, because you are obviously lacking in reading with comprehension department. So, Lazaridis shows that EEF (not Natufians, which lived 6-8 thousand years before EEF) descended from Basal Eurasian in 44% and in 56% from common ancestor of EEF and WHG, the West Eurasians. That's all it says, in relation to our conversation.
How did you get the direct connection of WHG to Natufians from this table is beyond me, or Angela and many other members of Eupedia.

 

[davef]

These white supremacists nut jobs are as bad as Afro_Centrics. I have been commenting on some of these articles from various News websites. The headers of many of these articles are so misleading. For example Russia Todays headline is "Ancient Egyptians have ancestry from Europe and the Middle East", from Europe what?

Ancestry from Europe? How can anyone make that claim even after just skimming the supplement? The only "European" connection the Ancient Egyptians had with Europe was that small amount of Anatolian like ancestry they had, going by the chart. They were no more European than Palestinians.

To Russia Today:
"From" Europe? "From" where? Denmark?

Lol

 

[Alan]

You're right. My faulty memory is to blame, I've been under the weather lately. And it's interesting how modern Levantine populations are different from ancients, that iranian_chl shook the Levantine gene pool into something new. The closest to those ancient egyptian samples is Bronze Age levant by a landslide. Maybe perhaps the ancient Levantine gene pool was much more Egyptian like. I'd safely bet on that assumption.

Not so much though. It seems they had allot of Iran_CHL admixture already during Late Neolithic/Bronze Age. However what did shook up the region seems to have been a combination of all (Iranian_Iron AGE, African etc), but especially a Sub Saharan African admixture via the Slave trade. Since SSA admixture is so divergent to any of the ancestry the ancient Levantines had. It is this component that drifts them significantly away from ancient once. The same reason why modern Egyptians do not overlap a 100% with ancient once and it seems like ancient Egyptians are more akine to modern Jordanians or Palestinians. This is because modern Egyptians have more SSA admixture that drifts them away on the PCA allot.

 

[bicicleur 2]

You're right. My faulty memory is to blame, I've been under the weather lately. And it's interesting how modern Levantine populations are different from ancients, that iranian_chl shook the Levantine gene pool into something new. The closest to those ancient egyptian samples is Bronze Age levant by a landslide. Maybe perhaps the ancient Levantine gene pool was much more Egyptian like. I'd safely bet on that assumption.

could be
after all much of the Levant was occupied by the Egyptians till the bronze age collapse

 

[patrician]

Southeast Europe consists of present day populations from the areas of Italy, Greece, and the western Balkan states from Bulgaria to Croatia.
It would appear that present day populations in Southeast Europe show some of the highest rates of genetic relatedness to the second wave of migration into Europe roughly 11,000 years ago. This wave of migration consisted of Neolithic farmers from the fertile crescent and expanded primarily into southern Europe, incorporating small scattered European hunter-gatherer communities along their path. The island of Sardinia, having early evidence of postglacial hunter-gatherer inhabitants, was not permanently settled until this migration of Neolithic farmers from the fertile crescent populated it roughly 8,000 – 7,000 years ago. Although a key position in early Mediterranean trade routes, the populations of Sardinia remained relatively isolated genetically, and today, represent a particularly unique connection to Southeast European Neolithic ancestry.

 

[Angela]

I have a problem with this claim too. Many people come to the conclusion they were Bedouin like because they cluster on 2 dimensional PCAs just next to them. But this is merely projection bias. When I run ancient Levant Neolithic samples through calculators and compare them with Bedouin samples. One thing get's obvious. modern Bedouins have allot more Iran_Neolithic like admixture while in older calculators Levant_neolithics more of the Eastmed and even significant Westmed admixture in combination with the Southwest Asian component. While Bedouins are almost exclusively of the Southwest Asian variant.
The Southwest Asian itself is a component made up on Bedouins as proxy and combines Levant_Neo and Iran_Neo ancestry with possibly little SSA admixture.
So with other words Bdouins main components are actually allot more Eastern shifted (towards Iran_Neolithic) but the ~6-8% SSA admixture in them pushes them further towards Southwest on the PCA which makes them appear to be very close to Levant_Neolithic. While in reality Bedouins are like predominantly Levant_Neolithic + allot of Iran_Neolithic + some SSA.

With other words we basically don't have any modern population that fits ancient Levantine samples. The best fit would still be modern Lebanese minus the Iran_CHL admixture or Palestinians minus Iran_CHL and the little SSA admixture

I very much agree with the bolded comment. I'm not so sure about the rest, and I'm not speaking here about the PCA but about the Admixture analysis.

The Palestinians have a great deal of Iran Chl. While Bedouin A seem to have about the same amount, Bedouin B have less than either.

So, Bedouin B have the "advantage" of having less Chl. than the Palestinians, and no SSA, while the Palestinians have a similar amount of Anatolian Neolithic as the ancients, but a lot of Iran Chl as well the SSA.

Some of the Saudis are also very close to Bedouin B and also have a bit more Anatolian Neolithic. Of course, a lot of Saudis have SSA, while this group, if my eyes don't deceive me, do not.

I'll have to go back to the Supplement if I have a chance today, and see what other measures of relatedness have to show.

Modern calculators are a much less reliable measure than these comparisons using the actual ancient genomes.

If people start to play around with these genomes, it's important they use the non-SSA admixed group.

Does anyone know if those are the Negev group?

 

[harena]

This one?
No Natufians, no levant Neolithic, not even Anatolian neolithic. Instead it shows connection of West Eurasian to EEF, though we know now that there was a direct gene donation from WHG to EEF, or even Anatolian Farmer. Quite outdated chart anyway.

That's not even in the 2016 Lazaridis paper I referenced, getting desperate much? This picture has been around since 2013 and is quite frankly outdated. It also hilariously contradicts what you claimed right below: WHG in Levant Neolithic mediated via Anatolia Neolithic.
Good try though.

Or this one? Again, no direct connection of WHG to Natufians! Doesn't even show ancestral connections through Basal Eurasian. There is known, indirect connection of WHG to Levant Neolithic mediated through Anatolian Neolithic, time in which Natufians didn't exist anymore.

Nope. This is Table 4.a where Natufians aren't even modeled. It only confirms that they derive 45% of their ancestry from Basal Eurasian, they didn't bother with the remaining 55% probably cause it's not the focus (neareastern farmers are, as per the title of the paper) of the chart. However this is consistent with the 55% WHG-related input they estimated in figure S4.10 and that I reported in my previous comment.
By the way even Anatolian farmers are admixed with something more like WHG-related rather than WHG, the authors described it as something like Switzerland HG Bichon but even more extreme. This is probably the best description of the WHG-related source in Natufians as well.

Let's remember how it started, and what you said:

Well, you didn't Remembered Correctly. One could have only hopped that you would notice it in time and corrected your statement. We would have avoided all of this unnecessary argumentation.

I'm going to explain to you what S4.10 actually says, because you are obviously lacking in reading with comprehension department. So, Lazaridis shows that EEF (not Natufians, which lived 6-8 thousand years before EEF) descended from Basal Eurasian in 44% and in 56% from common ancestor of EEF and WHG, the West Eurasians. That's all it says, in relation to our conversation.
How did you get the direct connection of WHG to Natufians from this table is beyond me, or Angela and many other members of Eupedia.

There isn't even EEF in fig. S4.10, what are you babbling about? Read the paper before pretending to explain anything.
You are also deeply delusional if you think anything like the broad "West Eurasian" group (Goyet, Vestonice, Kostenki14) can be somehow conflated with WHG/WHG-related; Iosif specifically employed WHG as proxy.
WHG (Villabruna cluster) is something specific that emerged in the late Upper Paleolithic and is sharply distinct from the pre-existing lineages in UP West Eurasia. Even El Miron (5ky older than Villabruna) who has proto-WHG ancestry plots nowhere near the WHG cluster.
So WHG is definitely more accurate than the West Eurasian nonsense you're pushing. Now you can keep splitting hair using WHG-like, WHG-related and whgatnot, the big picture stays roughly the same.

Quoting again for emphasis:

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.

The population structure of the ancient Near East was not independent of that of Europe (Supplementary Information, section 4), as evidenced by the highly significant (Z=-8.9) statistic f(Iran_N, Natufian;WHG, EHG) which suggests gene flow in ‘northeastern’ (Neolithic Iran/EHG) and ‘southwestern’ (Levant/WHG) interaction spheres (Fig. 4d).

 

[LeBrok]

That's not even in the 2016 Lazaridis paper I referenced, getting desperate much? This picture has been around since 2013 and is frankly outdated, especially considering the keener tools and ancient genomes we have today.



Nope. This is Table 4.a where Natufians aren't even modeled. It only confirms that they derive 45% of their ancestry from Basal Eurasian, they didn't bother with the remaining 55% probably cause it's not the focus (neareastern farmers are, as per the title of the paper) of the chart. However this is consistent with the 55% WHG-related input they estimated in figure S4.10 and that I reported in my previous comment.
By the way even Anatolian farmers are admixed with something more like WHG-related rather than WHG, the authors described it as something like Switzerland HG Bichon but even more extreme. This is probably the best description of the WHG-related source in Natufians as well.



Oh!



There isn't even EEF in fig. S4.10, what are you babbling about? Read the paper before pretending to explain anything.
You are also deeply delusional if you think anything like the broad "West Eurasian" group (Goyet, Vestonice, Kostenki14) can be somehow conflated with WHG/WHG-related; Iosif specifically employed WHG as proxy.
WHG (Villabruna cluster) is something specific that emerged in the late Upper Paleolithic and is sharply distinct from the pre-existing lineages in UP West Eurasia. Even El Miron (5ky older than Villabruna) who has proto-WHG ancestry plots nowhere near the WHG cluster.
So WHG is definitely more accurate than the West Eurasian nonsense you're pushing. Now you can keep splitting hair using WHG-like, WHG-related and whgatnot, the big picture stays roughly the same.

Quoting again for emphasis:

Ok, if you are so anxious of digging a bigger hole, go ahead and post the chart you are referring to. And remember it has to agree with your statement.

Originally Posted by harena
IIRC Lazaridis modeled Natufians roughly as 50% Basal Eurasian and 50% WHG;

Here is your last chance to come clean. Was your statement misleading or just wrong?

 

[Sile]

. So, Lazaridis shows that EEF (not Natufians, which lived 6-8 thousand years before EEF) descended from Basal Eurasian in 44% and in 56% from common ancestor of EEF and WHG, the West Eurasians. That's all it says, in relation to our conversation.
How did you get the direct connection of WHG to Natufians from this table is beyond me, or Angela and many other members of Eupedia.

thats a silly comment , ..............EEF lived 6-8 thousand years before EEF was created ?

All haplogroups from https://en.wikipedia.org/wiki/Haplogroup_GHIJK where WHG or EHG before become EEF ...............which of these then became EEF ?

 

[LeBrok]

thats a silly comment , ..............EEF lived 6-8 thousand years before EEF was created ?

All haplogroups from https://en.wikipedia.org/wiki/Haplogroup_GHIJK where WHG or EHG before become EEF ...............which of these then became EEF ?

In your head Natufians are EEF?! The Natufians are 6-8 ky older than EEF.

(not Natufians, which lived 6-8 thousand years before EEF)

 

[Sile]

In your head Natufians are EEF?! The Natufians are 6-8 ky older than EEF.

your the one that said it , it is embarrasing that you are trying to deflect it on me when you stated it

I questioned your silly comment ..............who told you this, Laz?

 

[Alan]

I very much agree with the bolded comment. I'm not so sure about the rest, and I'm not speaking here about the PCA but about the Admixture analysis.

The Palestinians have a great deal of Iran Chl. While Bedouin A seem to have about the same amount, Bedouin B have less than either.

So, Bedouin B have the "advantage" of having less Chl. than the Palestinians, and no SSA, while the Palestinians have a similar amount of Anatolian Neolithic as the ancients, but a lot of Iran Chl as well the SSA.

Some of the Saudis are also very close to Bedouin B and also have a bit more Anatolian Neolithic. Of course, a lot of Saudis have SSA, while this group, if my eyes don't deceive me, do not.

I'll have to go back to the Supplement if I have a chance today, and see what other measures of relatedness have to show.

Modern calculators are a much less reliable measure than these comparisons using the actual ancient genomes.

If people start to play around with these genomes, it's important they use the non-SSA admixed group.

Does anyone know if those are the Negev group?

I agree that small pockets of Bedouins do look quite similar to Levant_Neolithic or Egyptians. But here is the problem. They are isolated pockets. When I speak of populations I mean them as a whole as average of a population. As the people we see when we come across a ethnic Saudi or Palestinian or whoever. On Average unfortunately there is no modern population that fits ancient once 100%.

As you also pointed out the best fit are still Palestinians, Jordanians without the small amount of SSA admixture and with less Iran_CHL like admixture.

While ancient Egyptians would still be best decribed as modern Egyptians + additional SSA (8%).

 

[Alan]

Guys I think both sides here are talking bypassing each other. I get the point of harena as wel LeBrock. LeBrock is correct in saying that the admixture in Anatolian_Farmers and Natufians is not WHG per se because WHG (as the name indicates, Western Hunters and Gatherers) is modeled after mesolithic Hunters from Europe. It is definitely not the case that European Hunters and Gatherers donated the WHG like ancestry to Natufians. Since WHG and Natufians are roughly of same age.

What LeBrock is trying to say is that a group ancestral to these Bishon Hunter and Gatherer who most definitely came from a region spanning the Levant, Anatolia and Balkans contributed to Natufians (they most likely where there even before the Basal Eurasians).

Basically we have a proto WHG population that expanded first throughout Europe and the western part of the Near East.

It's just the different terminologies.