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holderlin
30-05-17, 18:44
https://www.nature.com/articles/ncomms15694

Check it out.

Very little SSA compared to modern Egyptians, and very similar to Bronze Age Levant

The three males' Y HG calls from Genetiker are below:

JK2134 Pre-Ptolemaic 776–569BC J1a2a2-Z2329 calls (https://genetiker.wordpress.com/y-snp-calls-for-jk2134/)
JK2911 Pre-Ptolemaic 769–560BC J2b1-PF7314 calls (https://genetiker.wordpress.com/y-snp-calls-for-jk2911/)
JK2888 Ptolemaic 97–2BC E1b1b1a1b2-V22 calls (https://genetiker.wordpress.com/y-snp-calls-for-jk2888/)

davef
30-05-17, 18:59
No surprise that they would be Levantine in nature.

Megalophias
30-05-17, 19:36
They did have SSA. Less than modern Egyptians though.

On the PCA modern Egyptians are close but shifted towards Arabs ISTM.

holderlin
30-05-17, 19:59
They did have SSA. Less than modern Egyptians though.

On the PCA modern Egyptians are close but shifted towards Arabs ISTM.

I guess they do say this, but compared to modern day populations it's very small. I can't even see it on the plots.

I edited the OP.

holderlin
30-05-17, 20:02
I'm a little bummed there's no Old Kingdom, but if simple spatial logic is applied they should look closer to Natufian with less Anatolian Neo, and Iranian Neo.

Angela
30-05-17, 20:33
Thanks, Holderlin.

We started a preliminary discussion based on the abstract here:
http://www.eupedia.com/forum/threads/33739-Ancient-Egyptian-dna-Kraus-et-al?highlight=SSA+ancient+Egyptians

"Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level."

I think some pertinent questions were raised, but they'll have to be examined in light of the data we now have from the actual paper.

"So the samples are from 1070 BC forward, and after the Hyksos and Sea Peoples, but also after the time of Rameses III and his SSA yDna, yes? Interesting."

I also wondered how the Copts would compare.

holderlin
30-05-17, 20:46
@Angela didn't see that, thanks.

Angela
30-05-17, 20:50
Actually, this is the time period and what they were examining:
"all sampled remains derive from this community in Middle Egypt and have been radiocarbon dated to the late New Kingdom to the Roman Period (cal. 1388BCE–426CE, Supplementary Data 1 (https://www.nature.com/articles/ncomms15694#s1)). In particular, we seek to determine if the inhabitants of this settlement were affected at the genetic level by foreign conquest and domination, especially during the Ptolemaic (332–30BCE) and Roman (30BCE–395CE) Periods."

The site is Abusir el-Meleq, which is sortNile of mid . I probably shouldn't comment as I'm just starting to read, but doesn't it seem an odd place to look for Greek and Roman introgression? It was in the delta, in Alexandria, where Greeks were perhaps half of the population.

Ah, it's near Fayum.

Ed. Honestly, is it my allergies or early senility. I made a stupid word substitution and a typo!

Hauteville
30-05-17, 20:51
They did have SSA. Less than modern Egyptians though.

On the PCA modern Egyptians are close but shifted towards Arabs ISTM.

No because on this graphic the ancient egyptian samples did not have yoruban-like admixture.

https://s16.postimg.org/m9inpse79/ncomms15694-f4.jpg (https://postimg.org/image/5yijth1pd/)host immagini (https://postimage.io/index.php?lang=italian)

Yetos
30-05-17, 21:08
Actually, this is the time period and what they were examining:
"all sampled remains derive from this community in Middle Egypt and have been radiocarbon dated to the late New Kingdom to the Roman Period (cal. 1388BCE–426CE, Supplementary Data 1 (https://www.nature.com/articles/ncomms15694#s1)). In particular, we seek to determine if the inhabitants of this settlement were affected at the genetic level by foreign conquest and domination, especially during the Ptolemaic (332–30BCE) and Roman (30BCE–395CE) Periods."

The site is Abusir el-Meleq, which is sort of mid isle. I probably shouldn't comment as I'm just starting to read, but doesn't it seem an odd place to look for Greek and Roman introgressio? It was in the delta, in Alexandria, where Greeks were perhaps half of the population.

Ah, it's near Fayum.


That makes me also wonder,

Angela
30-05-17, 21:22
Nice admixture graph. Slightly off-topic, but this visual is a nice illustration of why PCA is only one way of looking at the data. Unless I'm reading it wrong, on the PCA the ancient Egyptians look like they're sitting right on top of Bedouin A, and yet the admixture run shows they're quite different.

Strange that the Saudi group they tested has no SSA. Going by this it looks like the ancient Egyptians are closest to Bronze Age Levant and these strangely non SSA Saudis. Other things are about as expected. North African Jews picked up some Berber, but it was before the North Africans got all that SSA it looks like. Tunisians and Algerians are very similar. Bedouin A has SSA, Bedouin B doesn't. Anybody know if the Bedouin tribes that went to Palestine and Jordan were predominantly Bedouin A?

Well, here's one thing I was very wrong about, along with a lot of other people. The Druse were not a good proxy for the Neolithic migrations to Europe. They have a lot of Iran Chl, even a lot more than in the Levant Bronze Age. Maybe what they represent is the population in the Levant around the beginning of the modern era? Or, do they have more Iran Chl for one reason or another

Why on earth no Copts?

Do they do an analysis elsewhere using East Africans? Or would that just pick up all that shared ancestry? Is most of Saudi "African" ancestry actually East African? From what I remember even regular Saudis, not peripheral groups, have a ton of African mtDna.

Angela
30-05-17, 21:44
@Hauteville,

They may not show it in Admixture, but it's there. I have to read the Supplement, but they probably are using Mbuti for some of these tests.

" Finally, we used two methods to estimate the fractions of sub-Saharan African ancestry in ancient and modern Egyptians. Both qpAdm35 (https://www.nature.com/articles/ncomms15694#ref35) and the f4-ratio test39 (https://www.nature.com/articles/ncomms15694#ref39)reveal that modern Egyptians inherit 8% more ancestry from African ancestors than the three ancient Egyptians do, which is also consistent with the ADMIXTURE results discussed above. Absolute estimates of African ancestry using these two methods in the three ancient individuals range from 6 to 15%, and in the modern samples from 14 to 21% depending on method and choice of reference populations (see Supplementary Note 1 (https://www.nature.com/articles/ncomms15694#s1), Supplementary Fig. 6 (https://www.nature.com/articles/ncomms15694#s1), Supplementary Tables 5–8 (https://www.nature.com/articles/ncomms15694#s1)). We then used ALDER40 (https://www.nature.com/articles/ncomms15694#ref40) to estimate the time of a putative pulse-like admixture event, which was estimated to have occurred 24 generations ago (700 years ago), consistent with previous results from Henn and colleagues16 (https://www.nature.com/articles/ncomms15694#ref16). While this result by itself does not exclude the possibility of much older and continuous gene flow from African sources, the substantially lower African component in our ∼2,000-year-old ancient samples suggests that African gene flow in modern Egyptians occurred indeed predominantly within the last 2,000 years."

Well, that may be overstating it a tad, yes? It's not a huge jump from 6 to 14%, or from 15 to 22%, and this is just one site. Sites further south might have been quite different.

Well, I guess we know now that Ramses' African "Y" was not a fluke. The Egyptians of this era did have some SSA, even if it wasn't very substantial. It remains to be seen what it was like further back in time.

Angela
30-05-17, 21:52
Honestly, not the correct site, as they themselves implicitly acknowledge.

" Abusir el-Meleq’s proximity to, and close ties with, the Fayum are significant in the context of this study as the Fayum in particular saw a substantial growth in its population during the first hundred years of Ptolemaic rule, presumably as a result of Greek immigration33 (https://www.nature.com/articles/ncomms15694#ref33),43 (https://www.nature.com/articles/ncomms15694#ref43). Later, in the Roman Period, many veterans of the Roman army—who, initially at least, were not Egyptian but people from disparate cultural backgrounds—settled in the Fayum area after the completion of their service, and formed social relations and intermarried with local populations44 (https://www.nature.com/articles/ncomms15694#ref44). Importantly, there is evidence for foreign influence at Abusir el-Meleq. Individuals with Greek, Latin and Hebrew names are known to have lived at the site and several coffins found at the cemetery used Greek portrait image and adapted Greek statue types to suit ‘Egyptian’ burial practices2 (https://www.nature.com/articles/ncomms15694#ref2),45 (https://www.nature.com/articles/ncomms15694#ref45). The site’s first excavator, Otto Rubensohn, also found a Greek grave inscription in stone as well as a writing board inscribed in Greek46 (https://www.nature.com/articles/ncomms15694#ref46). Taken together with the multitude of Greek papyri that were written at the site, this evidence strongly suggests that at least some inhabitants of Abusir el-Meleq were literate in, and able to speak, Greek45 (https://www.nature.com/articles/ncomms15694#ref45). However, a general issue concerning the site is that several details of the context of the individuals analysed in this study were lost over time."

This verges on the silly. You need the context of the samples to make a determination that they are likely to show any introgression that occurred. It doesn't exist for these three samples.

How disappointing. If the Egyptian government allowed access to samples from more promising sites, we might get some answers as to the amount, if any, of Greek and Roman introgression, or if it was sort of like the German communities in the Balkans, where they lived alongside the natives for hundred of years, but didn't intermingle.

I1a3_Young
30-05-17, 22:04
Estimating phenotypesFinally, we analysed several functionally relevant SNPs in sample JK2911, which had low contamination and relatively high coverage. This individual had a derived allele at the SLC24A5 locus, which contributes to lighter skin pigmentation and was shown to be at high frequency in Neolithic Anatolia41 (https://www.nature.com/articles/ncomms15694#ref41), consistent with the ancestral affinity shown above. Other relevant SNPs carry the ancestral allele, including HERC2 and LCT, which suggest dark-coloured eyes and lactose intolerance (Supplementary Table 9 (https://www.nature.com/articles/ncomms15694#s1)).



Seems expected. I wonder if their procedures to rule out contamination were only for modern contamination or also apply to the mummy prep. These mummies would have been extensively handled and processed by possibly those of slave status. Or maybe not? Still makes me wonder.

Angela
30-05-17, 22:09
This is after the Hyksos, and its a Hyksos site, so perhaps explaining the Iran Chl. Like I said, wrong site.

Plus, depends what you mean by ancient, right? Maybe more introgression from the Near East lowered the amount of the SSA.

DuPidh
31-05-17, 02:01
Nice admixture graph. Slightly off-topic, but this visual is a nice illustration of why PCA is only one way of looking at the data. Unless I'm reading it wrong, on the PCA the ancient Egyptians look like they're sitting right on top of Bedouin A, and yet the admixture run shows they're quite different.

Strange that the Saudi group they tested has no SSA. Going by this it looks like the ancient Egyptians are closest to Bronze Age Levant and these strangely non SSA Saudis. Other things are about as expected. North African Jews picked up some Berber, but it was before the North Africans got all that SSA it looks like. Tunisians and Algerians are very similar. Bedouin A has SSA, Bedouin B doesn't. Anybody know if the Bedouin tribes that went to Palestine and Jordan were predominantly Bedouin A?

Well, here's one thing I was very wrong about, along with a lot of other people. The Druse were not a good proxy for the Neolithic migrations to Europe. They have a lot of Iran Chl, even a lot more than in the Levant Bronze Age. Maybe what they represent is the population in the Levant around the beginning of the modern era? Or, do they have more Iran Chl for one reason or another

Why on earth no Copts?

Do they do an analysis elsewhere using East Africans? Or would that just pick up all that shared ancestry? Is most of Saudi "African" ancestry actually East African? From what I remember even regular Saudis, not peripheral groups, have a ton of African mtDna.

Is today's Cyprus population the closest possible to Levant, at the time of ancient Egypt?
I am trying to picture how did the Levant people looked back then

Angela
31-05-17, 03:38
Is today's Cyprus population the closest possible to Levant, at the time of ancient Egypt?
I am trying to picture how did the Levant people looked back then

Levant Bronze Age is very similar to the ancient Egyptian sample, which I think will turn out to be close to the Egyptian Copts. They don't at all look Cypriot to me.

https://thetablet.org/wp-content/uploads/2013/08/copt.jpg

http://www.denverpost.com/wp-content/uploads/2016/12/afp_j0350.jpg?w=525

http://news.bbcimg.co.uk/media/images/63782000/jpg/_63782333_63782332.jpg

Greek Cypriots:
http://in-cyprus.com/wp-content/uploads/2016/10/STK_1563.jpg


Obviously, there are a few non-Cypriots in the following. :)
http://media.worldbulletin.net/250x190/2013/11/30/adsiz_1.jpg

Plus, didn't the paper on the Canaanites tell us that these Bronze Age Canaanite samples have no derived SLC45A2, so not only different than people in the Levant today, but also quite a bit darker than the people of the Anatolia Neolithic and the EEF of Europe, who did have reasonably high percentages of derived SLC45A2. In fact, I think a recent paper revised those estimates upwards from where they were a while ago.. This might suggest that most of the Iran Chl, like the CHG themselves, only had the derived SLC25A2 allele, and thus were rather darker than not only Anatolia Neolithic, but also Levant Neolithic, since some of them also had derived SLC45A2, although the Natufians did not.

The admixture run isn't optimal, but going by that the Bronze Age Levant doesn't look all that different from the Saudis. So, maybe tribal Saudis or Yeminis without obvious SSA?

http://c8.alamy.com/comp/F8N8NW/sanaa-yemen-10th-dec-2015-yemeni-tribal-men-attend-a-rally-against-F8N8NW.jpg



https://upload.wikimedia.org/wikipedia/commons/9/9d/Bedouin_family-Wahiba_Sands.jpg

Who knows, though?

LeBrok
31-05-17, 04:45
Interestingly, modern Near Easterners are the construct of BA mixing, a similar process as in Europe in BA. Well, there are some changes since, but not that dramatic.

Looks like modern Palestinians and Bedouin A are the closest to Levant BA and BA Egypt. Was Levant BA the Semitic birthplace?

davef
31-05-17, 05:10
Hmmm....by the graph, it seems that the ancient Egyptians were closest to modern north (east) Africans. Makes sense. I always figured that far northeast africans (by far I mean way up north near the Mediterranean and east as in near the Levant) were Levantines with a dash of Sub Saharan.

Angela
31-05-17, 06:17
Hmmm....by the graph, it seems that the ancient Egyptians were closest to modern north (east) Africans. Makes sense. I always figured that far northeast africans (by far I mean way up north near the Mediterranean and east as in near the Levant) were Levantines with a dash of Sub Saharan.

From the graphic posted I don't see that at all, unless you're coining your own definitions for population groups. Northeast Africans are Horners.

The only "Africans" the ancient Egyptians from this period plot close to are North Africans, who are mostly Levantines with SSA, more than half of it coming in the last 2000 years, presumably through the Arab slave trade, plus whatever traces of the prior population(s) are left. None of that is a surprise.

Anyone who has been paying attention to the papers knows that two major population flows moved out of the Near East, the western farmers, and then a few thousand years later a population related to the Iranian farmers. Both spread over vast distances and mixed with earlier populations where ever they went. The first group spread all along the southern coast of the Mediterranean, among many other places, and even deep into Africa. We can see the traces of the second major Near East group in northern Africa too, but in much smaller percentages.

Basically, as LeBrok pointed out, the Bronze Age may be the last really major population upheaval in western Eurasia. As I stated in another thread, the second gene flow out of the Near East, which was less consequential for most of Europe was like a pincer movement into Europe, I believe, with part of it going over the Caucasus and onto the steppe, and part of it going into southeastern and southern Europe, as well as all over the Near East, and some of it even reaching North Africa.

It looks like a modified version of the old Dienekes theory of the Womb of Nations to me, but as you have to consider also the western farmers, it's not just the Caucasus area, but the Anatolia/Levant region as well.

ThirdTerm
31-05-17, 07:19
Our analysis furthermore shows that derived alleles for the genes SLC24A5, known to be responsible for partially lighter skin pigmentation were present in both JK2888 and JK2911 (see Supplementary Note 6 for details). For further genes such as SLC45A2, LCT and EDAR we were unable to find derived alleles for both JK2888 and JK2911. For JK2134, there was no sufficient coverage after quality filtering at all the specific sites, which is why the analysis revealed no further clues.


Supplementary Data 3 shows that mtDNA haplogroups for the three ancient Egyptian samples JK2134 JK2888 and JK2911 are J1d, U6a2 and M1a1, respectively. J1d and its subclades are considered Near Eastern and U6a2 is close to the East African cluster U6a2a. M1a1 was also found in Ethiopia and the majority of the M1a lineages found in Africa had a more recent Eastern African origin. These ancient Egyptian mummies had partially light skin pigmentation without further light skin pigmentation genes and they probably resembled modern-day East Africans. Ethiopians are known to plot closer to Near Easterners in PCA, suggesting a much larger Eurasian genetic component in East Africa.

https://jewamongyou.files.wordpress.com/2011/10/ethiopian-women1.jpg

davef
31-05-17, 07:39
From the graphic posted I don't see that at all, unless you're coining your own definitions for population groups. Northeast Africans are Horners.

The only "Africans" the ancient Egyptians from this period plot close to are North Africans, who are mostly Levantines with SSA, more than half of it coming in the last 2000 years, presumably through the Arab slave trade, plus whatever traces of the prior population(s) are left. None of that is a surprise.

Anyone who has been paying attention to the papers knows that two major population flows moved out of the Near East, the western farmers, and then a few thousand years later a population related to the Iranian farmers. Both spread over vast distances and mixed with earlier populations where ever they went. The first group spread all along the southern coast of the Mediterranean, among many other places, and even deep into Africa. We can see the traces of the second major Near East group in northern Africa too, but in much smaller percentages.

Basically, as LeBrok pointed out, the Bronze Age may be the last really major population upheaval in western Eurasia. As I stated in another thread, the second gene flow out of the Near East, which was less consequential for most of Europe was like a pincer movement into Europe, I believe, with part of it going over the Caucasus and onto the steppe, and part of it going into southeastern and southern Europe, as well as all over the Near East, and some of it even reaching North Africa.

It looks like a modified version of the old Dienekes theory of the Womb of Nations to me, but as you have to consider also the western farmers, it's not just the Caucasus area, but the Anatolia/Levant region as well.
Sorry for mis-wording things, by northeast Africans I was referring to modern Egyptians, Tunisians, and Algerians. These groups are the closest to the ancient Egyptian samples studied in this study.

Hauteville
31-05-17, 10:05
Those samples have an extra Iran_Neolithic, maybe they are mixed with Hyksos more than purest ancient Egyptians.

Fire Haired14
31-05-17, 11:44
Interestingly, modern Near Easterners are the construct of BA mixing, a similar process as in Europe in BA. Well, there are some changes since, but not that dramatic.

For some parts of the Middle East it occurred before the BA. The three genetic components Caucasians are makeup of; EHG, EEF, CHG were present in the Caucasus by at least 4000 BC. The same could be true for Anatolia and Mesoptamia. IranChalolithic isn't radically different from Assyrians, Kurds, Persians, etc.

Maybe nothing like the expansion of Steppe ancestry in Europe occurred in the Middle East. It expanded from out of a pocket in Russia to most of Europe in about 500 years.

MarkoZ
31-05-17, 12:21
Looks like modern Palestinians and Bedouin A are the closest to Levant BA and BA Egypt. Was Levant BA the Semitic birthplace?

I think the southern Levant is most commonly proposed as the homeland of Semitic. Those Bedouin samples incidentally are from the Negev just south of the Levant.

DuPidh
31-05-17, 13:00
Levant Bronze Age is very similar to the ancient Egyptian sample, which I think will turn out to be close to the Egyptian Copts. They don't at all look Cypriot to me.

https://thetablet.org/wp-content/uploads/2013/08/copt.jpg

http://www.denverpost.com/wp-content/uploads/2016/12/afp_j0350.jpg?w=525

http://news.bbcimg.co.uk/media/images/63782000/jpg/_63782333_63782332.jpg

Greek Cypriots:
http://in-cyprus.com/wp-content/uploads/2016/10/STK_1563.jpg


Obviously, there are a few non-Cypriots in the following. :)
http://media.worldbulletin.net/250x190/2013/11/30/adsiz_1.jpg

Plus, didn't the paper on the Canaanites tell us that these Bronze Age Canaanite samples have no derived SLC45A2, so not only different than people in the Levant today, but also quite a bit darker than the people of the Anatolia Neolithic and the EEF of Europe, who did have reasonably high percentages of derived SLC45A2. In fact, I think a recent paper revised those estimates upwards from where they were a while ago.. This might suggest that most of the Iran Chl, like the CHG themselves, only had the derived SLC25A2 allele, and thus were rather darker than not only Anatolia Neolithic, but also Levant Neolithic, since some of them also had derived SLC45A2, although the Natufians did not.

The admixture run isn't optimal, but going by that the Bronze Age Levant doesn't look all that different from the Saudis. So, maybe tribal Saudis or Yeminis without obvious SSA?

http://c8.alamy.com/comp/F8N8NW/sanaa-yemen-10th-dec-2015-yemeni-tribal-men-attend-a-rally-against-F8N8NW.jpg



https://upload.wikimedia.org/wikipedia/commons/9/9d/Bedouin_family-Wahiba_Sands.jpg

Who knows, though?
There were comments from newspapers about this study as well. One paper I read on line was saying that the study showed that (many mummies of 96 of them, where they were able to extract DNA) mummies were carrying the gene for white skin. The population of Egypt back then was compared with Turkeys population today. Since Turkey today has all possible shades of European populations I don't know what they mean by Turkish. That's why I said probably Cyprus was the best candidate.

DuPidh
31-05-17, 13:15
Levant Bronze Age is very similar to the ancient Egyptian sample, which I think will turn out to be close to the Egyptian Copts. They don't at all look Cypriot to me.

https://thetablet.org/wp-content/uploads/2013/08/copt.jpg

http://www.denverpost.com/wp-content/uploads/2016/12/afp_j0350.jpg?w=525

http://news.bbcimg.co.uk/media/images/63782000/jpg/_63782333_63782332.jpg

Greek Cypriots:
http://in-cyprus.com/wp-content/uploads/2016/10/STK_1563.jpg


Obviously, there are a few non-Cypriots in the following. :)
http://media.worldbulletin.net/250x190/2013/11/30/adsiz_1.jpg

Plus, didn't the paper on the Canaanites tell us that these Bronze Age Canaanite samples have no derived SLC45A2, so not only different than people in the Levant today, but also quite a bit darker than the people of the Anatolia Neolithic and the EEF of Europe, who did have reasonably high percentages of derived SLC45A2. In fact, I think a recent paper revised those estimates upwards from where they were a while ago.. This might suggest that most of the Iran Chl, like the CHG themselves, only had the derived SLC25A2 allele, and thus were rather darker than not only Anatolia Neolithic, but also Levant Neolithic, since some of them also had derived SLC45A2, although the Natufians did not.

The admixture run isn't optimal, but going by that the Bronze Age Levant doesn't look all that different from the Saudis. So, maybe tribal Saudis or Yeminis without obvious SSA?

http://c8.alamy.com/comp/F8N8NW/sanaa-yemen-10th-dec-2015-yemeni-tribal-men-attend-a-rally-against-F8N8NW.jpg



https://upload.wikimedia.org/wikipedia/commons/9/9d/Bedouin_family-Wahiba_Sands.jpg

Who knows, though?
This one is a coment by "washington post" about the topic:The scientists compared these ancient genetics with those of 100 modern Egyptians and 125 modern Ethiopians that had been previously analyzed. If you ask Egyptians, they'll say that they have become more European recently, Krause said. “We see exactly the opposite,” he said.


So The post is saying that back then many Egyptians from this site looked more European

Fire Haired14
31-05-17, 13:41
I knew the reporters would miss interpret derived allele A111t(rs1426654) in ancient Egyptians. That mutation is overrated. For too long it was viewed as the cause of European light skin. But still today researchers overrate its affect on skin color.

Yeah, that mutation in ancient Egyptians indicates their skin wasn't as Black as night but it doesn't indicate they had "light skin" which is what the paper said. Now I bet some articles online are going to miss interprat that information and information about Egyptians relationship to Neolithic Europeans and conclude ancient Egyptians were white Europeans.

Just look at ancient Egyptian art. They depicted themselves with brown skin.

davef
31-05-17, 14:45
I knew the reporters would miss interpret derived allele A111t(rs1426654) in ancient Egyptians. That mutation is overrated. For too long it was viewed as the cause of European light skin. But still today researchers overrate its affect on skin color.

Yeah, that mutation in ancient Egyptians indicates their skin wasn't as Black as night but it doesn't indicate they had "light skin" which is what the paper said. Now I bet some articles online are going to miss interprat that information and information about Egyptians relationship to Neolithic Europeans and conclude ancient Egyptians were white Europeans.

Just look at ancient Egyptian art. They depicted themselves with brown skin.

I agree with you! I'm tired of euro centrists, Nordicists, and skinheads stating that they claim every ancient civilization bc that's crazy talk. And yes, by the data, the ancient Egyptians were NOT genetically close to european farmers. Not by a long shot.

I1a3_Young
31-05-17, 15:09
Skin genes are not like hair and eye genes, based on personal observations of mixed people. Hair and eyes have dominant and recessive genes, of which color is one component. Skin of mixed people is always a gradient between the parents. Mix a Nigerian and a Swede and you will always get the brown color in between, but never a white or black skin. The eyes and hair would be dark and less coarse than the Nigerian's, but the children of that mixed child could produce light hair or eyes if their partner had the correct genes.

Therefore, I'm not sure how you can say "light skin genes" as it appears to be much more fluid than other types of genes.

John Doe
31-05-17, 15:45
I agree with you! I'm tired of euro centrists, Nordicists, and skinheads stating that they claim every ancient civilization bc that's crazy talk. And yes, by the data, the ancient Egyptians were NOT genetically close to european farmers. Not by a long shot.

At the same time you have the We Wuz Kingz Afro-centrists who claim that ancient Chinese were black, the vikings were black, Shakespeare was black etc.

I1a3_Young
31-05-17, 15:48
At the same time you have the We Wuz Kingz Afro-centrists who claim that ancient Chinese were black, the vikings were black, Shakespeare was black etc.

Heh I have met those. Frustrating and amusing at the same time. I suppose there's an internal affinity towards tribalism that makes people behave this way. Afro master race! Nordic master race! Celtic master race! Italian master race! Iberian master race! Croatian master race! Japanese master race! etc.

davef
31-05-17, 16:02
At the same time you have the We Wuz Kingz Afro-centrists who claim that ancient Chinese were black, the vikings were black, Shakespeare was black etc.

I agree, they're just as bad.

bicicleur
31-05-17, 16:41
Skin genes are not like hair and eye genes, based on personal observations of mixed people. Hair and eyes have dominant and recessive genes, of which color is one component. Skin of mixed people is always a gradient between the parents. Mix a Nigerian and a Swede and you will always get the brown color in between, but never a white or black skin. The eyes and hair would be dark and less coarse than the Nigerian's, but the children of that mixed child could produce light hair or eyes if their partner had the correct genes.

Therefore, I'm not sure how you can say "light skin genes" as it appears to be much more fluid than other types of genes.

I don't think so.
I know of a case where a white woman cheated on her white husband with a black man and got a perfect white daughter, and the white husband was never aware of the cheating.
Then the white daughter got pregnant from her white boyfriend and got a black son.
Her white boyfriend rejected her and her black son, untill a DNA test proved what had realy happened.

Angela
31-05-17, 16:48
Look, for the ten thousandths time, gentlemen, pigmentation is a polygenic trait. There's no way we can get a fix on it without getting the results for a whole group of alleles and running them through algorithms. That's why the academics always speak in relative terms.

The allele in question does impact skin color. However, what is commonly perceived as "European" skin color pigmentation also seems to be very affected by derived SLC45A2. Going by memory, the paper on the Canaanites said that among today's Levantines, 1/3 (or was it 2/3?) have at least one copy of derived SLC45A2 along with the other major skin lightening allele. So, all they could say is that the Bronze Age Canaanites and the Levant Bronze Age people were probably darker than some of today's people from the same region. The ancient Egyptian samples also lack this second skin lightening allele, and they also possess some degree of SSA which the ancient samples from the Levant did not, so I highly doubt they were German looking or Greek Cypriot looking. Neither, however, did they look SSA. So, I guess racists on either side aren't happy.

Reporters always get things wrong. It's just the way it is.

holderlin
31-05-17, 16:50
We Wuz Kingz
:laughing::laughing::laughing:

Angela
31-05-17, 16:56
I agree with you! I'm tired of euro centrists, Nordicists, and skinheads stating that they claim every ancient civilization bc that's crazy talk. And yes, by the data, the ancient Egyptians were NOT genetically close to european farmers. Not by a long shot.I don't know what you mean by that. They had a lot of "farmer" ancestry. Perhaps it was more Levant Neolithic, but Levant Neolithic contained minority Anatolian Neolithic, just as Anatolian Neolithic contained minority Levant Neolithic. Plus, which European farmers do you mean? The early Neolithic farmers in Europe picked up almost no additional WHG. That only happened thousands of years later in the MN, when it went up to about 20-25% depending on the area.

Of course, it seems the Egyptians from the era in question did have some Iran Chl. type material, but it wasn't much. They did have, for a lower bound number, about 6% SSA, which European Neolithic people did not.

The skin pigmentation of European farmers also seems to have been quite different. On the other hand, everybody at that point in time was darker than today.

Angela
31-05-17, 16:59
I think that we should also keep in mind that this paper only covers a relatively recent period in Egyptian ancient history. We have no idea of the SSA profile of the ancient Egyptians before that time. It might have been higher, so any "crowing" seems a little premature. There were also Nubian rulers of Egypt, so who knows how that affected gene flow. Or even, as they imply, if the Old Kingdom wasn't significantly higher in SSA, we don't know the profile as you move further south toward Libya.

I1a3_Young
31-05-17, 17:09
I don't think so.
I know of a case where a white woman cheated on her white husband with a black man and got a perfect white daughter, and the white husband was never aware of the cheating.
Then the white daughter got pregnant from her white boyfriend and got a black son.
Her white boyfriend rejected her and her black son, untill a DNA test proved what had realy happened.

That is interesting. I've seen hundreds of mixes and never heard of that before. Do they have available public pics, like a FB profile or something? I believe you, but I find it so bizarre that it must be a rare occurrence.

Angela
31-05-17, 17:20
Sorry for mis-wording things, by northeast Africans I was referring to modern Egyptians, Tunisians, and Algerians. These groups are the closest to the ancient Egyptian samples studied in this study.

As I explained, they're not north-east Africans: they're North Africans. Plus, this group of ancient Egyptians may have had less SSA than modern Tunisians and Algerians, depending on the tools used. The authors go to great lengths to point out that although there is continuity in Egypt, the ancient Egyptians, who aren't so ancient, are closer to some other groups. From admixture it looks as if they're closer to minimally SSA admixed Saudis. I have to check the Supplement and the other types of analyses to make sure.

bicicleur
31-05-17, 17:53
That is interesting. I've seen hundreds of mixes and never heard of that before. Do they have available public pics, like a FB profile or something? I believe you, but I find it so bizarre that it must be a rare occurrence.

no I don't have any pics or links to some site, but it is a genuine case
I agree with you that most of the time the children have a complexion in between that of the parents, but appearantly it doesn't have to, although in that case I guess it happens in the 2nd generation

davef
31-05-17, 17:59
I don't know what you mean by that. They had a lot of "farmer" ancestry. Perhaps it was more Levant Neolithic, but Levant Neolithic contained minority Anatolian Neolithic, just as Anatolian Neolithic contained minority Levant Neolithic. Plus, which European farmers do you mean? The early Neolithic farmers in Europe picked up almost no additional WHG. That only happened thousands of years later in the MN, when it went up to about 20-25% depending on the area.

Of course, it seems the Egyptians from the era in question did have some Iran Chl. type material, but it wasn't much. They did have, for a lower bound number, about 6% SSA, which European Neolithic people did not.

The skin pigmentation of European farmers also seems to have been quite different. On the other hand, everybody at that point in time was darker than today.

Sorry, I was going by the chart Hauteville posted, page 1 of this thread. The ancient Egyptian samples have some Anatolian by that chart (indicated by the shred of "dark blue"), but not much. Natufian seems to be the dominant component.

I'll admit, I may not know what I'm talking about :).

Angela
31-05-17, 18:44
Once again I find myself mostly in agreement with Razib Khan:

https://gnxp.nofe.me/2017/05/30/ancient-egyptians-black-or-white/?utm_source=dlvr.it&utm_medium=twitter

Angela
31-05-17, 18:55
The Fayum mummy portraits might give us some idea what the people in the later part of this "ancient Egyptian" period looked like, although they might have a little admixture from Hellenistic and Roman periods.

https://upload.wikimedia.org/wikipedia/commons/thumb/0/09/Fayum-01.jpg/155px-Fayum-01.jpg

https://allkindsofhistory.files.wordpress.com/2014/12/fayum-girl-120-150.jpg?w=241&h=383

https://s-media-cache-ak0.pinimg.com/236x/f5/3f/50/f53f50e4556c65d63e66323d676c4d45.jpg

There were a few lighter ones too:
https://upload.wikimedia.org/wikipedia/commons/thumb/4/42/Fayum-13.jpg/220px-Fayum-13.jpg

It's to be expected given that there's going to be variation.

I don't think my Bedouin, Yemeni example is that far off. :)

Copts generally look different to me, more like some Samaritans if they were darker: not such fine feature in a lot of them, and more SSA. Perhaps the "SSA' in the Copts is less East African than in these ancient Egyptians?

Angela
31-05-17, 19:04
Just to throw it in...Nefertiti

http://i-cias.com/e.o/slides/nefertiti01.jpg

I think she's stunning.

Kemsit, the Pharaoh Mentuhotep's Nubian queen:
http://2.bp.blogspot.com/-oy8VYE0Nsx4/U8fA0Vm4jzI/AAAAAAAAHxs/JNGkSriMPi8/s1600/kemsit.jpg

I think the difference is obvious, yes?

davef
31-05-17, 19:24
Third one down from the top looks very Arabian so you may be right about ancient Egypt being close to Saudis.

Fire Haired14
31-05-17, 20:46
The Fayum mummy portraits might give us some idea what the people in the later part of this "ancient Egyptian" period looked like, although they might have a little admixture from Hellenistic and Roman periods.


It would be interesting to see if Natufian/LevantN heavy SW Asians look similar to Sardinians. I tend to think the stero typical Middle Eastern look derives from IranNeo-CHG.

A. Papadimitriou
31-05-17, 21:31
Once again I find myself mostly in agreement with Razib Khan:

https://gnxp.nofe.me/2017/05/30/ancient-egyptians-black-or-white/?utm_source=dlvr.it&utm_medium=twitter

Since he talks about various dynasties, how much SSA did the Nubian dynasty had?

Fire Haired14
31-05-17, 21:45
The ADMIXTURE analysis in Supplementary Info Figure 4 is the best I've seen. It isolates a Natufian(ish) component, IranNeo/CHG(ish) component, AnatoliaNeo(ish) component, and EuroHG(ish) component.

The results are consistent with what qpADM and D-stats give. Sardinia scores a little in the Natufoan(ish) and IranNeo/CHG(ish) components. What I think has made Sardinia so special is its lack of Steppe/ANE-heavy ancestry which all other Europeans have a lot of. Sardinia might have as much Near Eastern ancestry as other Italians but because they lack Steppe ancestry they pack a lot more AnatoliaNeo ancestry.

Angela
31-05-17, 21:59
It would be interesting to see if Natufian/LevantN heavy SW Asians look similar to Sardinians. I tend to think the stero typical Middle Eastern look derives from IranNeo-CHG.

I have no idea what you're talking about, as usual. Why would Sardinians look particularly southwest Asian?

Saudis are 65% SW Asian. Palestinians are 36% SWAsian

Sardinians are 8.7% SWAsian.

Fire Haired14
31-05-17, 22:08
I have no idea what you're talking about, as usual. Why would Sardinians look particularly southwest Asian?


Because Natufians, who makeup most of that SW Asian component in the paper, might be closely related to Anatolia Neolithic.

Angela
31-05-17, 22:20
Because Natufians, who makeup most of that SW Asian component in the paper, might be closely related to Anatolia Neolithic.
I knew you must have forgotten the percentages for SW Asian in Europeans, but you persist even after I provided the percentages for SW Asian in the post above?

I take it you've also forgotten that the early farmers who went to Europe were extremely close to Anatolia Neolithic, and that Anatolia Neolithic had only a minority component of Levant Neolithic, which was also not completely Natufian? Perhaps you want to review those papers and the stats for these populations.

In addition to all of that, of course, the Sardinians have a pretty big chunk of WHG.

So, again, I don't know why on earth you'd think Sardinians would look particularly southwest Asian.

Angela
31-05-17, 22:37
There's variation everywhere, so I don't think blanket generalizations are at all helpful, but no, most Sardinians don't look at all southwest Asian, if what you mean is Arabian or Palestinian looking. You've obviously not seen very many of them.

http://top10for.com/wp-content/uploads/2015/04/Giorgia-Palmas.jpg?1c5b41

http://www.paginainizio.com/frasi/fonti/elisabettacanalis.jpg

http://www.enciclopediadelledonne.it/wp-content/uploads/2014/03/1368maria_carta13.jpeg

http://www.azquotes.com/picture-quotes/quote-according-to-an-ancient-sardinian-legend-the-bodies-of-those-who-are-born-on-christmas-grazia-deledda-58-70-21.jpg

http://www.sandalyon.eu/uploadmeteora2/Giuseppe_dessy_wiki_14541758658408.jpg

http://www.maisonbarbagli.it/data/lavorazioni/7/big/2d1e1da4.jpg

Famous people from Saudi and Palestine:

https://s-media-cache-ak0.pinimg.com/originals/cb/fe/fe/cbfefe16cb67da3d46e7d122f327ed33.jpg

http://www.newswatchngr.com/wp-content/uploads/2017/02/Omar-Borkan-Al-Gala.jpg

https://publishingperspectives.com/wp-content/uploads/2017/04/500-Mohammed-Hasan-Alwan-ftw-256x300.jpg



https://pbs.twimg.com/profile_images/2186359197/tweet2.jpg

https://www.babelio.com/users/AVT_Alsanea-Rajaa_6665.jpeg

I can't imagine where you get these ideas.

harena
01-06-17, 01:15
He's implying that Anatolia Neolithic, Levant Neolithic and Natufians all hail from the same stock, Anatolia Neolithic is just more WHG admixed.

Alan
01-06-17, 02:35
Those samples have an extra Iran_Neolithic, maybe they are mixed with Hyksos more than purest ancient Egyptians.

The site where the samples come from have no record of Hyksos or Greek settlements + they are burried in typical Egyptian fashion. There is absolutely no way that they were mixed with Hyksos. They are Iran_Neo admixed because the ancient Egyptian derive most likely from late-Neolithic or Bronze Age Levant. This would explain why ancient Egytpain language is linguistically closer to Semitic than Berber. It is because it left the South Levant as a secondary wave of Afro_Asiatic speakers. After the Proto Berbers left earlier.

Alan
01-06-17, 02:37
This one is a coment by "washington post" about the topic:The scientists compared these ancient genetics with those of 100 modern Egyptians and 125 modern Ethiopians that had been previously analyzed. If you ask Egyptians, they'll say that they have become more European recently, Krause said. “We see exactly the opposite,” he said.


So The post is saying that back then many Egyptians from this site looked more European

Not more European but more Caucasian aka Near Eastern.

LeBrok
01-06-17, 03:15
He's implying that Anatolia Neolithic, Levant Neolithic and Natufians all hail from the same stock, Anatolia Neolithic is just more WHG admixed.Anatolian Neolithic was surprisingly more distinct than just WHG admixture. IIRC Anatolian Neolithic was 10% WHG, 20 Natufian and the rest (70%) their own stock, Anatolian farmers.

Well, they are related by ancient relatives belonging to 3 major admixtures/groups, though in different proportions, and they have drifted way through thousands of years of separation. Here are their genomes in HarappaWorld GedMatch run.



M041601
Merged

M54279
I0746


Natufian


Anatolian EF


Run time
6.39

Run time
10.20


S-Indian
-

S-Indian
-


Baloch
-

Baloch
-


Caucasian
13.98

Caucasian
35.90


NE-Euro
-

NE-Euro
3.91


SE-Asian
-

SE-Asian
-


Siberian
-

Siberian
-


NE-Asian
-

NE-Asian
-


Papuan
0.68

Papuan
-


American
-

American
-


Beringian
-

Beringian
-


Mediterranean
27.39

Mediterranean
46.12


SW-Asian
53.62

SW-Asian
14.03


San
-

San
-


E-African
4.33

E-African
-


Pygmy
-

Pygmy
-


W-African
-

W-African
-



They have mostly similar admixtures (living relatively close by), but in so different proportions that it makes them very distinct.

Angela
01-06-17, 03:51
Thank you, LeBrok.

LeBrok
01-06-17, 04:38
Here are the 3 ancestral populations of every Near Easterner today, well major ancestral components. Natufian, Anatolian and Iranian farmers. Iranian is quite different, though united with the first two by local Caucasian component.



M041601
Merged

M54279
I0746

M967114 I1290


Natufian


Anatolian EF

Iranian Neolithic
10 kya


Run time
6.39

Run time
10.20

Run time
7.91


S-Indian
-

S-Indian
-

S-Indian
6.13


Baloch
-

Baloch
-

Baloch
62.71


Caucasian
13.98

Caucasian
35.90

Caucasian
24.97


NE-Euro
-

NE-Euro
3.91

NE-Euro
-


SE-Asian
-

SE-Asian
-

SE-Asian
-


Siberian
-

Siberian
-

Siberian
-


NE-Asian
-

NE-Asian
-

NE-Asian
-


Papuan
0.68

Papuan
-

Papuan
0.35


American
-

American
-

American
-


Beringian
-

Beringian
-

Beringian
-


Mediterranean
27.39

Mediterranean
46.12

Mediterranean
-


SW-Asian
53.62

SW-Asian
14.03

SW-Asian
3.88


San
-

San
-

San
0.18


E-African
4.33

E-African
-

E-African
-


Pygmy
-

Pygmy
-

Pygmy
-


W-African
-

W-African
-

W-African
1.78

LeBrok
01-06-17, 04:51
Now, Levant Neolithic and BA samples, plus modern Lebanese, Palestinian, Bedouin and Egyptian.



M115616
I0867

M291439
I1706

Modern


Modern


Modern


Modern



Levant Neolithic

Levant BA

Lebanese

Palestinian

Bedouin


Egyptian



Run time
9.93

Run time
13

Run time


Run time


Run time


Run time



S-Indian
-

S-Indian
0.26

S-Indian
1

S-Indian
1

S-Indian
0

S-Indian
1


Baloch
-

Baloch
3.57

Baloch
11

Baloch
7

Baloch
5

Baloch
3


Caucasian
25.97

Caucasian
37.26

Caucasian
41

Caucasian
39

Caucasian
21

Caucasian
28


NE-Euro
-

NE-Euro
-

NE-Euro
3

NE-Euro
1

NE-Euro
2

NE-Euro
1


SE-Asian
0.07

SE-Asian
0.62

SE-Asian
1

SE-Asian
0

SE-Asian
0

SE-Asian
0


Siberian
-

Siberian
-

Siberian
1

Siberian
1

Siberian
0

Siberian
0


NE-Asian
0.06

NE-Asian
0.43

NE-Asian
1

NE-Asian
0

NE-Asian
0

NE-Asian
0


Papuan
-

Papuan
-

Papuan
0

Papuan
0

Papuan
0

Papuan
0


American
-

American
0.34

American
0

American
0

American
0

American
0


Beringian
-

Beringian
-

Beringian
0

Beringian
0

Beringian
0

Beringian
0


Mediterranean
32.53

Mediterranean
12.01

Mediterranean
13

Mediterranean
12

Mediterranean
7

Mediterranean
17


SW-Asian
39.86

SW-Asian
44.73

SW-Asian
23

SW-Asian
31

SW-Asian
56

SW-Asian
33


San
-

San
-

San
0

San
0

San
0

San
0


E-African
1.52

E-African
-

E-African
3

E-African
5

E-African
5

E-African
12


Pygmy
-

Pygmy
0.4

Pygmy
0

Pygmy
0

Pygmy
0

Pygmy
0


W-African
-

W-African
0.38

W-African
1

W-African
1

W-African
3

W-African
6

Angela
01-06-17, 05:20
Now, Levant Neolithic and BA samples, plus modern Lebanese, Palestinian, Bedouin and Egyptian.



M115616
I0867

M291439
I1706

Modern


Modern


Modern


Modern



Levant Neolithic

Levant BA

Lebanese

Palestinian

Bedouin


Egyptian



Run time
9.93

Run time
13

Run time


Run time


Run time


Run time



S-Indian
-

S-Indian
0.26

S-Indian
1

S-Indian
1

S-Indian
0

S-Indian
1


Baloch
-

Baloch
3.57

Baloch
11

Baloch
7

Baloch
5

Baloch
3


Caucasian
25.97

Caucasian
37.26

Caucasian
41

Caucasian
39

Caucasian
21

Caucasian
28


NE-Euro
-

NE-Euro
-

NE-Euro
3

NE-Euro
1

NE-Euro
2

NE-Euro
1


SE-Asian
0.07

SE-Asian
0.62

SE-Asian
1

SE-Asian
0

SE-Asian
0

SE-Asian
0


Siberian
-

Siberian
-

Siberian
1

Siberian
1

Siberian
0

Siberian
0


NE-Asian
0.06

NE-Asian
0.43

NE-Asian
1

NE-Asian
0

NE-Asian
0

NE-Asian
0


Papuan
-

Papuan
-

Papuan
0

Papuan
0

Papuan
0

Papuan
0


American
-

American
0.34

American
0

American
0

American
0

American
0


Beringian
-

Beringian
-

Beringian
0

Beringian
0

Beringian
0

Beringian
0


Mediterranean
32.53

Mediterranean
12.01

Mediterranean
13

Mediterranean
12

Mediterranean
7

Mediterranean
17


SW-Asian
39.86

SW-Asian
44.73

SW-Asian
23

SW-Asian
31

SW-Asian
56

SW-Asian
33


San
-

San
-

San
0

San
0

San
0

San
0


E-African
1.52

E-African
-

E-African
3

E-African
5

E-African
5

E-African
12


Pygmy
-

Pygmy
0.4

Pygmy
0

Pygmy
0

Pygmy
0

Pygmy
0


W-African
-

W-African
0.38

W-African
1

W-African
1

W-African
3

W-African
6


It's good to remind people that Levant Neolithic is not the same as Natufian. The transition brought more "Caucasus" and Med and decreased the SWAsian. I think that's admixture with Anatolian Neolithic, which shows up in the modeling.

Then in the Levant Bronze, Caucasian went up, which is in line with what these papers have been talking about, Baloch appears, but SW Asian also went up. Perhaps there was more movement from Arabia north? Virtually no SSA in the Levant Bronze Age, however, so whatever brought the additional SW Asian didn't carry it. Both the East African and West African came after that.

For SWAsian, it's 23 to 31, Lebanese to Palestinian. Are these Christian Lebanese? If they aren't, the differences might be larger.

Well, you can see not only the increase in the East African in modern Egyptians, but also the increase in West African.


Amazing how low the Med component drops. Anatolia Neolithic was 46% Med. So, I guess since Med is the Sardinian cluster, it's mostly Anatolian Neolithic plus WHG?

LeBrok
01-06-17, 06:07
It's good to remind people that Levant Neolithic is not the same as Natufian. The transition brought more "Caucasus" and Med and decreased the SWAsian. I think that's admixture with Anatolian Neolithic, which shows up in the modeling.

Then in the Levant Bronze, Caucasian went up, which is in line with what these papers have been talking about, Baloch appears, but SW Asian also went up. Perhaps there was more movement from Arabia north? Virtually no SSA in the Levant Bronze Age, however, so whatever brought the additional SW Asian didn't carry it. Both the East African and West African came after that.

For SWAsian, it's 23 to 31, Lebanese to Palestinian. Are these Christian Lebanese? If they aren't, the differences might be larger.

Well, you can see not only the increase in the East African in modern Egyptians, but also the increase in West African.


Amazing how low the Med component drops. Anatolia Neolithic was 46% Med. So, I guess since Med is the Sardinian cluster, it's mostly Anatolian Neolithic plus WHG?
Palestinians are almost true BA Levant, plus 5 percent of baloch and 6 percent of SSA. Amazing. I'm betting that ancient Jews will turn very similar and most likely Phoenicians too.

Here is Anatolian and EEF, BA Italian and Sardinian



M54279
I0746

M405327
I1506 NE1

Remedello Average

Modern from Harappa table



Anatolian EF

Hungary, Polgár-Ferenci-hát
7.2kya

Bronze Age (Neolithic Genome)
Sardinian



Run time
10.2

Run time
19.95

Run time


Run time



S-Indian
-

S-Indian
-

S-Indian
-

S-Indian



Baloch
-

Baloch
-

Baloch
-

Baloch



Caucasian
35.9

Caucasian
28.27

Caucasian
11.03

Caucasian
20


NE-Euro
3.91

NE-Euro
12.13

NE-Euro
21.25

NE-Euro
13


SE-Asian
-

SE-Asian
-

SE-Asian
0.61

SE-Asian



Siberian
-

Siberian
-

Siberian
-

Siberian



NE-Asian
-

NE-Asian
-

NE-Asian
-

NE-Asian



Papuan
-

Papuan
-

Papuan
-

Papuan



American
-

American
-

American
-

American



Beringian
-

Beringian
-

Beringian
-

Beringian



Mediterranean
46.12

Mediterranean
45.75

Mediterranean
60.61

Mediterranean
60


SW-Asian
14.03

SW-Asian
13.45

SW-Asian
5.50

SW-Asian
7


San
-

San
-

San
-

San



E-African
-

E-African
-

E-African
-

E-African



Pygmy
-

Pygmy
0.05

Pygmy
0.08

Pygmy



W-African
-

W-African
0.35

W-African
0.92

W-African

bicicleur
01-06-17, 08:22
Palestinians are almost true BA Levant, plus 5 percent of baloch and 6 percent of SSA. Amazing. I'm betting that ancient Jews will turn very similar and most likely Phoenicians too.

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

harena
01-06-17, 08:25
Anatolian Neolithic was surprisingly more distinct than just WHG admixture. IIRC Anatolian Neolithic was 10% WHG, 20 Natufian and the rest (70%) their own stock, Anatolian farmers.

Well, they are related by ancient relatives belonging to 3 major admixtures/groups, though in different proportions, and they have drifted way through thousands of years of separation. Here are their genomes in HarappaWorld GedMatch run.



M041601
Merged

M54279
I0746


Natufian


Anatolian EF


Run time
6.39

Run time
10.20


S-Indian
-

S-Indian
-


Baloch
-

Baloch
-


Caucasian
13.98

Caucasian
35.90


NE-Euro
-

NE-Euro
3.91


SE-Asian
-

SE-Asian
-


Siberian
-

Siberian
-


NE-Asian
-

NE-Asian
-


Papuan
0.68

Papuan
-


American
-

American
-


Beringian
-

Beringian
-


Mediterranean
27.39

Mediterranean
46.12


SW-Asian
53.62

SW-Asian
14.03


San
-

San
-


E-African
4.33

E-African
-


Pygmy
-

Pygmy
-


W-African
-

W-African
-



They have mostly similar admixtures (living relatively close by), but in so different proportions that it makes them very distinct.


I'm not too sure about backward modeling very ancient samples like that, some of those components are partly derived from Natufian/Anatolian Farmers not the other way around.
IIRC Lazaridis modeled Natufians roughly as 50% Basal Eurasian and 50% WHG; Levant Neolithic, Anatolian farmers, EEF and Copper Age Iberia are all on the same cline, just look at a PCA.

Fire Haired14
01-06-17, 08:42
Post at my blog about the new ancient Egyptian mtDNA results: First look at ancient Egyptian mtDNA (http://mtdnaatlas.blogspot.com/)

mtDNA doesn't get anymore SouthWest Asian than the ancient Egyptian's mtDNA. There isn't a lot of East African mtDNA in my database. The stuff I've read about East African mtDNA indicates their West Eurasian mtDNA shares a lot of similarities.

R0a, HV1, T1a, J2a2, N1, M1a might all ultimately derive from Natufian-like people. N1, T1a, J2a link Neolithic Anatolians with Natufian-rich people.

Think about this. Andronovo, Bronze age British, and these ancient Egyptians were roughly contemporary to each other. Each carries roughly the same frequency of T1a and I as the ancient Egyptians. That demonstrates the widespread distribution of Neolithic West Asian ancestry.

bicicleur
01-06-17, 08:44
the calls for Y-DNA of the 3 males :

https://genetiker.wordpress.com/2017/06/01/y-snp-calls-from-ancient-egypt/

Fire Haired14
01-06-17, 11:25
This paper's ADMIXTURE analysis is maybe the most interesting aspect of the paper. It's 100% consistent with results I and others have gotten using D-stats provided by David Wesoloski at Eurogenes. Recall that the ADMIXTURE isolated Natufian, AnatoliaNeolthic, CHG, and Europe HG centered components.

Here are some interesting details the ADMIXTURE analysis shows...

-Saami's European-side has more Euro_HG(WHG, EHG) ancestry than any Europeans including Lithuanians and Finns. D-stats indicate they have 10-15%(exact percentages might be wrong) Scandinavian Hunter Gatherer ancestry which was rich in EHG and also had its own unique alleles. D-stats and this paper's ADMIXTURE give Saami roughly 40% EuroHG ancestry, 20% CHG ancestry, 15% AnatoliaNeo ancestry, and 25% something East Asian-like.

-Southern Italians score as much in the Natufian component as Iranians which indicates their Near Eastern ancestors lived south and west of Iran.

-BedouinB might be mostly Natufian(ish). They score 70% in the Natufian component, 20% in the CHG component, and 20% in the AnatoliaN component.

-YemaniteJew, ancient Egyptians, and Jordan_EBA are all really similar to each other. They score 50% in the Natufian component, 20-30% in CHG, and 20-30% in AnatoliaN. All modern SouthWest Asians score an extra dose in CHG(30-40%) and significantly less in Natufian(35-40%).

-The Near Eastern ancestor of North African Jews and European Jews was probably similar to the average modern Levantie. The Near Eastern ancestor of Yemanite Jews was probably similar to Jordan_EBA and ancient Egyptians.

MarkoZ
01-06-17, 12:15
The site where the samples come from have no record of Hyksos or Greek settlements + they are burried in typical Egyptian fashion. There is absolutely no way that they were mixed with Hyksos. They are Iran_Neo admixed because the ancient Egyptian derive most likely from late-Neolithic or Bronze Age Levant. This would explain why ancient Egytpain language is linguistically closer to Semitic than Berber. It is because it left the South Levant as a secondary wave of Afro_Asiatic speakers. After the Proto Berbers left earlier.

However the predynastic sites that look like the best candidates for the Protoegyptians (the Naqada horizon) are rather concentrated in Upper Egypt. I guess only ancient DNA will tell, but in my mind that makes an origin from the Levant unlikely.

bicicleur
01-06-17, 12:29
However the predynastic sites that look like the best candidates for the Protoegyptians (the Naqada horizon) are rather concentrated in Upper Egypt. I guess only ancient DNA will tell, but in my mind that makes an origin from the Levant unlikely.

prior to Naqada was the 8.2 ka climate event, which attracted all kind of herders and farmers from SW Asia to the Nile Delta and beyond, into Northern Africa
after the 8.2 ka event, the Sahara became 'green again' till 5.9 ka when the Sahara desert expanded again, which drove many herders & farmers back into the Nile Valley
the Protoegyptians probable were in Northern Africa since 8.2 ka and their origin was SW Asia
of course, later chalcolithic influxes are also possible and likely

MarkoZ
01-06-17, 12:39
prior to Naqada was the 8.2 ka climate event, which attracted all kind of herders and farmers from SW Asia to the Nile Delta and beyond, into Northern Africa
after the 8.2 ka event, the Sahara became 'green again' till 5.9 ka when the Sahara desert expanded again, which drove many herders & farmers back into the Nile Valley
the Protoegyptians probable were in Northern Africa since 8.2 ka and their origin was SW Asia
of course, later chalcolithic influxes are also possible and likely

While I think that's possible, the most commonly proposed origin for Afrasian seems to be in the pre-neolithic Eastern Sahara and the Horn of Africa.

davef
01-06-17, 12:58
Because Natufians, who makeup most of that SW Asian component in the paper, might be closely related to Anatolia Neolithic.

Sorry, but if you go by Hauteville's charts posted in the first page of this thread, you'll find that Natufians aren't anywhere near Anatolian Neolithic farmers. They are way way different. They lack that "dark blue" component. Natufians were pretty much Bedouins if I recall. Leagues away from Anatolian.

bicicleur
01-06-17, 14:57
While I think that's possible, the most commonly proposed origin for Afrasian seems to be in the pre-neolithic Eastern Sahara and the Horn of Africa.

that is what I tought also, untill the Y-DNA of the Natufians was published about a year ago
since then, I'm pretty convinced that the Afroasiatic languages originated in the Levant along with haplo E1b1b1 and also spread along with this clade out of the Levant

as for the 8.2 ka event : before 8.2 ka the 'green Sahara' was full of HG, during the 8.2 ka event, which lasted a few centuries, the Sahara was empty, and after the event, the 'green Sahara' was full of herders

whatever happened in the Nile delta at that time, nobody knows because everything is burried under very deep layers of sediments

Aaron1981
01-06-17, 15:07
From the graphic posted I don't see that at all, unless you're coining your own definitions for population groups. Northeast Africans are Horners.

The only "Africans" the ancient Egyptians from this period plot close to are North Africans, who are mostly Levantines with SSA, more than half of it coming in the last 2000 years, presumably through the Arab slave trade, plus whatever traces of the prior population(s) are left. None of that is a surprise.

Anyone who has been paying attention to the papers knows that two major population flows moved out of the Near East, the western farmers, and then a few thousand years later a population related to the Iranian farmers. Both spread over vast distances and mixed with earlier populations where ever they went. The first group spread all along the southern coast of the Mediterranean, among many other places, and even deep into Africa. We can see the traces of the second major Near East group in northern Africa too, but in much smaller percentages.

Basically, as LeBrok pointed out, the Bronze Age may be the last really major population upheaval in western Eurasia. As I stated in another thread, the second gene flow out of the Near East, which was less consequential for most of Europe was like a pincer movement into Europe, I believe, with part of it going over the Caucasus and onto the steppe, and part of it going into southeastern and southern Europe, as well as all over the Near East, and some of it even reaching North Africa.

It looks like a modified version of the old Dienekes theory of the Womb of Nations to me, but as you have to consider also the western farmers, it's not just the Caucasus area, but the Anatolia/Levant region as well.

While related, the admixture in northern Europe is from mesolithic age CHG and doesn't appear male mediated, the admixture event in the western Middle East is Iran_CHL/Iran_NEO, which is a distant, younger relative. If you try to model north Europeans as Iran_CHL/NEO, it won't jive.

Let's face it, until J1, J2, G2...etc start showing up in droves on the neolithic steppe, I will still consider CHG admixture in northern Europe as female driven. We know R1 was originally WHG/EHG along with I.

MarkoZ
01-06-17, 15:23
While related, the admixture in northern Europe is from mesolithic age CHG and doesn't appear male mediated, the admixture event in the western Middle East is Iran_CHL/Iran_NEO, which is a distant, younger relative. If you try to model north Europeans as Iran_CHL/NEO, it won't jive.

Let's face it, until J1, J2, G2...etc start showing up in droves on the neolithic steppe, I will still consider CHG admixture in northern Europe as female driven. We know R1 was originally WHG/EHG along with I.

You might want to back that up, because Iran_ChL/EHG is exactly the model Lazaridis proposed for Yamnaya.

R1 wasn't originally WHG-EHG for god's sake. Stop being silly.

MarkoZ
01-06-17, 15:24
since then, I'm pretty convinced that the Afroasiatic languages originated in the Levant along with haplo E1b1b1 and also spread along with this clade out of the Levant


I guess more samples are needed. Though E-M35 should be around thousands of years before Natufian.

kingjohn
01-06-17, 15:28
no mtdna h3 was found in the ancient egyptions
it looks like it originated or in iberia or in morocco/ algeria area ...

LeBrok
01-06-17, 17:18
I'm not too sure about backward modeling very ancient samples like that, some of those components are partly derived from Natufian/Anatolian Farmers not the other way around. 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.

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

Levant Neolithic, Anatolian farmers, EEF and Copper Age Iberia are all on the same cline, just look at a PCA. 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.

Angela
01-06-17, 18:04
Palestinians are almost true BA Levant, plus 5 percent of baloch and 6 percent of SSA. Amazing. I'm betting that ancient Jews will turn very similar and most likely Phoenicians too.

Here is Anatolian and EEF, BA Italian and Sardinian



M54279
I0746

M405327
I1506 NE1

Remedello Average

Modern from Harappa table



Anatolian EF

Hungary, Polgár-Ferenci-hát
7.2kya

Bronze Age (Neolithic Genome)
Sardinian



Run time
10.2

Run time
19.95

Run time


Run time



S-Indian
-

S-Indian
-

S-Indian
-

S-Indian



Baloch
-

Baloch
-

Baloch
-

Baloch



Caucasian
35.9

Caucasian
28.27

Caucasian
11.03

Caucasian
20


NE-Euro
3.91

NE-Euro
12.13

NE-Euro
21.25

NE-Euro
13


SE-Asian
-

SE-Asian
-

SE-Asian
0.61

SE-Asian



Siberian
-

Siberian
-

Siberian
-

Siberian



NE-Asian
-

NE-Asian
-

NE-Asian
-

NE-Asian



Papuan
-

Papuan
-

Papuan
-

Papuan



American
-

American
-

American
-

American



Beringian
-

Beringian
-

Beringian
-

Beringian



Mediterranean
46.12

Mediterranean
45.75

Mediterranean
60.61

Mediterranean
60


SW-Asian
14.03

SW-Asian
13.45

SW-Asian
5.50

SW-Asian
7


San
-

San
-

San
-

San



E-African
-

E-African
-

E-African
-

E-African



Pygmy
-

Pygmy
0.05

Pygmy
0.08

Pygmy



W-African
-

W-African
0.35

W-African
0.92

W-African




Remedello isn't Bronze Age. It's basically just Middle Neolithic, although they already had copper.

In your prior post, interesting that the 6 point increase in SSA, plus a few other minor changes, lowered the SW Asian in Palestinians by 8 points.

bicicleur
01-06-17, 18:07
afaik the Natufians were not 100 % proper Natufian, they had some EEF admixture in them
I would also be surprised that they were 100 % E1b1, all samples we have are from 1 single site and about the same age.
I wouldn't be surprised to find some haplo G2 (but not G2a2) in Natufians, and some H2.

Angela
01-06-17, 18:27
While related, the admixture in northern Europe is from mesolithic age CHG and doesn't appear male mediated, the admixture event in the western Middle East is Iran_CHL/Iran_NEO, which is a distant, younger relative. If you try to model north Europeans as Iran_CHL/NEO, it won't jive.

Let's face it, until J1, J2, G2...etc start showing up in droves on the neolithic steppe, I will still consider CHG admixture in northern Europe as female driven. We know R1 was originally WHG/EHG along with I.

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.

Angela
01-06-17, 18:30
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.

Angela
01-06-17, 18:33
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.

Angela
01-06-17, 19:07
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
http://realhistoryww.com/world_history/ancient/Images_Egypt/Egypt_Nubian_Taharqa.jpg

Shebitku:
https://s-media-cache-ak0.pinimg.com/originals/88/9c/af/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.

https://i.ytimg.com/vi/l_n0_DjIxI4/hqdefault.jpg

http://www.touregypt.net/images/touregypt/ramesses3-8.jpg

harena
01-06-17, 22:12
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:

8761

Angela
01-06-17, 22:37
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.

Alan
02-06-17, 01:01
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.

A. Papadimitriou
02-06-17, 01:16
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.

Angela
02-06-17, 01:56
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 (https://www.nature.com/articles/ncomms15694#ref16). 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 (https://www.nature.com/articles/ncomms15694#ref49). 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 (https://www.nature.com/articles/ncomms15694#ref50). 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 (https://www.nature.com/articles/ncomms15694#ref51),52 (https://www.nature.com/articles/ncomms15694#ref52),53 (https://www.nature.com/articles/ncomms15694#ref53). 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 (https://www.nature.com/articles/ncomms15694#ref17). 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 (https://www.nature.com/articles/ncomms15694#ref54). 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 (https://www.nature.com/articles/ncomms15694#ref54).
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 (https://www.nature.com/articles/ncomms15694#ref43),55 (https://www.nature.com/articles/ncomms15694#ref55), or among the higher classes of Egyptian society55 (https://www.nature.com/articles/ncomms15694#ref55). Under Ptolemaic and Roman rule, ethnic descent was crucial to belonging to an elite group and afforded a privileged position in society55 (https://www.nature.com/articles/ncomms15694#ref55). 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 (https://www.nature.com/articles/ncomms15694#ref55). 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.

Alan
02-06-17, 03:21
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.

Promenade
02-06-17, 03:21
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.

Alan
02-06-17, 03:23
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.

LeBrok
02-06-17, 05:13
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.

davef
02-06-17, 06:10
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.

A. Papadimitriou
02-06-17, 09:01
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



Royal
Egypt
Deir el Bahari [Ramses III]

1155 BC
E1b1a



Hawass 2012 (http://www.ancestraljourneys.org/bibliography.shtml#Hawass2012)


Royal
Egypt
Deir el Bahari [Unknown man E - Pentawere?]

1155 BC?
E1b1a



Hawass 2012 (http://www.ancestraljourneys.org/bibliography.shtml#Hawass2012)


Tomb mummy
Egypt
Abusir el-Meleq [JK2134]

776-569 cal BC
J
J1d


Schuenemann 2017 (http://www.ancestraljourneys.org/bibliography.shtml#Schuenemann2017)


Tomb mummy
Egypt
Abusir el-Meleq [JK2911]

769-560 cal BC
J
M1a1


Schuenemann 2017 (http://www.ancestraljourneys.org/bibliography.shtml#Schuenemann2017)


Tomb mummy
Egypt
[DMG5]

402-385 BC


I2
73G, 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 analysis
Khairat 2013 (http://www.ancestraljourneys.org/bibliography.shtml)


Tomb mummy
Egypt
Abusir el-Meleq [JK2888]

97-2 cal BC
E1b1b1a1b2 [V22]
U6a2


Schuenemann 2017 (http://www.ancestraljourneys.org/bibliography.shtml#Schuenemann2017)

harena
02-06-17, 11:39
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:

8768

LeBrok
02-06-17, 16:49
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.

Angela
02-06-17, 16:53
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



Royal
Egypt
Deir el Bahari [Ramses III]

1155 BC
E1b1a



Hawass 2012 (http://www.ancestraljourneys.org/bibliography.shtml#Hawass2012)


Royal
Egypt
Deir el Bahari [Unknown man E - Pentawere?]

1155 BC?
E1b1a



Hawass 2012 (http://www.ancestraljourneys.org/bibliography.shtml#Hawass2012)


Tomb mummy
Egypt
Abusir el-Meleq [JK2134]

776-569 cal BC
J
J1d


Schuenemann 2017 (http://www.ancestraljourneys.org/bibliography.shtml#Schuenemann2017)


Tomb mummy
Egypt
Abusir el-Meleq [JK2911]

769-560 cal BC
J
M1a1


Schuenemann 2017 (http://www.ancestraljourneys.org/bibliography.shtml#Schuenemann2017)


Tomb mummy
Egypt
[DMG5]

402-385 BC


I2
73G, 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 analysis
Khairat 2013 (http://www.ancestraljourneys.org/bibliography.shtml)


Tomb mummy
Egypt
Abusir el-Meleq [JK2888]

97-2 cal BC
E1b1b1a1b2 [V22]
U6a2


Schuenemann 2017 (http://www.ancestraljourneys.org/bibliography.shtml#Schuenemann2017)




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.

Angela
02-06-17, 16:56
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.

holderlin
02-06-17, 18:26
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.

Angela
02-06-17, 19:51
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.

harena
02-06-17, 20:21
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
02-06-17, 20:43
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
02-06-17, 21:47
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
03-06-17, 01:59
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
03-06-17, 02:06
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
03-06-17, 02:20
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
03-06-17, 05:58
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
03-06-17, 06:06
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.
https://evolutionistx.files.wordpress.com/2016/01/model.png





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.



http://oi65.tinypic.com/311pgrq.jpg
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
03-06-17, 06:07
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
03-06-17, 08:03
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
03-06-17, 09:42
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
03-06-17, 15:54
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
03-06-17, 16:35
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.

https://s16.postimg.org/m9inpse79/ncomms15694-f4.jpg

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
03-06-17, 16:54
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.
https://evolutionistx.files.wordpress.com/2016/01/model.png


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.



http://oi65.tinypic.com/311pgrq.jpg


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
03-06-17, 17:24
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.


http://www.eupedia.com/forum/images/misc/quote_icon.png 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
03-06-17, 20:50
. 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
03-06-17, 20:55
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
03-06-17, 23:01
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
04-06-17, 01:43
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.

https://s16.postimg.org/m9inpse79/ncomms15694-f4.jpg

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
04-06-17, 01:51
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.

LeBrok
04-06-17, 01:57
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?Let's try it agian. I said this:
(not Natufians, which lived 6-8 thousand years before EEF)
Now you understand, that you didn't understand the first time? Though, not surprising for old members of Eupedia.

Angela
04-06-17, 02:11
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%).

I hesitate to give more space to this, because we largely agree. However, I don't concur, going by the Admixture run, that Palestinians are the closest population. They have way too much Iran Chl. for that. Imo, the closest are either Saudis without SSA or Bedouin B. I have no idea if Bedouin B is more isolated or Bedouin A is more isolated. It looks to me as if perhaps Bedouin B is just those Bedouin without all that additional SSA.

For more definitive answers I think we'll have to wait for what other tools show. That may change my opinion.

As for the discussion between Harena and LeBroc, a lot of the problem with the hobbyist community is that they use pop. genetics terms way too loosely, confusing not only themselves but others. Anatolia Neolithic is about 10%? WHG. If you go around saying that Natufians were 50% WHG it's wrong and confusing to other people.

Plus, the point is that these populations were distinct from one another, just as Anatolia Neolithic was distinct from Iranian Neolithic no matter that they shared some "components" from thousands of years before the Neolithic.

harena
04-06-17, 03:25
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.



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


With pleasure, if you can pinpoint and quote the actual insults I got an infraction for in my previous post. Otherwise it's you the one who has to worry about coming out clean i'm afraid.

Sile
04-06-17, 03:38
Let's try it agian. I said this:
(not Natufians, which lived 6-8 thousand years before EEF)
Now you understand, that you didn't understand the first time? Though, not surprising for old members of Eupedia.



And you know I told you for over 2 years that the fertile crescent and the bulk of the levant where populated from people north of the zargos mountains......I also stated the Natufians came via NE-Anatolia

LeBrok
04-06-17, 03:57
And you know I told you for over 2 years that the fertile crescent and the bulk of the levant where populated from people north of the zargos mountains......I also stated the Natufians came via NE-Anatolia :confused2: Exactly my point. ...and you also travel through time in your time machine, and visit parallel universes.
Let's leave it like this.

LeBrok
04-06-17, 03:59
With pleasure, if you can pinpoint and quote the actual insults I got an infraction for in my previous post. Otherwise it's you the one who has to worry about coming out clean i'm afraid.
Bla, bla, bla, where is the chart?

davef
04-06-17, 07:17
https://www.google.com/imgres?imgurl=https%3A%2F%2Fcdn.meme.am%2Fcache%2F instances%2Ffolder686%2F42428686.jpg&imgrefurl=https%3A%2F%2Fmemegenerator.net%2Finstan ce%2F42428686%2Fhomer-simpson-popcorn-time-to-take-out-the-popcorn-and-watch-show&docid=JlZIEOIF1M1ZjM&tbnid=6OdmDEc9f_S3IM%3A&vet=10ahUKEwju6P6it6PUAhUBTCYKHfmxDwQ4ZBAzCDcoNTA1 ..i&w=400&h=400&itg=1&hl=en&safe=off&client=safari&bih=441&biw=320&q=show%20it%20homer%20simpson&ved=0ahUKEwju6P6it6PUAhUBTCYKHfmxDwQ4ZBAzCDcoNTA1&iact=mrc&uact=8

davef
04-06-17, 07:26
Hey wait a minute, they have the internet on computers now? D'oh!
Can't post image...must be some way...d'oh!

Hey harena, my man, can you be a bro and post that chart?

Angela
04-06-17, 18:24
I hesitate to give more space to this, because we largely agree. However, I don't concur, going by the Admixture run, that Palestinians are the closest population. They have way too much Iran Chl. for that. Imo, the closest are either Saudis without SSA or Bedouin B. I have no idea if Bedouin B is more isolated or Bedouin A is more isolated. It looks to me as if perhaps Bedouin B is just those Bedouin without all that additional SSA.

For more definitive answers I think we'll have to wait for what other tools show. That may change my opinion.

As for the discussion between Harena and LeBroc, a lot of the problem with the hobbyist community is that they use pop. genetics terms way too loosely, confusing not only themselves but others. Anatolia Neolithic is about 10%? WHG. If you go around saying that Natufians were 50% WHG it's wrong and confusing to other people.

Plus, the point is that these populations were distinct from one another, just as Anatolia Neolithic was distinct from Iranian Neolithic no matter that they shared some "components" from thousands of years before the Neolithic.

I just want to point out that I think Alan is absolutely correct when he says the following:

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

It's the additional SSA that pulls modern Egyptians away from the ancient Egyptians in this sample. That's another reason why so much of the commentary in the press is so wrong.

harena
06-06-17, 10:37
Bla, bla, bla, where is the chart?

Still see no evidence of insults, I'm waiting..


Hey wait a minute, they have the internet on computers now? D'oh!
Can't post image...must be some way...d'oh!

Hey harena, my man, can you be a bro and post that chart?

No problem on my part, I do really want to share it and discuss but I cannot let Lebrok's infraction slip. I believe what he did is incompatible with his position of admin on this forum.

Either he apologizes, or I want him demoted from his role.

Olympus Mons
06-06-17, 12:06
.....I believe what he did is incompatible with his position of admin on this forum.

Either he apologizes, or I want him demoted from his role.

I do not know what he did or for that matter what you, Harena, is talking about (and have no time to look for) but I want to see the explanation, because Moderators and admin in this sort of forums sometime forget that it should come with a responsibility (although not the style of Lebrok from what I have seen of him). Already got infractions that I do not understood why and just to see the same persons do the same or worst.

Odysseus
06-06-17, 13:08
The Bronze age Levants obviously looked like vikings.

Sent from my WAS-LX1 using Eupedia Forum mobile app (http://r.tapatalk.com/byo?rid=89698)

Alan
06-06-17, 15:11
I just want to point out that I think Alan is absolutely correct when he says the following:

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

It's the additional SSA that pulls modern Egyptians away from the ancient Egyptians in this sample. That's another reason why so much of the commentary in the press is so wrong.

And that is what so freakn furstrates me I have seen comments and articles saying even things like "ancient Egyptians closer to Europeans than to modern once" what the heck?

LeBrok
06-06-17, 16:38
Still see no evidence of insults, I'm waiting..



No problem on my part, I do really want to share it and discuss but I cannot let Lebrok's infraction slip. I believe what he did is incompatible with his position of admin on this forum.

Either he apologizes, or I want him demoted from his role.


I do not know what he did or for that matter what you, Harena, is talking about (and have no time to look for) but I want to see the explanation, because Moderators and admin in this sort of forums sometime forget that it should come with a responsibility (although not the style of Lebrok from what I have seen of him). Already got infractions that I do not understood why and just to see the same persons do the same or worst.
Read the forum rules. If you still clueless why you got infractions, I can't help you.

davef
06-06-17, 20:13
The Bronze age Levants obviously looked like vikings.

Sent from my WAS-LX1 using Eupedia Forum mobile app (http://r.tapatalk.com/byo?rid=89698)

Is this sarcasm? :)

davef
06-06-17, 20:42
And that is what so freakn furstrates me I have seen comments and articles saying even things like "ancient Egyptians closer to Europeans than to modern once" what the heck?

According to the chart posted by Angela and Hauteville in this thread, the Modern Egyptians have more SSA than the Ancient Egyptian samples of this study, so these samples might be closer to Europeans in the same way Palestinians are (lack of SSA). It's meaningless, really.

And if by "closer to european" they mean "Europeans are closer to ancient Egyptians than modern Levantines and North Africans" they're probably just disappointed with the outcome of this study and want to delude themselves. Anyone with half a brain and minute knowledge of ancient genetics can tell from the chart that a Tunisian minus a dash of SSA does not make a Swede... on the flip side, a Swede with a dash of SSA does not make a Tunisian.

Angela
06-06-17, 20:56
The general conclusions to be taken from the paper are, I think, clear. When analyzing samples, all the results from the different tools have to be analyzed and put into a pattern. You can't just take one result showing more closeness to Europeans than to modern Egyptians and make outlandish claims. This is not new, however. It's done all the time in the amateur community to support one agenda or another.

All of that said, these samples have a tiny number of snps in common with modern gene arrays used in things like the gedmatch calculators. Any results by amateurs trying to compare these ancients to modern populations is not going to be accurate, whether it's going to be done by Egyptians, Copts, modern Levantines etc to see if they "descend" from them, or the Sikeliots of the world who would try to fit them into some sort of agenda.

We have to try to get a grip on how these tools work, and their limitations.

One heartening thing is that in this case, both the Nordicists and the Afro-Centrists have been discomfited. The marvels of ancient Egypt were largely created by people genetically similar to the people who created the marvels of the Near East, and no, they weren't very "Nordic like" or WHG, or steppe like either.

Odysseus
07-06-17, 12:57
I agree with you

Alan
07-06-17, 13:15
According to the chart posted by Angela and Hauteville in this thread, the Modern Egyptians have more SSA than the Ancient Egyptian samples of this study, so these samples might be closer to Europeans in the same way Palestinians are (lack of SSA). It's meaningless, really.

And if by "closer to european" they mean "Europeans are closer to ancient Egyptians than modern Levantines and North Africans" they're probably just disappointed with the outcome of this study and want to delude themselves. Anyone with half a brain and minute knowledge of ancient genetics can tell from the chart that a Tunisian minus a dash of SSA does not make a Swede... on the flip side, a Swede with a dash of SSA does not make a Tunisian.

Thats the point some news outlets are misinterpreting the results. The paper clearly points out that modern Egypt = 92% ancient Egypt + 8% SSA.

The study also says ancient Egyptians were closer to Middle Easterners and Europeans than modern Egyptians are. Well the reason for that is not them having European ancestry, but Egyptians and Europeans sharing ancient West Asian/Near Eastern genes. Also this sentence is easy to "missinterpret" into ancient Egyptians are closer to Europeans than they are to modern Egyptians. It's one word changing it's position and the sentence gets a whole different meaning so it can fit in some peoples agendas.

Let me give an example. A Chinese with a Swedish great grandfather will be closer to Europeans than a 100% Chinese will be. But does that make the Chinese with a little Swedish ancestry closer to Europeans as to other fellow Chinese?

Aaron1981
23-06-17, 21:01
Ancient Egyptians are absolutely nothing like Europeans. EEF isn't even European really but my ancestors absorbed them thousands of years ago.

Angela
23-06-17, 21:18
Ancient Egyptians are absolutely nothing like Europeans. EEF isn't even European really but my ancestors absorbed them thousands of years ago.

Europeans didn't exist until the three major ancestral components admixed after 2500 BC. I can't even say nice try, but definitely no cigar.

davef
24-06-17, 06:43
Ancient Egyptians are absolutely nothing like Europeans. EEF isn't even European really but my ancestors absorbed them thousands of years ago.

But the EEF weren't anything like Ancient Egyptians either. Not even close. The samples used in this article were very close to Bronze Age Levantines and the closest modern populations are North Africans and modern Levantines.

Jovialis
24-06-17, 13:53
But the EEF weren't anything like Ancient Egyptians either. Not even close. The samples used in this article were very close to Bronze Age Levantines and the closest modern populations are North Africans and modern Levantines.

https://www.nature.com/articles/ncomms15694/figures/5

The article has this graphic that demonstrates which population is closest.

According to the map in figure A. Sardinians and the Basque have the highest frequency of similarity with Ancient Egyptians in modern populations.

In ancient times, the Linearbandkeramik and Neolithic Anatolians also shared a strong similarity. Thus, they were a lot like the EEF too.

NOTE: I could be wrong, so if someone can point out how I'm misinterpreting this graphic; it would be much appreciated.

davef
24-06-17, 15:08
https://www.nature.com/articles/ncomms15694/figures/5

The article has this graphic that demonstrates which population is closest.

According to the map in figure A. Sardinians and the Basque have the highest frequency of similarity with Ancient Egyptians in modern populations.

In ancient times, the Linearbandkeramik and Neolithic Anatolians also shared a strong similarity. Thus, they were a lot like the EEF too.

NOTE: I could be wrong, so if someone can point out how I'm misinterpreting this graphic; it would be much appreciated.
No offense, but by that logic, Lithuanians are closer to ancient Egypt than Modern Egyptians. It's likely you're misinterpreting the chart (then again, I don't know how to interpret it myself...but since those groups are at the top, it's likely you misinterpreted it as higher on the chart=more related. It can't be since Scots are higher on that chart than modern populations of the Mideast and Jews).

If you take a look at some of the charts posted a few pages back in this thread, you'll see that Ancient Egyptians were Bronze Age Levantine like , and nowhere near Anatolian farmers.

Jovialis
24-06-17, 15:16
No offense, but by that logic, Lithuanians are closer to ancient Egypt than Modern Egyptians. It's likely you're misinterpreting the chart (then again, I don't know how to interpret it myself...but since those groups are at the top, it's likely you misinterpreted it as higher on the chart=more related. It can't be since Scots are higher on that chart than modern populations of the Mideast and Jews).

If you take a look at some of the charts posted a few pages back in this thread, you'll see that Ancient Egyptians were Bronze Age Levantine like , and nowhere near Anatolian farmers.

Yes, figure B is kind of weird. I'm not sure how to read it. But I was actually referring to figure A:

http://i.imgur.com/GenzlSf.jpg (http://imgur.com/GenzlSf)

(a) Outgroup f3-statistics measuring shared drift of the three ancient Egyptian samples and other modern and ancient populations,

The circles are representative of the modern populations. The brightest orange is over Sardinia.

davef
24-06-17, 17:24
Yes, figure B is kind of weird. I'm not sure how to read it. But I was actually referring to figure A:

http://i.imgur.com/GenzlSf.jpg (http://imgur.com/GenzlSf)

(a) Outgroup f3-statistics measuring shared drift of the three ancient Egyptian samples and other modern and ancient populations,

The circles are representative of the modern populations. The brightest orange is over Sardinia.

I see...I don't know how to explain that either since it conflicts with the charts posted a page ago. Maybe someone can chime in and help explain this.

Alan
25-06-17, 03:09
But the EEF weren't anything like Ancient Egyptians either. Not even close. The samples used in this article were very close to Bronze Age Levantines and the closest modern populations are North Africans and modern Levantines.

What the paper is trying to say (and what is not incorrect) is that technically ancient Egyptians are closer to modern Europeans than modern Egyptians are because they have less SSA and little more farmer DNA. And the closest component in Europeans to the ancestry of Egyptians is EEF. EEF or Anatolian_Neo is quite similar to Levant-Neolithic even if little less UHG/WHG like and more Basal.

The problem I have with the articles however is, that they make of small side effects headlines. Looking at the ancient Egyptian DNA one of the LEAST things you would think of is that they are closer to Europeans than modern Egyptians are. This wouldn't be so bad if many people weren't so stupid and use this to misinterpret things.

People generally with strong agendas (most humans have an agenda but some are more open minded to accept facts than other) will use these articles.

I see Afro_Centrics who claim now Basal Eurasian as Black African because they were extremely owned by the Egyptian paper. These guys are ridiculous. Both sites don't or can't accept the facts.

Alan
25-06-17, 03:18
According to the chart posted by Angela and Hauteville in this thread, the Modern Egyptians have more SSA than the Ancient Egyptian samples of this study, so these samples might be closer to Europeans in the same way Palestinians are (lack of SSA). It's meaningless, really.



Palestinians don't lack SSA (far from it) they just have less. There was a increase of SSA ancestry in all of the regions where the ancient Levantines expanded (Arabian Peninsula and the Levant). Palestinians have like 8% SSA while modern Egyptians 14%. Ancient Egyptians most likely had some variation like all ancient groups. Some where close to zero SSA other up to 20%. Thats my prediction. But one thing from these ancient samples if for sure. the Proto Egyptians most likely had non to very little SSA. And the SSA admixture came with the time via Nubians and later Slave trade.

And if by "closer to european" they mean "Europeans are closer to ancient Egyptians than modern Levantines and North Africans" they're probably just disappointed with the outcome of this study and want to delude themselves. Anyone with half a brain and minute knowledge of ancient genetics can tell from the chart that a Tunisian minus a dash of SSA does not make a Swede... on the flip side, a Swede with a dash of SSA does not make a Tunisian.

Correct, it's not so much the scientists it is the news outlets that are writing their articles in a way where they leave too much room for misinterpretations, be it on purpose or not.

Alan
25-06-17, 03:25
Yes, figure B is kind of weird. I'm not sure how to read it. But I was actually referring to figure A:

http://i.imgur.com/GenzlSf.jpg (http://imgur.com/GenzlSf)

(a) Outgroup f3-statistics measuring shared drift of the three ancient Egyptian samples and other modern and ancient populations,

The circles are representative of the modern populations. The brightest orange is over Sardinia.

This is only measuring shared drift not shared ancestry. on the PCAs and the other graphs you can clearly see with whom they share most ancestry.

Jovialis
25-06-17, 11:41
This is only measuring shared drift not shared ancestry. on the PCAs and the other graphs you can clearly see with whom they share most ancestry.

I see, yes, Ancient Egyptians are closer to the modern populations round Palestine, and the Levant.

But what exactly is meant by shared drift, in regards to the chart I pointed out?

Angela
25-06-17, 18:09
https://www.nature.com/articles/ncomms15694/figures/5

The article has this graphic that demonstrates which population is closest.

According to the map in figure A. Sardinians and the Basque have the highest frequency of similarity with Ancient Egyptians in modern populations.

In ancient times, the Linearbandkeramik and Neolithic Anatolians also shared a strong similarity. Thus, they were a lot like the EEF too.

You have to be careful with terminology. This is a shared drift diagram. The shared drift is largest, obviously, with EEF, Anatolia Neolithic, and Levant Neolithic. After that, with Bronze Age Levant. Then and only then with Sardinia and Basques as far as modern populations, because they are the modern populations with the largest amount of what we could call ancient "western" Neolithic ancestry ancestry, i.e. Anatolia/Levant.

First, as to genetic drift in general, it's the evolutionary mechanism which produces random changes in a population over time. It's different from natural selection, whereby only beneficial changes become fixed. In genetic drift the changes occur by chance, and so both beneficial and disadvantageous mutations can become fixed. It occurs more often in small populations. Bottlenecks and founder effects are examples of when it's most operative. (Sorry if I'm telling you what you already know.)

When geneticists are talking about shared genetic drift or shared drift patterns, they're saying that the populations in question share a long genetic history. Shared drift means shared evolutionary history. In terms of Sardinians/Basques and Egyptians, they both have lots of that ancient Neolithic ancestry.

What happened with the Egyptians is that they got a bigger dose of "eastern" Neolithic ancestry, plus the SSA.

I hope I explained that properly. If someone else wants to have a go, be my guest.

Jovialis
25-06-17, 18:23
You have to be careful with terminology. This is a shared drift diagram. The shared drift is largest, obviously, with EEF, Anatolia Neolithic, and Levant Neolithic. After that, with Bronze Age Levant. Then and only then with Sardinia and Basques as far as modern populations, because they are the modern populations with the largest amount of what we could call ancient "western" Neolithic ancestry ancestry, i.e. Anatolia/Levant.

First, as to genetic drift in general, it's the evolutionary mechanism which produces random changes in a population over time. It's different from natural selection, whereby only beneficial changes become fixed. In genetic drift the changes occur by chance, and so both beneficial and disadvantageous mutations can become fixed. It occurs more often in small populations. Bottlenecks and founder effects are examples of when it's most operative. (Sorry if I'm telling you what you already know.)

When geneticists are talking about shared genetic drift or shared drift patterns, they're saying that the populations in question share a long genetic history. Shared drift means shared evolutionary history. In terms of Sardinians/Basques and Egyptians, they both have lots of that ancient Neolithic ancestry.

What happened with the Egyptians is that they got a bigger dose of "eastern" Neolithic ancestry, plus the SSA.

I hope I explained that properly. If someone else wants to have a go, be my guest.

Thank you for the explanation! I'm not familiar with the terms. I was a history and poli-sci major; the little I know about genetics is self-taught from reading articles online.

davef
26-06-17, 15:05
You have to be careful with terminology. This is a shared drift diagram. The shared drift is largest, obviously, with EEF, Anatolia Neolithic, and Levant Neolithic. After that, with Bronze Age Levant. Then and only then with Sardinia and Basques as far as modern populations, because they are the modern populations with the largest amount of what we could call ancient "western" Neolithic ancestry ancestry, i.e. Anatolia/Levant.

First, as to genetic drift in general, it's the evolutionary mechanism which produces random changes in a population over time. It's different from natural selection, whereby only beneficial changes become fixed. In genetic drift the changes occur by chance, and so both beneficial and disadvantageous mutations can become fixed. It occurs more often in small populations. Bottlenecks and founder effects are examples of when it's most operative. (Sorry if I'm telling you what you already know.)

When geneticists are talking about shared genetic drift or shared drift patterns, they're saying that the populations in question share a long genetic history. Shared drift means shared evolutionary history. In terms of Sardinians/Basques and Egyptians, they both have lots of that ancient Neolithic ancestry.

What happened with the Egyptians is that they got a bigger dose of "eastern" Neolithic ancestry, plus the SSA.

I hope I explained that properly. If someone else wants to have a go, be my guest.
Wait, if the Egyptians were like Neolithic farmers then how can we explain those charts and pca in the last page?

Angela
26-06-17, 17:44
Wait, if the Egyptians were like Neolithic farmers then how can we explain those charts and pca in the last page?

I didn't say they're like Neolithic farmers. I said they have shared genetic drift with Neolithic farmers, as do Sardinians.

davef
26-06-17, 18:32
I didn't say they're like Neolithic farmers. I said they have shared genetic drift with Neolithic farmers, as do Sardinians.

Got it. I guess I'll need to read up on what shared genetic drift is.

Jovialis
27-06-17, 00:48
Got it. I guess I'll need to read up on what shared genetic drift is.

Yea, this is something I will need to look into myself.

ihype02
01-10-17, 15:32
Levant Bronze Age is very similar to the ancient Egyptian sample, which I think will turn out to be close to the Egyptian Copts. They don't at all look Cypriot to me.
https://thetablet.org/wp-content/uploads/2013/08/copt.jpg
http://www.denverpost.com/wp-content/uploads/2016/12/afp_j0350.jpg?w=525
http://news.bbcimg.co.uk/media/images/63782000/jpg/_63782333_63782332.jpg
Greek Cypriots:
http://in-cyprus.com/wp-content/uploads/2016/10/STK_1563.jpg
Obviously, there are a few non-Cypriots in the following. :)
http://media.worldbulletin.net/250x190/2013/11/30/adsiz_1.jpg
Plus, didn't the paper on the Canaanites tell us that these Bronze Age Canaanite samples have no derived SLC45A2, so not only different than people in the Levant today, but also quite a bit darker than the people of the Anatolia Neolithic and the EEF of Europe, who did have reasonably high percentages of derived SLC45A2. In fact, I think a recent paper revised those estimates upwards from where they were a while ago.. This might suggest that most of the Iran Chl, like the CHG themselves, only had the derived SLC25A2 allele, and thus were rather darker than not only Anatolia Neolithic, but also Levant Neolithic, since some of them also had derived SLC45A2, although the Natufians did not.
The admixture run isn't optimal, but going by that the Bronze Age Levant doesn't look all that different from the Saudis. So, maybe tribal Saudis or Yeminis without obvious SSA?
http://c8.alamy.com/comp/F8N8NW/sanaa-yemen-10th-dec-2015-yemeni-tribal-men-attend-a-rally-against-F8N8NW.jpg
https://upload.wikimedia.org/wikipedia/commons/9/9d/Bedouin_family-Wahiba_Sands.jpg
Who knows, though?
The second picture that you used was taken after a bomb killed several victims.

IronSide
10-04-18, 15:21
I hoped this paper would have focused more on the ethnogenesis of modern and Ancient Egyptians beyond the question of them having SSA ancestry or not?

Like how, when, and by whom the Iran_N ancestry in Ancient Egyptians appeared? what was the structure of the population before them?

SSA is interesting, but why focus on that alone?

Well, given the extreme interest in SSA in Near Easterners, someone up thread wondered why Saudis wouldn't have it? the admixture run was wrong in not detecting that in Saudis, who do have East African ancestry. similar to Dinka.

from Lazaridis et al(2016), a negative f3 statistic of the form f3(Saudi, Anatolia_N, Dinka) = -0.00326, Z_score = -5.1

That means it must exist, the allele frequency in the Saudi population is intermediate between Dinka and Anatolia_N or any population ancestral to them. it exists from 1% to 5% in various Saudi tribal groups, the origin of that I would assume is ancient, because the British Roman outlier also had it.

Angela
10-04-18, 15:28
I hoped this paper would have focused more on the ethnogenesis of modern and Ancient Egyptians beyond the question of them having SSA ancestry or not?

Like how, when, and by whom the Iran_N ancestry in Ancient Egyptians appeared? what was the structure of the population before them?

SSA is interesting, but why focus on that alone?

Well, given the extreme interest in SSA in Near Easterners, someone up thread wondered why Saudis wouldn't have it? the admixture run was wrong in not detecting that in Saudis, who do have East African ancestry. similar to Dinka.

from Lazaridis et al(2016), a negative f3 statistic of the form f3(Saudi, Anatolia_N, Dinka) = -0.00326, Z_score = -5.1

That means it must exist, the allele frequency in the Saudi population is intermediate between Dinka and Anatolia_N or any population ancestral to them. it exists from 1% to 5% in various Saudi tribal groups, the origin of that I would assume is ancient, because the British Roman outlier also had it.

Well, it's not exactly easy to get ancient samples from Egypt. The researchers are sort of reduced to using old samples in museums. Let's hope for more in the future.

markozd
10-04-18, 16:34
I hoped this paper would have focused more on the ethnogenesis of modern and Ancient Egyptians beyond the question of them having SSA ancestry or not?

Like how, when, and by whom the Iran_N ancestry in Ancient Egyptians appeared? what was the structure of the population before them?

SSA is interesting, but why focus on that alone?

Well, given the extreme interest in SSA in Near Easterners, someone up thread wondered why Saudis wouldn't have it? the admixture run was wrong in not detecting that in Saudis, who do have East African ancestry. similar to Dinka.

from Lazaridis et al(2016), a negative f3 statistic of the form f3(Saudi, Anatolia_N, Dinka) = -0.00326, Z_score = -5.1

That means it must exist, the allele frequency in the Saudi population is intermediate between Dinka and Anatolia_N or any population ancestral to them. it exists from 1% to 5% in various Saudi tribal groups, the origin of that I would assume is ancient, because the British Roman outlier also had it.

I'm also interested in this. If it isn't too far off-topic, have you taken a look at the Taforalt paper? The ADMIXTURE analysis suggests that the African admixture in Natufian, Iran_Hotu/Iran_Neo and so forth is related to a component that is modal in the Hadza. A very unlikely source, but it looks quite solid. It's even more pronounced in the Taforalt samples and still very significant in modern Berbers, while in the Levant/Europe it seems to be reduced relative to ancient samples. The 'Hadza Component' is also what differentiates Dinka from West Africans.

https://i.imgur.com/yeCh09G.png

IronSide
10-04-18, 16:53
I'm also interested in this. If it isn't too far off-topic, have you taken a look at the Taforalt paper? The ADMIXTURE analysis suggests that the African admixture in Natufian, Iran_Hotu/Iran_Neo and so forth is related to a component that is modal in the Hadza. A very unlikely source, but it looks quite solid. It's even more pronounced in the Taforalt samples and still very significant in modern Berbers, while in the Levant/Europe it seems to be reduced relative to ancient samples. The 'Hadza Component' is also what differentiates Dinka from West Africans.

Unfortunately, I haven't, many times ADMIXTURE detected African related components in Natufians and Levant Neolithic, that would definitely explain haplogroup E, but then came the Lazaridis paper.


No evidence for admixture related to sub-Saharan Africans in
Natufians. We computed the statistic f4(Natufian, Other Ancient; African, Chimp) varying African to be
Mbuti, Yoruba, Ju_hoan_North, or the ancient Mota individual. Gene flow between Natufians and
African populations would be expected to bias these statistics positive. However, we find most of
them to be negative in sign and all of them to be non-significant (|Z|<3), providing no evidence that
Natufians differ from other ancient samples with respect to African populations.

The Natufians don't share more alleles with (Mbuti - Yoruba - Ju_hoan_North - Mota) than the amount the EHG or WHG shares, which is null.

this f4 test f4(Natufian, Other Ancient; African, Chimp) tests whether the population African shares alleles with the Natufians that Other Ancient and Chimp don't, if yes it would be positive, but it wasn't. see the bolded statement above.

IronSide
10-04-18, 17:03
https://i.imgur.com/yeCh09G.png

Interesting puzzle, why would they have Hadza like admixture ?

markozd
10-04-18, 17:20
Unfortunately, I haven't, many times ADMIXTURE detected African related components in Natufians and Levant Neolithic, that would definitely explain haplogroup E, but then came the Lazaridis paper.



The Natufians don't share more alleles with (Mbuti - Yoruba - Ju_hoan_North - Mota) than the amount the EHG or WHG shares, which is null.

this f4 test f4(Natufian, Other Ancient; African, Chimp) tests whether the population African shares alleles with the Natufians that Other Ancient and Chimp don't, if yes it would be positive, but it wasn't. see the bolded statement above.

I had looked at this, but I think I didn't notice that Lazaridis also used Mota as an outgroup, which should according to the analysis above have the Hadza component. This is very confusing.

I find it quite difficult to fully understand intra-African diversity to be honest. What causes the Hadza to have such an unusual position in the PCA relative to South & West Africans? Based on haplotypes I'd exclude recent Eurasian admixture.

IronSide
10-04-18, 17:26
I had looked at this, but I think I didn't notice that Lazaridis also used Mota as an outgroup, which should according to the analysis above have the Hadza component. This is very confusing.

I find it quite difficult to fully understand intra-African diversity to be honest. What causes the Hadza to have such an unusual position in the PCA relative to South & West Africans? Based on haplotypes I'd exclude recent Eurasian admixture.

Maybe pure Basal Eurasians admixed into them, but then the Natufians and Iran_N would share ancestry with them more than the EHG for example, but they don't. a puzzle indeed.