Sunday, June 14, 2015

Copts: an example of Pre-Islamic and Arab conquest Egypt?



What you see above in the middle & in red are the Nagada Copts (residents of Khartoum, Sudan) from the recent autosomal DNA study on Sudan (Dobon et al.). That's them in a Global PCA (Principal Component Analysis) made by the author of Eurogenes upon my request. [1]




They interestingly look to be more Eurasian / West Eurasian / West Asian than their Muslim Egyptian counterparts ("Egyptian" samples). As you can see in the Global PCA, they pull more north toward West Asians and straddle between Muslim Egyptians and Palestinians. Palestinians are about ~5 to 10% African admixed (I'm speaking of components like the East African cluster and perhaps "Niger-Congo" here) while Muslim Egyptians are about ~20 to 25% on average, much like Northwest Africans whom they cluster close & who are known to be at that level. [2]






You can see in the new study's own PCA above that the data is more or less the same, the Copt samples pull more to the right on the X axis like Qataris while Egyptians pull more to the left; they once again clearly prove more West Eurasian / West Asian than their Muslim counterparts.

Muslim Egyptians often show small trace levels of Ancient North Eurasian ancestry (ANE), if I recall correctly though; their region is mostly a near dead zone for this kind of ancestry especially when you go south to the Horn and now seemingly even North Sudan where there is more or less no ANE ancestry about. The situation is the same to their west where Maghrebis / Northwest Africans seem to lack ANE input altogether



Northwest Africa / The Maghreb



Though Maghrebis have Western European Hunter-Gatherer (WHG) ancestry as has been noticed via Eurogenes K=8 and even Lazaridis et al.'s old ADMIXTURE analysis from 2013. [3]

Muslim Egyptians and Copts both show trace or low levels of WHG ancestry however there's really no way of knowing if this is real WHG ancestry or perhaps something very ancient that could have come out of West Asia similar to WHG (many I know tend to refer to this as "UHG/Unknown Hunter-Gatherer") so this WHG might not entirely be real though some of it could be.

At any rate it seems to me as though these Nagada Copts, the descendants of migrants who came from Egypt within the last 2 centuries as Dobon et al. notes, might honestly be representative of Copts as a whole. I say this because I have seen a random Egyptian Copt from Upper Egypt's results and she came out quite similar to them. No ANE, low WHG levels, ~15% East African / Sub-Saharan African and clearly more West Eurasian than Egyptians, in fact from what I've heard of her results and seen, she seems quite identical to these samples.

Her results from Eurogenes K=7:


ANE: 0.38%
WHG-UHG: 7.70%
ASE: 0.0%
East Eurasian: 1.54%
West African: 0.0%
 East African: 11.87%
ENF: 78.52%

.

She's "LifeisDandy"and the users to the far right are Europeans (rich in WHG. "Jusarius" is a Finn) and some ("Stellacritic" is Northwest African) to her south like the Assyrian and Iraqi (IQ) Mandaean samples are about 10-15% ANE

The results above are based on Eurogenes K=7 which was somewhat less fine tuned than
K=8 especially at times with its WHG estimates. It would give Northwest Africans something along the lines of 20-30% WHG ancestry which is ridiculous, those are in fact Italic & Greek levels of WHG ancestry. So her "WHG" score in those above results is most likely quite inflated.

She seems just like the new Nagada Sudanese Copts David Wesolowski ran through K=8: ~15% Sub-Saharan (in this case it seems to be entirely East African), ~80-90% ENF/ the West Asian
component that carries Basal Eurasian, and finally; small trace levels of WHG that probably
isn't entirely real WHG.

Like LifeisDandy in Eurogenes K=7, their "Sub-Saharan African" ancestry seems to be solely East African and not at all Niger-Congo (sometimes referred to as "West-Central African") based. You can see this in Dobon et al.'s own ADMIXTURE analyses like with the following run at K=3 where Copts show none of the light blue Yoruba (YRI) component but the Egyptian samples do:






Now, the reason this is all actually interesting is because. as I've stated in the past, Christian and non-Western (Ashkenazim + Sephardim) or Northwest African (Maghrebim) Jews from West Asia's Arabized regions often come off as distinct from their Muslim counterparts to some degree and seem to have avoided waves of more recent admixture that's affected their Muslim counterparts or at least absorbed much less of it.


The Spread of the initial Caliphates

This admixture can vary from being Niger-Congo ancestry to Peninsula Arabian ancestry
that is higher in some Muslim populations and either lower in their Christians (or Jews) or in the case of Niger-Congo ancestry completely absent.

One can only for now imagine that this new Niger-Congo input that isn't present in the Christian and Jewish groups who at times look like isolates in their home regions or display some substructure when compared to their Muslim kinsman [4] might just be a legacy from The Arab Slave Trade?

At any rate, a good example of these newer waves of admixture especially in terms of newer African ancestry absorbed likely through the Slave Trade would be Yemenite Muslims and Yemenite Jews.




Most Yemenite Muslims I've encountered either in studies or outside of them tend to come out with North African levels of African admixture, at a level of ~15-25% as you can see with how they plot at the same level as Mozabites, Moroccans, Egyptians and so on with only one of those samples just ending up at the very south of the Nagada Copts. 

Some Yemenite Muslims can indeed be about ~15% African in my experience, that isn't necessarily abnormal. But as a whole they're clearly more admixed than Saudis, Qataris and so on (fellow Arabians of the Peninsula). [5]


The Arabian Peninsula


Yemenite Jews in contrast are at African admixture levels comparable to those of Levantines who are more along the lines of ~5-15% African admixed. [6] Yemenite Jews' African admixture is also likely much more ancient as they only show East African cluster based African ancestry and none of the seemingly newer Niger-Congo input in Yemenite Muslims. 

I'd go on and on but it's generally obvious that they avoided various forms of outside admixture (not just Niger-Congo admixture) that Yemenites of a Muslim extraction simply did not.


Notice how Yemenite Muslims ("Yemen") show the Yoruba / Niger-Congo component whilst Yemenite Jews only show the pink Dinka / East African cluster component [3]

This perhaps seems to be the case with our new Copt samples as well. I personally wouldn't be too surprised if these Copts are a reliable genetic example of Christian and Late Period EgyptIranians, Anatolians and Caucasians are very rich in Ancient North Eurasian ancestry and from glancing at this recent incredulous Bronze Age Ancient Genomes study on Eurasia; it seems the Caucasus was rich in ANE as far back as the Bronze Age, Anatolia and the Iranian Plateau likely were too in my humble opinion. 

The point is, from what David says about the WHG and ANE levels in these Copts & even the levels LifeisDandy shows; it's clear that they really don't have Persian or Greek admixture. Persian or Iranian admixture would've likely brought with it notable ANE ancestry and Greek admixture would've brought with it much more notable and solid WHG ancestry (not negligible trace levels that might even be actual WHG admixture).


The Achaemenid Empire, the first great Persian empire
 
Although Bedouin admixture can't entirely be ruled out as one friend has noted. Many or most Arabian Bedouin do not show ANE or WHG ancestry in K=8, they're much like these Copts and mostly just look like a cross between East African/ Sub-Saharan ancestry (~5-15%) and ENF ancestry (the West Asian component that carriers Basal Eurasian with it) though some can show some Niger-Congo input.

Honestly, I think it's entirely possible that some of these ethno-religious isolates of West Asia do have influences likely owed to the Arab Conquest. Christians in the Levant do in fact show Arabian admixture at a non-negligible level in some independent ADMIXTURE runs or studies. [6]

Nevertheless, these populations did seemingly avoid admixture their Muslim counterparts have endured (though sometimes not at all entirely) whether it be Peninsula Arabian admixture or African admixture most likely owed to the Slave Trade or some other events.
These Copts who are honestly just descended from Egyptian migrants who arrived to Sudan within the last 2 centuries (as this new Sudan autosomal DNA based study notes) & Egyptian Copts like "LifeisDandy" among others seem to keep to this pattern. They seem more West Eurasian than their Muslim counterparts, lack some outside input in them such as Niger-Congo admixture & are most likely a better representation of what Egypt was like genetically before its Islamization and Arabization.

But this is merely an assumption on my part based on how they're keeping to an already well-known pattern among the Christians & non-Western or Northwest African Jews of "The Middle East" (Assyrians, Lebanese Christians, Yemenite Jews etc.) who often to some degree even to geneticists seem to perhaps be a better representation of their region's pre-Islamic & pre-Arab conquest population. [7]

The way they lack Niger-Congo input exactly like Lebanese Christians & Yemenite Jews do whilst their Muslim counterparts (Lebanese Muslims, Yemenite Muslims and Egyptian Muslims) actually have such admixture is especially compelling.





That alone to me establishes that they've at least avoided some admixture from the outside but the question as to whether or not these Copts lack Peninsula Arabian influences is still up in the air from what I can tell. Frankly, I'm not an expert on Egyptian autosomal DNA data and don't know if Egyptians Muslims themselves lack Arabian input or have any.

Granted, from looking at the ADMIXTURE results from Dobon et al. above; one is left to wonder given that Egyptians at K=10 and several other Ks seem more similar to Qataris than Copts. But that can be a bit skewed in that these new Copt samples are forming their own mixed component (similar to how some Mozabites or Tunisian Berbers form a "Maghrebi" component or Somalis form components like "Ethio-Somali") from K=5 and onward, but you'd expect the Egyptian samples to show more of this component than they are in my humble opinion.



Reference List:








Notes:

1. For the record, it has been known for a while now that Yemenite Jews are pretty much mostly native to the Arabian Peninsula, it's pretty clear that they aren't a Levantine migrant group that came to Arabia and mixed with the locals too as they don't share IBD segments with other Jews like Iraqi or Sephardi Jews while these Jews do share IBD segments with one another. [-]

2. To touch upon that Lazaridis et al. ADMIXTURE run I linked you to; you can see that Northwest Africans like Mozabites and Tunisians have WHG admixture by observing K=16 in that run for example where Northwest Africans show the blue WHG/ Loschbour based component alongside EEF (pink).

3. I referenced Hodgson et al. ("[5]") when I mentioned that Yemenite Muslims are more African admixed than Saudis and Qataris because you can view that data in that study's ADMIXTURE analysis. (names of the components)

4. My old post on ANE's spread that I linked to in this post needs to be updated a bit/ followed up perhaps with a newer post giving everyone a clearer image of what seems to for now be Ancient North Eurasian ancestry's spread across the world. Also, populations like Negevite Bedouins and Copts likely do have some negligible ANE-related ancestry owed to Caucasus Hunter-Gatherer-related admixture (which they show).

5. Link to note

6. Keep in mind that Coptic is a dead language (only used for liturgy) and that Copts are indeed simply Christian Egyptian Arabic speakers just like Maronites in Lebanon don't really speak Aramaic anymore.

Extra share:

A new variant of the Pan-Northeast Africa PCA where Tunisians, Moroccans, Mozabites and Morccan Jews have been added. A mapping of the group clusters in it I made.

Special thanks to:

David Wesolowski, the author of Eurogenes.

15 comments:

  1. Does anyone know the particular locale of origin for the Muslim Egyptian sample used in this study?

    Whether they were rural farmers or city-dwellers might make a significant difference in how much their ancestors were affected by admixture since the 7th Century.

    It's generally assumed that the influx of newcomers to Egypt was concentrated in cities like Cairo and Alexandria, and more in the Delta than in the Thebaid. In older literature, the Muslim Fellahin of the countryside, as well as the Copts, were often cited as good representatives of the pre-Islamic Egyptian populace, if only on physiological grounds.

    What we really need is a detailed genetic survey of Egypt by both region and religious affiliation. Better yet, we need that plus ancient DNA from skeletons representing various periods of Egyptian antiquity, from pre-Dynastic times onward.

    I've long been puzzled by the absence of published data on ancient Egyptian genomes at a time when we're getting such a harvest of data on older humans from Europe and Asia. Given the greater abundance of material to work with in Egypt, one would think we'd know a lot more by now. Does this have something to do with chemical peculiarities of the mummification process? Or could it just be that political conditions in Egypt had simply made it difficult for scientists to have opportunities to apply the techniques pioneered in recent years to the study of ancient Egyptian remains?

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    1. "Does anyone know the particular locale of origin for the Muslim Egyptian sample used in this study?

      Whether they were rural farmers or city-dwellers might make a significant
      difference in how much their ancestors were affected by admixture since the 7th Century.

      It's generally assumed that the influx of newcomers to Egypt was concentrated in cities like Cairo and Alexandria, and more in the Delta than in the Thebaid. In older literature, the Muslim Fellahin of the countryside, as well as the Copts, were often cited as good representatives of the pre-Islamic Egyptian populace, if only on physiological grounds."


      I don't know if they were city-dwellers or rural farmers but they seem to be the usual Lower Egyptian samples passed around between various studies. The study didn't collect the non-Copt Egyptian samples themselves but got them from an outside database. I'll email one of the authors one last question and see if he can give me any details on these Egyptians but they seem like the usual Lower Egyptian samples in studies. To my knowledge; there aren't a great many samples from Upper Egypt (or even samples from all over modern Egypt) in studies.

      "What we really need is a detailed genetic survey of Egypt by both region and religious affiliation. Better yet, we need that plus ancient DNA from skeletons representing various periods of Egyptian antiquity, from pre-Dynastic times onward."


      I couldn't agree more to be honest. What I did here with these Copts is really just "reasonable speculating" with some backing; what we truly need is a comprehensive look at Egypt on a genetic level= samples from all over and ancient DNA. We won't have a concrete image of Egypt's demographic history until we do.


      "Does this have something to do with chemical peculiarities of the mummification process? Or could it just be that political conditions in Egypt had simply made it difficult for scientists to have opportunities to apply the techniques pioneered in recent years to the study of ancient Egyptian remains?"

      I'm not aware of any real difficulties being posed by some of these ancient remains in Egypt being mummified. But I'm no expert on how to sample mummies, of course. I honestly don't know why there haven't been ancient DNA results from Egypt yet. I can try and think of various explanations like "political issues". The country has been pretty unstable over the last few years and the last few years has been when ancient DNA testing really started taking off so that might be the cause.

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    2. Are copts descendants of the ancient egyptians or are they an admixture of foreign invaders and ancient egyptians,or are they just foreign invaders who adopted egyptian language and culture because their language is close of the ancient egyptian langugage

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    3. They likely are, in some part, descended from the "Ancient Egyptians" but I don't think they're their unbroken and direct descendants as there likely were (i.e. the Hyksos) West Asian incursions into Egypt since its early days (likely bringing in new ancestral elements) but the only way to answer your question with any sort of "concrete-ness" would be to get substantial Ancient Egyptian ancient DNA from numerous periods and then compare those samples to modern Copts. And that, sadly, hasn't been done yet, and if it has; it hasn't been made public. Which is why I cautiously just assume they're likely a good example of pre-Islamic/Christian Egypt (likely more true for Lower Egypt).

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    4. I always heard the Cops were descendants of the Greeks. Any truth to this? Some of them (phenotypically) look largely largely Levantine or Caucus to me. Nonetheless if you had to take a guess on the origin of the Copts -- what would your guess or theory be overall?

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    5. They're certainly not "Greeks" based on how they cluster in PCAs and their various mixture models. They basically cluster with Yemenite Jews, Negevite Bedouins and Saudis. They don't seem to show any signs of notable Southern European admixture or any notable shift toward Caucasian populations but you're right on the Levantine comparison; they are shifted, at the very least, toward Southern Levantines (Negevite Bedouins, Palestinians, Jordanians etc.) but this doesn't really mean they come from these populations, they're just very similar to them on a basal level.

      As for where I, personally, think they come from... I think they're very much "natives" to Northeast Africa (perhaps particularly Lower Egypt) whose ancestors, over-time, absorbed waves of admixture from West Asia (particularly the Levant) since perhaps the days of the Hyksos. We'll see someday via ancient DNA. :-)

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  2. "They basically cluster with Yemenite Jews, Negevite Bedouins and Saudis."

    Would this indicate they're heavily Arabian admixed? I mean even if their existence does predate that of the Arab conquest. I wouldn't surprised if they originally came from the Achaemenids, Christianized during Byzantine Egypt, and then (more recently) largely Arabian admixed. However a lot of Copts look whiter than modern Arab Egyptians.

    I have a hard time believing they're natives to Northeast Africa.

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    1. "Would this indicate they're heavily Arabian admixed? I mean even if their existence does predate that of the Arab conquest. I wouldn't surprised if they originally came from the Achaemenids, Christianized during Byzantine Egypt, and then (more recently) largely Arabian admixed."

      Being very similar to Arabians on a basal level doesn't necessarily imply admixture from them. It's like with Western Jews and the Maltese which are two very, basally, similar population-sets but when you get a look at their Y-DNA and mtDNA profiles; they're clearly distinct populations, as far as I recall. Similar case here. Copts seemingly have a lot of Y-DNA E-M35 subclades (more than they have J1) whilst most Arabians are overflowing with J1 founder-effects.

      And there's seemingly not much proof of "Achaeminid" (Iranian) admixture. They don't have enough Caucasus-Hunter-Gather-related ancestry and/or ANE-related ancestry that differs from those of Southern Levantines and various Arabians, nor do they show the right Haplogroups to indicate such admixture.

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    2. Can I get a source for Coptic y-DNA? E-M35 is of Northeast African origin. Correct? Nonetheless the Copts are certainly an interesting bunch and I largely blame the country of Egypt for us not having DNA results for the Ancient Egyptians as they could release these results but they're holding these results hostage. Most DNA studies we do have on Ancient Egyptians are from STR (Short Tandem Repeat) studies that are known for their high error rate when it comes to sequencing of the human genome and studies that are largely inconsistent and contradictory in nature.

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  3. It's interesting how much the sudanese resemble horners, always assumed they were more west african-like. The Copts seem to be largely related to them, only with less native East African ancestry, while Muslim Egyptians seem to be, in fact, Arab Egytpians, at least the sample featured in that study.

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    1. You mean Sudanese in general ("South" & "North") or just Nubians and the "Arabs"? I see your point in both cases. They do have more West-Central African admixture (which is not present in the Horn). Groups like Dinkas have maybe 20-35% or so while Nubians and co. have less but definitely have some notable amounts. But yes, the majority of their "African" ancestry seems to be anchored in the "East African cluster" often formed by Nilo-Saharan speakers like Dinkas and Anuaks.

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    2. Just Nubians and Arabs, although some of the same applies to the Southern ones.

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    3. both horners and sudanese West Euroasian admixture happened during a prehistoric back migration through sudan. sudanese nubians and arabs are the same btw. the sudanese arabs are nubians with one of their paternal ancestors being arab. the only ethnic arab tribe in sudan is rashida.

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    4. "both horners and sudanese West Euroasian admixture happened during a prehistoric back migration through sudan."

      I'm aware:

      http://www.anthrogenica.com/showthread.php?9499-Gedmatch-populations-approximation&p=208306&viewfull=1#post208306

      "sudanese nubians and arabs are the same btw. the sudanese arabs are nubians with one of their paternal ancestors being arab. the only ethnic arab tribe in sudan is rashida."

      Only somewhat true. It depends on the Sudanese Arab subgroup, some were formerly Chadic speakers like various Baggara-Arabs but yes, the more Nile-Valley farmer types were often Nubian speakers until they were Arabized and acquired some Arabian admixture (most noticeable through some of their J1 subclades). But the two populations are again not "the same". It again really depends on the Sudanese Arab subgroup you're speaking of... Some have notably more West-Eurasian admixture than most Nubians in Sudan ('least the samples I've seen) while others are indeed practically identical to them in term s of autosomal DNA.

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  4. http://www.unz.com/gnxp/the-egyptians-live/?utm_source=rss&utm_medium=rss&utm_campaign=the-egyptians-live

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