Wednesday, June 10, 2015

Sudanese Arabs, Beni-Amer Beja and Nubians: Autosomal DNA data

An amazing new study came out recently with several Sudanese samples of Sudanese Arab, Beni-Amer Beja, Nubian, Darfurian, Copt, Nilote, Fulani and various other Sudanese origins.  [1]


[1]

The data is quite exciting as we can finally compare the populations of Sudan to other Mainland East Africans such as Horners and Southeast Africans. I contacted David Wesolowski (the author of the Eurogenes genome blog) and asked him to run the new samples into a Global PCA/ cluster as well as another PCA (Principal Component Analysis) which he made into a sort of Pan Northeast Africa PCA with Arabians, Levantines, Maasais and Fulanis thrown in:






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The results seem quite interesting. There's intriguing information on several of these population sets but my main interest in this particular blog post are the Sudanese Arab, Nubian and Beja samples. The Beja seem mostly more West Asian/ West Eurasian than Ḥabeshas (Amhara-Tigrinya), Somalis, Ethiopian Jews, Wolaytas & Oromos and seemingly within a ~50-60% West Asian range of admixture. However in the Northeast African PCA they form a cluster with Horners like Somalis, Ḥabeshas, Oromos and Wolaytas while Sudanese Arabs and Nubians form their own cluster:





  In conjunction with this, they also come out extremely similar to this paper's Ethiopian samples (who are mostly a composite of Amharas and Tigrinyas accompanied by 2 Oromos) when put through the study's ADMIXTURE runs:




It seems to me that whilst they are actually often more West Eurasian/ West Asian than Horners like Ḥabeshas, Oromos and Somalis; these Cushitic speaking Beja still seem to share a gross amount of ancestry with Horners based on how they plot in the Pan Northeast Africa PCA and their greater similarity to Ḥabeshas/ these Ethiopian samples than to Nubians and Sudanese Arabs in this study's ADMIXTURE runs.


Information (including locations) on the various sampled populations:






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Overall, these Beja seem quite homogeneous. All clustering very close in the Global PCA, demonstrating a generally close/ uniform distance from non-Eurasian admixed Africans (f.e. Yorubas and South Sudanese) and West Eurasians. However one must wonder if this is because virtually all of the samples were gathered from one location/ town and are of the same Beja subgroup/ tribe (the Beni-Amer).

In contrast, the Sudanese Arab and Nubian samples were gathered from a variety of locations. 
Sudanese Arab locations:




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However, from what a friend tells me, Hadendoas were sampled a long time ago in Tishkoff et al. [2] alongside Beni-Amers and both groups seemed to look extremely similar so it's entirely possible that these Beni-Amer are representative of virtually all to most Bejas but we'll see in due time, I suppose.

Sudanese Arabs and  Nubians in terms of admixture levels are a different story from Beni-Amer Bejas however and are notably quite diverse in terms of admixture levels:






The more left a sample/ person pulls-> the more West Asian/ West Eurasian they are. That's what I mean by "Admixture Levels"; how much a population splits between West Asian ancestry and the kind of mostly non-Eurasian admixed African ancestry you'd find in a Dinka for example. 

Sudanese Arabs and Nubians seem very heterogeneous in this regard. Some few Sudanese Arabs and Nubians actually seem to be at a Somali level of West Asian ancestry (~40% or so), others sit between Somalis and Ḥabeshas (~40-50%) whilst many seem practically identical to Ḥabeshas & Ethiopian Jews in terms of admixture levels (~50%), on the other hand; a great number of them (more Sudanese Arabs than Nubians) seem well-over Ḥabesha levels of admixture (>50%).

As you can see Beni-Amer Bejas-:



 
-who form a cluster with non-Ari Horners are much more homogeneous and often more West Asian than Ḥabeshas (>50%) though a good number of them are more or less at a Ḥabesha level of West Asian ancestry. 

Sudanese Arabs & Nubians seem to be more similar to each other (forming a cluster with one another) than they are to non-Ari Horners like Ḥabeshas, Wolaytas, Somalis, Ethiopian Jews & Oromos (forming their own sort of cluster) while Beni-Amer Bejas seem more similar to these same Horners but sit at a sort of intermediate position between them and North Sudanese like Sudanese Arabs and Nubians.





There are two other PCAs that David Wesolowski made upon a request from a friend (user Lol_Race):



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In these PCAs, that friend requested that Hadzas be added because it was curious how Somalis alongside Oromos, Wolaytas, Ḥabeshas & Ethiopian Jews were seemingly pulling up toward Aris who are the current best representation we have of the Omotic component

He hoped the Hadza being added would maybe introduce something similar enough to Ari Blacksmiths and Ari Cultivators & the ancestry in Somalis that might be similar to Omotic speakers like Aris. This, in turn, could perhaps separate Somalis from Ḥabeshas a little bit in a PCA since, due to some older analyses that I've touched on in the past, Somalis seemingly don't have Omotic admixture despite what studies like Hodgson et al. and Shriner et al. seem to posit. However, the separation he was hoping to see simply did not occur:





Somalis, Beni-Amer Bejas, Wolaytas, Ḥabeshas, Ethiopian Jews & Oromos all consistently formed a cluster together in both new PCAs where Hadzas were included. Leading both him and me to wonder whether or not Somalis do actually have at least a tiny amount of Omotic admixture? Though I personally suggested that this could be something else binding the populations of the Horn (including Aris) together. No truly strong inkling as to what it might be however.

I also do wonder if these Beni-Amer Bejas have any Omotic admixture because if they lack it; it would make a good case for linguists who pose the rather plausible idea that Cushitic speakers (the pre-historic peoples who likely make up a large chunk of the ancestry in most Cushitic and Ethiopian Semitic speaking peoples) originally came from further up north in Northeast Africa/ essentially down from areas like Egypt and Sudan and into the Horn.



Northeast Africa

That leads me to talking about a possible ADMIXTURE analysis. David over at Eurogenes put together a small dataset from these various populations that one could run through an ADMIXTURE calculator:




If anyone is interested in running them through any number of ADMIXTURE calculators then go on ahead. If you download all of the samples by yourself then you may sadly encounter very poor labeling of the samples but I emailed some of the authors and managed to get a spreadsheet that properly labels every sample with its ethnic designation:






The original data was really just ID numbers for each sample and it was pretty much impossible to know which sample belonged to which population. If anyone with a good calculator for helping spot Omotic admixture like the kind in an old fellow Somali's following spreadsheet- :




-is out there then it would be quite appreciated if you could run these samples through such an ADMIXTURE analysis and email me the results: Awaleking@gmail.com. Or really just post it here in the comment section. I'm going to try fiddling with them myself in the meantime and see what I can share.

 This is certainly not the last post I'm going to be making on this subject. This is honestly more of a rushed post where I'm ecstatically trying to get some of this new and incredibly interesting information out, I'll probably do several follow ups on this paper, especially once I have enough interesting data via ADMIXTURE. I'll even touch upon populations other than the ones focused on in this post. Stay tuned...



Reference List:





Notes:

1. David over at Eurogenes did attempt to run some of the samples through Eurogenes K=8 and while I haven't seen the data directly myself-> it seems to be that Sudanese Arabs, Nubians and Beni-Amer Beja (most likely all Beja as well) lack Ancient North Eurasian and Western European Hunter-Gatherer input much like the substantially West Asian admixed populations of the Horn such as Somalis, Habeshas, Ethiopians Jew & so on.

2. David did note that the chip used in this paper didn't overlap well with the chips usually used in other studies so a much lower number of markers than usual were used for these PCAs (15,000 SNPs when most other PCAs he's made tend to use more than 150,000 SNPs), there could be some differences in clustering noticeable with more markers, nothing radical but some groups could show slightly more variation from each other.

3. The Ethiopian samples from this new paper also seem to basically be diaspora folk as they reside in Khartoum, Sudan. The Ethiopians David used in his PCAs however are basically from Pagani et al. / the ones you usually see in papers like Hodgson et al. , Shriner et al. and so on.

4. Beni-Amers in Eritrea are thought to mix with Tigres (Ethiopian Semitic speaking pastoralists, linguistically very closely related to Tigrinyas). I wonder if the case is similar at all for these Sudanese ones or if meaningful mixing (enough to show in terms of  the Beni-Amer's general autosomal DNA) between these two groups even in Eritrea truly occurs. Though Tigres have yet to be sampled in any study, to my knowledge.  

5. If you're wondering why Ethiopian Semitic speakers and Cushitic speakers would likely share in some decent amount of ancient/ pre-historic ancestry: [-]


Very Special Thanks to:


All the authors involved in this study and David Wesolowski (the author of Eurogenes).


Recommended reads:

Population Genomics of Bronze Age Eurasia, Allentoft et al.  , it's unrelated to this but is extremely exciting and something I simply had to share. I'll make posts on this in due time as well.

 

6 comments:

  1. One of the most interesting things this study reveals is the genetic distinctiveness of the Coptic Christians in comparison with Muslim Egyptians. This, to my knowledge, is the first time such a marked difference between these two populations has been documented. If you look at the supplementary data in this paper, it remains visible right on up through K=10.

    Does this, in fact, suggest that Egypt experienced a major demographic change in association with the Arab-Muslim conquest? Or could it be that the Copts have simply become more distinctive as a result of genetic drift over the last 1400 years?

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    1. "One of the most interesting things this study reveals is the genetic distinctiveness of the Coptic Christians in comparison with Muslim Egyptians."

      I agree, we went into this in some length at the forum I linked to at some point in the above blog post:

      http://www.forumbiodiversity.com/showthread.php/44363-Sudan-autosomal-study/page6

      "This, to my knowledge, is the first time such a marked difference between these two populations has been documented. If you look at the supplementary data in this paper, it remains visible right on up through K=10."

      It's not simply that but these Nagada Copts who are basically migrants from Egypt in the last 200 years or so-> are actually more Eurasian than their Muslim counterparts. They actually sit in the global PCA between Southern Arab Levantines (f.e. Palestinians) and Muslim Egyptians:

      https://drive.google.com/file/d/0B2ARnUeK-Y8WSjNlNUZlYUdhWU0/view

      David over at Eurogenes ran a few of them through Eurogenes K=8 and they seem to come out ~15% "Sub-Saharan African" & ~85% ENF. They more or less completely lack Ancient North Eurasian (ANE) and Western European Hunter-Gatherer (WHG) admixture. They show trace levels of WHG but that probably is not WHG as even he admits; it's probably something old in the Middle East similar to WHG ("UHG"/ "Unknown Hunter-Gatherer").

      "Does this, in fact, suggest that Egypt experienced a major demographic change in association with the Arab-Muslim conquest? Or could it be that the Copts have simply become more distinctive as a result of genetic drift over the last 1400 years?"

      I think it's mostly likely to be the option in your first question. Christian Middle Easterners actually show this pattern rather often where there's often a substructure between Muslims & their Christian counterparts:

      http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003316

      Even Yemenite Jews look to perhaps be a preservation of the pre-Islamic Arabian Peninsula (or at least Yemen). They lack the "Niger-Congo" input (their African input is solely "East African") many modern Yemenite Arab Muslims will show and seem to lack various other forms of outside admixture Muslim Yemenites have incurred from what I've noticed.

      The Christian and non-Western (Ashkenazi, Sephardi) & Northwest African (Tunisian, Moroccan etc.) Jewish populations of the Middle East often seem like a frozen in time example of what their region may have looked like prior to its Arabization and Islamization.

      Mind you, these Copts and Muslim Egyptians still seem quite close. It's clear Egypt went through some "demographic changes" thanks to its Islamization and Arabization but I won't over-blow it and say the changes were extremely profuse but they're clearly non-negligible.

      ---

      On another note; I do think these Copts maybe representative of all Copts. I've seen another random Copt's results (a girl who was tested on 23andme, I believe) and she seemed to be pretty much identical to these Copts; no ANE, small amount of WHG that's probably not real WHG, mostly ENF and ~15% "East African"/ "Sub-Saharan African". Her and these new Copt samples seem very alike if not identical and she's an Egyptian Copt from Upper Egypt.

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  2. Very very interresting study. It looks like Nubians are distinct from Horners and plot through a different axis which corelates with linguistic affiliation while on the other hand Bejas are still close to other Cushitic speakers and are probably resulting of a further north expansion (?). Cheers.

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  3. This DNA test is flawed! there is no habesha DNA..... The amharas are the only habesha if they're lucky claimers with the tigray people of ethiopia. Also, I don't think the amhara and Eritrean DNA would match, neither would it match with the Somalis either btw.

    What you should rather study is the genetic between Eritreans: the distinct behiher tigrinya tribe, beja, tigre, kunama, saho and afar with the Sudense and Egyptian population! THAT would be interesting. Reason is our african dna is supposed to come from in between Sudan Egypt, That's not the case for Ethios!

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    1. "The amharas are the only habesha if they're lucky claimers with the tigray people of ethiopia. Also, I don't think the amhara and Eritrean DNA would match, neither would it match with the Somalis either btw."

      With all due respect... What you "think" is irrelevant here. Amharas and Tigrinyas are both considered "Habesha" and genetically; they form a very close group with only incredibly small differences in terms of autosomal DNA. They're quite close and many members of either group will even seem "identical" and overlap like they do in the following PCA:

      https://drive.google.com/file/d/0B2ARnUeK-Y8WTkZSNHNOV0JXZWM/view?usp=sharing

      Amharas can sometimes be a bit heterogeneous due to assimilating some other groups like Agaws for one but even then; no strong difference.

      And while Somalis are more distinct from them than they are from each other; these two populations are undeniably closely related to Somalis. There's no arguing about this or getting "opinionated", it's a genetic fact, deal with it or don't; that's not my problem.

      "What you should rather study is the genetic between Eritreans: the distinct behiher tigrinya tribe, beja, tigre, kunama, saho and afar with the Sudense and Egyptian population! THAT would be interesting."

      What? Are you some kind of odd Eritrean nationalist who's been duped into thinking there's some huge difference between you and "Ethiopians" like Amharas and Oromos? I hate to break this to you but if you're a Biher Tigrinya, unless you have recent "foreign" ancestry (from Sudan or Arabia and so on) you're barely distinct from your average Ethiopian Amhara (and basically identical to Ethiopian Tigrinyas) and are closely related to, though markedly more distinct from, populations like Oromos or Somalis. Eritreans are much closer to the Cushitic and Ethiopian Semitic speaking populations I touch upon on this blog than to any population in Sudan other than Bejas. As for your suggestion about studying Sahos and such populations-> would love too but as it stands; we lack autosomal DNA data for Sahos and Tigres as well as Afars.

      But you're right in some sense; comparing "Eritreans" like Tigrinyas to Bejas should be an interesting endeavor but you seem to be operating under some misguided view that there's some kind of substantial genetic division between Cushitic & Ethiopian Semitic speaking "Eritrean" & "Ethiopian" populations... There really isn't for the most part.

      "Reason is our african dna is supposed to come from in between Sudan Egypt, That's not the case for Ethios!"

      Not true... The "African ancestry" in populations like Tigrinyas in Eritrea is no different from what you'd find in an Oromo or an Amhara in Ethiopia. It's mostly a mixture of "Omotic" Ari-related ancestry and "the East African cluster" with the latter component being shared substantially with various other East African populations (I have a post about it; look it up). From observing Sudanese populations so far; seems they're mostly bereft of the "Omotic" ancestry in various Horn African populations and are more "recently" related to Nilo-Saharan speaking groups like Dinkas, Masalits and Furs than we are which makes perfect sense as populations like Nubians are basically Nilo-Saharan speakers themselves.

      "This DNA test is flawed!"

      No, you just don't seem to like what you're seeing but as I said; not my problem.

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  4. Question. Would you agree with saying that the Copts are the closest to Ancient Lower/Northern Egyptians while modern day Upper/Southern Egyptians to North Sudanese are the closest to Ancient Upper/Southern Egyptians? Here's an example of the second:

    http://i.4cdn.org/his/1489980429103.jpg

    The art shows brown or red subjects and a notable amount of fair skinned specimens (if only as women).

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