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:

Global PCA

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Pan Northeast Africa PCA

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:

Karima

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Shendi

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New Halfa

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):

 PCA 1

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PCA 2

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:

Dataset

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:

Information and labels for the Samples

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- :

Bandar's run K=7

-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:

1. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape, Dobon et al.

2. The Genetic Structure and History of Africans and African Americans, Tishkoff et al.

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.