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Thread: Autosomal DNA data from Sudan, Dobon et al. 2015

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    Autosomal DNA data from Sudan, Dobon et al. 2015

    Not many African members here but for anyone who's interested-> there are various new Sudanese samples from a new study:

    Quote Originally Posted by Dobon et al. Abstract
    East Africa is a strategic region to study human genetic diversity due to the presence of ethnically, linguistically, and geographically diverse populations. Here, we provide new insight into the genetic history of populations living in the Sudanese region of East Africa by analysing nine ethnic groups belonging to three African linguistic families: Niger-Kordofanian, Nilo-Saharan and Afro-Asiatic. A total of 500 individuals were genotyped for 200,000 single-nucleotide polymorphisms. Principal component analysis, clustering analysis using ADMIXTURE, FST statistics, and the three-population test were used to investigate the underlying genetic structure and ancestry of the different ethno-linguistic groups. Our analyses revealed a genetic component for Sudanese Nilo-Saharan speaking groups (Darfurians and part of Nuba populations) related to Nilotes of South Sudan, but not to other Sudanese populations or other sub-Saharan populations. Populations inhabiting the North of the region showed close genetic affinities with North Africa, with a component that could be remnant of North Africans before the migrations of Arabs from Arabia. In addition, we found very low genetic distances between populations in genes important for anti-malarial and anti-bacterial host defence, suggesting similar selective pressures on these genes and stressing the importance of considering functional pathways to understand the evolutionary history of populations.

    Link

    I asked David/ Polako/ the author of Eurogenes/ Generalisimo via email to acquire the samples and run them against other East Africans and some West Asian populations (in PCAs) so we could see how they compare and well, I'll just copy and past what I ended up getting and posted on ABF:

     
    Quote Originally Posted by Awale
    Well, ladies and gentlemen! Polako made two PCAs for us as well as a small dataset available in case one wants to run some of these new samples through an ADMIXTURE calculator.

     
    Quote Originally Posted by David/ Polako
    The chip they used is really crap; it doesn't overlap well with the usual chips. But the attached PCA look OK, as long as none of the samples are mislabeled.

    Btw, here you can download a small dataset with these new samples that you can run with ADMIXTURE.


    Here is the Global PCA and it shows you each group's admixture levels rather well based on how much they pull toward West Asians and North Africans:



    I apologize though for how messy it can get given how Polako labels each sample with its ethnic designation.

    This is a sort of Pan Northeast Africa PCA with Levantines, Arabians & Maasai thrown in:



    And finally, here is the dataset Davidski-man/ the King of the Poles gave us to use for an ADMIXTURE analysis:



    ---

    A Katrilion Bajillion thanks to David/ Polako!



    Interesting things to note, some of which I mention at my blog:

    • The Beni-Amer Bejas seem to perhaps share more ancestry with Horners such as Habeshas and form a cluster with Horners at large while Sudanese Arabs and Nubians form their own, however they (the Bejas) do sort of look to be intermediates between Horners and North Sudanese (Sudanese Arabs + Nubians). They also look to mostly be more West Eurasian than Habeshas though, putting them at >50% range of West Eurasian/ West Asian ancestry.

      ---
    • The Nagada Copts are basically the descendants of immigrants to Sudan within the last 2 centuries and are more West Eurasian than your average Muslim Egyptian; they also seem to lack ANE & WHG input. Granted, they show trace levels of WHG but that as David/ Generalismo notes after running them through the K8 ADMIXTURE analysis; is probably not real WHG but something WHG-like from West Asia ("UHG"). At any rate; the study itself confirms that they mostly lack Niger-Congo input (the "YRI"/ Yoruba component at K=2) unlike their Muslim Egyptian counterparts who do have Niger-Congo admixture. These Copts basically only have East African admixture so they're more or less about ~85% "ENF" and ~15% East African much like a Copt whose results I touch upon at my blog whilst wondering if these Copts can be taken as a good example of Pre-Islamic and Pre-Arab Conquest Egypt-> What do you think of them?

      ---
    • David ran some of these Sudanese samples through Eurogenes K=8 & Sudanese Arabs, Nubians & Beni-Amer Bejas seem to be bereft of ANE & WHG ancestry much like Horners such as Somalis & Habeshas. They like Horners seem to be mostly just "ENF" admixed. But some of the samples from what he's said do show trace amounts of WHG (Horners don't show this) but that again probably isn't real WHG.

      ---
    • There seems to be a good amount of heterogeneity amongst Sudanese Arabs and Nubians in terms of West Eurasian ancestry levels. Some few are about as West Eurasian as Somalis (~40%), some seem to sit between Somalis & Habeshas, others are at Habesha levels whilst many such as Shukrya Arabs seem more admixed than Habeshas (>50% West Eurasian)

      ---
    • The Fulani samples seem to be of two separate groups, one that seems practically as African as the Gumuz and one that looks more blatantly West Eurasian/ Northwest African admixed and pulls toward North Africans and West Asians on a PCA however when Northwest Africans are thrown into this PCA; both the less admixed Fulanis and more admixed Fulanis pull downward on the Y axis as Northwest Africans do; displaying a clear affinity for them from what I can tell. This is in line with how Fulanis tend to show "Maghrebi/ Northwest African" admixture in other studies like Hodgson et al. 2014: [Hogson et al. 2014 ADMIXTURE run] [names of the various components]. David ran them through Eurogenes K=8 and it seems that like Northwest Africans/ Maghrebis the more West Eurasian admixed Fulani samples are showing WHG ancestry (~5-6%). So it looks to me that Fulanis (at least the more clearly Northwest African admixed ones) do carry some WHG like Northwest Africans do.



    Some "mappings" I made of the various groups that form clusters together in the PCAs:

     


    .




    Detailed info on the samples I acquired from the paper's authors via email:



    For those of you capable of tinkering with them; David put together a small dataset of samples from this new study someone could run through an ADMIXTURE analysis if they cared to:



    --

    Many thanks to David btw! And while I don't see too many members interested in African genetics here; these Copts are certainly interesting so... Discuss...
    Last edited by Awale; 06-25-2015 at 03:02 AM.
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    Great work, Awale! Awesome first post!

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    Quote Originally Posted by Ezana View Post
    Great work, Awale! Awesome first post!
    Heh, thanks. Btw, Lol_Race (he's told me a bit about you so I'm sure you're familiar with him :-)) and I noticed something a bit OT bit still interesting about the "Northeast Africa" plot:



    It's that Somalis alongside Northern Highlanders (Habeshas + Beta Israels) & Oromos are seemingly pulling toward Aris and showing what looks like an Omotic affinity. Lol_Race asked David to throw in Hadzas to perhaps introduce something similar to Aris that may have been able to slightly differentiate Somalis from Omotic admixed Horners but the pulling toward Aris seemed to stick:



    Why is this weird? Well... It's making it seem like Somalis may actually have Omotic admixture. As you may know; Bandar from the old ABF days created a run that was pretty good at spotting Omotic by removing the most inbred Ari Blacksmiths & in this run Somalis generally came up 0% Omotic except for Ethiopians Somalis who had some folks among them (alongside two heavily Omotic admixed outliers) showing Omotic admixture. Now, David suggested that the lower number of markers he was forced to use for these PCAs (due to the rather poor overlap between Dobon et al.'s chip and the chips used by other studies) might just change this up a bit.

    So I recently asked him to try and replicate those two above PCAs but exclude the Sudanese samples entirely so he could then use the usual high number of markers-> if things stay the same if and when he turns up with those PCAs and Somalis keep pulling toward Aris alongside other Horners-> Do you think it could mean Bandar's run was wrong and Somalis perhaps do have at least some Omotic admixture?

    I wonder if these Bejas also have Omotic admixture; I asked Ethiohelix to run them through an ADMIXTURE analysis and while he said he was pretty rusty; he does know how to spot Omotic admixture IIRC so we'll see about these Bejas, I guess... If they lack Omotic admixture then it does lend some good credence (as Lol_Race mentioned on ABF) that Cushitic speakers originally came from further up north in Northeast Africa. Granted, that idea makes enough good sense to me from a linguistic standpoint alone..
    Last edited by Awale; 06-25-2015 at 01:05 AM.
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    1) On the graphs whats the different between dark blue and green, they both appear to be west eurasian related. Is the green a berber specific component?
    2) Also take into consideration noth african populations in algeria and morroco have WHG around 15%, so its very possible that the WHG found in copts is from that source and not UHG/EHG related

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    Quote Originally Posted by tamilgangster View Post
    1) On the graphs whats the different between dark blue and green, they both appear to be west eurasian related. Is the green a berber specific component?
    You mean this graph? The dark blue one just looks like a Southwest Asian-esque component peaking in Qataris in this dataset (mostly ENF with some East African, I'd wager).

    The dark green component definitely doesn't seem to have much to do with Northwest Africans; otherwise it would have been perhaps much more profuse in the Fulani samples. Seems like these Copts are just forming their own component...

    2) Also take into consideration noth african populations in algeria and morroco have WHG around 15%, so its very possible that the WHG found in copts is from that source and not UHG/EHG related
    Hmm, perhaps. But keep in mind that what WHG they do have is very minimal (1-3%). One thing I would notice though is the PCA David made with Northwest Africans present:

    https://drive.google.com/file/d/0B2A...pSU2VsUEk/view

    Notice how all Northwest African/ Maghrebi admixed groups (Morrocan Jews who have been known to have some Northwest African admixture [-] & Fulanis) pull down on the Y axis with Northwest Africans-> displaying what looks to be their affinity for them. And notice that these Copts don't do the same... I can't totally deny the possibility but I doubt they have meaningful Northwest African admixture or got their trace amounts of WHG from them. If they share any ancestry with Northwest Africans; my money would be that this would mostly be much more ancient shared ancestry-> owed perhaps to the original Berber speakers who migrated into Northwest Africa who probably weren't WHG admixed at all.
    Last edited by Awale; 06-25-2015 at 01:35 PM.
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    Excellent work, Awale. A worthwhile read.

    My main impression is that the PCA plots tend to mirror geographic clines in a broad sense. Additionally, I'm taken aback (in a positive way) regarding the clustering patterns here; the summation of North Africa, the Levant and the Arabian Peninsula occupy a proportionally smaller clustering space than the neighbouring non-North African groups. I'm immediately reminded of the coined phrase regarding Eurasia being a "subset of African genetic diversity".

    I'd be curious to see what the ANE frequencies are among these folks. It does appear, as you've covered in your earlier blog entries and stated definitively here, that almost all of the West Eurasian-derived scores among NE Africans is ENF. Given the presence of R1b-V88 in Chadic speakers and the current popular working hypothesis regarding the Y-DNA R1-M173 bifurcation in the Eurasian steppe, I do wonder whether even a trace of this is anywhere to be seen in NE Africa, as it lies more or less en route between Eurasia and Cameroon.

    In that respect, I wonder if anyone with ADMIXTURE familiarity is interested in running these samples to see if anything comes up.

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    Quote Originally Posted by DMXX View Post
    My main impression is that the PCA plots tend to mirror geographic clines in a broad sense. Additionally, I'm taken aback (in a positive way) regarding the clustering patterns here; the summation of North Africa, the Levant and the Arabian Peninsula occupy a proportionally smaller clustering space than the neighbouring non-North African groups. I'm immediately reminded of the coined phrase regarding Eurasia being a "subset of African genetic diversity".
    Well, a good amount of modern African diversity is also ultimately owed to Eurasian input, so I'd keep that in mind. One of the main things (if not in some cases the main thing) pulling Horners, North Sudanese, the Maasai and various Fulanis away from where groups like Nilotes are clustering is ultimately their West Eurasian ancestry.

    It does appear, as you've covered in your earlier blog entries and stated definitively here, that almost all of the West Eurasian-derived scores among NE Africans is ENF.
    Yes, this is often why Peninsular Arabians and now these Copts tend to seem like the best example of the kinds of West Asians the East African ancestors of Horners mixed with episodically; it's because these new Copt samples and Arabians tend to mostly just be ENF (mostly lacking ANE & WHG-UHG) when it comes to their West Eurasian ancestry.

    Given the presence of R1b-V88 in Chadic speakers and the current popular working hypothesis regarding the Y-DNA R1-M173 bifurcation in the Eurasian steppe, I do wonder whether even a trace of this is anywhere to be seen in NE Africa, as it lies more or less en route between Eurasia and Cameroon.
    Hmm, there are people better suited to helping you figure this out (Beyoku, Lol_Race, Pgbk87 et al. ; I'll message them about your musings )

    In that respect, I wonder if anyone with ADMIXTURE familiarity is interested in running these samples to see if anything comes up.
    Yeah, it would be very interesting to see what would turn up. Adding Somalis into the mix would be very interesting so we could see just how much ancestry would prove to look "shared" between Somalis & Bejas (fellow Cushitic speakers) given that at K=7 what looks to be a sort of pseudo-Cushitic component like "Ethio-Somali" forms (making up a good degree of the Maasai's ancestry and a whole lot of the Beja and Ethiopian samples' ancestry) but that ADMIXTURE run as Lol_Race noted to me at ABF is rather unstable:

     
    Quote Originally Posted by Lol_Race
    That Cushitic component doesn't look particularly stable, probably due to the mere 14K SNPs used, as well as the lack of important samples, like Somalis. Other than the major Cushitic contribution, Maasai should also show significant Nilo-Saharan and Bantu, but that K=7 run isn't picking up on the NS at all. It makes them look predominantly Niger-Congo, which is misleading (should be closer to 20%).

    The "Fulani" component is also problematic, and not informative for East African populations.
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    I can add these to my dataset and keep whatever passes the 50% threshold for coverage. I'll run them in admixture after a while. I'm plugging in some other stuff at the moment.

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    Quote Originally Posted by Chad Rohlfsen View Post
    I can add these to my dataset and keep whatever passes the 50% threshold for coverage. I'll run them in admixture after a while. I'm plugging in some other stuff at the moment.
    That would be great but do you have any Somali & Habesha samples? Or at least the Horner samples from Pagani et al.; running them alongside the "Afar", Somali and Habesha samples from that study is pretty key.
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    I have tons of Africans, including Somalis, Ethiopian Jews, etc. I've got like 2700 samples, of which 200 are ancient. I even have Indian tribals and the Onge.

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