Sudanese autosomal genetics

26 May
Location of the samples
There is a new paper dealing with Sudanese genetics, which is  of some interest, in my opinion:
Most interestingly they spot a cline and divide (both) between Egypt and Tropical Africa and differential genetics for Somalis, one of three outgroups (the other two being Egyptians and Ugandans from Karamoja region (Nilotic ethnicities).

Fig. 5 (blue: my annotations)
The structure shows (as much as a mere three components allow) a duality of some clinal value (i.e. not absolute but relative) with a divide cutting across Sudan: not just between North and South according to the latest political split but also placing Darfur, Kordofan and the Nuba along with Tropical Africa as well. 
Instead Central, North and Eastern Sudanese look much like Egyptians. Somalis are clearly different however but you’d never know based only on K=2. That’s why it is important to explore these analysis to some depth, greater than K=3 in any case, a very shallow depth for such a diverse region. 

PC Analysis:

Fig. 6A
Fig. 6B

Notice that PC2 and PC3 are of similar values. PC1 however is more than double in importance and marks a cline between Egypt (and the Sudanese Copts) and the Nuba. PC2 and PC3 only show distinctions between Copts and Egyptians and Copts and Somalis respectively. 
I wonder if this last is caused because of random peculiarities of the 15 ancestry informative markers used in this study, which seem a bit too few not to cause random distortions, specially in such a poorly understood region as is East Africa.

Posted by on May 26, 2011 in African genetics, autosomal DNA, Sudan


6 responses to “Sudanese autosomal genetics

  1. Etyopis

    May 26, 2011 at 7:52 pm

    Interesting low resolution Autosomal study, thanks for sharing Maju.I doubt that some of their conclusions can hold much water however as they are missing a huge swath of sampling area between Somalia and Sudan, i.e. Ethiopia and Eritrea, leading candidate regions for the origin of Afroasiatic languages. If they included these regions, as well as increased the size of the microsattelite markers used, the variation explained by language versus geography would have been almost equal, as Tishkoff et. al found and noted in her study.Interesting study anyhow.

  2. Maju

    May 26, 2011 at 8:14 pm

    Yes, it's not too revealing because of its very low resolution and relatively small comparison area. It is still a reference to keep in mind. That's about it.

  3. Andrew Oh-Willeke

    May 27, 2011 at 5:42 pm

    "also placing Darfur, Kordofan and the Nuba along with Tropical Africa as well."Not surprising, but evidence that there will be more genocide unless North Sudan grants more regional autonomy and learns to function as a multinational state.

  4. Maju

    May 29, 2011 at 8:46 am

    It is surprising to me: I would have expected the divide to be at the 1st cataract if anywhere or to be more gradual. Nubians (1st to 2nd cataract originally y Egypt, also in Northernmost Sudan) are generally considered black in Egypt, while regular Egyptians are considered white. But we get here that Egyptians, Nubians, and most Sudanese appear to cluster together in the structure analysis (less clearly so in the PC analysis maybe). That's puzzling to me. The limited numbers of AIMs (only 15!) and the shallowness of the structure analysis may be behind these issues. I guess it's better than nothing but I also hope for a better paper soon that clarifies our doubts.

  5. Alexander Philip

    November 16, 2013 at 2:16 am

    “manipulation and trolling are also very much unwelcome here”…”The author reserves the right to delete any abusive comment”…mmm that's interesting !

    “Not surprising, but evidence that there will be more genocide unless North Sudan grants more regional autonomy and learns to function as a multinational state.”

    Dear Mr author, you do not consider the above quoted comment to be “abusive” or “manipulative” ?!

  6. Maju

    November 16, 2013 at 2:28 am

    No. It's a legitimate opinion, which I happen to share in essence (not in form because I do not believe in multiethnic states with colonial or otherwise imperialist borders but in the right to self-determination of every single people-nation with a traditional territory, especially those whose identity is not based on mere religious brainwashing since childhood, as happens in abhorrent pseudo-national entities like Pakistan or the Apartheid Regime in Palestine). It may be a bit off-topic but not enough for me.

    Also the author of that comment is a respected commented here which has never given me any reason to exert the always problematic act of censorship, unlike so many others.


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