June 09, 2015

Nilo-Saharan component

Scientific Reports 5, Article number: 9996 doi:10.1038/srep09996

The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape

Begoña Dobon et al.

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.



Awale said...

Would it be possible for you to get the samples and run them through an ADMIXTURE analysis with Somalis, Ari Blacksmiths, Gumuz, Oromos and Ethiopian Tigrinyas and Amharas as well as Pagani's "Afar" samples?

When you get the data/ samples they'll likely be poorly labelled (just digits/ codes) but I contacted the authors and you can see each samples information right here:


It would be very interesting to see things like whether or not the Beja sampels have any "Omotic" admixture for example.


andrew said...

One of the most interesting discoveries in the paper is not noted in the abstract.

"It is interesting to note that Nuba populations constitute an homogeneous group, even if some speak Kordofanian (of the Niger-Kordofanian family) and others different languages of two branches of the Nilo-Saharan family. Their genetic composition denotes their Nilo-Saharan origin, with linguistic replacements in some groups."

Kordofanian languages have long been interesting to linguists because they are an outlier island of Niger-Congo languages to the Northeast of the contiguous West to Central African territory of the other, non-Bantu, Niger-Congo languages. The fact that Kordofanian language speakers show strong genetic signs of being descendants of Nilo-Saharan languages speaking people who experienced language shift at some point, has great significance in interpreting this outlier case. In particular, it disfavors the hypothesis that non-Bantu Niger-Congo languages once had a much greater range that contracted in prehistoric times for reasons unknown.

AdygheChabadi said...

This study is helpful to my studies of the Kushite/ Meroitic language. According to this study, The Kushites/ Meroites were not Nilotic and, therefore, not genetically related to the ancestral Nubians, Eastern Sudanic speakers, or other Nilo-Saharans. This might also be a sign that their language, Kushite/ Meroitic, was also non-Nubian/ Nilo-Saharan. This study did find that modern Nubian are primarily made up of what was the remnant population of Kush/ Meroe which means that there was no very massive intrusion after the fall of Meroe in 350 CE. The invaders were clearly not a large band since excluding recent Arab admixture the population of Northern Sudan, like Egypt, is closer to the Berbers genetically than anything Nilotic. It would appear that the Noba/ Nuba (ancestral Nubians), who would have carried Darfurian/ Nilotic genes (the Nubian urheimat is in Darfur), exerted what is called "elite dominance" over the population of the collapsed Kushite/ Meroitic kingdom. Their numbers (the Noba/ Nuba) could not have been massive at all. The Nubians are between 60% and 68% of the Coptic source population. This would make ~30% (more or less) of their genes Nilotic on the average. This would show that the Kushites/ Meroities did not go anywhere, they are still present, at least, genetically anyway.

Furthermore, it does not surprise me that the Beja are so close to the Nubians who genetically make up the remnants of the Kushites, they have lived in close proximity for 1000's of years. The Beja and Kushites have a long history. What is surprising is the difference between Egypt and the Nubians. The Kushites had been in contact with Egypt since the pre-Dynastic period. It looked like the Egypt sample was heavily influenced by Southwest Asian (Arabian) genes. I am sure at K=13 they would seperate out more and not look quite so similar (looks like at K=10 some components are clumped together). The genetic sharing between the Copts and the Nubians is unsurprising as well. The near identical admixture profiles of the Sudanese Arabs to the Nubians also confirms rather unsurprisingly that those Arabs are local Islamic converts. The very close admixture results for the Beja and Ethiopians are also unsurprising.

So this added genetic information will help to flesh out some things linguistically and historically for my research.