In this study we present an extensive genome-wide data set characterizing East African human genetic diversity in populations from Sudan, South Sudan and Ethiopia. We further analyse the Nilo-Saharan ancestral component within the variation of South-Saharan Africans.
Nubians are the only Nilo-Saharan speaking group that does not cluster with groups of the same linguistic affiliation, but with Sudanese Afro-Asiatic speaking groups (Arabs and Cushitic Beja) and Afro-Asiatic Ethiopians.
Y-chromosome and mitochondrial DNA studies reported Nubians to be more similar to Egyptians and Ethiopians than to other Nilo-Saharan populations.....
A random subset of 18 individuals from each population was selected to avoid sample size bias. Columns represent individuals, where the size of each colour segment represents the proportion of ancestry from each cluster. Although k = 3 is the statistically supported model, here we show the results from k = 2 through k = 5 as they explain several ancestral components: North African/Middle Eastern (dark blue), Sub-Saharan (light blue), Coptic/Cushitic (dark green), Nilo-Saharan (light green) and Fulani (pink). MKK = Maasai from Kinyawa, Kenya; LWK = Luhya from Webuye, Kenya; YRI = Yoruba from Ibadan, Nigeria.
Populations from the North-East cluster: Beja, Ethiopians, Arabs and Nubians (Table 2) may be explained as admixture products of an ancestral North African population (similar to Copts).
Nubians are the only Nilo-Saharan speaking group that does not cluster with groups of the same linguistic affiliation, but with Sudanese Afro-Asiatic speaking groups (Arabs and Beja) and Afro-Asiatic Ethiopians (Supplementary Fig. S1a). Y-chromosome and mitochondrial DNA studies reported Nubians to be more similar to Egyptians than to other Nilo-Saharan populations1,8: Nubians were influenced by Arabs as a direct result of the penetration of large numbers of Arabs into the Nile Valley over long periods of time following the arrival of Islam around 651 A.D20.
Interestingly, our analyses shows a unique ancestry for Sudanese Nilo-Saharan speaking groups (Darfurians and Nuba) related to Nilotes of South Sudan, but not to other Sudanese populations or sub-Saharan populations (Fig. 3). This ancestral component is not present in places where the Bantu expansion left a strong footprint and creates a different genetic background that is not found among most African populations. Tishkoff et al.5. reported a common ancestry of Nilo-Saharan speaking populations. We also found this relationship of Nilo-Saharan Sudanese populations with other Nilo-Saharan populations from Kenya (Maasai), but not as strong, as Maasai show their own genetic component at k = 6, which is different from the Sudanese component (Supplementary Fig. S7) and do not cluster with our Nilo-Saharan speaking populations. In a previous Y-chromosome study8, most Nilo-Saharan speaking populations, except Nubians, showed little evidence of gene flow with other Sudanese populations.
The presence of the core of Nilo-Saharan languages in the confluence of the two Nile rivers suggests that the Sudanese region is the place of origin of the Nilo-Saharan linguistic family despite their fragmented distribution, as shown by the location of the Nubian language21,22. 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.
Population displacement, whether it is followed with cultural or genetic exchange with local populations, would explain why not every Nilo-Saharan speaking group has this genetic component (as is the case of Nubians) and not every population that has it is mainly formed by Nilo-Saharan speakers (as is the case of Niger-Kordofanian speaking Nuba).
References:
https://www.nature.com/articles/srep09996/tables/2
https://www.nature.com/articles/srep09996
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