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The Genetics of East African Populations: A Nilo-Saharan Component in the African Genetic Landscape

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The Genetics of East African Populations: A Nilo-Saharan Component in the African Genetic Landscape

Begoña Dobon et al. Sci Rep.

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.

Figures

Figure 1
Figure 1. Map of studied region in East Africa showing Sudan, South Sudan and Ethiopia, and the approximate locations of eight populations genotyped in this study.
Nomadic Fulani are not shown in the map due to their wide distribution in the west, central and east of the Sudan. The inset in the top shows the locations of Sudan, South Sudan and Ethiopia in East Africa. Modified from d-maps.com.
Figure 2
Figure 2. Principal component analysis of the populations from the Sudanese region in the context of the African continent.
Plot shows a) PC1 and PC2 and b) PC2 and PC3 and the variation explained by them. Sudanese populations cluster in four groups according to their geographic location, with PC1 representing a north-east to south-west axis in East Africa. Populations not genotyped in this study are shown with grey filled symbols. MKK = Maasai from Kinyawa, Kenya; LWK = Luhya from Webuye, Kenya; YRI = Yoruba from Ibadan, Nigeria.
Figure 3
Figure 3. ADMIXTURE results for the 14 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 (dark green), Nilo-Saharan (light green) and Fulani (pink). MKK = Maasai from Kinyawa, Kenya; LWK = Luhya from Webuye, Kenya; YRI = Yoruba from Ibadan, Nigeria.
Figure 4
Figure 4. Genes associated with resistance/susceptibility to malaria.
Sampling distribution of the sample mean pairwise FST between populations. Average FST value of genes associated with resistance/susceptibility to malaria (♦) is significantly lower than the mean FST score of the sampling distribution in all pairwise comparisons. COP = Copts; NOR = Beja, Ethiopians, Arabs and Nubians; SOU = Darfurians, Nuba and Nilotes; FUL = Fulani. The sampling distribution is drawn from the mean FST value of subsets of randomly selected genic SNPs with a sample size equal to the number of common SNPs between populations in the selected genes (n) and with similar MAF (10,000 permutations).
Figure 5
Figure 5. Anti-bacterial host defence related genes.
Sampling distribution of the sample mean pairwise FST between populations. All pairwise comparisons, except COP vs. NOR, have an average FST value of anti-bacterial host defence related genes (♦) that is significantly lower than the mean FST score of the sampling distribution. COP = Copts; NOR = Beja, Ethiopians, Arabs and Nubians; SOU = Darfurians, Nuba and Nilotes; FUL = Fulani. The sampling distribution is drawn from the mean FST value of subsets of randomly selected genic SNPs with a sample size equal to the number of common SNPs between populations in the selected genes (n) and with similar MAF (10,000 permutations).
Figure 6
Figure 6. Anti-fungal host defence related genes.
Sampling distribution of the sample mean pairwise FST between populations. Only three pairwise comparisons have an average FST value of anti-fungal host defence related genes (♦) that is significantly lower than the mean FST score of the sampling distribution: COP vs. SOU, COP vs. FUL, and NOR vs. SOU. COP = Copts; NOR = Beja, Ethiopians, Arabs and Nubians; SOU = Darfurians, Nuba and Nilotes; FUL = Fulani. The sampling distribution is drawn from the mean FST value of subsets of randomly selected genic SNPs with a sample size equal to the number of common SNPs between populations in the selected genes (n) and with similar MAF (10,000 permutations).

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