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. 2015 Nov 26;7(12):3484-95.
doi: 10.1093/gbe/evv236.

Extensive Admixture and Selective Pressure Across the Sahel Belt

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Free PMC article

Extensive Admixture and Selective Pressure Across the Sahel Belt

Petr Triska et al. Genome Biol Evol. .
Free PMC article

Abstract

Genome-wide studies of African populations have the potential to reveal powerful insights into the evolution of our species, as these diverse populations have been exposed to intense selective pressures imposed by infectious diseases, diet, and environmental factors. Within Africa, the Sahel Belt extensively overlaps the geographical center of several endemic infections such as malaria, trypanosomiasis, meningitis, and hemorrhagic fevers. We screened 2.5 million single nucleotide polymorphisms in 161 individuals from 13 Sahelian populations, which together with published data cover Western, Central, and Eastern Sahel, and include both nomadic and sedentary groups. We confirmed the role of this Belt as a main corridor for human migrations across the continent. Strong admixture was observed in both Central and Eastern Sahelian populations, with North Africans and Near Eastern/Arabians, respectively, but it was inexistent in Western Sahelian populations. Genome-wide local ancestry inference in admixed Sahelian populations revealed several candidate regions that were significantly enriched for non-autochthonous haplotypes, and many showed to be under positive selection. The DARC gene region in Arabs and Nubians was enriched for African ancestry, whereas the RAB3GAP1/LCT/MCM6 region in Oromo, the TAS2R gene family in Fulani, and the ALMS1/NAT8 in Turkana and Samburu were enriched for non-African ancestry. Signals of positive selection varied in terms of geographic amplitude. Some genomic regions were selected across the Belt, the most striking example being the malaria-related DARC gene. Others were Western-specific (oxytocin, calcium, and heart pathways), Eastern-specific (lipid pathways), or even population-restricted (TAS2R genes in Fulani, which may reflect sexual selection).

Keywords: Sahel; admixture; genome-wide diversity; selection.

Figures

F<sc>ig</sc>. 1.—
Fig. 1.—
Location of studied samples and population structure across Sahel. (A) Geographic locations of the populations studied here, with subsistence system and family language affiliation identified. The colored zones indicate the current climate zones. Numbers 1 to 13 refer to groups studied here: 1 – Fulani; 2 – Songhai; 3 – Mossi; 4 – Gurunsi; 5 – Gurmantche; 6 – Kanembu; 7 – Daza; 8 – Nubians; 9 – Sudanese Arabs; 10 – Oromo; 11 – Samburu; 12 – Turkana; and 13 – Somali. Numbers 14 to 19 refer to groups from 1000 Genomes project and Li et al. (2008): 14 – Gambian in Western Division; 15 – Mandenka in Senegal; 16 – Mende in Sierra Leone; 17 – Yoruba in Ibadan, Nigeria; 18 – Esan in Nigeria; and 19 – Luhya from Kenya. (B) PCA1 versus PCA2. (C) Admixture analysis for K = 7 ancestral populations (each represented by a color). Each vertical line is an individual.
F<sc>ig</sc>. 2.—
Fig. 2.—
Top-10 iHS in each Sahelian population and matching selected genes in Italians. Some of the regions contain many genes, and only the first and last genes are indicated, with interesting genes reported inside brackets.
F<sc>ig</sc>. 3.—
Fig. 3.—
Selected genes in informative metabolic pathways (KEGG database). (A) Oxytocin signaling pathway. (B) Vascular smooth muscle contraction. (C) Calcium signaling pathway. (D) Glycerolipid metabolism. (E) Glycerophospholipid metabolism. (F) Malaria. (G) Taste transduction. GWD – Gambia; MSL – Mende; YRI – Yoruba; ESN – Esan; LWK – Luhya.
F<sc>ig</sc>. 4.—
Fig. 4.—
Locus zoom of a few enriched ancestry regions. (A) Chromosome 2 in Oromo. (B) Chromosome 1 in Sudanese Arabs + Nubians. (C) Chromosome 12 in Fulani. (D) Chromosome 2 in Turkana + Samburu.

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