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

Overview

Journal Sci Rep

Specialty Science

Date 2015 May 29

PMID 26017457

Citations 15

Authors

Begona Dobon

Hisham Y Hassan

Hafid Laayouni

Pierre Luisi

Isis Ricano-Ponce

Alexandra Zhernakova

Cisca Wijmenga

Hanan Tahir

David Comas

Mihai G Netea

Jaume Bertranpetit

Affiliations

Soon will be listed here.

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.

Citing Articles

Genomic and physiological mechanisms of high-altitude adaptation in Ethiopian highlanders: a comparative perspective.

Seifu W, Bekele-Alemu A, Zeng C Front Genet. 2025; 15():1510932.

PMID: 39840284 PMC: 11747213. DOI: 10.3389/fgene.2024.1510932.

Factors associated with completeness in documentation of diagnostic work-up and treatment in patients with breast cancer in Sudan.

Eltoum N, Caston N, Gutnik L, Alazm M, Mohamed F, Abdalkarem L Ecancermedicalscience. 2024; 17:1632.

PMID: 38414946 PMC: 10898882. DOI: 10.3332/ecancer.2023.1632.

Bi-allelic PRRT2 variants may predispose to Self-limited Familial Infantile Epilepsy.

Koko M, Elseed M, Mohammed I, Hamed A, Abd Allah A, Yahia A Eur J Hum Genet. 2024; 32(10):1338-1342.

PMID: 38316952 PMC: 11500335. DOI: 10.1038/s41431-024-01541-x.

Clinical phenotyping and genetic diagnosis of a large cohort of Sudanese families with hereditary spinocerebellar degenerations.

Yahia A, Hamed A, Mohamed I, Elseed M, Salih M, El-Sadig S Eur J Hum Genet. 2023; 32(10):1214-1226.

PMID: 37012327 PMC: 11499676. DOI: 10.1038/s41431-023-01344-6.

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia.

Sirak K, Fernandes D, Lipson M, Mallick S, Mah M, Olalde I Nat Commun. 2021; 12(1):7283.

PMID: 34907168 PMC: 8671435. DOI: 10.1038/s41467-021-27356-8.

References

Krings M, Salem A, Bauer K, Geisert H, Malek A, Chaix L . mtDNA analysis of Nile River Valley populations: A genetic corridor or a barrier to migration?. Am J Hum Genet. 1999; 64(4):1166-76. PMC: 1377841. DOI: 10.1086/302314. View

Stajich J, Block D, Boulez K, Brenner S, Chervitz S, Dagdigian C . The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002; 12(10):1611-8. PMC: 187536. DOI: 10.1101/gr.361602. View

Kwiatkowski D . How malaria has affected the human genome and what human genetics can teach us about malaria. Am J Hum Genet. 2005; 77(2):171-92. PMC: 1224522. DOI: 10.1086/432519. View

Patterson N, Price A, Reich D . Population structure and eigenanalysis. PLoS Genet. 2006; 2(12):e190. PMC: 1713260. DOI: 10.1371/journal.pgen.0020190. View

Barreiro L, Laval G, Quach H, Patin E, Quintana-Murci L . Natural selection has driven population differentiation in modern humans. Nat Genet. 2008; 40(3):340-5. DOI: 10.1038/ng.78. View

Gardner M, Bertranpetit J, Comas D . Worldwide genetic variation in dopamine and serotonin pathway genes: implications for association studies. Am J Med Genet B Neuropsychiatr Genet. 2008; 147B(7):1070-5. DOI: 10.1002/ajmg.b.30717. View

Sikora M, Ferrer-Admetlla A, Mayor A, Bertranpetit J, Casals F . Evolutionary analysis of genes of two pathways involved in placental malaria infection. Hum Genet. 2008; 123(4):343-57. DOI: 10.1007/s00439-008-0483-y. View

Hassan H, Underhill P, Cavalli-Sforza L, Ibrahim M . Y-chromosome variation among Sudanese: restricted gene flow, concordance with language, geography, and history. Am J Phys Anthropol. 2008; 137(3):316-23. DOI: 10.1002/ajpa.20876. View

Tishkoff S, Reed F, Friedlaender F, Ehret C, Ranciaro A, Froment A . The genetic structure and history of Africans and African Americans. Science. 2009; 324(5930):1035-44. PMC: 2947357. DOI: 10.1126/science.1172257. View

10.

Campbell M, Tishkoff S . The evolution of human genetic and phenotypic variation in Africa. Curr Biol. 2010; 20(4):R166-73. PMC: 2945812. DOI: 10.1016/j.cub.2009.11.050. View

11.

Scheinfeldt L, Soi S, Tishkoff S . Colloquium paper: working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history. Proc Natl Acad Sci U S A. 2010; 107 Suppl 2:8931-8. PMC: 3024023. DOI: 10.1073/pnas.1002563107. View

12.

Hunter-Zinck H, Musharoff S, Salit J, Al-Ali K, Chouchane L, Gohar A . Population genetic structure of the people of Qatar. Am J Hum Genet. 2010; 87(1):17-25. PMC: 2896773. DOI: 10.1016/j.ajhg.2010.05.018. View

13.

Wang K, Li M, Hakonarson H . ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010; 38(16):e164. PMC: 2938201. DOI: 10.1093/nar/gkq603. View

14.

Sikora M, Laayouni H, Calafell F, Comas D, Bertranpetit J . A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations. Eur J Hum Genet. 2010; 19(1):84-8. PMC: 3039508. DOI: 10.1038/ejhg.2010.141. View

15.

Peltonen L, Altshuler D, de Bakker P, Deloukas P, Gabriel S, Gwilliam R . Integrating common and rare genetic variation in diverse human populations. Nature. 2010; 467(7311):52-8. PMC: 3173859. DOI: 10.1038/nature09298. View

16.

Fadhlaoui-Zid K, Rodriguez-Botigue L, Naoui N, Benammar-Elgaaied A, Calafell F, Comas D . Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley. Am J Phys Anthropol. 2011; 145(1):107-17. DOI: 10.1002/ajpa.21472. View

17.

cerny V, Pereira L, Musilova E, Kujanova M, Vasikova A, Blasi P . Genetic structure of pastoral and farmer populations in the African Sahel. Mol Biol Evol. 2011; 28(9):2491-500. DOI: 10.1093/molbev/msr067. View

18.

Babiker H, Schlebusch C, Hassan H, Jakobsson M . Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci. Investig Genet. 2011; 2(1):12. PMC: 3118356. DOI: 10.1186/2041-2223-2-12. View

19.

Alexander D, Lange K . Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics. 2011; 12:246. PMC: 3146885. DOI: 10.1186/1471-2105-12-246. View

20.

Trynka G, Hunt K, Bockett N, Romanos J, Mistry V, Szperl A . Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet. 2011; 43(12):1193-201. PMC: 3242065. DOI: 10.1038/ng.998. View