High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation

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From: American Journal of Human Genetics(Vol. 107, Issue 3)
Publisher: Elsevier B.V.
Document Type: Report
Length: 628 words

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Keywords Nilo-Saharan; population genetic variation; signatures of selection Summary Africa contains more human genetic variation than any other continent, but the majority of the population-scale analyses of the African peoples have focused on just two of the four major linguistic groups, the Niger-Congo and Afro-Asiatic, leaving the Nilo-Saharan and Khoisan populations under-represented. In order to assess genetic variation and signatures of selection within a Nilo-Saharan population and between the Nilo-Saharan and Niger-Congo and Afro-Asiatic, we sequenced 50 genomes from the Nilo-Saharan Lugbara population of North-West Uganda and 250 genomes from 6 previously unsequenced Niger-Congo populations. We compared these data to data from a further 16 Eurasian and African populations including the Gumuz, another putative Nilo-Saharan population from Ethiopia. Of the 21 million variants identified in the Nilo-Saharan population, 3.57 million (17%) were not represented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects. We found greater genetic differentiation between the Nilo-Saharan Lugbara and Gumuz populations than between any two Afro-Asiatic or Niger-Congo populations. F3 tests showed that Gumuz contributed a genetic component to most Niger-Congo B populations whereas Lugabara did not. We scanned the genomes of the Lugbara for evidence of selective sweeps. We found selective sweeps at four loci (SLC24A5, SNX13, TYRP1, and UVRAG) associated with skin pigmentation, three of which already have been reported to be under selection. These selective sweeps point toward adaptations to the intense UV radiation of the Sahel. Author Affiliation: (1) College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda (2) College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda (3) Centre for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK (4) Institut de Recherche en Sciences de la Santei (IRSS) - Unitei de Recherche Clinique de Nanoro (URCN), Nanoro, Burkina-Faso (5) Institute of Genomics, University of Tartu, 51010 Tartu, Estonia (6) Department of Biology, University of Padova, Via U. Bassi, 58/B - 35121 Padova, Italy (7) Universite Jean Lorougnon Guede (UJLoG) de Daloa, Cote d'Ivoire (8) Institut National de Recherche Biomedicale, Avenue de la Democratie, Kinshasa Gombe, P.O. Box 1197 Kinshasa, Democratic Republic of Congo (9) Faculty of Science, University of Dschang, P.O. Box 67, Dschang, Cameroon (10) University of Malawi, College of Medicine, Department of Basic Medical Sciences, Private Bag 360, Chichiri, Blantyre 3, Malawi (11) Institute, Centre International de Recherche-Developpement sur l'Elevage en zones Subhumides (CIRDES), 01 BP 454 Bobo-Dioulasso 01, Burkina Faso (12) Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka, Zambia (14) Institut de Recherche pour le Developpement (IRD), IRD-CIRAD 177, TA A-17/G, Campus International de Baillarguet, 34398 Montpellier, France (15) Programme National de Lutte contre la Trypanosomose Humaine Africaine, BP 851, Conakry, Guinee (16) Wellcome Centre for Integrative Parasitology, Biodiversity Animal Health and Comparative Medicine, Glasgow G61 1QH, UK (17) Earlham Institute Norwich Research Park Innovation Centre, Colney Ln, Norwich NR4 7UZ, UK * Corresponding author Article History: Received 3 July 2020; Accepted 13 July 2020 (miscellaneous) Published: August 10, 2020 Byline: Julius Mulindwa (1,2), Harry Noyes (3), Hamidou Ilboudo (4), Luca Pagani (5,6), Oscar Nyangiri (1), Magambo Phillip Kimuda (1), Bernardin Ahouty (7), Olivier Fataki Asina (8), Elvis Ofon (9), Kelita Kamoto (10), Justin Windingoudi Kabore (11,15), Mathurin Koffi (7), Dieudonne Mumba Ngoyi (8), Gustave Simo (9), John Chisi (10), Issa Sidibe (11), John Enyaru (2), Martin Simuunza (12), Pius Alibu (2), Vincent Jamonneau (14), Mamadou Camara (15), Andy Tait (16), Neil Hall (17), Bruno Bucheton (14,15), Annette MacLeod (16), Christiane Hertz-Fowler (3), Enock Matovu [matovue@covab.mak.ac.ug] (1,*), Enock Matovu, Issa Sidibe, Dieuodonne Mumba, Mathurin Koffi, Gustave Simo, John Chisi, Vincent P. Alibu, Annette Macleod, Bruno Bucheton, Christianne Hertzfowler, Alison Elliot, Mamadou Camara, Ozlem Bishop, Julius Mulindwa, Oscar Nyangiri, Magambo Phillip Kimuda, Elvis Ofon, Bernadin Ahouty, Justin Kabore

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Gale Document Number: GALE|A640354566