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

Julius Mulindwa; Harry Noyes; Hamidou Ilboudo; Luca Pagani; Oscar Nyangiri; Magambo Phillip Kimuda; Bernardin Ahouty; Olivier Fataki Asina; Elvis Ofon; Kelita Kamoto; Justin Windingoudi Kabore; Mathurin Koffi; Dieudonne Mumba Ngoyi; Gustave Simo; John Chisi; Issa Sidibe; John Enyaru; Martin Simuunza; Pius Alibu; Vincent Jamonneau; Mamadou Camara; Andy Tait; Neil Hall; Bruno Bucheton; Annette MacLeod; Christiane Hertz-Fowler; Enock Matovu; Dieuodonne Mumba; Vincent P. Alibu; Annette Macleod; Christianne Hertzfowler; Alison Elliot; Ozlem Bishop; Bernadin Ahouty; Justin Kabore; the TrypanoGEN Research Group of the H3Africa Consortium

doi:10.1016/j.ajhg.2020.07.007

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

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

Julius Mulindwa, Harry Noyes, Hamidou Ilboudo, Luca Pagani, Oscar Nyangiri, Magambo Phillip Kimuda, Bernardin Ahouty, Olivier Fataki Asina, Elvis Ofon, Kelita Kamoto, …

American journal of human genetics, Vol.107(3), pp.473-486

03/09/2020

DOI: https://doi.org/10.1016/j.ajhg.2020.07.007

PMID: 32781046

Résumé

Nilo-Saharan

population genetic variation

signatures of selection

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.

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Titre: High Levels of Genetic Diversity within Nilo-Saharan Populations: Implications for Human Adaptation
Créateurs - sans rôle: Julius Mulindwa - College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
Harry Noyes - Centre for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK
Hamidou Ilboudo - Institut de Recherche en Sciences de la Santeì (IRSS) - Uniteì de Recherche Clinique de Nanoro (URCN), Nanoro, Burkina-Faso
Luca Pagani - Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
Oscar Nyangiri - College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
Magambo Phillip Kimuda - College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O. Box 7062, Kampala, Uganda
Bernardin Ahouty - Université Jean Lorougnon Guédé
Olivier Fataki Asina - Institut National de Recherche Biomedicale, Avenue de la Democratie, Kinshasa Gombe, P.O. Box 1197 Kinshasa, Democratic Republic of Congo
Elvis Ofon - Faculty of Science, University of Dschang, P.O. Box 67, Dschang, Cameroon
Kelita Kamoto - University of Malawi, College of Medicine, Department of Basic Medical Sciences, Private Bag 360, Chichiri, Blantyre 3, Malawi
Justin Windingoudi Kabore - Institute, Centre International de Recherche-Développement sur l’Elevage en zones Subhumides (CIRDES), 01 BP 454 Bobo-Dioulasso 01, Burkina Faso
Mathurin Koffi - Université Jean Lorougnon Guédé
Dieudonne Mumba Ngoyi - Institut National de Recherche Biomedicale, Avenue de la Democratie, Kinshasa Gombe, P.O. Box 1197 Kinshasa, Democratic Republic of Congo
Gustave Simo - Faculty of Science, University of Dschang, P.O. Box 67, Dschang, Cameroon
John Chisi - University of Malawi, College of Medicine, Department of Basic Medical Sciences, Private Bag 360, Chichiri, Blantyre 3, Malawi
Issa Sidibe - Institute, Centre International de Recherche-Développement sur l’Elevage en zones Subhumides (CIRDES), 01 BP 454 Bobo-Dioulasso 01, Burkina Faso
John Enyaru - Makerere University
Martin Simuunza - Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka, Zambia
Pius Alibu - College of Natural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
Vincent Jamonneau - Institut de Recherche pour le Développement (IRD), IRD-CIRAD 177, TA A-17/G, Campus International de Baillarguet, 34398 Montpellier, France
Mamadou Camara - Programme National de Lutte contre la Trypanosomose Humaine Africaine, BP 851, Conakry, Guinée
Andy Tait - Wellcome Centre for Integrative Parasitology, Biodiversity Animal Health and Comparative Medicine, Glasgow G61 1QH, UK
Neil Hall - Earlham Institute Norwich Research Park Innovation Centre, Colney Ln, Norwich NR4 7UZ, UK
Bruno Bucheton - Institut de Recherche pour le Développement (IRD), IRD-CIRAD 177, TA A-17/G, Campus International de Baillarguet, 34398 Montpellier, France
Annette MacLeod - Wellcome Trust
Christiane Hertz-Fowler - Centre for Genomic Research, University of Liverpool, Liverpool L69 7ZB, UK
Enock Matovu - Makerere University
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
the TrypanoGEN Research Group of the H3Africa Consortium
Détails de publication: American journal of human genetics, Vol.107(3), pp.473-486
Éditeur: Elsevier Inc
Nombre de pages: 14
Identifiants: 99139934709311
Unité académique: Intéractions hôtes-vecteurs-parasites-environnement maladies tropicales - INTERTRYP
Langue: English
Type de ressource: Journal article