High levels of genetic diversity within Nilo-Saharan populations: implications for human adaptation

Mulindwa, J. et al. (2020) High levels of genetic diversity within Nilo-Saharan populations: implications for human adaptation. American Journal of Human Genetics, 107(3), pp. 473-486. (doi: 10.1016/j.ajhg.2020.07.007) (PMID:32781046) (PMCID:PMC7477016)

Abstract

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.

• Item Type: Articles
• Additional Information: This study was funded by the African Academy of Sciences/Wellcome project ID H3A/18/004 as part of the H3Africa consortia.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Matovu, Dr Enock and MacLeod, Professor Annette and Tait, Professor Andy
• Authors: Mulindwa, J., Noyes, H., Ilboudo, H., Pagani, L., Nyangiri, O., Kimuda, M. P., Ahouty, B., Asina, O. F., Ofon, E., Kamoto, K., Kabore, J. W., Koffi, M., Ngoyi, D. M., Simo, G., Chisi, J., Sidibe, I., Enyaru, J., Simuunza, M., Alibu, P., Jamonneau, V., Camara, M., Tait, A., Hall, N., Bucheton, B., MacLeod, A., Hertz-Fowler, C., and Matovu, E.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine
• Journal Name: American Journal of Human Genetics
• Publisher: Elsevier (Cell Press)
• ISSN: 0002-9297
• ISSN (Online): 1537-6605
• Published Online: 10 August 2020
• Copyright Holders: Copyright © 2020 The Authors
• First Published: First published in American Journal of Human Genetics 107(3): 473-486
• Publisher Policy: Reproduced under a Creative Commons license