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, (doi: 10.1016/j.ajhg.2020.07.007) (PMID:32781046) (In Press)

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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:In Press
Refereed:Yes
Glasgow Author(s) Enlighten ID:MacLeod, Professor Annette and Tait, Professor Andrew and Matovu, Dr Enock
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 > Institute of Biodiversity Animal Health and Comparative Medicine
College of Medical Veterinary and Life Sciences > School of 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 2020
Publisher Policy:Reproduced under a Creative Commons license

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