Evidence of population specific selection inferred from 289 genome sequences of Nilo-Saharan and Niger-Congo linguistic groups in Africa



Mulindwa, Julius, Noyes, Harry ORCID: 0000-0002-0656-200X, Ilboudo, Hamidou, Nyangiri, Oscar, Koffi, Mathurin, Mumba, Dieudonne, Simo, Gustave, Enyaru, John, Chisi, John, Simuunza, Martin
et al (show 8 more authors) (2017) Evidence of population specific selection inferred from 289 genome sequences of Nilo-Saharan and Niger-Congo linguistic groups in Africa.

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Abstract

Abstract Background There are over 2000 genetically diverse ethno-linguistic groups in Africa that could help decipher human evolutionary history and the genetic basis of phenotypic variation. We have sequenced 300 genomes from Niger-Congo populations from six sub-Saharan African countries (Uganda, Democratic Republic of Congo, Cameroon, Zambia, Ivory Coast, Guinea) and a Nilo-Saharan population from Uganda. Of these, we analysed 289 samples for population structure, genetic admixture, population history and signatures of selection. These samples were collected as part of the TrypanoGEN consortium project [1]. Results The population genetic structure of the 289 individuals revealed four clusters, which correlated with ethno-linguistic group and geographical latitude. These were the West African Niger-Congo A, Central African Niger-Congo B, East African Niger-Congo B and the Nilo-Saharan. We observed a spatial distribution of positive natural selection signatures in genes previously associated with AIDS, Tuberculosis, Malaria and Human African Trypanosomiasis among the TrypanoGEN samples. Having observed a marked difference between the Nilo-Saharan Lugbara and Niger-Congo populations, we identified four genes ( APOBEC3G , TOP2B , CAPN9 , LANCL2 ), which are highly differentiated between the two ethnic groups and under positive selection in the Lugbara population (_iHS -log p > 3.0, Rsb -log p > 3.0, Fst > 0.1 bonferroni p > 1.8x10e4). Conclusion The signatures that differentiate ethnically distinct populations could provide information on the specific ecological adaptations with respect to disease history and susceptibility/resistance. For instance in this study we identified APOBEC3G which is believed to be involved in the susceptibility of the Nilo-Saharan Lugbara population to Hepatitis B virus infection.

Item Type: Article
Uncontrolled Keywords: for the TrypanoGEN Research Group, as members of The H3Africa Consortium
Depositing User: Symplectic Admin
Date Deposited: 26 May 2020 09:16
Last Modified: 16 Sep 2020 08:34
DOI: 10.1101/186700
Open Access URL: https://www.biorxiv.org/content/10.1101/186700v2.f...
URI: http://livrepository.liverpool.ac.uk/id/eprint/3088568