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Genomic evidence for population specific selection in Nilo-Saharan and Niger-Congo linguistic groups in Africa

Julius Mulindwa, View ORCID ProfileHarry Noyes, Hamidou Ilboudo, Oscar Nyangiri, Mathurin Koffi, Dieudonne Mumba, Gustave Simo, John Enyaru, John Chisi, Martin Simuunza, Pius Alibu, Veerle Lejon, Vincent Jamonneau, Annette MacLeod, Bruno Bucheton, Christiane Hertz-Fowler, Issa Sidibe, Enock Matovu, The TrypanoGEN Research Group, as members of The H3Africa Consortium
doi: https://doi.org/10.1101/186700
Julius Mulindwa
1Makerere University, Kampala, Uganda, Bobo-Dioulasso, Burkina Faso
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Harry Noyes
2Centre for Genomic Research, University of Liverpool, UK
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  • ORCID record for Harry Noyes
Hamidou Ilboudo
3Centre International de Recherche-Développement sur l’Elevage en zone Subhumide (CIRDES)
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Oscar Nyangiri
1Makerere University, Kampala, Uganda, Bobo-Dioulasso, Burkina Faso
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Mathurin Koffi
4Université Jean Lorougnon Guédé (UJLoG), Daloa, Côte d’Ivoire
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Dieudonne Mumba
5Institut National de Recherche Biomedicale, Kinshasa, Democratic Republic of Congo
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Gustave Simo
6Faculty of Science, University of Dschang, Cameroon
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John Enyaru
1Makerere University, Kampala, Uganda, Bobo-Dioulasso, Burkina Faso
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John Chisi
7University of Malawi, College of Medicine, Department of Basic Medical Sciences, Blantyre, Malawi
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Martin Simuunza
8Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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Pius Alibu
1Makerere University, Kampala, Uganda, Bobo-Dioulasso, Burkina Faso
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Veerle Lejon
9Institut de Recherche pour le Développement (IRD), IRD-CIRAD 177, Montpellier, France
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Vincent Jamonneau
9Institut de Recherche pour le Développement (IRD), IRD-CIRAD 177, Montpellier, France
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Annette MacLeod
10Wellcome Center for Molecular Parasitology, University Place, Glasgow, UK
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Bruno Bucheton
9Institut de Recherche pour le Développement (IRD), IRD-CIRAD 177, Montpellier, France
11Programme National de Lutte contre la Trypanosomose Humaine Africaine, Conakry, Guinea
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Christiane Hertz-Fowler
2Centre for Genomic Research, University of Liverpool, UK
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Issa Sidibe
3Centre International de Recherche-Développement sur l’Elevage en zone Subhumide (CIRDES)
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Enock Matovu
1Makerere University, Kampala, Uganda, Bobo-Dioulasso, Burkina Faso
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1.0 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 analysed 298 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. These samples were collected as part of the TrypanoGEN consortium project http://www.trypanogen.net.

Results The population genetic structure of the 298 individuals revealed four clusters which correlated with ethno-linguistic group and geographical latitude, that is, West African Niger-Congo A, Central African Niger Congo, East African Niger-Congo B and the Nilo-Saharan.

We observed a spatial distribution of positive natural selection signatures in genes 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, (_iHS −log p > 3.0, Rsb −log p > 3.0, Fst > 0.1 bonferroni p > 1.8x10e4)], which are highly differentiated between the two ethnic groups and under positive selection in the Lugbara population.

Conclusion The signatures that differentiate ethnically distinct populations provide information on the specific ecological adaptations with respect to disease history and susceptibility/ resistance; as demonstrated in this study where APOBEG3G is believed to be involved in the susceptibility of the Nilo-Saharan Lugbara population to Hepatitis B virus infection.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted September 10, 2017.
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Genomic evidence for population specific selection in Nilo-Saharan and Niger-Congo linguistic groups in Africa
Julius Mulindwa, Harry Noyes, Hamidou Ilboudo, Oscar Nyangiri, Mathurin Koffi, Dieudonne Mumba, Gustave Simo, John Enyaru, John Chisi, Martin Simuunza, Pius Alibu, Veerle Lejon, Vincent Jamonneau, Annette MacLeod, Bruno Bucheton, Christiane Hertz-Fowler, Issa Sidibe, Enock Matovu, The TrypanoGEN Research Group, as members of The H3Africa Consortium
bioRxiv 186700; doi: https://doi.org/10.1101/186700
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Genomic evidence for population specific selection in Nilo-Saharan and Niger-Congo linguistic groups in Africa
Julius Mulindwa, Harry Noyes, Hamidou Ilboudo, Oscar Nyangiri, Mathurin Koffi, Dieudonne Mumba, Gustave Simo, John Enyaru, John Chisi, Martin Simuunza, Pius Alibu, Veerle Lejon, Vincent Jamonneau, Annette MacLeod, Bruno Bucheton, Christiane Hertz-Fowler, Issa Sidibe, Enock Matovu, The TrypanoGEN Research Group, as members of The H3Africa Consortium
bioRxiv 186700; doi: https://doi.org/10.1101/186700

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