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

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

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dc.contributor.author Julius Mulindwa
dc.contributor.author Harry Noyes
dc.contributor.author Hamidou Ilboudo
dc.contributor.author Oscar Nyangiri
dc.contributor.author Mathurin Koffi
dc.contributor.author Dieudonné Mumba
dc.contributor.author Gustave Simo
dc.contributor.author John Enyaru
dc.contributor.author John Chisi
dc.contributor.author Martin Simuunza
dc.contributor.author Vincent P. Alibu
dc.contributor.author Vincent Jammoneau
dc.contributor.author Annette MacLeod
dc.contributor.author Bruno Bucheton
dc.contributor.author Christiane Hertz-Fowler
dc.contributor.author Issa Sidibé
dc.contributor.author Enock Matovu
dc.date.accessioned 2021-01-11T13:51:40Z
dc.date.available 2021-01-11T13:51:40Z
dc.date.issued 2017
dc.identifier.uri https://combine.alvar.ug/handle/1/49422
dc.description.abstract 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. 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.
dc.publisher Cold Spring Harbor Laboratory
dc.title Evidence of population specific selection inferred from 289 genome sequences of Nilo-Saharan and Niger-Congo linguistic groups in Africa
dc.type Preprint
dc.identifier.doi 10.1101/186700
dc.identifier.mag 3098687747; 2754397801
dc.identifier.lens 013-245-982-578-263
dc.identifier.spage 186700
dc.subject.lens-fields Ethnic group
dc.subject.lens-fields Genomics
dc.subject.lens-fields Genetic admixture
dc.subject.lens-fields Malaria
dc.subject.lens-fields African trypanosomiasis
dc.subject.lens-fields Population
dc.subject.lens-fields Genetic structure
dc.subject.lens-fields Natural selection
dc.subject.lens-fields Evolutionary biology
dc.subject.lens-fields Biology
dc.subject.lens-fields Ethnic group
dc.subject.lens-fields Demography
dc.subject.lens-fields Malaria
dc.subject.lens-fields African trypanosomiasis
dc.subject.lens-fields Acquired immunodeficiency syndrome (AIDS)
dc.subject.lens-fields Population
dc.subject.lens-fields Population specific
dc.subject.lens-fields Genetic structure
dc.subject.lens-fields Natural selection
dc.subject.lens-fields Biology


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