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Admixture Into and Within Sub-Saharan Africa

View ORCID ProfileGeorge B.J. Busby, Gavin Band, Quang Si Le, Muminatou Jallow, Edith Bougama, Valentina Mangano, Lucas Amenga-Etego, Anthony Enimil, Tobias Apinjoh, Carolyne Ndila, Alphaxard Manjurano, Vysaul Nyirongo, Ogobara Doumbo, Kirk A. Rockett, Dominic P. Kwiatkowski, Chris C.A. Spencer, In Association with the Malaria Genomic Epidemiology Network
doi: https://doi.org/10.1101/038406
George B.J. Busby
1Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
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  • ORCID record for George B.J. Busby
  • For correspondence: george@well.ox.ac.uk spencer@well.ox.ac.uk
Gavin Band
1Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
2Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Quang Si Le
1Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
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Muminatou Jallow
3Medical Research Council Unit, Serrekunda, The Gambia
4Royal Victoria Teaching Hospital, Banjul, The Gambia
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Edith Bougama
5Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso
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Valentina Mangano
6Dipartimento di Sanita Publica e Malattie Infettive, University of Rome La Sapienza, Rome, Italy
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Lucas Amenga-Etego
7Navrongo Health Research Centre, Navrongo, Ghana
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Anthony Enimil
8Komfo Anokye Teaching Hospital, Kumasi, Ghana
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Tobias Apinjoh
9Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
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Carolyne Ndila
10KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
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Alphaxard Manjurano
11Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
12Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Vysaul Nyirongo
13Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
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Ogobara Doumbo
14Malaria Research and Training Centre, Faculty of Medicine, University of Bamako, Bamako, Mali
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Kirk A. Rockett
1Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
2Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Dominic P. Kwiatkowski
1Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
2Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Chris C.A. Spencer
1Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
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  • For correspondence: george@well.ox.ac.uk spencer@well.ox.ac.uk
15MalariaGEN consortium;
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Abstract

Understanding patterns of genetic diversity is a crucial component of medical research in Africa. Here we use haplotype-based population genetics inference to describe gene-flow and admixture in a collection of 48 African groups with a focus on the major populations of the sub-Sahara. Our analysis presents a framework for interpreting haplotype diversity within and between population groups and provides a demographic foundation for genetic epidemiology in Africa. We show that coastal African populations have experienced an influx of Eurasian haplotypes as a series of admixture events over the last 7,000 years, and that Niger-Congo speaking groups from East and Southern Africa share ancestry with Central West Africans as a result of recent population expansions associated with the adoption of new agricultural technologies. We demonstrate that most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of large-scale population movements over the last 4,000 years. Our in-depth analysis of admixture provides an insight into haplotype sharing across different geographic groups and the recent movement of alleles into new climatic and pathogenic environments, both of which will aid the interpretation of genetic studies of disease in sub-Saharan Africa.

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Posted February 01, 2016.
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Admixture Into and Within Sub-Saharan Africa
George B.J. Busby, Gavin Band, Quang Si Le, Muminatou Jallow, Edith Bougama, Valentina Mangano, Lucas Amenga-Etego, Anthony Enimil, Tobias Apinjoh, Carolyne Ndila, Alphaxard Manjurano, Vysaul Nyirongo, Ogobara Doumbo, Kirk A. Rockett, Dominic P. Kwiatkowski, Chris C.A. Spencer, In Association with the Malaria Genomic Epidemiology Network
bioRxiv 038406; doi: https://doi.org/10.1101/038406
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Admixture Into and Within Sub-Saharan Africa
George B.J. Busby, Gavin Band, Quang Si Le, Muminatou Jallow, Edith Bougama, Valentina Mangano, Lucas Amenga-Etego, Anthony Enimil, Tobias Apinjoh, Carolyne Ndila, Alphaxard Manjurano, Vysaul Nyirongo, Ogobara Doumbo, Kirk A. Rockett, Dominic P. Kwiatkowski, Chris C.A. Spencer, In Association with the Malaria Genomic Epidemiology Network
bioRxiv 038406; doi: https://doi.org/10.1101/038406

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