Admixture into and within sub-Saharan Africa

George B.J. Busby, Gavin Band, Quang Si Le, Muminatou Jallow, Edith Bougama, Valentina D. Mangano, Lucas N. Amenga-Etego, Anthony Enimil, Tobias O. Apinjoh, Carolyne M. Ndila, Alphaxard Manjurano, Vysaul Nyirongo, Ogobara Doumba, Kirk A. Rockett, Dominic P. Kwiatkowski, Chris C.A. Spencer, Aaron Vanderwal, Abier Elzein, Aceme Nyika, Alieu MendyAlistair Miles, Andrea Diss, Angeliki Kerasidou, Angie Green, Anna E. Jeffreys, Bronwyn MacInnis, Catherine Hughes, Catherine Moyes, Christina Hubbart, Cinzia Malangone, Claire Potter, Daniel Mead, David Barnwell, Dushyanth Jyothi, Eleanor Drury, Elilan Somaskantharajah, Eliza Hilton, Ellen Leffler, Gareth Maslen, George Busby, Geraldine M Clarke, Ioannis Ragoussis, Jacob Almagro Garcia, Jane Rogers, Jantina deVries, Jennifer M G Shelton, Jiannis Ragoussis, Jim Stalker, Joanne Rodford, John O'Brien, Julie Evans, Kate Rowlands, Katharine Cook, Kathryn Fitzpatrick, Katja Kivinen, Kerrin Small, Kimberly J. Johnson, Lee Hart, Magnus Manske, Marilyn McCreight, Marryat Stevens, Matti Pirinen, Meike Hennsman, Michael Parker, Miguel SanJoaquin, Nuno Seplúveda, Olivia Cook, Olivo Miotto, Panos Deloukas, Rachel Craik, Rebecca Wrigley, Renee Watson, Richard D Pearson, Robert Hutton, Samuel Oyola, Sarah Auburn, Shivang Shah, Si Quang Le, Sile Molloy, Susan Bull, Susana Campino, Taane G. Clark, Valentín Ruano-Rubio, Victoria Cornelius, Yik Ying Teo, Patrick Corran, Nilupa Silva, Paul Risley, Alan Doyle, Jennifer Evans, Rolf Horstmann, Chris Plowe, Patrick Duffy, Dan Carucci, Michael Gottleib, Adama Tall, Alioune Badara Ly, Amagana Dolo, Anavaj Sakuntabhai, Odile Puijalon, Abdou Bah, Abdoulie Camara, Abubacar Sadiq, Aja Abie Khan, Amie Jobarteh, Anthony Mendy, Augustine Ebonyi, Bakary Danso, Bintou Taal, Climent Casals-Pascual, David J. Conway, Emmanuel Onykwelu, Fatoumatta Sisay-Joof, Giorgio Sirugo, Haddy Kanyi, Haddy Njie, Herbert Obu, Horeja Saine, Idrissa Sambou, Ismaela Abubakar, Jalimory Njie, Jula Jaiteh, Kalifa A. Bojang, Kebba Jammeh, Kumba Sabally-Ceesay, Lamin Manneh, Landing Camara, Lawrence Yamoah, Madi Njie, Margaret Pinder, Mariatou Jallow, Mohammed Aiyegbo, Momodou Jasseh, Momodou Lamin Keita, Momodou Saidy-Khan, Ndey Ceesay, Oba Rasheed, Pa Lamin Ceesay, Pamela Esangbedo, Ramou Cole-Ceesay, Rasaq Olaosebikan, Simon Correa, Sophie Njie, Stanley Usen, Yaya Dibba, Abdoulaye Barry, A. Djimdé, Abdourahmane H. Sall, Amadou Abathina, Amadou Niangaly, Awa Dembele, Belco Poudiougou, Elizabeth Diarra, Kariatou Bamba, Mahamadou A. Thera, Ogobara Doumbo, Ousmane Toure, Salimata Konate, Sibiry Sissoko, Mahamadou Diakite, Amadou T. Konate, David Modiano, Edith C. Bougouma, Germana Bancone, Issa N. Ouedraogo, Jaques Simpore, Sodiomon B. Sirima, Marita Troye-Blomberg, Abraham R. Oduro, Abraham V.O. Hodgson, Anita Ghansah, Francis Nkrumah, Frank Atuguba, Kwadwo A. Koram, Michael D. Wilson, Nana Akosua Ansah, Nathan Mensah, Patrick A. Ansah, Thomas Anyorigiya, Victor Asoala, William O. Rogers, Alex Osei Akoto, Alex Owusu Ofori, Daniel Ansong, David Sambian, Emmanuel Asafo-Agyei, Justice Sylverken, Sampson Antwi, Tsiri Agbenyega, Adebola E. Orimadegun, Folakemi Anjol Amodu, Olajumoke Oni, Olayemi O. Omotade, Olukemi Amodu, Subulade Olaniyan, Andre Ndi, Clarisse Yafi, Eric Akum Achidi, Eric Mbunwe, Judith Anchang-Kimbi, Regina Mugri, Richard Besingi, Tobias O. Apinjoh, Vincent Titanji, Ahmed Elhassan, Ayman Hussein, Hiba Mohamed, Ibrahim Elhassan, Muntaser Ibrahim, Gilbert Kokwaro, Tom Oluoch, Alexander Macharia, Charles Newton, Daniel H. Opi, Dorcas Kamuya, Evasius Bauni, Kevin Marsh, Norbert Peshu, Sassy Molyneux, Sophie Uyoga, Thomas N Williams, Vicki Marsh, Behzad Nadjm, Caroline Maxwell, Chris Drakeley, Eleanor Riley, Frank Mtei, George Mtove, Hannah Wangai, Hugh Reyburn, Sarah Joseph, Deus Ishengoma, Martha Lemnge, Theonest Mutabingwa, Julie Makani, Sharon Cox, Ajib Phiri, Annie Munthali, David Kachala, Labes Njiragoma, Malcolm E. Molyneux, Mike Moore, Neema Ntunthama, Paul Pensulo, Terrie Taylor, Richard Carter, Deepika Fernando, Nadira Karunaweera, Rajika Dewasurendra, Prapat Suriyaphol, Malaria Genomic Epidemiology Network

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Abstract

Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology.

Original languageEnglish
Article numbere15266
Pages (from-to)1-44
Number of pages44
JournaleLife
Volume5
Issue numberJUN2016
DOIs
Publication statusPublished - 21 Jun 2016
Externally publishedYes

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    Busby, G. B. J., Band, G., Le, Q. S., Jallow, M., Bougama, E., Mangano, V. D., Amenga-Etego, L. N., Enimil, A., Apinjoh, T. O., Ndila, C. M., Manjurano, A., Nyirongo, V., Doumba, O., Rockett, K. A., Kwiatkowski, D. P., Spencer, C. C. A., Vanderwal, A., Elzein, A., Nyika, A., ... Malaria Genomic Epidemiology Network (2016). Admixture into and within sub-Saharan Africa. eLife, 5(JUN2016), 1-44. [e15266]. https://doi.org/10.7554/eLife.15266.001