George B.J. BusbyGavin BandQuang Si LeMuminatou JallowEdith BougamaValentina D. ManganoLucas N. Amenga-EtegoAnthony EnimilTobias ApinjohCarolyne M. NdilaAlphaxard ManjuranoVysaul NyirongoOgobara DoumbaKirk A. RockettDominic P. KwiatkowskiChris C.A. SpencerAaron VanderwalAbier ElzeinAceme NyikaAlieu MendyAlistair MilesAndrea DissAngeliki KerasidouAngie GreenAnna E. JeffreysBronwyn MacInnisCatherine HughesCatherine MoyesChristina HubbartCinzia MalangoneClaire PotterDaniel MeadDavid BarnwellDushyanth JyothiEleanor DruryElilan SomaskantharajahEliza HiltonEllen LefflerGareth MaslenGeorge BusbyGeraldine M. ClarkeIoannis RagoussisJacob Almagro GarciaJane RogersJantina deVriesJennifer SheltonJiannis RagoussisJim StalkerJoanne RodfordJohn O'BrienWellcome Trust Centre for Human GeneticsWellcome Trust Sanger InstituteMedical Research Council UnitRoyal Victoria Teaching Hospital GambiaCentre National de Recherche et de Formation sur le PaludismeUniversità degli Studi di Roma La SapienzaNavrongo Health Research CenterKomfo Anokye Teaching HospitalUniversity of BueaWellcome Trust Research Laboratories NairobiKilimanjaro Christian Medical CollegeLondon School of Hygiene & Tropical MedicineUniversity of Malawi College of MedicineUniversity of BamakoNational Institute for Biological Standards and ControlWellcome TrustBernhard Nocht Institut fur Tropenmedizin HamburgUniversity of Maryland, BaltimoreNational Institute of Allergy and Infectious DiseasesFoundation for the National Institutes of HealthInstitut Pasteur de DakarInstitut Pasteur, ParisMedical Research Council Laboratories GambiaUniversity of GhanaKwame Nkrumah University of Science and Technology2018-12-112019-03-142018-12-112019-03-142016-06-21eLife. Vol.5, No.JUN2016 (2016)2050084X2-s2.0-84975491862https://repository.li.mahidol.ac.th/handle/20.500.14594/43005© Busby et al. 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.Mahidol UniversityBiochemistry, Genetics and Molecular BiologyImmunology and MicrobiologyArticleSCOPUS10.7554/eLife.15266.001