title: Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.
abstract: The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.
authors.affiliation: Department of Zoology, University of Oxford, OX1 3PS, UK francesco.montinaro@gmail.com.
authors.forename: Francesco
authors.initials: F
authors.lastname: Montinaro
authors.affiliation: Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK.
authors.forename: George B J
authors.identifier: 0000-0003-4148-6222
authors.initials: GB
authors.lastname: Busby
authors.affiliation: Department of Zoology, University of Oxford, OX1 3PS, UK.
authors.forename: Miguel
authors.initials: M
authors.lastname: Gonzalez-Santos
authors.affiliation: School of Medicine, University of Namibia, Private Bag 13301 Windhoek, Namibia.
authors.forename: Ockie
authors.initials: O
authors.lastname: Oosthuitzen
authors.affiliation: School of Medicine, University of Namibia, Private Bag 13301 Windhoek, Namibia.
authors.forename: Erika
authors.initials: E
authors.lastname: Oosthuitzen
authors.affiliation: Dipartimento di Biologia Ambientale, Università "La Sapienza," 00185 Rome, Italy.|Istituto Italiano di Antropologia, 00185 Rome, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Anagnostou
authors.affiliation: Dipartimento di Biologia Ambientale, Università "La Sapienza," 00185 Rome, Italy.|Istituto Italiano di Antropologia, 00185 Rome, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Destro-Bisol
authors.affiliation: Institute of Public Health, Catholic University, 00168 Rome, Italy.
authors.forename: Vincenzo L
authors.initials: VL
authors.lastname: Pascali
authors.affiliation: Department of Zoology, University of Oxford, OX1 3PS, UK.
authors.forename: Cristian
authors.initials: C
authors.lastname: Capelli
mesh_terms: D000353:Africa, Southern; D044383:Black People / Q000235:genetics*; D000072441:DNA, Ancient / Q000032:analysis* / Q000737:chemistry; D005787:Gene Frequency; D040342:Genetic Structures; D014644:Genetic Variation; D005828:Genetics, Population / Q000379:methods; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D007927:Lesotho; D009276:Namibia; D058974:Phylogeography / Q000379:methods
chemical_list: D000072441:DNA, Ancient
keywords: African prehistory; Khoesan; ancient structure; sub-Saharan Africa