title: Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries.
abstract: Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.
authors.affiliation: South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 8000, South Africa.
authors.forename: Caitlin
authors.initials: C
authors.lastname: Uren
authors.affiliation: Department of Ecology and Evolution, Stony Brook University, New York 11794.
authors.forename: Minju
authors.initials: M
authors.lastname: Kim
authors.affiliation: Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts 02114 Program in Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142.
authors.forename: Alicia R
authors.initials: AR
authors.lastname: Martin
authors.affiliation: Department of Ecology and Evolution, Stony Brook University, New York 11794.
authors.forename: Dean
authors.initials: D
authors.lastname: Bobo
authors.affiliation: Department of Genetics, Stanford University, California 94305.
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Gignoux
authors.affiliation: South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 8000, South Africa.
authors.forename: Paul D
authors.initials: PD
authors.lastname: van Helden
authors.affiliation: South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 8000, South Africa.
authors.forename: Marlo
authors.initials: M
authors.lastname: Möller
authors.affiliation: South African Medical Research Council Centre for Tuberculosis Research, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, 8000, South Africa brenna.henn@stonybrook.edu egvh@sun.ac.za.
authors.forename: Eileen G
authors.initials: EG
authors.lastname: Hoal
authors.affiliation: Department of Ecology and Evolution, Stony Brook University, New York 11794 brenna.henn@stonybrook.edu egvh@sun.ac.za.
authors.forename: Brenna M
authors.initials: BM
authors.lastname: Henn
mesh_terms: D000353:Africa, Southern; D044383:Black People / Q000235:genetics*; D004272:DNA, Mitochondrial / Q000235:genetics*; D005006:Ethnicity / Q000235:genetics*; D051456:Gene Flow; D005828:Genetics, Population; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D010802:Phylogeny; D058974:Phylogeography / Q000379:methods; D020641:Polymorphism, Single Nucleotide
chemical_list: D004272:DNA, Mitochondrial
keywords: KhoeSan; ancestry; pastoralism; population structure