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Fine-scale human population structure in southern Africa reflects ecological boundaries

Caitlin Uren, Minju Kim, Alicia R Martin, Dean Bobo, Christopher R Gignoux, Paul D van Helden, Marlo Möller, Eileen G Hoal, Brenna M Henn
doi: https://doi.org/10.1101/038729
Caitlin Uren
1SA MRC Centre for TB Research, DST/NRF 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
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Minju Kim
2Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
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Alicia R Martin
3Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114
4Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142
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Dean Bobo
2Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
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Christopher R Gignoux
5Department of Genetics, Stanford University, Stanford, CA 94305
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Paul D van Helden
1SA MRC Centre for TB Research, DST/NRF 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
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Marlo Möller
1SA MRC Centre for TB Research, DST/NRF 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
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Eileen G Hoal
1SA MRC Centre for TB Research, DST/NRF 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
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  • For correspondence: brenna.henn@stonybrook.edu egvh@sun.ac.za
Brenna M Henn
2Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794
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  • For correspondence: brenna.henn@stonybrook.edu egvh@sun.ac.za
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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 about 2,000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about population history within southern Africa. We examine new genome-wide polymorphism data and whole mitochondrial genomes for more than one hundred 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 recent ancestry with other Khoe-speaking forager populations that forms 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, approximately 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 impact from eastern African genetic diffusion.

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Posted February 03, 2016.
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Fine-scale human population structure in southern Africa reflects ecological boundaries
Caitlin Uren, Minju Kim, Alicia R Martin, Dean Bobo, Christopher R Gignoux, Paul D van Helden, Marlo Möller, Eileen G Hoal, Brenna M Henn
bioRxiv 038729; doi: https://doi.org/10.1101/038729
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Fine-scale human population structure in southern Africa reflects ecological boundaries
Caitlin Uren, Minju Kim, Alicia R Martin, Dean Bobo, Christopher R Gignoux, Paul D van Helden, Marlo Möller, Eileen G Hoal, Brenna M Henn
bioRxiv 038729; doi: https://doi.org/10.1101/038729

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