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Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University.ORCID iD: 0000-0002-8160-9621
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
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2012 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 338, no 6105, 374-379 p.Article in journal (Refereed) Published
Abstract [en]

The history of click-speaking Khoe-San, and African populations in general, remains poorly understood. We genotyped ∼2.3 million SNPs in 220 southern Africans and found that the Khoe-San diverged from other populations ≥100,000 years ago, but structure within the Khoe-San dated back to about 35,000 years ago. Genetic variation in various sub-Saharan populations did not localize the origin of modern humans to a single geographic region within Africa; instead, it indicated a history of admixture and stratification. We found evidence of adaptation targeting muscle function and immune response, potential adaptive introgression of UV-light protection, and selection predating modern human diversification involving skeletal and neurological development. These new findings illustrate the importance of African genomic diversity in understanding human evolutionary history.

Place, publisher, year, edition, pages
2012. Vol. 338, no 6105, 374-379 p.
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-181302DOI: 10.1126/science.1227721ISI: 000309955800039OAI: oai:DiVA.org:uu-181302DiVA: diva2:555719
Available from: 2012-09-21 Created: 2012-09-21 Last updated: 2016-04-14
In thesis
1. Reconstructing the Human Past using Ancient and Modern Genomes
Open this publication in new window or tab >>Reconstructing the Human Past using Ancient and Modern Genomes
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The study of DNA variation is one of the most promising avenues for learning about the evolutionary and historical past of humans and other species. However, the difficulty associated with obtaining DNA directly from ancient remains have for long kept genomic studies of population history trapped in time; confined to interpreting patterns of modern-day variation without direct historical observations. In this thesis, I outline new approaches for the retrieval, analysis and interpretation of large-scale genomic data from ancient populations, including solutions to overcome problems associated with limited genome coverage, modern-day contamination, temporal differences between samples, and post-mortem DNA damage. I integrate large-scale genomic data sets from ancient remains with modern-day variation to trace the human past; from traits targeted by natural selection in the early ancestors of anatomically modern humans, to their descendants' interbreeding with archaic populations in Eurasia and the spread of agriculture in Europe and Africa. By first reconstructing the earliest population diversification events of early modern humans using a novel large-scale genomic data set from Khoe-San populations in southern Africa, I devise a new approach to search for genomic patterns of selective sweeps in ancestral populations and report evidence for skeletal development as a major target of selection during the emergence of early modern humans. Comparing publicly available genomes from archaic humans, I further find that the distribution of archaic human ancestry in Eurasia is more complex than previously thought. In the first direct genomic study of population structure in prehistoric populations, I demonstrate that individuals associated with farming- and hunter-gatherer complexes in Neolithic Scandinavia were strongly genetically differentiated, and direct comparisons with modern-day populations as well as other prehistoric individuals from Southern Europe suggest that this structure originated from Northward expansion of Neolithic farming populations. Finally, I develop a bioinformatic approach for removing modern-day contamination from large-scale ancient DNA sequencing data, and use this method to reconstruct the complete mitochondrial genome sequence of a Siberian Neandertal that is affected by substantial modern-day contamination.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2013. 68 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 1069
population genetics, paleogenomics, human evolution
National Category
Evolutionary Biology Genetics
Research subject
Evolutionary Genetics
urn:nbn:se:uu:diva-206787 (URN)978-91-554-8744-7 (ISBN)
Public defence
2013-10-18, Zootissalen, Evolutionary Biology Centre, Norbyvägen 18C, Uppsala, 10:00 (English)
Available from: 2013-09-27 Created: 2013-09-04 Last updated: 2014-01-23

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Schlebusch, Carina M.Skoglund, PontusSjödin, PerGattepaille, Lucie M.Li, SenJakobsson, Mattias
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