title: Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history.
abstract: The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/'hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100-150 kyr ago. In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80-100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations.
authors.affiliation: 1] Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, Pennsylvania 16802, USA [2] Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore 637551, Singapore.
authors.forename: Hie Lim
authors.initials: HL
authors.lastname: Kim
authors.affiliation: 1] Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, Pennsylvania 16802, USA [2] Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA.
authors.forename: Aakrosh
authors.initials: A
authors.lastname: Ratan
authors.affiliation: Departments of Anthropology and Biology, Pennsylvania State University, 513 Carpenter Building, University Park, Pennsylvania 16802, USA.
authors.forename: George H
authors.initials: GH
authors.lastname: Perry
authors.affiliation: 1] Department of Geography, Ohio State University, 154 North Oval Mall, Columbus, Ohio 43210, USA [2] Campus do Litoral Paulista, Unesp-Univ Estadual Paulista, São Vicente 11330-900, Brazil.
authors.forename: Alvaro
authors.initials: A
authors.lastname: Montenegro
authors.affiliation: Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, Pennsylvania 16802, USA.
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.affiliation: 1] Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, 310 Wartik Lab, University Park, Pennsylvania 16802, USA [2] Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27, Singapore 637551, Singapore.
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
mesh_terms: D000353:Africa, Southern; D044383:Black People / Q000235:genetics*; D003710:Demography; D005260:Female; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D008297:Male; D017422:Sequence Analysis, DNA