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Population history of modern humans and genetic ancestry of an individual genome
Speaker(s): Dr Hie Lim Kim, Senior Research Fellow SCELSE, SBS, LKCMedicine, Nanyang Technological University
When: 18 June 2015 (9:30 am)
Where: CR4 (SBS-01n-24)
Type: Seminars


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. We sequenced the complete genomes of five Namibian Khoisan individuals and one Bantu-speaking agriculturist from southern Africa to an average coverage of 27~55-fold. Population genetic analyses using a 420K SNP dataset from 1,462 worldwide individuals demonstrate that two genomes from the Ju/’hoansi (northern Khoisan) population contain exclusive Khoisan ancestry. The two genomes allow us to infer early history of major modern human populations. In order, coalescent analysis was applied to the six southern African genomes we sequenced and eight publicly available whole genomes from various populations. Our analyses reveal that the Khoisan and their ancestors have maintained their large effective population size following their split from non-Khoisan populations ~100-150 kya. In contrast, the ancestor populations of the non-Khoisans, including Bantu speakers and non-Africans, dramatically declined after the split and lost more than half of their genetic diversity. This is in stark contrast to the current census size of the Khoisan hunter-gatherers, which is drastically smaller compared to that of the Bantu-speaking population. Based on paleoclimate records and models, it is predicted that the precipitation in southern Africa increased ~80-100 kya while west-central Africa became drier. We hypothesize that these climate differences in central and southern Africa might be related to the divergent ancestral population histories among modern humans.