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Genome Biol. 2019 Apr 26;20(1):77. doi: 10.1186/s13059-019-1684-5.

Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations.

Author information

Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.
Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA.
CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028, Barcelona, Spain.
Universitat Pompeu Fabra (UPF), Barcelona, Spain.
College of Science, Department of Biology, Taibah University, Al Madinah, Al Monawarah, Saudi Arabia.
Higher Institute of Biotechnology of Beja, University of Jendouba, Avenue Habib Bourguiba, BP, 382, 9000, Beja, Tunisia.
Oncology Data Analytics Program, Bellvitge Biomedical Research Institute (ICO-IDIBELL), Consortium for Biomedical Research in Epidemiology and Public Health, Hospitalet de Llobregat, Barcelona, Spain.
Department of Archaeology, University of Helsinki, Helsinki, Finland.
Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa.
School of Medicine, The Lebanese American University, Beirut, 1102-2801, Lebanon.
Institució Catalana de Recerca i Estudis Avançats, ICREA, 08003, Barcelona, Spain.
Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF/CSIC), Universitat Pompeu Fabra, 08003, Barcelona, Spain.



Population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at the genome level.


Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems, and lifestyles within Africa through analysis of whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, with the hunter-gatherer groups being more genetically differentiated and having larger effective population sizes throughout most modern-human history. Admixture signals are found between neighbor populations from both hunter-gatherer and agriculturalists groups, whereas North African individuals are closely related to Eurasian populations. Regarding archaic gene flow, we test six complex demographic models that consider recent admixture as well as archaic introgression. We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage.


The present study represents an in-depth genomic analysis of a Pan African set of individuals, which emphasizes their complex relationships and demographic history at population level.


Africa; Archaic introgression; Genome diversity; Human population genetics; Whole-genome sequences

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