Lorente-Galdós, Belén, 1981-Lao Grueso, Oscar, 1976-Serra Vidal, Gerard, 1989-Santpere Baró, Gabriel, 1981-Kuderna, Lukas, 1989-Arauna, Lara RFadhlaoui-Zid, KarimaPimenoff, Ville N.Soodyall, HimlaZalloua, Pierre A.Marquès i Bonet, Tomàs, 1975-Comas, David, 1969-2019-04-302019-04-302019Lorente-Galdos B, Lao O, Serra-Vidal G, Santpere G, Kuderna LFK, Arauna LR et al. 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. Genome Biol. 2019;20(1):77. DOI: 10.1186/s13059-019-1684-51474-7596http://hdl.handle.net/10230/37159Background: 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. Results: 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. Conclusion: 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.application/pdfeng© The Author(s). 2019. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.info:eu-repo/semantics/articlehttp://dx.doi.org/10.1186/s13059-019-1684-5Human population geneticsGenome diversityWhole-genome sequencesAfricaArchaic introgressioninfo:eu-repo/semantics/openAccess