Background: 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.

This study was funded by the Spanish MINECO grants CGL-2013-44351-P, CGL-2016-75389-P, and the “Unidad de Excelencia Maria de Maeztu” MDM2014-0370. BLG was supported with a Beatriu de Pinós (BP-DGR 2014) fellowship. O.L. was supported by a Ramón y Cajal grant from the Spanish Ministerio de Economia y Competitividad (MEIC) with reference RYC-2013-14797, a BFU2015-68759-P (MEIC/FEDER) grant and the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 937). O.L. also acknowledges the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership; Centro de Excelencia Severo Ochoa; CERCA Programme / Generalitat de Catalunya; the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) through the Instituto de Salud Carlos III; Generalitat de Catalunya through Departament de Salut and Departament d’Empresa i Coneixement; the co-financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program. GSV was supported by a FI (2017FI_B2 00010) scholarship. LFKK was supported by an FPI fellowship associated with BFU2014-55090-P (MINECO/FEDER, UE). VNP was financially supported by the Ministry of Health, Government of Catalonia [grant SLT002/16/00496] and a grant from Otto A. Malmi Foundation (Finland). TMB is supported by BFU2017-86471-P (MINECO/FEDER, UE), U01 MH106874 grant, Howard Hughes International Early Career, Obra Social "La Caixa" and Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880).