In-depth genomic analysis of a Pan African set of individuals, that emphasizes their complex relationships and demographic history at population level. Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from unknown Neanderthal sister taxa into sub-Saharan populations

The population demography and gene flow among African groups, as well as the putative archaic introgression of ancient hominins, have been poorly explored at genome level despite being the cradle of humankind.Here, we examine 15 African populations covering all major continental linguistic groups, ecosystems and lifestyles within Africa, by analyzing the whole-genome sequence data of 21 individuals sequenced at deep coverage. We observe a remarkable correlation among genetic diversity and geographic distance, being the hunter-gatherer groups the ones more genetically differentiated and with larger effective population sizes through 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. Concerning archaic gene flow, we test four demographic models considering recent admixture as well as archaic introgression, identifying the fingerprint of an archaic introgression in the sub-Saharan populations tested (~8.8% in Khoisan, ~5.8% in Mbuti Pygmies, and 3.3% in Mandenka) from a ghost archaic population related to Neanderthals