North African Populations Carry the Signature of Admixture with Neandertals

Abstract

One of the main findings derived from the analysis of the Neandertal genome was the evidence for admixture between Neandertals and non-African modern humans. An alternative scenario is that the ancestral population of non-Africans was closer to Neandertals than to Africans because of ancient population substructure. Thus, the study of North African populations is crucial for testing both hypotheses. We analyzed a total of 780,000 SNPs in 125 individuals representing seven different North African locations and searched for their ancestral/derived state in comparison to different human populations and Neandertals. We found that North African populations have a significant excess of derived alleles shared with Neandertals, when compared to sub-Saharan Africans. This excess is similar to that found in non-African humans, a fact that can be interpreted as a sign of Neandertal admixture. Furthermore, the Neandertal's genetic signal is higher in populations with a local, pre-Neolithic North African ancestry. Therefore, the detected ancient admixture is not due to recent Near Eastern or European migrations. Sub-Saharan populations are the only ones not affected by the admixture event with Neandertals.

Genetic variation in Tunisia in the context of human diversity worldwide

“…Simple characterizations of groups and regions based on limited initial information is understandable, but will need to be updated and new perspectives obtained by additional analyses. For example, Sanchez‐Quinto et al (2012) characterize the Tunisian population as homogeneous and inbred based on a small relatively inbred Tunisian sample reported by Henn et al (2012); but that broad characterization is now untenable in the context of our more extensive sampling of populations in Tunisia which shows that the Henn et al Tunisian sample is something of an outlier for Tunisia as a whole.…”

Influence of IFNL3.rs12979860 and IFNL4.ss469415590 polymorphism on clearance of hepatitis C virus infection among Egyptians

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IBD Sharing between Africans, Neandertals, and Denisovans

“…Only few studies have looked at Neandertal ancestry among African populations (Lachance et al 2012; Sanchez-Quinto et al 2012; Wang et al 2013; Llorente et al 2015) and mostly came to the conclusion that Neandertal ancestry in Africans is probably due to Eurasian backflow admixture. However, archaic hominins lived longer side by side within than outside of Africa and this led to plentiful opportunities for gene flow within Africa that should not be dismissed (Hammer et al 2011).…”