Cell 2020 Feb 20; 180(4):677-687. doi: 10.1016/j.cell.2020.01.012.

Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals

Lu Chen, Aaron B Wolf, Wenqing Fu, Liming Li, Joshua M Akey

Admixture has played a prominent role in shaping patterns of human genomic variation, including gene flow with now-extinct hominins like Neanderthals and Denisovans. Here, we describe a novel probabilistic method called IBDmix to identify introgressed hominin sequences, which, unlike existing approaches, does not use a modern reference population. We applied IBDmix to 2,504 individuals from geographically diverse populations to identify and analyze Neanderthal sequences segregating in modern humans. Strikingly, we find that African individuals carry a stronger signal of Neanderthal ancestry than previously thought. We show that this can be explained by genuine Neanderthal ancestry due to migrations back to Africa, predominately from ancestral Europeans, and gene flow into Neanderthals from an early dispersing group of humans out of Africa. Our results refine our understanding of Neanderthal ancestry in African and non-African populations and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date.

The importance is this paper lies in the demonstration that Neanderthal genomic matches are found in all of the modern human populations. This means that we now have direct evidence for shared descent between a Eurasian hominin species and modern humans (including Sub-Saharan Africans), while having no evidence for shared genetic ancestry between African hominins and any modern humans. On the one hand, it creates another difficulty for an out-of-Africa model for the origin of modern humans. On the other hand, it further decreases the likelihood of Out-of-America I because now, for out-of-America I to work, it needs to show that Neaderthals, too, originated in the Americas.

The paper does interpret the shared genomic material between Neanderthals and modern humans as evidence for two-way admixture – from Neanderthals to modern humans and from modern humans to Neanderthals but this solution runs counter to homozygosity levels data that shows dramatic difference in diversity between ancient hominins (Neanderthals and Denisovans), on the one hand, and each and every modern human population, on the other. Any admixture events would have evened those metrics out.