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Neanderthal Genetic Ancestry Found in Present-Day African Populations

NEW YORK – New research suggests that Neanderthal ancestry may be more widespread than previously appreciated, turning up in individuals from East Asia, Europe, and even Africa.

As they reported online on Thursday in Cell, the researchers, from Princeton University, the University of Washington, and Microsoft, used an "identity by descent"-based statistical approach called IBDmix to tease out Neanderthal archaic ancestry in genotyping data from more than 2,500 Eurasian, American, or African participants in the 1,000 Genomes Project. With this strategy, they uncovered Neanderthal sequences in each of the populations, including distinct adaptive introgression events providing clues to the challenges faced by past human populations.

The team noted that Neanderthal ancestry in Africans may have been missed or underestimated in the past by failing to take into account migrations of individuals with European ancestry back into Africa after the out-of-Africa migration. Consequently, the results have also refined estimates around the proportion of Neanderthal ancestry in non-African populations.

"Collectively, these results show that Neanderthal ancestry estimates in East Asians and Europeans were biased due to unaccounted-for back-migrations from European ancestors into Africa," senior and corresponding author Joshua Akey, a researcher at Princeton, said in a statement.

For their analyses, the researchers analyzed genotyping profiles for 2,504 individuals from populations around the world, using the population reference-free IBDmix method and available Altai Neanderthal sequences to identify stretches of archaic ancestry in the participants. They noted that this approach is designed to specifically pick up Neanderthal ancestry, and may miss ancestry stemming from other, unknown archaic hominins.

The team detected subtle differences in the proportion of Neanderthal ancestry in the European, East Asian, and South Asian individuals. Both East and South Asian individuals carried around 55 Mb of Neanderthal-related sequence, on average, compared to an average of 51 Mb of Neanderthal sequence in the European individuals.

From these and other findings, the authors estimated that "most of the Neanderthal ancestry that individuals have today can be traced back to a common hybridization event involving the population ancestral to all non-Africans, occurring shortly after the out-of-Africa dispersal," Akey explained.

On the other hand, the team found that African individuals had an average of 17 Mb of Neanderthal-related ancestry, representing roughly 0.3 percent of the genome. Using real and simulated population genotyping profiles, the investigators found that the Neanderthal sequences present in Africans share closer ties to those in Europeans than in East Asians — a pattern suspected of stemming from back-to-Africa migrations by Europeans with Neanderthal ancestry.

"[O]ur data show that out-of-Africa and in-to-Africa dispersals must be accounted for when interpreting archaic hominin ancestry in contemporary human populations," the authors wrote, noting that "the legacy of gene flow with Neanderthals likely exists in all modern humans, highlighting our shared history."

When they focused on the specific Neanderthal sequences that have persisted in different present-day human populations, which offered adaptive introgression hints, the researchers saw 51 Neanderthal haplotypes that were particularly common. In the African individuals, for example, they tracked down more than a dozen haplotypes that fell in parts of the genome containing genes from immune, ultraviolet light response, and other pathways contributing to environmental response.

"Our results refine catalogs of genomic regions where Neanderthal sequence was deleterious and advantageous and demonstrate that remnants of Neanderthal genomes survive in every modern human population studied to date," Akey said, noting that the new results "provide insight into the evolutionary history of these populations, the selective pressures they faced, and current variation in health and disease."

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