Every Modern Human Population Has Neanderthal Ancestry, New Genetic Analysis Finds

Neanderthals are an extinct species of ancient humans. Petr Student/Shutterstock

Neanderthal genomes survive in every modern population studied to date, according to a new international genetic analysis. In particular, Europeans and Africans share more Neanderthal DNA with each other than they do with East Asians. The findings provide important new insight into human history and the dispersal of Neanderthal ancestry across the planet.

To come to their conclusions, researchers at Princeton University developed a new method for detecting ancient ancestry that addresses biases and limitations with previous analyses. The new statistical method is called IBDmix, which draws its name from the genetic principle “identity by descent” (IBD).

“IBDmix operates by taking a pair of genomes, one human and one Neanderthal, and reads along these genomes base-by-base, determining the likelihood that at a given site the two genomes are identical by descent (IBD),” senior study author Aaron Wolf told IFLScience. “Each site is given a score based on the probability of IBD, and groups of sites can be strung together to maximize that score and define larger segments of Neanderthal ancestry in a human genome.”

Characteristics determined by IBD are then used to identify and distinguish regions present in the modern human genome that are derived from modern humans interbreeding with Neanderthals. This method was used to identify Neanderthal sequences in more than 2,500 individuals from the 1,000 Genomes Project, an international database of human genetic variation from individuals across the planet. For the first time, researchers determined that about 0.3 percent of Africans’ genomes contained Neanderthal ancestry, with more than 94 percent of this sequence also being shared with non-Africans.

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Most Neanderthal ancestry can be "traced back to one common hybridization event involving the population ancestral to all non-Africans, occurring shortly after the Out-of-Africa dispersal," said the researchers.

“Our claim that most Neanderthal ancestry can be traced to a common hybridization event is significant because many previous studies have hypothesized multiple hybridization events contributing to Neanderthal ancestry in modern humans,” said Wolf, adding that his team’s results show that the difference in Neanderthal ancestry between European and East Asian populations is much lower than previously thought.  

However, genetics do not explain when or how ancient humans migrated from Africa and such determinations require anthropological and archaeological evidence. History was “much more interesting” than previously thought, say the researchers. The findings suggest that there is one hybridization event, but early humans likely left Africa in many waves over the course of tens of thousands of years. Gene flow likely went in both directions, with modern humans coming from Africa around 200,000 years ago and hybridizing with Neanderthals, thereby introducing modern human DNA into the genomes of Neanderthals.
 
"All genetics can tell us about is what happened in the past among those individuals who contribute ancestry to present-day populations. Therefore, although the vast majority of all non-Africans can trace their ancestry to a single out of Africa dispersal, this doesn’t mean there weren’t other migrations out of Africa in history, but they would be 'invisible' to genetics," study co-author Joshua Akey told IFLScience. 
 

The researchers add that IBDmix works off of already known genomes and is not suitable to discover sequences shared between modern humans and unknown individuals. Further research will need to account for both out-of- and into-Africa dispersals when looking at global patterns of genomic variation.

To address these concerns, the study authors hope to develop their method further and apply it to additional populations, characterize targeted sequences, and study what this means for modern human health and disease.

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