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Mystery solved: How and why humans have Neanderthal DNA

Approximately 40,000 years ago, Neanderthals, long-time inhabitants of the western part of the Eurasian continent, met the incoming Homo sapiens from Africa. These two species shared the region for several millennia, leading to the infusion of Neanderthal DNA into the Homo sapiens genome. 

Neanderthal DNA 

Recently, researchers at the University of Geneva (UNIGE) have been meticulously analyzing how the DNA from Neanderthals has been distributed in Homo sapiens over the last 40,000 years. Their findings, published in the journal Science Advances, indicate subtle variations across time and geography, shedding light on the intertwined history of these two species.

The advances in genome sequencing and comparative analysis have shown that Neanderthals and Homo sapiens did interbreed. From these interactions, present-day Eurasians carry about two percent of Neanderthal-origin DNA. However, this percentage is not consistent across Eurasia: Neanderthal DNA is slightly more abundant in Asian genomes compared to European ones.

One theory proposes that the variances between Asian and European populations could be due to different impacts of natural selection on Neanderthal-origin genes. 

Migratory flows

However, the UNIGE scientists have proposed an alternative theory based on migratory flows: when a migrating population merges with a local population, the local population’s DNA tends to increase in proportion with distance from the migrating group’s point of origin.

With Homo sapiens originating from Africa and Neanderthals predominantly located in Europe, the theory is that the farther one travels from Africa, the higher the proportion of Neanderthal DNA. 

Focus of the study

To validate this, the researchers utilized a database from Harvard Medical School which contains over 4,000 genomes of individuals from Eurasia over the past 40 millennia.

“Our study is mainly focused on European populations since we are obviously dependent on the discovery of bones and the state of conservation of DNA. It turns out that archaeological excavations have been much more numerous in Europe, which greatly facilitates the study of the genomes of European populations,” explained lead author Claudio Quilodrán, an expert in Population Genetics and Ecology at UNIGE.

What the researchers learned 

The team’s statistical findings reveal that, after Homo sapiens migrated from Africa, European Paleolithic hunter-gatherers had a slightly higher proportion of Neanderthal DNA than their Asian counterparts. 

This observation is in line with paleontological records, emphasizing Neanderthals’ dominance in western Eurasia, notably with no Neanderthal remains found east of Siberia’s Altai region.

Neolithic transition 

However, the researchers observed a significant shift during the Neolithic transition, about 10,000 to 5,000 years ago: there was a reduction in the proportion of Neanderthal DNA in European genomes, resulting in a slightly lower percentage than in Asian populations. 

This shift aligns with the arrival of the first farmers from Anatolia and the Aegean region, who carried less Neanderthal DNA. Their integration further diluted the Neanderthal DNA concentration in Europe.

Study significance 

The fusion of ancient genome research and archaeological data provides a window into the evolutionary journey of hybrid species. 

“In addition, we are beginning to have enough data to describe more and more precisely the percentage of DNA of Neanderthal origin in the genome of Sapiens at certain periods of prehistory,” said study senior author Mathias Currat, a professor of Genetics and Evolution at UNIGE.

“Our work can therefore serve as a reference for future studies to more easily detect genetic profiles that deviate from the average and might therefore disclose an advantageous or disadvantageous effect.”

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