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Ancient genomes reveal hidden history of human adaptation

Certain genetic changes due to environmental pressures likely more common in ancient humans than previously thought
3 November 2022

It is widely believed that the genetics of our human ancestors did not change in response to environmental pressures as much as that of other animals due to our enhanced ability to overcome such pressures with new tools and technologies rather than with biological adaptations. However, a new study comparing modern human genomes with ancient human DNA finds that certain genetic changes in humans may have been more common than previously thought.

The team studied a type of genetic change, called a hard selective sweep, in which a rare genetic variant becomes common across all members of a group in response to external pressure, like a virus or climate change. These hard selective sweeps are commonly observed within the genomes of animals but have appeared to be rare in humans.

“Our results confirm hard selective sweeps were part of human genetic adaptation, suggesting we may not be so different from other animal species,” said Christian Huber, assistant professor of biology, Penn State. “Broadly, our discovery challenges the prevailing view of human adaptation and provides insights into how humans have adapted to the novel environmental pressures they encountered as we spread across the planet.”

Using data from publicly available repositories, the researchers compiled and analyzed genetic information from more than 1,000 ancient human remains from across Eurasia, with the oldest sample around 45,000 years old.

map of Europe with dots and arrows
Each human symbol represents a sample, and the colors indicate different populations classified into broad groupings according to archaeological records of material culture and lifestyle. Sample ages are represented in the bottom panel in thousand years before present (BP). The green lines depict the generalized migration route of Anatolian Early Farmers (EF) into Europe ~8,500 years ago, where they mixed with Western Hunter-Gatherers (WHG) to create the European Early Farmers. Similarly, the pink arrows represent the generalized movement of Steppe Pastoralists, which resulted in mixing with Late Farmers (LF) ~5,000 years ago, giving rise to Late Neolithic/Bronze Age (LNBA) societies. Credit: Christian Huber, Penn State

The team discovered more than 50 cases of hard selective sweeps in which an initially rare beneficial genetic variant became prevalent across all members of an ancient human group. Although the researchers have not yet identified the specific environmental drivers of these hard selective sweeps, they did observe that one of the variants was associated with the immune system, for example.

By contrast, the team did not find similar evidence of selective sweeps in the modern human genomes they analyzed.

“Historical mixing between human groups over the past 8,000 years may have hidden signs of genetic changes in modern human genomes, while the ancient genomes predating these intermixing events still retain traces of the signals,” said Huber. “Our results confirm hard selective sweeps were indeed part of the repertoire of human genetic adaptation.”

The results were published in the journal Nature Ecology and Evolution.

Other authors on the paper include Yassine Souilmi, group leader, University of Adelaide, and Ray Tobler, postdoctoral fellow, Australian National University. Researchers based at the Mayo Clinic, the Garvan Institute of Medical Research, the Max Planck Institute for the Science of Human History in Germany, the University of New South Wales and Massey University in New Zealand also contributed to the research paper.

The Australian Research Council, Australian National Database Service, Nectar Cloud and University of Adelaide Environment Institute supported this work.

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Sara LaJeunesse
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