Ancient DNA reveals a hidden history of human adaptation

Humans may be just as vulnerable to environmental change as other animals, according to our new research, which analyzes genetic data from more than a thousand people who have lived in Europe and Asia over the past 45,000 years.

We found traces of more than 50 “hard sweeps,” where a rare genetic variant was rapidly swept through a population — most likely after a change in conditions that left those lacking the variant extinct. The most striking breakthrough occurred in early Anatolian farmers in a genetic region associated with the immune system called MHC-III.

Hard sweeps have often been observed in other species, but until now there has been little evidence of them in humans. Traces of the hard sweeps had been obscured by frequent intermingling of populations over the past 8,000 years.

Our results show that humans’ famous ability to adapt our behavior and develop new tools and techniques is not always enough to survive in difficult times.

How natural selection works

Modern humans live in a wide variety of natural environments, from the frozen arctic to the sultry tropical rainforest.

Unlike most animals, humans can draw on cultural innovations – like fire and clothing – to overcome the challenges these environments present.

However, these innovations may not always have been sufficient to cope with the new environmental conditions. This is where genetic variability between individuals comes into play.

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Individuals with genetic variations that make them better equipped for the new conditions will tend to leave more offspring. As a result, these beneficial variants will become more common in future generations.

This process of genetic adaptation was called “natural selection” by Charles Darwin almost 200 years ago.

How humans adapt

Using statistical tools to search for evidence of hard sweeps, researchers have found abundant evidence of past adaptive events in many animals and plants, but little in human genomes. More specifically, hard sweeps are remarkably rare in humans.

As a result, some have speculated that genetic adaptation is rare in humans, perhaps because cultural innovations have largely made it unnecessary. Others have suggested that selection occurred across many moderately favorable genetic variants, resulting in subtle and difficult-to-detect signals.

hidden signals

Almost 40 years ago, new technologies were developed to extract tiny amounts of DNA from archaeological skeletal remains. This has made it possible to study the genomes of ancient populations and changed our view of how ancient human groups and civilizations are related to one another.

Ancient DNA research has shown that over the past 10,000 years, interbreeding between genetically different populations has been particularly common in Eurasia.

We thought these events might have erased historical sweep signals from modern human genomes—but that ancient genomes that arose before these commingling events might still contain traces of the signals.

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Around 10,000 years ago, after the end of the last Ice Age, there was much greater genetic diversity among hunter-gatherers living in Europe than among people living there today.

In fact, the genetic differences between ancient European hunter-gatherer groups were as great as the differences observed today between modern-day populations in western Europe and eastern Asia.

This extreme genetic differentiation collapsed over the past 8,000 years due to multiple migrations and interbreeding events, making modern Europeans much more genetically homogeneous.

Hard Sweeps in Human History

In our new research, published today in Nature Ecology & Evolution, we revisited this question by scanning more than a thousand ancient human genomes from across Eurasia.

We wondered: could these relatively recent mixing events have masked historical selective sweeps, making them invisible in modern human genomes?

To test this idea, we first ran some computer simulations based on genetic mixing estimates from studies of ancient Eurasian genomes. The simulation results suggested that ancient selection signals may indeed be severely diluted in modern genomes.

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Next, we compiled and analyzed genetic information from more than 1,000 ancient human remains, with the oldest sample being around 45,000 years old.

We compared selection signals in ancient genomes with those from modern genomes. The old data contained many more hard-swept signals than the modern samples. Recent sweeps were particularly prone to deletion because they were rare or absent from at least one of the mixed populations.

Our results confirm that hard sweeps were indeed part of the human genetic adaptation repertoire. This suggests that we may not be all that different from other animal species.

The genetic basis of adaptation

Genetic evidence of historical interbreeding events between different populations is growing. This is true not only for humans but also for other species, suggesting that such interbreeding is fairly common in nature.

If these mixing events are widespread, our study suggests that hard sweeps were also more common than we currently assume. Overall, we may have a biased view of how species have genetically adapted to environmental stresses.

To better understand how adaptation works at the genetic level, we need to develop new statistical methods to disentangle signals from hard sweeps and other selection events.

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