Landmark ancient-genome study shows surprise acceleration of human evolution

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The biggest ever study of ancient human DNA shows that human evolution has accelerated over the past 10,000 years.

Researchers identified hundreds of gene variants that evolved through natural selection in ancient people from western Eurasia — Europe and the Middle East — after the dawn of agriculture. Changes to these genes had widespread ramifications for the health of present-day populations.

“We are seeing dramatic changes,” says David Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts, who co-led the 15 April Nature study1. However, some researchers remain unconvinced by the scale of the findings and results that show natural selection has affected gene variants underlying highly complex traits, such as mental illness and cognition.

Adapting to agriculture

Homo sapiens emerged in Africa around 200,000 to 300,000 years ago, before expanding to nearly every corner of the planet. The advent of farming introduced new foods, pathogens and other challenges, as people began living in larger groups and in closer proximity to animals.

Humans clearly adapted to these upheavals. But genomic studies of present-day and ancient people have uncovered only a smattering of genetic signs of natural selection, particularly for advantageous genes that have surged to high frequency, or ones that have proved to be harmful and become less common.

The best‑known example of such ‘directional selection’ is a genetic variant that maintains production of the lactose enzyme into adulthood, which enables many people of European ancestry to digest milk throughout their lives.

To supercharge the search, Reich, Ali Akbari, a computational geneticist at Harvard Medical School, and their colleagues amassed the largest-ever collection of genomic data from ancient humans — from a total of 15,836 individuals from western Eurasia — including more than 10,000 newly sequenced genomes.

Efforts to identify gene variants that became more or less common owing to directional selection can be thwarted by random fluctuations, known as genetic drift, and population shifts that can drastically alter the genetic make-up of regions’ inhabitants, such as the replacement of European hunter-gatherers by farmers from the Middle East.

To overcome this, Akbari and Reich’s team first looked for genetic variants that consistently appeared more or less frequently in different groups living at different times. They then discounted changes that could be explained by forces other than selection, identifying 479 variants that showed strong signs of directional selection.

These changes paint a picture of populations whose biology was in flux, as hunter-gatherer lifestyles gave way to farming across Europe. The study also found that evolution accelerated during the Bronze Age, which began around 5,000 years ago, possibly reflecting an intensification of lifestyle changes that started in the Neolithic period starting around 10,000 years ago, says Reich. “This is an economically and culturally transformative time.”

Immunity genes

The method that Akbari and Reich’s team developed was designed to spot consistent changes in a gene variant’s frequency in a population, either increasing or decreasing. But the frequency of two-thirds of the variants that they identified moved more like rollercoasters. A gene variant linked to the heightened risk of developing multiple sclerosis, which had been identified in a previous study2, shot up in frequency about 6,000 years ago. The latest study suggests that the variant has become less common in some European groups in the past 2,000 years.

Genes involved in immunity are among the most common targets for directional selection. A variant linked to tuberculosis susceptibility became less common in the past 3,000 years, confirming another previous result3. But before this, it shot up in frequency, possibly owing to the emergence of other pathogens. A variant that confers HIV resistance in modern humans became more common between 6,000 and 2,000 years ago, possibly because it also protected against plague-causing bacteria.

Evolution has also shaped the appearance of Europeans. Akbari and Reich’s team found ten variants linked to lighter skin tone that had signals of selection. A cause of male pattern baldness became much less common over the past 7,000 years, contributing to an estimated 1–2% decrease in the prevalence of baldness.