How Potato Farming Shaped AMY1 Genes in the Peruvian Andes

High in the Peruvian Andes, the earliest farmers made a straightforward decision: they dug up wild potatoes and replanted them.

That change transformed what they ate each day, while also altering their biology in ways they could not have recognised.

New research indicates that the choice produced an enduring imprint in human DNA. Scientists have identified a pronounced genetic signature among Indigenous Andean populations.

The pattern is directly associated with the emergence of potato farming roughly 10,000 years ago.

Potatoes influenced digestion in the Andes

At the centre of the story is a gene known as AMY1. It regulates the production of salivary amylase, an enzyme that starts breaking down starch as soon as food reaches the mouth.

The number of AMY1 copies people possess varies considerably. While some individuals have only a small number, others have many. This variation influences how effectively the body starts to digest starchy foods, including potatoes and rice.

Those carrying more AMY1 copies produce more amylase, giving them an initial advantage when processing starch.

A population favoured by natural selection

The researchers examined thousands of people from around the globe, and one population stood well above all others.

Indigenous Peruvian Andeans had a median of ten AMY1 copies, compared with a worldwide average of about seven. Certain people in the Andes possessed as many as 20 copies.

This was not a broad trend found across every Indigenous American population. Instead, it was especially pronounced in particular Andean groups.

Scientists initially considered more straightforward explanations. They assessed ancestry patterns to exclude external influence, but the findings remained unchanged.

They also investigated whether random genetic drift might account for the pattern. Simulations demonstrated that chance by itself could not generate copy numbers this high.

The evidence instead indicated one distinct driver: natural selection.

Genetic adaptation to diet

Natural selection acting on a gene produces recognisable signals in the surrounding DNA, and the team detected these signals near the amylase region.

They also found a particular genetic variant associated with the increase. This variant spread rapidly among Andean populations.

The signal is as powerful as some of the most widely recognised examples of human adaptation.

Study co-author Omer Gokcumen is a professor of biological sciences at the University at Buffalo.

“Biologists have long suspected that different groups of humans have evolved genetic adaptations in response to their diets,” said Gokcumen.

“But there are very few cases where the evidence is this strong.”

The timeline of the genetic change

The chronology makes the finding still more striking: the genetic shift started around 10,000 years ago.

That coincides with the first domestication of potatoes in the Andes. Once potatoes became a staple, people with higher numbers of AMY1 copies had a modest advantage.

Across many generations, that benefit accumulated, increasing the number of gene copies throughout the population.

Evolution in action

This was a slow process rather than a single event. Minor differences in survival and reproduction gradually accumulated.

“Evolution is chiseling a sculpture, not constructing a building,” said Gokcumen. “It’s not as if Indigenous Andeans gained additional AMY1 copies once they started eating potatoes.

“Instead, those with lower copy numbers were eliminated from the population over time, perhaps because they had fewer offspring, and the ones with the higher copy numbers remained.”

AMY1 lies within a complicated DNA region containing repeated sections. These sections can become misaligned during cell division.

The process may produce additional copies of the gene, or it can remove copies. Among Andean populations, the balance moved towards acquiring more copies.

Advanced sequencing techniques verified that this established mechanism is responsible for the high copy numbers observed today.

Effects on the body

A greater number of AMY1 copies results in more amylase in saliva, accelerating the breakdown of starch in the mouth.

The alteration could also influence the microbiome. As different sugars become available to bacteria, microbial communities may change.

The health consequences are still uncertain. Research has found no strong association with body weight, although some evidence points to quicker spikes in blood sugar after consuming starch.

There may be disadvantages as well. Greater amylase activity in the mouth could raise the risk of tooth decay. Dental problems are highly common among children in parts of Peru.

Potato-related genes in the Andes

Starchy foods are central to many cultures, yet this pronounced genetic pattern is seen mainly in the Andes.

Researchers offer several possible explanations. Potatoes are a key component of the Andean diet and often provide a substantial proportion of daily calories.

Conditions at high altitude could be another factor. Living in these settings places particular demands on the body.

Other genes connected with starch in Andean populations also display evidence of selection, suggesting a wider dietary adaptation.

“The high-altitude Andes are known for being a rich region for understanding human evolutionary adaptation, for instance, hypoxia, in which tissues do not get enough oxygen,” said Abigail W. Bigham, co-author of the study.

“This new research highlights how the Andes are useful for understanding human evolutionary adaptation to other selective environmental pressures like diet.”

A wider lesson

The research extends beyond a single gene, showing that human populations can adapt rapidly when new food sources emerge.

It also questions oversimplified views of diet and evolution. Human biology is not frozen in the past; it continues to shift alongside culture and the environment.

“There are ideas out there like the paleo diet, which is adapted to the Paleolithic environment and says we’re not suited to eat foods that come post-domestication,” said Bigham.

“But I think this research shows that human populations have responded and evolved to changing food conditions within the last 10,000 years. Our metabolic pathways are not simply a product of that Paleolithic past.”

The Andean case provides a clear example of recent human evolution. A change in diet produced a measurable genetic shift, and that change persists today.

Each mouthful of starch starts to break down in the mouth. In the Andes, however, the process holds a deeper past, reflecting generations of adaptation linked to one crop.

A decision about farming ultimately became a biological signature.