For thousands of years, potatoes have been central to life in the Andes. Indigenous Andean communities were the first to domesticate the starch-rich crop, turning it into a dietary staple long before potatoes spread around the world. Now, researchers have found evidence that this ancient reliance on potatoes may also have shaped human evolution.
Indigenous people in Peru today carry more copies of a gene involved in starch digestion than any other known population. A new study co-led by researchers at UCLA and the University at Buffalo suggests that natural selection began favoring Indigenous Andeans with especially high numbers of the salivary amylase gene, known as AMY1, around the same period that potatoes became established in the Andean highlands roughly 6,000 to 10,000 years ago.
The findings were published recently in the journal Nature Communications.
A Genetic Advantage for Digesting Starch
People who carry more copies of AMY1 generally produce greater amounts of the amylase enzyme in their saliva and are believed to process starch more efficiently, according to Abigail Bigham, an associate professor of anthropology at UCLA who studies populations in the Peruvian Andes and the Himalayas of Nepal.
For the study, Bigham and her team of evolutionary anthropologists collected DNA from Peruvian Andean Quechua speakers. They then compared those samples with genomic databases containing thousands of DNA samples from dozens of present-day human populations.
“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 Bigham, whose previous work with co-author Kelsey Jorgensen, then a postdoctoral scholar with Bigham, provided evidence of selection in the starch digestion pathway of Andean peoples. “This new research highlights how the Andes are useful for understanding human evolutionary adaptation to other selective environmental pressures like diet.”
Co-corresponding author Omer Gokcumen, a University at Buffalo professor of biological sciences, has previously shown that the first duplication of AMY1 occurred in humans at least 800,000 years ago. He said the new findings provide unusually strong evidence that natural selection acted on this gene in the Andes after potato cultivation began.
“Biologists have long suspected that different groups of humans have evolved genetic adaptations in response to their diets,” he said, “but there are very few cases where the evidence is this strong.”
How Potato Farming Shaped Andean Evolution
The ancestors of Indigenous Andeans already possessed different numbers of AMY1 copies before settling in the highlands and domesticating potatoes. Some individuals carried relatively few copies, while others carried many.
Once potatoes became an important food source, however, people with higher AMY1 copy numbers appear to have gained an evolutionary advantage.
The researchers estimated that beginning about 10,000 years ago, people with roughly 10 or more copies had a 1.24% survival or reproductive advantage per generation.
“Evolution is chiseling a sculpture, not constructing a building,” Gokcumen said. “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.”
Over many generations, that process produced a striking difference. Indigenous people living in Peru today carry an average of 10 AMY1 copies, approximately two to four more copies than any of the other 83 populations examined in the study.
A Potato Farming Signature in Human DNA
The researchers also compared Indigenous Peruvians with the Maya, an Indigenous population in Mexico that shares evolutionary history with Andean peoples but does not have a tradition of potato farming.
On average, Indigenous Peruvians carried 10 copies of AMY1, compared with six among the Maya.
That difference supported the idea that potato cultivation played an important role, but the researchers had to rule out another major event in Indigenous American history.
Following European contact in the 15th century, Indigenous populations across the Americas declined dramatically because of disease, famine, violence, conflict and the rapid loss of genetic diversity.
The researchers therefore had to determine whether this severe population bottleneck could have reduced the number of people carrying fewer AMY1 copies, creating the appearance of natural selection even if potato consumption was not the cause.
Separating those possibilities was one of the study’s major challenges.
Using state-of-the-art ultra-long DNA sequencing technologies together with newly available comparative datasets, the team found that high AMY1 copy numbers had already become more common in the Andes several thousand years before Europeans arrived.
That timing supports the conclusion that natural selection associated with diet, rather than the later population collapse, was responsible for the genetic pattern seen today.
What Ancient Potatoes Reveal About Human Adaptation
Bigham said the findings could encourage broader research into human populations living at high elevations, where people face challenges that extend beyond low oxygen. Daily life can also involve limited food resources along with intense exposure to cold temperatures and ultraviolet rays.
The research also raises a much broader question about how humans may continue adapting to modern diets. For many people today, foods and cuisines from around the world are more accessible than ever, yet genetic adaptation remains part of the human story.
“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,” she said. “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.”
Other collaborators on the research included researchers from the University of Kansas, Pennsylvania State University, the University of Pennsylvania, the University of Puerto Rico at Cayey, Syracuse University, Cayetano Heredia University in Peru and Bilkent University in Turkey.
The work was supported by the National Science Foundation, National Institutes of Health, and the Leakey Foundation.