Peruvian indigenous have a digestive superpower; researchers think it may be linked to potatoes

Table of Contents

Indigenous people of the Andes were the first to domesticate the potato, making the starch-rich crop a dietary staple for this high-altitude population long before it spread to the rest of the world. Today, their descendants in Peru carry the highest known numbers of a gene involved in starch digestion of any population in the world.

Now, a study co-led by researchers from UCLA and the University at Buffalo has discovered that natural selection began favoring Indigenous Andeans with an unusually high number of salivary amylase genes, or AMY1, during the period when potatoes were first grown in the Andean highlands, roughly 6,000 to 10,000 years ago.

Their findings were published in the journal Nature Communications.

Key takeaways
#

A new study by researchers at UCLA and the University at Buffalo shows that Indigenous Andean populations carry unusually high numbers of a gene involved in starch digestion, an adaptation shaped by natural selection during the transition to high-altitude living and major dietary shifts 6,000–10,000 years ago.
Those with roughly 10 copies or more of salivary amylase genes, or AMY1, had a 1.24% survival or reproductive advantage per generation, the researchers found.
The findings highlight how culture, diet and environment interact to shape human genomes, with implications for understanding metabolism, the microbiome and gene–diet interactions relevant to human health.

People with a high number of AMY1 copies tend to produce more of the amylase enzyme in their saliva and are thought to digest starch more effectively, said Abigail Bigham, an associate professor of anthropology at UCLA who studies populations in the Peruvian Andes and the Himalayas of Nepal.

Bigham and her team of evolutionary anthropologists collected DNA from Peruvian Andean Quechua speakers for the study — data that was then compared with genomic databases containing thousands of DNA samples from dozens of modern 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 post-doctoral 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 whose research showed that the initial duplication of AMY1 occurred in humans at least 800,000 years ago, said the findings clearly demonstrated the role of natural selection 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,” Gokcumen said, “but there are very few cases where the evidence is this strong.”

Evolution is a sculptor, not a builder
#

Ancestors of Indigenous Andeans, the researchers said, already carried copies of AMY1 — some with fewer copies, some with more — before they settled into the highlands and domesticated potatoes. When they began growing potatoes, however, those with higher copy numbers gained an evolutionary advantage.

Starting about 10,000 years ago, those with roughly 10 copies or more had a 1.24% survival or reproductive advantage per generation, the researchers found.

“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.”

The result? Indigenous people living in Peru today carry an average of 10 AMY1 copies, approximately two to four copies more than any of the 83 populations examined in the study.

Indigenous history in the genome: Did contact with Europeans play a role?
#

Indigenous people in Peru were found, on average, to carry more copies of AMY1 — 10 versus 6 — than the Maya, an Indigenous population in Mexico with a shared evolutionary history but without a tradition of potato farming.

While the researchers suspected that Andeans’ higher number of AMY1 copies was related to their history of potato cultivation, they still had to account for the dramatic decline in the Indigenous population of the Americas following contact with Europeans in the 15th century, which resulted in disease, famine, violence, conflict and a rapid loss of genetic diversity in a short period of time.

Was it possible that this population bottleneck — rather than natural selection — could have disproportionately removed individuals with lower AMY1 copy numbers? Disentangling the two factors was a major challenge.

In the end, the use of state-of-the-art ultra-long DNA sequencing technologies, along with newly available comparative datasets, allowed the researchers to demonstrate that high numbers of copies of the gene rose in frequency in the Andes several thousand years before Europeans appeared on the scene.

What does it mean now that we all eat French fries?
#

The study, Bigham said, opens the door to wider research into the lives of people who live at high altitudes and whose daily realities include access to limited foodstuffs and extreme exposure to cold temperatures and ultraviolet rays.

It also raises questions about how humans will evolve from modern food offerings, particularly as access to both diets and global cuisine has, for many, become commonplace. Genetic adaptation, Bigham said, continues to be a factor.

“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.

Citation
#

The study Rapid adaptive increase of amylase gene copy number in Indigenous Andeans was published in Nature Communications. Authors: Kendra Scheer, Luane J. B. Landau, Kelsey Jorgensen, Charikleia Karageorgiou, Lindsey Siao, Can Alkan, Angelis M. Morales Rivera, Christopher Osborne, Obed A. Garcia, Laurel Pearson, Melisa Kiyamu, María Rivera-Ch, Fabiola León-Velarde, Frank S. Lee, Tom Brutsaert, Abigail W. Bigham & Omer Gokcumen