Humans’ Ability To Digest Carbs Predates the Agricultural Revolution

Humans have been primed to enjoy carbohydrate-rich foods for a lot longer than previously thought, according to a new study.

After analyzing and mapping the genomes of 98 participants, researchers from the University of Buffalo found that humans have had multiple copies of the gene that codes for salivary amylase for at least the past 45,000 years.

According to further analysis of 68 ancient genomes, even our Neanderthal cousins seemed to have multiple duplications of this AMY1 gene.

This kind of genetic variation means that the tongues of both hominid species were prepared for a carb-rich diet thousands of years before the agricultural revolution offered such a lifestyle.

The results were published in Science.

Homo carbohydrate

The AMY1 gene codes for salivary amylase, the enzyme that breaks down carbohydrates like starch.

To determine just when in human history modern humans evolved so many copies of the gene, the Buffalo researchers performed optical genome mapping and long-read sequencing on the genomes of 98 participants recruited from distinct genetic populations.

“We studied a diverse group of individuals,” Omer Gokcumen, a professor of evolutionary anthropology at the University of Buffalo, told Technology Networks.

“In fact, the majority of our samples were non-European. This gave us a good snapshot of the ‘common’ variation in the amylase region across different populations.”

To look further back in time, Gokcumen and his colleagues also mapped the AMY1 gene in 68 ancient human genomes and 38 archaic genomes (from other hominids), all sourced from archaeological remains.

They found that pre-agricultural hunter-gatherers already had an average of four to eight AMY1 copies per cell. This suggests that many humans and other hominids already had the ability to consume carbohydrates more than 800,000 years ago, well before the domestication of plants like wheat that led to starchy diets.

Indeed, Gokcumen posits that the agricultural revolution may have been the environmental pressure that finally brought this ability to the fore.

“In the case of the AMY1 gene, its duplications happened before the agricultural transition simply by chance,” he explained. “These early duplications made the region genetically unstable, which in turn facilitated further recombination errors and led to additional duplications over time. As a result, humans today have a highly variable AMY1 region with a wide diversity in the number of salivary amylase gene copies.”

“Later, when humans began consuming more starch-rich foods, there was an adaptive pressure to select individuals who had higher AMY1 copy numbers, as they could more effectively process starchy foods.”

According to Gokcumen, individuals with a higher number of AMY1 copies would have been able to digest starch even more efficiently, an ability that, upon the dawn of the agricultural revolution, would have benefited them and their offspring.

The findings correlate with Gokcumen’s previous research, which found that domesticated animals (dogs, pigs) living alongside humans possess more copies of amylase-producing genes than animals not reliant on starch-heavy diets.

For the moment, however, Gokcumen is only applying his agricultural-trigger theory to European human lineages, because, despite drawing on plenty of participants with non-European DNA for the modern-day analysis, the ancient DNA samples used in the study were largely from European sites.

“One caveat is that for the analysis of ancient genomes, we were limited mostly to European samples due to their availability,” he said. “As a result, we could demonstrate an increase in amylase copy number over the last 4,000 years among European farmers. How this recent history – particularly the last 10 to 5 thousand years – differs in other parts of the world, particularly in terms of dietary changes and the impact on amylase gene variation, remains an open and exciting area of study.”

Reference: Yilmaz F, Karageorgiou C, Kim K, et al. Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation. Science. 2024. doi: 10.1126/science.adn0609

Omer Gokcumen, a professor of evolutionary anthropology at the University of Buffalo, was speaking to Leo Bear-McGuinness, Science Writer and Editor at Technology Networks.