Our love of carbs may date back to the Neanderthals 

If you’ve ever found it challenging to cut back on carbs, ancient DNA might offer an explanation. 

New research reveals that humans have carried multiple copies of a gene responsible for breaking down starch, allowing us to efficiently digest foods that are high in carbs like bread and pasta. 

This genetic adaptation dates back far longer than previously thought, suggesting that our capacity to process starchy foods was an essential part of human evolution.

Modern human diets and carbs 

A study led by scientists from the University of Buffalo (UB) and The Jackson Laboratory (JAX) sheds new light on how duplications of the salivary amylase gene (AMY1) began over 800,000 years ago, long before the advent of agriculture. 

These early duplications set the stage for the genetic diversity seen today, influencing how effectively modern humans digest starch. 

The study’s findings, published in the journal Science, offer critical insights into our evolutionary history and the role of diet in shaping our genomes.

Key enzyme for starch digestion

The AMY1 gene produces amylase, an enzyme that starts breaking down starch in the mouth. More AMY1 copies mean higher amylase production, which can improve the digestion of starches. 

Study senior author Omer Gokcumen is a professor in the Department of Biological Sciences at UB. 

“The idea is that the more amylase genes you have, the more amylase you can produce and the more starch you can digest effectively,” said Gokcumen. 

Amylase also plays a role in giving bread its characteristic taste as it breaks starch down into sugars.

The research team, including co-author Charles Lee, professor and Robert Alvine Family Endowed Chair at JAX, used advanced genome sequencing techniques, such as optical genome mapping and long-read sequencing, to study the AMY1 gene region in detail. 

Traditional sequencing methods struggled to differentiate between the nearly identical gene copies in this region, but long-read sequencing enabled the researchers to map these variations with greater accuracy.

Genetic diversity of ancient hunter-gatherers 

By analyzing the genomes of 68 ancient humans, including a 45,000-year-old sample from Siberia, the team discovered that pre-agricultural hunter-gatherers already had a wide range of AMY1 copies, typically between four and eight per diploid cell. 

This genetic diversity suggests that early humans in Eurasia were equipped to digest starchy foods well before they began domesticating plants.

The study also revealed that AMY1 gene duplications were present in Neanderthals and Denisovans, indicating that these genetic variations began more than 800,000 years ago, long before the evolutionary split between modern humans and these ancient relatives. 

“This suggests that the AMY1 gene may have first duplicated more than 800,000 years ago, well before humans split from Neanderthals and much further back than previously thought,” said co-author Kwondo Kim, a scientist at the Lee Lab at JAX.

Genetic ripples of variation

The initial duplication of the AMY1 gene served as a starting point for further genetic variation, allowing humans to adapt to diverse diets over time. 

As populations spread across different regions, having flexibility in the number of AMY1 copies provided an evolutionary advantage, especially in environments where starchy foods became more available.

“Following the initial duplication, leading to three AMY1 copies in a cell, the amylase locus became unstable and began creating new variations,” said co-author Charikleia Karageorgiou, a scientist at UB. 

“From three AMY1 copies, you can get all the way up to nine copies, or even go back to one copy per haploid cell.” This variation enabled humans to adapt to different dietary needs as they encountered new food sources.

How farming influenced genetic variation

The shift from a hunter-gatherer lifestyle to farming had a profound impact on the evolution of AMY1 copy numbers. While early humans already possessed multiple AMY1 copies, the rise of agriculture brought a surge in starch consumption, leading to further increases in gene copies.

In particular, the average number of AMY1 copies among European farmers rose significantly over the past 4,000 years as their diets became increasingly starch-rich.

“Individuals with higher AMY1 copy numbers were likely digesting starch more efficiently and having more offspring,” Gokcumen explained. 

“Their lineages ultimately fared better over a long evolutionary timeframe than those with lower copy numbers, propagating the number of the AMY1 copies.” 

This trend mirrors findings from a recent study led by the University of California, Berkeley and published in the journal Nature, which reported that European populations expanded their average AMY1 copy number from four to seven over the last 12,000 years.

Interestingly, this genetic adaptation is not limited to humans. Gokcumen’s earlier research found that domesticated animals like dogs and pigs, which lived alongside humans, also developed higher AMY1 copy numbers compared to their wild counterparts, suggesting a parallel adaptation to starch-heavy diets.

Potential for metabolic health insights

The study’s findings open new avenues for understanding how variations in AMY1 copy numbers may affect metabolic health and glucose metabolism in humans. 

“Given the key role of AMY1 copy number variation in human evolution, this genetic variation presents an exciting opportunity to explore its impact on metabolic health and uncover the mechanisms involved in starch digestion and glucose metabolism,” said lead author Feyza Yilmaz, an associate computational scientist at JAX.

Future research could investigate how different AMY1 levels influence individual responses to high-carb diets, providing critical insights into nutrition and health. 

Understanding the evolutionary timeline of AMY1 gene duplications might also help researchers pinpoint when and how these genetic changes were most beneficial for human populations, shedding light on the interplay between genetics, diet, and adaptation.

A legacy of carbs written in DNA

This groundbreaking study highlights how ancient genetic adaptations continue to shape human biology today. 

By tracing the evolution of the AMY1 gene across thousands of years, researchers have revealed the deep roots of our ability to eat carbs and digest starch, a skill that has been essential for survival across diverse environments and changing lifestyles. 

These insights not only deepen our understanding of human evolution but also pave the way for exploring the connections between ancient DNA, diet, and modern health.

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