Our love of carbohydrates may date back to Neanderthals

If you’ve ever had a hard time cutting your carbs, ancient DNA might provide an explanation.

New research shows that humans carry multiple copies of a gene responsible for breaking down starch, allowing us to efficiently digest carbohydrate-rich foods like bread and pasta.

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

Modern human nutrition and carbohydrates

A study conducted by scientists at the University at Buffalo (UB) and 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 laid the foundation for today’s genetic diversity and influenced how effectively modern humans digest starch.

The results of the study, published in the journal Scienceprovide important insights into our evolutionary history and the role of nutrition in shaping our genomes.

Key enzyme for starch digestion

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

The study’s lead 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,” Gokcumen said.

Amylase also helps give bread its distinctive flavor by breaking down starch into sugar.

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 examine the AMY1 gene region in detail.

Traditional sequencing methods had difficulty distinguishing between the nearly identical gene copies in this region, but long-read sequencing allowed researchers to map these variations with greater precision.

Genetic diversity of ancient hunters and gatherers

By analyzing the genomes of 68 ancient humans, including a 45,000-year-old sample from Siberia, the team discovered that pre-agriculture 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 able to digest starchy foods long before the domestication of plants.

The study also found that AMY1 gene duplications were present in Neanderthals and Denisovans, suggesting 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, long before humans separated from Neanderthals, and much further back than previously thought,” said co-author Kwondo Kim, scientist at the Lee Lab at JAX.

Genetic waves of variation

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

As populations spread across different regions, flexibility in AMY1 copy numbers represented an evolutionary advantage, particularly in environments where starchy foods were more available.

“After the initial amplification, which resulted in three AMY1 copies in a cell, the amylase locus became unstable and began to generate new variations,” said co-author Charikleia Karageorgiou, a scientist at UB.

“From three AMY1 copies, you can get up to nine copies, or even go down to one copy per haploid cell.” This variation allowed people to adapt to different nutritional needs as they encountered new food sources.

How agriculture influenced genetic variation

The shift from hunter-gatherer lifestyle to agriculture had a profound impact on the evolution of AMY1 copy numbers. While early humans already had multiple AMY1 copies, the rise of agriculture led to an increase in starch consumption, which led to a further increase in gene copies.

In particular, the average number of AMY1 copies among European farmers increased significantly over the last 4,000 years as their diets became increasingly starchy.

“Individuals with higher AMY1 copy numbers likely digested starch more efficiently and had more offspring,” Gokcumen explained.

“Their lineages ultimately performed better than those with lower copy numbers over a long evolutionary period, spreading the AMY1 copy number.”

This trend reflects the results of a recent study conducted by the University of California, Berkeley and published in the journal Naturewho reported that the average AMY1 copy number of the European population increased from four to seven over the last 12,000 years.

Interestingly, this genetic adaptation is not limited to humans. Gokcumen’s previous research found that domesticated animals such as dogs and pigs that lived alongside humans also evolved higher AMY1 copy numbers compared to their wild counterparts, suggesting a parallel adaptation to high-starch diets.

The study’s results open new avenues for understanding how variations in AMY1 copy number may impact metabolic health and glucose metabolism in humans.

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

Future research could examine how different AMY1 levels influence individual responses to high-carbohydrate diets and provide important insights into nutrition and health.

Understanding the evolutionary timing of AMY1 gene duplications could also help researchers determine exactly when and how these genetic changes were most beneficial to human populations, shedding light on the interplay between genetics, nutrition and adaptation.

A heritage of carbohydrates embedded in the DNA

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

By tracing the evolution of the AMY1 gene over millennia, researchers have uncovered the deep roots of our ability to eat carbohydrates and digest starches – an ability that has been essential for survival in different environments and changing lifestyles.

These findings not only deepen our understanding of human evolution, but also pave the way for research into the connections between ancient DNA, nutrition and modern health.

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