If you’ve ever struggled with cutting back on carbs, ancient DNA might hold some answers.
A recent study from the University at Buffalo and the Jackson Laboratory (JAX) uncovers how the salivary amylase gene (AMY1) evolved, aiding human adaptation to starchy foods and potentially dating back over 800,000 years—long before agriculture began.
Researchers have known that humans possess multiple copies of the AMY1 gene, which plays a crucial role in breaking down complex carbohydrates like those found in bread and pasta. However, determining the timing and reasons behind the gene’s duplication has been challenging. This study provides significant insights into the genetic evolution of AMY1.
Understanding the Amylase Advantage
“The idea is that the more amylase genes you have, the more amylase you can produce, and the more starch you can digest effectively,” explains Omer Gokcumen, PhD, a professor in the Department of Biological Sciences at the University at Buffalo. Amylase, an enzyme produced by the AMY1 gene, is essential for breaking down starch into glucose and contributes to the flavor of bread.
Using advanced techniques like optical genome mapping and long-read sequencing, the researchers mapped the AMY1 gene region in unprecedented detail. Traditional sequencing methods struggled to differentiate between the nearly identical gene copies, but the new methods provided clarity on AMY1 evolution.
Insights from Ancient Genomes
By analyzing the genomes of 68 ancient humans, including a 45,000-year-old specimen from Siberia, the team discovered that pre-agricultural hunter-gatherers had an average of four to eight AMY1 copies per diploid cell. This suggests that variations in AMY1 gene copies existed long before humans began domesticating plants and consuming large amounts of starch.
Interestingly, AMY1 duplications were also found in Neanderthals and Denisovans. “This suggests that the AMY1 gene may have first duplicated more than 800,000 years ago, well before humans split from Neanderthals,” says Kwondo Kim, a lead author of the study from the Lee Lab at JAX.
Genetic Variation and Dietary Adaptation
The study emphasizes how initial duplications of AMY1 created a foundation for significant genetic variation. As humans migrated across diverse environments, having different numbers of AMY1 copies provided advantages for adapting to varying diets, particularly those rich in starch.
“Following the initial duplication, leading to three AMY1 copies in a cell, the amylase locus became unstable and began creating new variations,” notes Charikleia Karageorgiou, another lead author at UB. This variability allowed for copy numbers to fluctuate significantly, from three to as many as nine copies or even down to one.
The Impact of Agriculture on AMY1 Variation
The research also explores how agriculture influenced AMY1 variation. Although early hunter-gatherers had multiple gene copies, European farmers experienced a marked increase in AMY1 copies over the last 4,000 years, likely due to their starch-rich diets. Gokcumen’s previous work indicated that domesticated animals living alongside humans also exhibit higher AMY1 gene copy numbers.
“Individuals with higher AMY1 copy numbers were likely digesting starch more efficiently and having more offspring,” Gokcumen explains. As a result, lineages with higher AMY1 copies thrived over generations, enhancing the prevalence of this gene.
Future Directions for Research
The findings align with a recent study led by the University of California, Berkeley, which reported that Europeans expanded their average AMY1 copy number from four to seven over the last 12,000 years. “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,” says Feyza Yilmaz, an associate computational scientist at JAX and a lead author of the study.
The research, supported by the National Science Foundation and the National Human Genome Research Institute, highlights the importance of AMY1 in understanding human adaptation and health. Future studies may reveal the precise effects and timing of selection, providing valuable insights into genetics, nutrition, and metabolic health.
