A recent investigation sheds light on the duplication of the salivary amylase gene, suggesting that this genetic change may have significantly influenced human adaptation to starchy foods as far back as 800,000 years ago, well before farming began.
If you’ve ever found it challenging to cut back on carbs, ancient DNA might hold the key.
It is well-known that humans possess several copies of a gene that enables the initial breakdown of complex carbohydrate starch in the mouth, which is crucial for digesting starchy foods such as bread and pasta. However, pinpointing when and how the number of these genes increased has been a complex task for researchers.
A groundbreaking study led by the University at Buffalo and the Jackson Laboratory (JAX) uncovers that the duplication of the salivary amylase gene (AMY1) not only facilitated human adaptation to starchy diets but also likely began more than 800,000 years ago, predating agriculture.
Published in the advanced online edition of Science on October 17, the research illustrates how early duplications of the AMY1 gene contributed to the genetic diversity we see today, which affects our ability to digest starches efficiently.
According to Omer Gokcumen, PhD, the study’s lead author and a professor in the Department of Biological Sciences at UB, “The more amylase genes you have, the greater the amount of amylase you can produce, enhancing your ability to digest starch.”
Amylase is an enzyme that decomposes starch into glucose and also contributes to the flavor of bread.
Gokcumen and his research team, including co-senior author Charles Lee from JAX, employed advanced techniques such as optical genome mapping and long-read sequencing to explore the AMY1 gene region in remarkable detail. Traditional short-read sequencing often fails to differentiate between similar gene copies, but long-read sequencing allowed them to effectively map out how AMY1 duplications evolved in contemporary humans.
Ancient hunter-gatherers and Neanderthals already had multiple AMY1 copies
By examining the genomes of 68 ancient humans, including a 45,000-year-old sample from Siberia, the researchers discovered that pre-agricultural hunter-gatherers possessed an average of four to eight AMY1 copies in their diploid cells. This indicates that humans roamed Eurasia with a wide range of high AMY1 counts long before they began cultivating plants and consuming large amounts of starch.
Additionally, the study highlighted the presence of AMY1 gene duplications in Neanderthals and Denisovans.
Kwondo Kim, a lead author from the Lee Lab at JAX, stated, “This indicates that the initial duplication of the AMY1 gene likely happened over 800,000 years ago, predating the separation of humans and Neanderthals and further back than previously assumed.”
Gokcumen emphasized that “the early duplications in our genomes set the stage for significant genetic diversity in the amylase region, enabling humans to adjust to changing diets as starch consumption increased with new technologies and lifestyles.”
The seeds of genetic variation
The original duplication of AMY1 acted like a ripple effect, creating genetic opportunities that later influenced human evolution. As humans spread across various environments, the variability in AMY1 copies provided an edge for adapting to diets, especially those high in starch.
Charikleia Karageorgiou, another lead author from UB, noted, “After the initial duplication, which resulted in three AMY1 copies, the amylase region became unstable and began generating new variations. From three copies, the number could expand to nine or even revert to one per haploid cell.”
The complicated legacy of farming
This research also explores how the rise of agriculture influenced AMY1 variation. While early hunter-gatherers had several gene copies, European farmers experienced an increase in average AMY1 copies over the past 4,000 years, likely due to a starch-rich diet. Previous studies by Gokcumen revealed that domesticated animals such as dogs and pigs also have more amylase gene copies compared to those not on starch-heavy diets.
Gokcumen commented, “Individuals with a higher number of AMY1 copies probably digested starch more effectively and produced more offspring. Consequently, their lineages thrived over the long term compared to those with fewer copies, leading to an increase in the frequency of AMY1 copies.”
The findings align with a study led by the University of California, Berkeley, published last month in Nature, which showed that the average number of AMY1 copies in humans in Europe expanded from four to seven over the last 12,000 years.
Feyza Yilmaz, an associate computational scientist at JAX and a lead author, expressed, “Considering the crucial role of AMY1 copy number variation in human evolution, this genetic diversity provides an exciting chance to investigate its impact on metabolic health and to unveil the mechanisms behind starch digestion and glucose processing.” She added, “Future studies could clarify how and when this selection occurred, offering valuable insights into genetics, diet, and health.”
Other UB contributors to this research include PhD students Petar Pajic and Kendra Scheer.
This study was a collaboration with the University of Connecticut Health Center and received support from the National Science Foundation and the National Human Genome Research Institute, part of the National Institutes of Health.
