Our ancient DNA may have shaped our love for bread, pasta, rice and other carbohydrates. We have long known that our species carries multiple copies of the genes that allow us to break down complex carbohydrates in our mouths. This first step in metabolizing starchy foods is well documented, but it has been more difficult to determine how and when the number of carbohydrate-processing genes increased.
New research indicates that early duplications of the salivary amylase gene (AMY1) may have begun more than 800,000 years ago, long before humans began farming. These duplications opened the door to the large genetic variations that still exist today and help us digest starchy foods. The findings are detailed in a study published Oct. 17 in the journal’s advanced online issue Science.
All in the amylase
Amylase is a digestive enzyme which breaks down starch into glucose that the body can use as fuel. It is produced in the pancreas and salivary glands and also gives bread its flavor.
“The idea is that the more amylase genes you have, the more amylase you can produce and the more starch you can effectively digest,” study co-author and University at Buffalo evolutionary anthropologist Omer Gokcumen. said in a statement.
[Related: How farming helped humans evolve to get more energy from carbs.]
In the studyGokcumen used optical genome mapping and long-read sequencing to determine the AMY1 gene region. Typically, short-read sequencing methods have difficulty accurately distinguishing gene copies in this region because their sequences are nearly identical. Long-read sequencing allowed the team to look at the genes of modern-day humans and get a clearer picture of how AMY1 duplications evolved over time.
They analyzed the genomes of 68 ancient people, including a 45,000-year-old sample from Siberia. They saw that hunter-gatherers already had an average of four to eight AMY1 copies per diploid cell before agriculture. This suggests that early humans in Eurasia already had a wide variety of AMY1 copies long before they started domesticating plants like wheat and increasing starch intake.
The team also found that AMY1 gene duplications occurred in both Neanderthals and Denisovans.
“This suggests that the AMY1 gene first duplicated more than 800,000 years ago, long before humans split from Neanderthals and much further back than previously thought,” said study co-author Kwondo Kim. computational biologist at the Jackson Laboratory for Genomic Medicine. in Connecticut, said in a statement.
According to the teamthese initial duplications in our genomes laid the foundation for large variations in the amylase region. It allowed our species to adapt to major changes in diet, while dramatically increasing starch consumption.
Initiating genetic variation
This initial duplication of AMY1 was like the first domino to fall in a series that created a huge genetic opportunity that would go on to shape our species. As humans spread across warmer and cooler environments with different food sources, flexibility in AMY1 copy numbers allowed them to adapt to new diets, especially diets rich in starch.
“After the initial duplication, which led to three AMY1 copies in a cell, the amylase locus became unstable and began to create new variations,” study co-author and University at Buffalo evolutionary geneticist Charikleia Karageorgiou said in a statement. “From three AMY1 copies you can get up to nine copies, or even go back to one copy per haploid cell.”
The study also shows how agriculture itself influenced AMY1 variation. Early hunter-gatherers had multiple gene copies, but early European farmers saw the average number of AMY1 copies increase over the past 4,000 years. This is probably due to their starchy diets. Previous research showed that domesticated animals that live alongside humans also have higher AMY1 copy numbers compared to animals that are not as dependent on starchy diets.
“Individuals with higher AMY1 copy numbers likely digested starch more efficiently and produced more offspring,” Gokcumen said. “Their descendants ultimately fared better over a long evolutionary period than those with lower copy numbers, propagating AMY1 copy numbers.”
[Related: Scientists build intricate Neolithic family tree from 7,000-year-old DNA.]
These findings are also consistent with a study published in September which showed that humans in Europe have expanded their average number of AMY1 copies from four to seven over the past 12,000 years.
“Given the key role of AMY1 copy number variation in human evolution, this genetic variation provides an exciting opportunity to investigate its impact on metabolic health and uncover the mechanisms involved in starch digestion and glucose metabolism,” studied co-author Jackson Laboratory computational scientist Feyza. Yilmaz said in a statement. “Future research could reveal its precise effects and timing selection, which could provide critical insights into genetics, nutrition and health.”