Changes in Ancient DNA Led to Human Craving for Carbohydrates

Genes passed down from the incredibly distant past play a key role in the ability of human beings to break down and process carbohydrates. But archaic human species didn’t all possess this ability, and that is why genetic scientists have long been curious about the changes in ancient DNA that helped us develop the capacity to digest these energy-producing starches.

Now, a new study from the University of Buffalo and the Jackson Laboratory for Genomic Medicine has revealed some fascinating information that sheds light on this development, relating to events that happened more than 800,000 years ago. It was at this time that a gene essential for producing starch-digesting saliva was duplicated for the first time, within the genome of an archaic human ancestor. This was a critically important first step on the pathway of genetic change that turned us into the carbohydrate-loving creatures that we are today.

A Revolution in Starch Break Down

Modern humans carry multiple copies of this gene, which is known as the salivary amylase gene (AMY1). Without its presence, we wouldn’t be able to break down complex carbohydrates at the point where we begin chewing. This is a vital and indispensable step that allows us to metabolize foods loaded with starches, including staples of the human diet like rice, pasta, and bread.

"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 the study's corresponding author, Dr. Omer Gokcumen, a University of Buffalo professor in the Department of Biological Sciences, in a Jackson Laboratory press release.

Amylase is an enzyme that breaks starch down into glucose, and among other things this process that gives carbohydrate-laden foods their delicious taste.

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A graphical representation of the amylase gene locus and how it evolved to influence how humans digest complex carbohydrates like bread and pasta. (The Jackson Laboratory)

Tracing the proliferation of this gene back to its historical roots has proven to be extraordinarily difficult for researchers. But breakthroughs in genetic technology offer new possibilities to solve ancient mysteries related to evolution and changes in ancient DNA, as the new study completed by the University of Buffalo and Jackson Laboratory researchers clearly shows.

This distinguished team of genetic experts used optical genome mapping and long-read sequencing to analyze the region of the human genome where the vital salivary amylase gene (AMY1) is located. The usual method of short-read sequencing makes it incredibly difficult to distinguish between the gene copies in this region, since it only detects the DNA sequences that the various copies share. But long-read sequencing reveals far more precise genetic detail, allowing scientists to not only differentiate between specific AMY1 duplications, but to calculate when the duplication process created the various copies.

As the researchers explain in a new article just published in the journal Science, their findings suggest the earliest proliferation of the AMY1 gene occurred more than 800,000 years ago.

They analyzed the genomes of 68 ancient humans, including a 45,000-year-old genome recovered from human remains discovered in Siberia. These studies showed that ancient hunter-gatherers already had between four and eight AMY1 copies per cell, meaning the process of proliferation must have begun long before the agricultural revolution that made it possible to grow, harvest, and/or produce significant quantities of high-carbohydrate foods. Interestingly, AMY1 duplications were also found in genomes recovered from the skeletal remains of Neanderthals and Denisovans, which dated back a bit farther the human skeletal samples.

“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,” Jackson Laboratory geneticist and study co-author Kwondo Kim stated, highlighting the paradigm-changing nature of his team’s discoveries.

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Ancient DNA Duplication as a Driver of Evolution

Once the initial duplications occurred, more duplications were inevitable, the scientists say.

“The initial duplications in our genomes laid the groundwork for significant variation in the amylase region, allowing humans to adapt to shifting diets as starch consumption rose dramatically with the advent of new technologies and lifestyles,” Dr. Gokcumen said.

In other words, the capacity for duplication in this gene provided an evolutionary advantage, after the invention of agriculture made it possible to grow starchy crops in abundance and on an annual basis. In fact, the researchers found that European farmers have experienced a significant increase in the average number of AMY1 copies found in their genomes over the past 4,000 years, as would be expected under such circumstances.

Sprawling wheat field ready to be harvested near the end of summer (Holly Victoria Norval/CC BY 2.0)

"Individuals with higher AMY1 copy numbers were likely digesting starch more efficiently and having more offspring,” Dr. 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."

Other studies examining changes in ancient DNA have produced results consistent with the latest findings.

For example, a study at the University of California-Berkeley published earlier this year in Nature found that the average number of AMY1 copies in the genomes of Europeans had increased from four to seven over the past 12,000 years. Meanwhile, previous research carried out by Dr. Gokcumen revealed that domesticated animals that consume a lot of starches also have higher numbers of AMY1 copies than non-starch-consuming animals. This is yet more evidence that links farming and the increased consumption of carbohydrates with rampant AMY1 duplication.

Top image: Leavened wheat bread, consumed since the time of Ancient Egypt and Babylon   Source: Scott Bauer/U.S. Department of Agriculture/CC BY 2.0

By Nathan Falde