How starchy foods shaped human genomes

Starchy foods have played a pivotal role in human evolution, influencing not only our diets but also our genetic makeup.

A recent study has revealed that the rise of agriculture – around 12,000 years ago – and the subsequent increase in starchy staples like wheat and grains, significantly impacted the human genome.

Researchers from the United States, Italy, and the United Kingdom found that our ability to digest carbohydrates has significantly evolved over time. This is closely linked to the rise of agriculture and the increase of starchy foods in our diets.

The evolutionary power of starchy foods

The ability to extract energy from starchy foods has increased remarkably during this period, as shown by an expansion in the number of genes encoding enzymes that break down starch – jumping from an average of eight to over 11.

“The copy number of amylase genes had increased in Europeans since the dawn of agriculture, but we had never been able to sequence this locus fully before. It is extremely repetitive and complex,” said Peter Sudmant, assistant professor of integrative biology at the University of California, Berkeley, and one of the lead authors of the study.

This increase in amylase genes closely matched the rise and spread of agriculture across Europe from the Middle East, aligning with changes in dietary patterns.

Decoding the amylase locus

The researchers meticulously examined the genome’s amylase locus, where the salivary amylase gene (AMY1) and two pancreatic amylase genes (AMY2A and AMY2B) reside.

“If you take a piece of dry pasta and put it in your mouth, eventually it’ll get a little bit sweet. That’s your salivary amylase enzyme breaking the starches down into sugars,” explained Sudmant.

While this happens in all humans and other primates, the human genome contains a significantly higher number of amylase gene copies compared to our primate relatives, such as chimpanzees and Neanderthals, who possess only a single copy of AMY1.

UC Berkeley postdoctoral fellow Runyang Nicolas Lou, one of the study’s co-authors, elaborated: “Our study found that each copy of the human genome harbors one to 11 copies of AMY1, zero to three copies of AMY2A, and one to four copies of AMY2B. Copy number is correlated with gene expression and protein level and thus the ability to digest starch.”

Survival advantage and global adaptation

The presence of multiple amylase genes provided a survival advantage, with the incidence of chromosomes carrying multiple copies increasing sevenfold over the last 12,000 years.

This evolution was not confined to Europe. The researchers found evidence of similar patterns in other agricultural populations globally, regardless of which starchy plant was domesticated.

Erik Garrison, a co-lead author from the University of Tennessee Health Science Center, highlighted the broader implications of the findings: “One of the exciting things we were able to do here is probe both modern and ancient genomes to dissect the history of structural evolution at this locus.”

The dawn of a new method

Another breakthrough in the study was the development of a new method for identifying diseases involving genes with multiple copies, like amylase.

This method also opens doors to exploring rapidly duplicating genes related to the immune system, skin pigmentation, and mucus production.

The research hints at a potential link between higher AMY1 copies and increased tooth decay, though further investigation is needed.

Joana Rocha, a co-author from UC Berkeley, compared the genomic structure of the amylase locus to “sculptures made of different Lego bricks.”

Long-read sequencing techniques allowed the team to reconstruct these complex genetic structures with unprecedented accuracy, shedding light on human evolutionary history and its genetic diversity.

This research, funded by the U.S. National Institutes of Health, is part of an expanding effort to better understand how genetic adaptations have shaped human health and disease through our changing diets over millennia.

Starchy foods and human health

The evolutionary relationship between starchy foods and human genetics continues to shape modern health.

As our ancestors adapted to carbohydrate-rich diets, today’s populations still show varying abilities to digest starch, potentially influencing susceptibility to conditions such as obesity and diabetes.

Understanding this genetic adaptation to starchy foods not only offers insights into our past but also provides valuable information for addressing contemporary health challenges linked to diet and metabolism.

The study is published in the journal Nature.

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