Our bodies absolutely need carbohydrates for energy. It’s a matter of survival. So much so, that some human populations have actually increased the number of genes that help break down starches and sugars over the past 12,000 years. In that time, Europeans have gone from an average of eight starch breaking down genes to over 11.
The adaptation tracks a shift from a hunter-gatherer lifestyle to a more agrarian one, as agriculture spread across Europe from the Middle East. High-carbohydrate staples like wheat dramatically increased in the human diet and the ability to efficiently absorb all of that energy was advantageous. The findings are detailed in a study published September 4 in the journal Nature.
Focus on the ‘amylase locus’
Some of the roughly 19,900 known genes in the human genome can create the specific proteins that a gene codes for called enzymes. Enzymes have a variety of functions and amylase is the one that helps the body break down carbohydrates. Amylase is produced in the saliva and the pancreas to digest the starch into sugar that fuels the body.
“If you take a piece of dry pasta and put it in your mouth, eventually it’ll get a little bit sweet,” study co-author and University of California, Berkeley, biologist Peter Sudmant said in a statement. “That’s your salivary amylase enzyme breaking the starches down into sugars. That happens in all humans, as well as in other primates.”
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Having more copies of a gene typically means that an organism has higher levels of the proteins that the genes code for specific enzymes. Bonobo, chimpanzee, and Neanderthal genomes have one copy of the gene AMY1. This gene on chromosome 1 codes for the salivary amylase. Their genomes also have one copy of the two pancreatic amylase genes, AMY2A and AMY2B. All three of these genes are located near one another in a region of the primate genome scientists call the amylase locus. However, human genomes are a little different.
“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,” study co-author and UC Berkeley postdoctoral fellow Runyang Nicolas Lou said in a statement. “Copy number is correlated with gene expression and protein level and thus the ability to digest starch.”
With genetic analysis, the team found that about 12,000 years ago, humans across Europe had an average of four copies of the salivary amylase gene. Over time, that number has increased to about seven. The combined number of copies of the two pancreatic amylase genes also increased by half a gene on average. This increase in carb genes suggests that there must be a powerful survival advantage in having chromosomes with multiple copies of amylase genes.
Lifestyle shifts
Importantly, the team also found evidence of an increase in amylase genes in other agricultural populations around the world. The region of the chromosomes where these amylase genes are located also looks similar in all of these populations, no matter what starchy plant was domesticated in that culture.
According to the team, this demonstrates that as agriculture arose in populations around the world, it appears to have rapidly changed the human genome in incredibly similar ways to use this increased access to carbohydrates to our advantage. The rate of evolution leading to changes in amylase gene copy number was about 10,000 times faster than that of single DNA base pair changes in the human genome.
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“It has long been hypothesized that 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,” Sudmant said. “Now, we’re finally able to fully capture these structurally complex regions, and with that, investigate the history of selection of the region, the timing of evolution and the diversity across worldwide populations. Now, we can start thinking about associations with human disease.”
One of these suspected associations is with tooth decay. Some earlier research suggests that having more copies of AMY1 is associated with more cavities. This might be because the saliva does a better job of converting starch in chewed food into sugar, which feeds the bacteria that eat teeth.
Long-read sequencing
The study also took advantage of a genetic sequencing process called long-read sequencing. This allows scientists to read DNA sequences thousands of base pairs long to accurately capture where repetitive stretches are located.
At the time of the study, the Human Pangenome Reference Consortium (HPRC) had collected long-read sequences of 94 human haploid genomes. The team used these genomes to assess the variety of contemporary amylase regions. They then assessed that same region in 519 ancient European genomes. Using the genomes from the HPRC–called a pangenome–gave a more inclusive reference that more accurately captures human diversity.
Joana Rocha, a study co-author and UC Berkeley postdoctoral fellow, compared the region where amylase genes cluster to, “sculptures made of different Lego bricks.Those are the haplotype structures. Previous work had to take down the sculpture first and infer from a pile of bricks what the sculpture may have looked like. Long-read sequencing and pangenomic methods now allow us to directly examine the sculpture and thus offer us unprecedented power to study the evolutionary history and selective impact of different haplotype structures.”
[Related: The final missing piece of the human genome has been decoded.]
Scientists can use long-read sequencing to explore other areas of the genome, including those involved in our immune systems, skin pigmentation, and the production of mucus. These spots have all undergone rapid gene duplication in recent human history.
“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,” study co-author and University of Tennessee Health Science Center computational biologist Erik Garrison said in a statement.
These methods can also be applied to other species, particularly those that are often around humans. Dogs, pigs, rats, and mice all have more copies of the amylase gene than their more wild relatives, likely to take advantage of our table scraps and trash.