Over the past 12,000 years, people in Europe have dramatically increased their ability to digest carbohydrates, expanding the number of genes they have for enzymes that break down starch from an average of eight to more than 11, according to a new study by US researchers, Italy and Great Britain.
The increase in the number of genes encoding these enzymes follows the spread of agriculture across Europe from the Middle East, and with it an increasingly starchy human diet rich in carbohydrate staples such as wheat and other grains. Having more copies of a gene usually translates into higher levels of the protein the genes code for – in this case the enzyme amylase, which is produced in saliva and the pancreas to break down starches into sugar to fuel the body. provided.
The study, published today (September 4) in the journal Naturealso provides a new method for identifying the causes of diseases involving genes with multiple copies in the human genome, such as the genes for amylase.
The research was led by Peter Sudmant, assistant professor of integrative biology at the University of California, Berkeley, and Erik Garrison of the University of Tennessee Health Science Center in Memphis.
“If you put a piece of dry pasta in your mouth, it ends up being a little sweet,” Sudmant said. “That is your salivary amylase enzyme that breaks down starch into sugars. This happens in all humans, but also in other primates.”
The genomes of chimpanzees, bonobos and Neanderthals all have one copy of the gene on chromosome 1 that codes for the salivary amylase, also called AMY1. The same applies to the two pancreatic amylase genes, AMY2A and AMY2B. These three genes are located close together in a region of the primate genome known as the amylase locus.
However, human genomes harbor vastly different numbers of each amylase gene.
“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,” said UC Berkeley postdoctoral fellow Runyang Nicolas Lou, one of the five first authors of the book. the paper. “Copy number is correlated with gene expression and protein level and therefore with the ability to digest starch.”
The researchers found that while people across Europe had an average of about four copies of the salivary amylase gene about 12,000 years ago, that number has increased to about seven. The combined copy number of the two pancreatic amylase genes also increased by half a gene (0.5) on average in Europe during this period.
Survival benefit of multiple amylase genes
Overall, the incidence of chromosomes with multiple copies of amylase genes (that is, more total copies than chimpanzees and Neanderthals) has increased sevenfold over the past 12,000 years, suggesting that this provided a survival advantage for our ancestors.
The researchers also found evidence for an increase in amylase genes in other agricultural populations around the world, and that the region of the chromosomes where these amylase genes are located appears to be the same in all these populations, regardless of which specific starchy plant that culture domesticated. The findings show that as agriculture emerged independently around the world, the human genome appears to have rapidly changed in nearly identical ways in different populations to cope with increased dietary carbohydrates.
In fact, the researchers found that the rate of evolution leading to changes in amylase gene copy number was 10,000 times faster than that of changes in individual DNA base pairs in the human genome.
“It has long been hypothesized that the number of copies of amylase genes has increased in Europeans since the dawn of agriculture, but we had never before been able to fully sequence this locus. It is extremely repetitive and complex,” Sudmant said. “Now we are finally able to fully map these structurally complex regions, exploring the history of region selection, the timing of evolution, and diversity among global populations. Now we can start thinking about associations with human disease.”
A suspected link is with tooth decay. Previous studies have suggested that having more copies of AMY1 is associated with more cavities, perhaps because saliva does a better job of converting starch in chewed food into sugar, which feeds bacteria that eat away at teeth.
The research also provides a method for exploring other parts of the genome — for example, those involving the immune system, skin pigmentation and mucus production — that have undergone rapid gene duplication in recent human history, Garrison said.
“One of the exciting things we’ve been able to do here is examine both modern and ancient genomes to parse the history of structural evolution at this site,” he said.
These methods can also be applied to other species. Previous studies have shown that animals that hang out near people – dogs, pigs, rats and mice – have more copies of the amylase gene than their wilder relatives, apparently to benefit from the food we throw away.
“This is really the limit in my opinion,” Garrison said. “We can for the first time look at all these regions that we could never look at before, and not just in humans – in other species too. Human disease research has really struggled to identify associations at complex loci, such as amylase. Because the mutation rate is so high, traditional association methods can fail. We are very excited about how far we can push our new methods to identify new genetic causes of diseases.
From hunter-gatherer to agricultural
Scientists have long suspected that humans’ ability to digest starch increased after our ancestors shifted from a hunter-gatherer lifestyle to a settled, agricultural lifestyle. This shift was shown to be associated with more copies of the amylase genes in people from societies that domesticated plants.
But the region of the human genome where these copies are located is difficult to study because traditional sequencing – so-called short-read sequencing techniques that cut the genome into pieces of about 100 base pairs, sequence the millions of pieces and then put them back together in a genome – was unable to distinguish gene copies from each other. Complicating matters further is that some copies are reversed, that is, they are flipped over and read from the opposite strand of DNA.
Long-term sequencing allows scientists to resolve this region, reading DNA sequences thousands of base pairs long to accurately capture repetitive stretches. At the time of the study, the Human Pangenome Reference Consortium (HPRC) had collected long-read sequences from 94 human haploid genomes, which Sudmant and colleagues used to assess the diversity of contemporary amylase regions, called haplotypes. The team then assessed the same region in 519 ancient European genomes. The HPRC data helped avoid a common bias in comparative genomic studies using a single, averaged human genome as a reference. The HPRC genomes, also called a pangenome, provide a more inclusive reference that more accurately captures human diversity.
Joana Rocha, a postdoctoral researcher at UC Berkeley and co-first author of the paper, compared the area where amylase genes cluster to what she called “sculptures made from different Lego bricks.” Those are the haplotype structures. Previous work had to knock down the sculpture. first and deduce from a pile of stones what the sculpture may have looked like. Long-term sequencing and pangenomic methods now allow us to directly examine the sculpture and thus provide us with unprecedented power to study the evolutionary history and selective impact of different haplotype structures. “
Using specially developed mathematical models, the researchers identified 28 distinct haplotype structures among 94 long-read genomes and thousands of realigned short-read human genomes, all of which are clustered into 11 groups, each with a unique combination of AMY1, AMY2A and AMY2B copies. figures.
“These remarkably complex, crazy structures — regions of gene duplication, inversion and deletion in the human genome — have evolved independently over and over again in different human populations, even before the rise of agriculture,” Sudmant said.
Analysis of the many contemporary human genomes also pointed to an origin 280,000 years ago of an initial duplication event that added two copies of AMY1 to the human genome.
“That particular structure, which is prone to high mutation rates, arose 280,000 years ago and paved the way for later, when we developed agriculture, for people to have more copies to have better fitness, and then for selection of these copy numbers,” Sudmant said. “Using our methods, we were able to truly date the first duplication event for the first time.”
Alma Halgren, a bioengineering graduate from UC Berkeley, and Davide Bolognini and Alessandro Raveane of Human Technopole in Milan, Italy, are also first authors of the paper. Other co-authors include Andrea Guarracino of UTHSC, Nicole Soranzo of Human Technopole and the University of Cambridge in the United Kingdom, and Jason Chin of the Foundation for Biological Data Science in Belmont, California. Sudmant’s research is funded by the Institute of General Medical Sciences of the US National Institutes of Health (R35GM142916).
