How Agriculture Shaped the Human Genome for Starch Digestion
How Agriculture Shaped the Human Genome for Starch Digestion
The Genetic Impact of Agriculture on Human Evolution
Over the last 12,000 years, a pivotal shift occurred in the human genome, driven by the advent of agriculture and the shift to a carbohydrate-rich diet. A new study conducted by an international research team, including scientists from the University of California, Berkeley, and the University of Tennessee Health Science Center, has revealed that humans have dramatically increased their capacity to digest starches, marking a significant moment in human evolution. This research sheds light on how the rise of agriculture accelerated the evolution of genes associated with energy extraction from starchy foods.
The study, published in Nature1, focuses on a set of genes responsible for producing amylase, an enzyme that plays a crucial role in breaking down starch into sugars. This process allowed early humans to extract more energy from crops like wheat and grains, which became staples in post-agricultural societies. By analyzing both ancient and modern genomes, the research demonstrates that the number of genes coding for amylase has increased significantly in human populations since the dawn of agriculture, highlighting the transformative impact of this dietary shift on human evolution.
Genetic Evidence of Human Adaptation to Starchy Diets
The research team found that the number of copies of amylase genes in human genomes has risen from an average of eight in ancient populations to over 11 in contemporary humans. This increase, which occurred over the past 12,000 years, reflects the adaptation to an agriculture-based diet rich in carbohydrates. The gene responsible for amylase production, AMY1, saw the most significant increase in copy number, particularly in European populations where agriculture first took root.
According to the study’s co-author, UC Berkeley postdoctoral researcher Runyang Nicolas Lou,
"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."
This remarkable increase in the number of amylase genes aligns with the spread of agricultural practices across Europe and beyond. As human societies shifted from hunting and gathering to farming, the need for greater energy extraction from starchy foods became more pronounced, favoring individuals with more copies of the amylase genes. This evolutionary process, known as gene copy number variation, allowed early farmers to thrive on diets heavily reliant on cultivated crops.
The Role of Agriculture in Driving Genetic Evolution
The spread of agriculture brought with it a significant evolutionary pressure on humans to adapt to new diets. As crops like wheat, barley, and rice became primary food sources, individuals with more copies of the amylase gene were able to break down starch more efficiently, gaining a survival advantage. The rapid evolution of these genes underscores the strong selection pressure exerted by the shift to an agrarian lifestyle.
The study's findings suggest that this increase in amylase genes occurred much faster than other genetic changes in the human genome. In fact, the rate of evolution leading to the rise in amylase gene copies was found to be 10,000 times faster than that of single DNA base pair mutations. This rapid genetic change highlights the profound impact of agriculture on human biology. Co-author Peter Sudmant, assistant professor of integrative biology at UC Berkeley,
"It has long been hypothesized that the copy number of amylase genes 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. 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."
New Methods Unlock the Complexity of the Amylase Locus
One of the major breakthroughs of this study was the development of new methods for analyzing the amylase locus of the human genome, which is notoriously difficult to study due to its repetitive nature. Traditional sequencing techniques, which rely on short-read sequencing, were unable to accurately capture the multiple copies of the amylase gene present in human genomes. By using long-read sequencing and advanced pangenomic methods, the research team was able to overcome these challenges and gain unprecedented insight into the evolutionary history of the amylase gene family.
Joana Rocha, a postdoctoral fellow at UC Berkeley, likened the complexity of the amylase locus to a,
"sculpture made of different Lego bricks. 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."
By analyzing both modern and ancient genomes, the researchers were able to trace the evolution of the amylase gene back to its origins around 280,000 years ago, long before the advent of agriculture. However, it was the rise of farming that drove the rapid expansion of these genes in human populations, as the ability to digest starch became increasingly vital to survival.
The Broader Implications of Gene Copy Number Variation
The insights gained from studying the amylase gene family have far-reaching implications for understanding human evolution and adaptation. Gene copy number variation, the process by which genes are duplicated or deleted in the genome, plays a critical role in human health and disease. The study’s findings not only shed light on the evolutionary forces that shaped the human genome but also offer new avenues for exploring the genetic basis of complex traits and diseases.
According to study co-author Erik Garrison of the University of Tennessee Health Science Center,
"This is really the frontier, in my opinion. We can, for the first time, look at all of these regions that we could never look at before, and not just in humans — other species, too. Human disease studies have really struggled in identifying associations at complex loci, like amylase."
One potential application of these findings is in understanding the genetic factors that contribute to diseases such as tooth decay. Previous research has suggested that individuals with more copies of the AMY1 gene may be more prone to cavities, as their saliva is more efficient at converting starch into sugar, which feeds bacteria that damage teeth.
A New Chapter in Human Evolutionary Studies
The study marks a significant step forward in understanding how human genomes have evolved in response to changes in diet and lifestyle. The ability to digest starch more efficiently gave early agricultural societies a clear advantage, allowing them to thrive on cultivated crops and paving the way for the growth of civilizations.
As agriculture continues to shape human societies and economies, understanding the genetic mechanisms behind this evolutionary process is essential. The methods developed in this study offer a powerful tool for exploring other complex regions of the human genome and their role in health and disease, opening new possibilities for research in anthropology, archaeology, and human genetics.
Through this groundbreaking research, the team has uncovered the genetic evidence of humanity’s evolutionary journey from hunter-gatherers to farmers, highlighting the profound impact that diet and environment have had on shaping the human genome over millennia.
Bolognini, D., Halgren, A., Lou, R. N., Raveane, A., Rocha, J. L., Guarracino, A., Soranzo, N., Chin, C.-S., Garrison, E., & Sudmant, P. H. (2024). Recurrent evolution and selection shape structural diversity at the amylase locus. Nature. https://doi.org/10.1038/s41586-024-07911-1