Different genetic traits can be beneficial (for example, fending off disease) or harmful (making humans more susceptible to illness), depending on the environment. The theory behind these evolutionary trade-offs is called balancing selection. In new research, University at Buffalo evolutionary biologist Omer Gokcumen and colleagues scoured the genomes of hundreds of modern humans from around the world and four groups of ancient human ancestors, including Neanderthals and Denisovans. They looked for structural changes in genes, like deletions, that date back to more than 700,000 years ago — before modern humans split from their ancestors, and found large numbers of such ancient genes in modern humans.
Aqil et al. demonstrate an excess of polymorphisms in present-day humans that predate the modern human-Neanderthal split, which cannot be explained solely by selectively neutral scenarios. Image credit: Neanderthal Museum.
The persistence of versions of genes that cause severe disease in human populations has long perplexed scientists. It is common for many versions of a gene to exist.
But scientists expect that over time natural selection will eliminate versions of genes harmful to human health.
Sometimes, there are good reasons that a disease-causing gene may persist.
For example, having two copies of a particular gene variant causes a condition, called sickle cell disease.
But having one sickle cell-causing copy of the gene and one non-disease-causing copy protects against malaria.
As a result, the version of the gene that causes sickle cell is more common in people from areas where malaria is prevalent despite the risks to people who end up with two copies.
Researchers call this phenomenon balancing selection because trade-offs in the gene’s benefits and risks cause it to persist in the population.
Dr. Gokcumen and colleagues explored the phenomenon by analyzing thousands of modern human genomes alongside ancient hominin groups, such as Neanderthal and Denisovan genomes.
“Our research has implications for understanding human diversity, the origin of diseases, and biological trade-offs that may have shaped human evolution,” Dr. Gokcumen said.
“The study shows that many biologically relevant variants have been segregating among our ancestors for hundreds of thousands, or even millions, of years. These ancient variations are our shared legacy as a species.”
The work builds upon genetic discoveries in the past decade, including when scientists uncovered that modern humans and Neanderthals interbred as early humans moved out of Africa.
It also coincides with the growth of personalized genetic testing, with many people now claiming that a small percentage of their genome comes from Neanderthals. But, as the new study show, humans share much more in common with Neanderthals than those small percentages indicate.
This additional sharing can be traced back to a common ancestor of Neanderthals and humans that lived about 700,000 years ago.
This common ancestor bequeathed to the Neanderthals and modern humans a shared legacy in the form of genetic variation.
The authors explored this ancient genetic legacy, focusing on a particular type of genetic variation: deletions.
“The deletions are strange because they affect large segments. Some of us are missing large chunks of our genome,” Dr. Gokcumen said.
“These deletions should have negative effects and, as a result, be eliminated from the population by natural selection.”
“However, we observed that some deletions are older than modern humans, dating back millions of years ago.”
The researchers used computational models to show an excess of these ancient deletions, some of which have persisted since our ancestors first learned to make tools, some 2.6 million years ago.
Furthermore, the models found that balancing selection can explain this surplus of ancient deletions.
“Our study contributes to the growing body of evidence suggesting that balancing selection may be an important force in the evolution of genomic variation among humans,” said Alber Aqil, a Ph.D. candidate at the University at Buffalo.
The team found that deletions dating back millions of years are more likely to play an outsized role in metabolic and autoimmune conditions.
Indeed, the persistence of versions of genes that cause severe disease in human populations has long baffled scientists since they expect natural selection to get rid of these versions of genes.
It is, after all, very unusual for potentially disease-causing variation to persist for such long periods.
The scientists argue that balancing selection can solve this riddle.
“These variations may protect against infectious diseases, outbreaks, and starvation, which have occurred periodically throughout human history,” Aqil said.
“Thus, the findings represent a considerable leap in our understanding of how genetic variations evolve in humans.”
“A variant may be protective against a pathogen or starvation while also underlying certain metabolic or autoimmune disorders, like Crohn’s disease.”
The study was published online in the journal eLife.
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Alber Aqil et al. 2023. Balancing selection on genomic deletion polymorphisms in humans. eLife 12: e79111; doi: 10.7554/eLife.79111
Source : Breaking Science News