Genes for immunity forged in a germ-filled past are often blamed for making our bodies overreact to harmless triggers such as pollen or food. But evolution may not be so one-sided.

Some infection-fighting gene variants that spread over the past 10,000 years appear to reduce the risk of asthma and other allergies, not increase it, researchers report in a preprint posted to bioRxiv.org.

The finding challenges a long-standing idea that modern allergies are simply the price we pay for immune systems tuned to a dirtier past. That idea is “too simplistic,” says evolutionary geneticist Will Barrie of the University of Cambridge in England, who was not involved in the research. The hypothesis developed out of observations that many gene variants that help fight infection are also implicated in autoimmune diseases, in which the immune system goes off the rails and mistakenly attacks the body’s healthy tissues. But determining when those variants rose in frequency — and thus whether protection against past infections truly came at the cost of greater autoimmune risk today — has been difficult without ancient DNA datasets spanning major transitions in human history.

Recently, those datasets have grown large enough for researchers to confidently track genetic changes across the Stone Age, the rise of agriculture and later periods. For example, a recent analysis of human genomes from 15,836 individuals who lived between 18,000 and 200 years ago identified hundreds of genetic variants shaped by natural selection after the shift to agriculture transformed people’s diets, environments and lifestyles.

Many of those changes were linked to immune function, reinforcing the idea that pathogens became dominant evolutionary forces as people moved into denser societies, researchers report April 15 in Nature. But that study stopped short of showing how those ancient immune adaptations shape disease risk today, leaving the hypothesis about past germs and modern allergies or asthma largely untested.

To probe the hypothesis, Harvard geneticist Javier Maravall López and colleagues integrated the Nature study’s ancient DNA datasets with modern genetic studies of disease risk. A clear pattern in the data showed humans retained and passed on gene variants that helped protect them from tuberculosis, influenza and intestinal pathogens, and, as expected, these same variants also tended to increase people’s risk for developing immune-mediated conditions such as inflammatory bowel disease.