The Black Death didn’t just wipe out millions of Europeans during the 14th century. It left a mark on the human genome, favoring those who carried certain immune system genes, according to a new study. Those changes may help explain why Europeans respond differently from other people to some diseases and have different susceptibilities to autoimmune disorders.

Geneticists know that human populations evolve in the face of disease. Certain versions of our genes help us fight infections better than others, and people who carry those genes tend to have more children than those who don’t. So the beneficial genetic versions persist, while other versions tend to disappear as those carrying them die. This weeding-out of all but the best genes is called positive selection. But researchers have trouble pinpointing positively selected genes in humans, as many genes vary from one individual to the next.

Enter Mihai Netea, an immunologist at Radboud University Nijmegen Medical Centre in the Netherlands. He realized that in his home country, Romania, the existence of two very distinct ethnic groups provided an opportunity to see the hand of natural selection in the human genome. A thousand years ago, the Rroma people—commonly known as gypsies—migrated into Europe from north India. But they intermarried little with European Romanians and thus have very distinct genetic backgrounds. Yet, by living in the same place, both of these groups experienced the same conditions, including the Black Plague, which did not reach northern India. So the researchers sought genes favored by natural selection by seeking similarities in the Rroma and European Romanians that are not found in North Indians.

Netea; evolutionary biologist Jaume Bertranpetit of Pompeu Fabra University in Barcelona, Spain; and their colleagues looked for differences at more than 196,000 places in the genomes of 100 Romanians of European descent and 100 Rroma. For comparison, the researchers also cataloged these differences in 500 individuals who lived in northwestern India, where the Rroma came from. Then they analyzed which genes had changed the most to see which were most favored by selection.

Genetically, the Rroma are still quite similar to the northwestern Indians, even though they have lived side by side with the Romanians for a millennium, the team found. But there were 20 genes in the Rroma and the Romanians that had changes that were not seen in the Indians’ versions of those genes , Netea and his colleagues report online today in the Proceedings of the National Academy of Sciences. These genes “were positively selected for in the Romanians and in the gypsies but not in the Indians,” Netea explains. “It’s a very strong signal.”

Those genes included one for skin pigmentation, one involved in inflammation, and one associated with susceptibility to autoimmune diseases such as rheumatoid arthritis. But the ones Netea and Bertranpetit were most excited about were a cluster of three immune system genes found on chromosome 4. These genes code for toll-like receptors, proteins which latch on to harmful bacteria in the body and launch a defensive response. “We knew they must be important for host defense,” Netea says.

What events in history might have favored these versions of the genes in gypsies and Romanians, but not in Indians? Netea and his colleagues tested the ability of the toll-like receptors to react to Yersinia pestis, the bacterium that caused the Black Death. They found that the strength of the immune response varied depending on the exact sequence of the toll-like receptor genes.

Netea and Bertranpetit propose that the Rroma and European Romanians came to have the same versions of these immune system genes because of the evolutionary pressure exerted by Y. pestis. Other Europeans, whose ancestors also faced and survived the Black Death, carried similar changes in the toll-like receptor genes. But people from China and Africa—two other places the Black Death did not reach—did not have these changes. (There have been multiple plagues throughout history around the world, but none have been so deadly as the Black Death, which killed an estimated one in every four Europeans, and so exerted very strong selection.) The similarities in the other genes were likely caused by other conditions experienced by Rroma and Europeans, but not Indians.

"The use of two populations living in the same geographic area is very clever," says human population geneticist Oscar Lao of Erasmus MC in Rotterdam, the Netherlands, who was not involved in the study. "This experimental evidence is very important," he adds. It shows that the Black Death bacterium does indeed interact with the proteins coded for by the genes favored by natural selection. "That should be the goal for all those type of analyses."

"It's a nice hypothesis that they are putting forward," agrees Lluis Quintana-Murci, a human population geneticist at the Pasteur Institute in Paris who was not involved in the study. The genetic changes may have modern-day effects. "The presence of these particular versions of these genes may give the evolutionary basis for why certain populations are more at risk” for certain types of diseases, says Douglas Golenbock, an immunologist at the University of Massachusetts Medical School in Worcester. "The side effect seems to be that the Europeans have a more proinflammatory immune system than those who have never experienced Black Death."

However, Lao and Quintana-Murci wonder if the convergence in these genes might be explained another way. It's possible that these favorable versions were introduced into the Rroma by interbreeding between the Rroma and the Romanians, they suggest. Additional sequencing of the converged genetic regions should answer this question, Quintana-Murci says. It’s also important to check how these toll-like receptors respond to other deadly bacteria to see if other diseases might have been the cause of the changes. That will likely happen, Quintana-Murci adds. "This will inspire other labs to see if other bacterial infections could also explain the [selection]."