DNA tests revealed that 64 skulls discovered at Chichén Itzá in 1967 all belonged to children

In 1967, workers building a small airport behind Chichén Itzá, an ancient Mayan city in Mexico, unearthed human remains. Archaeologists called to the site discovered a chultún — an underground rainwater storage container that, in Mayan mythology, was seen as an entrance to the subterranean land of the dead. Connected to the cistern was a cave containing more than 100 human remains, almost all of them children.

Nearly 60 years later, ancient DNA extracted from 64 of the children offers new insights into the religious rituals of the ancient Maya and their links to modern descendants. In a paper published in the journal Nature, an international group of researchers revealed that the children — victims of sacrifices between 500 and 900 AD — were all local Maya children who may have been selected to be sacrificed in sibling pairs.

Research into the genome of Mayan children began as an effort to uncover the genetic legacy of Mesoamerica’s deadliest pandemic. In 1545, an outbreak of Salmonella enterica spread across what is now Mexico. Over the next century, the disease killed up to 90 percent of the indigenous population.

Pandemics often leave a mark on the immune genes of survivors. In the mid-2000s, Rodrigo Barquera —now immunogeneticist at the Max Planck Institute— and his colleagues attempted to uncover this genetic legacy by comparing the DNA of precolonial remains with that of people born after the calamity.

The children found at the chultún were one of those pre-Columbian groups who likely never encountered the pandemic in their lifetime. In 2015, the team received permission to destroy a small portion of their skulls to sequence the DNA. The results indicated that all 64 skulls belonged to boys.

“We kept repeating the tests because we couldn’t believe that they were all boys,” Barquera said.

Subsequent genetic testing showed that many of the children were related, including two sets of identical twins. It is not known why these children were chosen for sacrifice, Barquera said. But it is possible that siblings or close relatives were selected to reflect the trials of the Hero Twins.figures in Mayan cosmology who went through cycles of sacrifice and rebirth.

Barquera and his colleagues compared the children’s DNA to that of modern Maya living in Tixcacaltuyub, a town about an hour’s drive from Chichén Itzá, and found strong genetic continuity between the two groups. As Barquera expected, the 1545 pandemic left an imprint on the Maya, bequeathing to Tixcacaltuyub residents at least one genetic variant associated with immunity to salmonella.

Barquera and colleagues traveled to Tixcacaltuyub to share their findings in schools and with study participants. He said participants were delighted to receive confirmation that they were genetically related to the builders of Chichén Itzá.

“People who live near these archaeological sites ask, ‘Why do you have so much respect for the people who built these sites and then treat the indigenous people who live around them as inferior?’” she said. Now they can say, “Look, we are related to the people who made these pyramids. So stop being racist toward us.”