Nation & World

History of Chichén Itzá written in DNA

Research using new method upends narrative on ritual sacrifices, yields discovery on resistance built to colonial-era epidemics

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Photo by Johannes Krause

For more than 100 years, the ancient Maya city of Chichén Itzá has been a source of archaeological fascination. 

Human remains discovered early in the 20th century inspired what biomolecular archaeologist Christina Warinner called “lurid accounts” of ritual sacrifices of female virgins. Not until the early 21st century did researchers piece together enough skeletal evidence to cast doubt on the narrative. 

Chichén Itzá rose to prominence around 800 A.D., remaining powerful and populous for more than two centuries and serving as a destination for pilgrimages through and after the Spanish colonial period. 

Now Warinner, the John L. Loeb Associate Professor of the Social Sciences, and an international team of genetic scientists have turned that story on its head. Their state-of-the-art research, published this week in Nature, reveals that boys — especially twins — were the focus of sacrifices in the legendary city-state. The investigation also yielded broader insights into the victims’ familial ties and diets, colonial-era epidemics, and the whereabouts of Chichén Itzá’s descendants today. 

“This is the first study that uses ancient DNA, isotopes, and bioarchaeology to draw a better picture of what was going on there,” said lead author Rodrigo Barquera, an immunogeneticist and postdoctoral researcher at the Max Planck Institutes for Evolutionary Anthropology in Germany, where Warinner is also a group leader. 

Chichén Itzá rose to prominence around 800 A.D., remaining powerful and populous for more than two centuries and serving as a destination for pilgrimages through and after the Spanish colonial period. 

The regional capital’s architecture reflects a number of styles and evolved as Chichén Itzáns built political, cultural, and religious alliances near and far. For instance, El Castillo, the site’s 75-foot temple, was constructed in the style of the Toltecs, who ruled an area hundreds of miles away near present-day Mexico City. Those connections piqued Barquera’s curiosity about the provenance of individuals put to rest in or near the Sacred Cenote, a watery sinkhole where ritual offerings of gold, jade, and human lives were made. 

El Castillo.

Photo by Johannes Krause

“We really wanted a better picture of the people who lived and died there,” Barquera said. “Were they from the Maya region? Somewhere else in Mesoamerica? Or even farther away?” 

To find out, the research team embarked upon in-depth genetic analysis of children ritually buried in a chultún, or man-made cistern, not far from the Sacred Cenote. Warinner, who is also the Sally Starling Seaver Associate Professor at Harvard Radcliffe Institute, noted that chultúns and caves have long been depicted in ancient Maya art and myths as portals to the underworld. “There’s a repeating pattern between these subterranean structures, water, and child burials,” she said.

The Yucatan Peninsula’s hot, humid weather has been a complicating factor in ancient DNA research until now. Recent technological advances as well as the chultún’s relatively temperature-stable setting, which helped preserve the victims’ skeletons, enabled Barquera’s analysis. He chose to focus on bone from the petrous portion of the inner ear. 

“It’s the best site to find DNA,” he explained, adding that focusing on the left side enabled researchers to avoid duplicates. “We were lucky that out of the more than 100 individuals thought to have been buried there, we were able to collect the left petrous bone for 64 of them.”

Killed around the ages of 3 or 4, these children were mostly interred between the years 800 and 1,050 A.D., which was the era of Chichén Itzá’s political apex. All originated from local Maya populations. They also all proved to be male, with two sets of identical twins in the sample. 

Further analysis revealed that at least a quarter of the boys were closely related otherwise. But DNA wasn’t all they had in common. Stable isotope research — or using the chemistry of bones and teeth to investigate ancient foods — showed their diets were extremely similar, as if they lived in the same household. “This was true not only for the twins but for each set of related individuals,” Barquera noted. 

“They seemed to have been selected in pairs,” added Warinner, who also pointed to the importance of twins in Maya sacred texts like the Popol Vuh. “It suggests a very specific ritual activity.”

The researchers also studied people living today in Tixcacaltuyub, located about an hour by car from the ruins. Residents of this local Maya community were already working on various initiatives with researchers from the Autonomous University of Yucatán. Scientists hoped to compare the population’s DNA with that of the ancient children.

Tixcacaltuyub community members.

Photo by Pilar Márquez Vega

Partnering with local academics proved vital, according to Barquera. These Yucatán-based healthcare professionals and anthropology experts helped him travel to the town and explained what the ancient DNA study hoped to accomplish. Also helpful were copies of “Adventures in Archaeological Science,” a coloring book Warinner created with colleagues at the Max Planck Institute, now translated into Yucatec Maya as well as Spanish. 

The community was thrilled by these findings, he added, given the prevalence of racism against Indigenous populations in Mexico today. Now they can claim ancestral ties to the people who built the great city of Chichén Itzá.

“The books were intended for kids, but they work for everyone,” Barquera offered. “They show what we do in an accessible way.”

Genetic sampling revealed that Tixcacaltuyub residents are, in fact, “close living relatives to the people buried at Chichén Itzá,” Barquera explained. The community was thrilled by these findings, he added, given the prevalence of racism against Indigenous populations in Mexico today. Now they can claim ancestral ties to the people who built the great city of Chichén Itzá.

“We have seen researchers go into communities or archaeological sites in the past to take samples or data for their papers without returning anything,” said Barquera, who grew up in Mexico and worked in various Mexico City clinics and immunology labs before pursuing his Ph.D. in Europe. “What we wanted to do was give back.”

The study’s final discovery concerns the genetic legacies of colonial-era epidemics, which exacted a devastating toll on the Maya and other Indigenous peoples. The story begins in 2006 with Warinner’s Ph.D. dissertation research on Teposcolula-Yucundaa, a cemetery in Mexico’s Oaxaca region associated with the 1545 outbreak of a mysterious illness the Aztecs termed cocoliztli, or pestilence. The infection killed an estimated 5 million to 15 million, or up to 80 percent of Mexico’s Indigenous population. 

“It fundamentally changed the population of Mexico,” Warinner said. “But nobody knew what it was.”

Warinner returned in 2018 for an ancient DNA study that identified a form of Salmonella enterica in individuals buried at the cemetery. “Today it’s a very rare strain,” Warinner said. “But we now know it was quite widespread in Europe at the time of colonialism and was likely introduced during the Spanish conquest.”

For his part, Barquera was still working in Mexico City in the early 2000s when he started noticing a recurring allele, or genetic variant arising from a mutation, while conducting tests on donors and patients prior to organ transplantation. He remembers bringing the matter to his supervisor. 

“I told him, ‘This is weird! How can it be that all over Mexico we see this allele in such high frequency?’ We knew it had to come from somewhere. We thought maybe it had to do with resistance to something. But back then, we never came to a conclusion, because we didn’t have the analytical tools to prove anything.” 

In the Chichén Itzá study, the research team identified a shift in the very allele Barquera flagged years before. Today, he said, the genetic variant is “one of the most prominent — if not the most prominent — in Mexico and Central America,” but its prevalence proved low in the Maya of Chichén Itzá.

Subsequent analyses showed the variant was protective against Salmonella, which Warinner and colleagues had linked to the epidemics of 16th-century Mexico. “This is where things really come together,” Warinner said.

Cocoliztli is known to have reappeared in 1576, killing another 2 million people. “The mortality rate was so high,” Warinner said, “scientists have long speculated as to whether it shifted the immune profiles of Indigenous peoples of the Americas.” 

And now, she said, studying individuals buried at Chichén Itzá has revealed the immunological response to the bacteria’s deadly spread across colonial Mexico. 

After all these years, it remains written in the nation’s DNA.