Two conquering empires and more than 500 years of colonial rule failed to erase the cultural and genetic traces of indigenous Peruvians, a new study finds. This runs contrary to historical accounts that depict a complete devastation of northern Peru’s ancient Chachapoya people by the Inca Empire.

The Chachapoyas—sometimes referred to as “Warriors of the Clouds” because they made their home in the Amazonian cloud forests—are mainly known today for what they built: fortified hilltop fortresses and intricate sarcophagi overlooking their villages from sheer, inaccessible cliff sides. The little we know about their existence before the arrival of the Spanish comes to us via an oral history passed along by the Inca to their Spanish conquerors—in other words, the winners' version of history.

Now, a study tracking the genetic and linguistic history of modern Peruvians is revealing that the Chachapoyas may have fared better than these mainstream historical accounts would have us believe. As Chiara Barbieri, a post-doctoral researcher from the Max Planck Institute for the Science of Human History, puts it: “Some of these historical documents were exaggerated and a little bit biased in favor of the Inca.”

Many of these early reports stem from two historians who essentially wrote the book on the Inca Empire during the time period from 1438 to 1533: Inca Garcilaso de la Vega, the son of a conquistador and Incan princess who published chronicles on the Inca Empire in the early 17th century, and Pedro de Cieza de Leon, a Spanish conquistador from a family of Jewish converts who travelled through the area in the mid-16th century, and wrote one of the first lengthy histories of the Inca people and Spanish conquests.

According to Cieza de Leon’s account, it was in the 1470s, about midway through the Inca Empire, that paramount leader Túpac Inca Yupanqui first attacked the Chachapoyas in what is today northern Peru. He quickly found that the Warriors of the Clouds were not the type to give up without a fight. Cieza de Leon described the first battle between Yupanqui and the Chachapoyas in the first part of his Chronicle of Peru:

The Chachapoyas Indians were conquered by them, although they first, in order to defend their liberty, and to live in ease and tranquillity, fought with such fury that the Yncas fled before them. But the power of the Yncas was so great that the Chachapoyas Indians were finally forced to become servants to those Kings, who desired to extend their sway over all people.

Beaten but not defeated, the Chachapoyas rebelled again during the reign of Yupanqui’s son after the latter died. Huayna Capac had to re-conquer the region, but encountered many of the difficulties his father had, according to Cieza de Leon:

Among the Chachapoyas the Inca met with great resistance; insomuch that he was twice defeated by the defenders of their country and put to flight. Receiving some succour, the Inca again attacked the Chachapoyas, and routed them so completely that they sued for peace, desisting, on their parts, from all acts of war. The Inca granted peace on conditions very favourable to himself, and many of the natives were ordered to go and live in Cuzco, where their descendants still reside.

De la Vega’s account, written nearly 50 years after Cieza de Leon’s in the early 17th century, tells a similar story of a decisive conquest and subsequent forced dispersal of the Chachapoyas around the Inca Empire. The Inca often used this strategy of forced dispersal, which they referred to by the Quechua word mitma, to dissuade future rebellion in the vast region they came to control. (Quechua, according to the new study, is the most widely-spoken language family of the indigenous Americas.)

“We have some records in the Spanish history that the Inca had replaced the population completely, moving the Chachapoyas for hundreds of kilometers and replacing them with people from other parts of the empire,” Barbieri says.

These and other accounts are some of the only historical notes we have of the Inca, who lacked any system of writing other than the quipu, or knot records. The quipu system of cords used different types of knots to indicate numbers, and was used for accounting and other records.

“We know a lot about what the Inca did because Inca kings, or high officials, were talking to Spanish historians,” Barbieri says. “So the piece of history of this region that we know is very much biased towards what the Inca elite were telling the Spaniards. What we don’t know was what happened before that—everything that happened before the 16th century.”

That is now changing, thanks to a genetic study on which Barbieri was lead author, published recently in Scientific Reports.

Many researchers had thought the local variant of the Quechua language family spoken by the Chachapoyas had died out, says Barbieri’s coauthor Paul Heggarty, a linguist also at the Max Planck institute. Then, a colleague heard a local dialect spoken in the area. Researchers with their team found fewer than 10 people who actually spoke the Chachapoyas variant, and confirmed it to be distinct from other Quechua languages spoken in the Andes to the south of the Chachapoyas region and north in modern day Ecuador.

“We collected and transcribed actual recordings so that anyone can ‘confirm’ the differences by listening on our website,” Heggarty says.

There was also a genetic component to the research. The researchers traveled between small villages, taking saliva samples from volunteers in the region in February 2015, particularly from those who spoke Quechua, or whose parents or grandparents spoke Quechua. They analyzed DNA from the samples, honing in on genetic markers unique to the Americas.

They found that in contrast with people who live south of the Andes, who tend to have more mixed genes, some genetic profiles in Chachapoyas were not found anywhere else, even in other Andean regions. “The Chachapoya stayed a bit isolated genetically,” Barbieri says, adding that the presence of these genes proves thay some of the historical documents were exaggerated and biased in favor of the Inca conquerors' version of events. “We are denying this effect of moving and replacing an entire population.”

The idea that the Chachapoya weren’t completely displaced was not entirely new, according to Barbieri and Heggarty. Some histories hold that the Chachapoya, still rankled over their defeat and at least partial displacement, lent a hand to the Spanish in their conquest of the Inca. “It was the same sort of thing you often get: my enemy’s enemy is my friend,” Barbieri says.

While the "Warriors of the Clouds"—a term Heggarty says likely came from romanticized notions from scholars—may have satisfied a lust for revenge against their Inca conquerors by siding with the Spanish, the alliance did not exactly make them best friends. According to Cieza de León, one of Francisco Pizarro’s captains conquered the Chachapoyas area and “reduced the natives to the service of his Majesty.” Some Spanish were granted the right to demand tribute and forced labor from the local people in the area.

There have been few bio-archaeological studies in the area, says Kenneth Nystrom, a biological anthropologist at the State University of New York New Paltz who has published studies looking at the skeletal remains of Chachapoyas. “It was interesting to read those results, but also how they linked in the linguistic analysis of the Quechua,” says Nystrom, who was not involved in the new research.

Nystrom adds another wrench to the mix: The modern concept we have of the area being a unified culture before the Inca arrived, he says, may not have been exactly true. While there was some continuity between the communities in the area in terms of iconography and architectural style, Nystrom concludes that the Chachapoya may not have self-identified as a unified culture.

“There may have been some kind of loose association between the groups, but what I ultimately suggest is that when the Inca came in, they said ‘You guys are all Chachapoyas and we’re going to treat you as an administrative unit,’” Nystrom says. This was a political move: By bringing together the disparate communities in an area, including in some case the possible forcible displacement of families, they found the conquered populations easier to govern.

Today, only a few dozen people in the region still speak the Chachapoya form of Quechua. “We can’t do anything to keep it alive when there are only a few people speaking the language,” she says. “This Quechua is going to die.”

That may be true. But there is another linguistic layer that has yet to be revealed: the Chachapoya language. The form of Quechua that some Chachapoyas speak today is a the superimposed language that arrived around the time, or shortly before, the Inca conquest of Chachapoyas. The original language of these people has been dead for centuries, with trace remains found only in a few place names and the surnames of some regional residents, says Barbieri.

“There is another layer which is even more mysterious, which is the ancient language of the Chachapoya,” she says.