Remnants of round houses in Kuelap, the ruined citadel city of Chachapoyas.

The Chachapoyas, the “Warriors of the Clouds,” were a people that lived in the northern elevations of Peru, and put up a long-running struggle against the Inca Empire, which they eventually lost. Traditional tales told to the first Spanish conquerors of the New World about a century after their final defeat held that the Inca forcibly relocated the Chachapoyas to the corners of the massive empire, so they could never again pose a threat.

But a new deep dive into the DNA of these “warriors” indicates their current descendants live on in the same region – and were never fully dispersed to the rest of the Inca Empire, according to a paper in the journal Scientific Reports.

“This unique genetic profile challenges the routine assumption of large-scale population relocations by the Incas,” they conclude.

The Chachapoyas were conquered in the 15th century, the century before the Spanish conquistador Francisco Pizarro captured the Inca Emperor Atahualpa in 1532. But they left traces behind: especially the fortress of Kuelap, known as the “Machu Picchu of the north,” as well as an archaeological trail including other ruins, sarcophagi and pottery.

One of the cultural remnants that was considered to back up the Inca account of having dispersed the Chachapoyas throughout the Empire was the presence of Quechua, one of the most ancient and direct links to the pre-conquest history of the Americas. The spread of the language, which is currently spoken throughout the Western Hemisphere, was thought to be exemplified by diaspora of various people, including the Chachapoyas.

But the DNA showed differently.

The 119 genetic samples from around the former Inca Empire included samples from the Chachapoyas communities currently. The DNA was sequenced for mitochondrial comparison based on maternal lineage, and Y-chromosome networks based on paternal inheritance. (The mitochondrial work was completed through Illumina tools including the Genome Analyzer platform, and the HiSeq 2500; the Y-STR analysis was done through the PowerPlex Y23 System made by Promega, in concert with the GeneMapper data analyzer made by Life Technologies).

Various computing techniques to compare the DNA, and to reconstruct the genetic history of the Americas, were run through further programs that constructed phylogenetic trees and Bayesian Skyline plots.

They noted that the Chachapoyas are more isolated than the rest of the former Inca Empire.

“We were able to pinpoint a genetic signal in Chachapoyas that turned out to be far more diverse than we expected, especially in the male line, from father to son,” said Chiara Barbieri, of the Max Planck Institute for the Science of Human History, one of the authors. “What’s more, here the native component is quite different from the main genetic network in the highlands of central and southern Peru.”

The language clues seem to match the DNA evidence, added Paul Heggarty, another Max Planck author, who is a linguist.

“Linguists need to rethink their traditional view of the family tree of Quechua languages, and the history of how they spread through the Andes,” said Heggarty. “It seems that Quechua reached Chachapoyas without any big movement of people. This also doesn’t fit with the idea that the Incas force out the Chachapoyas population wholesale.”