NEW YORK (GenomeWeb) – A new genomic study suggests a Peruvian population living in the Chachapoyas region has retained some of the sequences passed down from ancient indigenous individuals in the area, despite centuries of interactions with representatives from the Inca Empire.
Researchers from Germany and Peru did mitochondrial whole-genome sequencing and/or targeted Y chromosome short tandem repeat sequencing on 119 individuals with suspected Chachapoyas ancestry using linguistic clues. As they reported today in Scientific Reports, the mitochondrial and Y chromosome sequences revealed an indigenous ancestry component that was not erased by long-term contact with the Incas, which began in the late 1400s and corresponded to other large-scale population shifts.
"[I]t seems that some genetic legacy of the Chachapoyas did indeed resist Inca impacts, all the way through to today," co-first author Chiara Barbieri, a molecular anthropology researcher at the Max Planck Institute for the Science of Human History, said in a statement.
Members of the Chachapoyas culture — nicknamed the Warriors of the Clouds — are native to a region in northern Peru where the Andes mountains meet the Amazon rainforest, the team explained. There, the population built the walled settlement of Kuelap (sometimes called the Machu Picchu of the North), though their occupation in the region is thought to have been upended by the arrival of the Incan population.
"In the earliest historical accounts, Spanish chronicles make extensive mention of Chachapoyas for its long resistance to Inca conquest — and then as a clear example of the Inca state policy of forced resettlements," the authors noted. "Chachapoyas is taken as one of a few regions where the recalcitrant local population was essentially completely removed and replaced — making this a test case for the ability of population genetics to challenge or confirm the (proto-)historical record, of questionable veracity here."
To explore this history, the researchers focused on 119 individuals with suspected indigenous ancestry based on their cultural and linguistic histories. Although many people still speak the native Chachapoyas language Quechua in other parts of the world, they explained, the language is much rarer in the Chachapoyas region, where only a few elders still speak it.
Using in-solution capture and Illumina HiSeq 2500 sequencing, the team sequenced mitochondrial genomes from 116 of the participants, starting with DNA isolated from saliva samples. It assigned 113 of those individuals to half a dozen geographic groups, and noted that most participants belonged to Native American haplogroups.
The researchers then focused in on 88 men from the Native American haplogroup Q for a SNaPshot-based analysis of 23 STR markers in a non-recombinant Y chromosome region. Together, the mitochondrial sequences and Y chromosome markers suggest that a distinct, genetically diverse Chachapoyas ancestry component has persisted in northern Peru, they reported.
"[H]ere the native component is quite different from the main genetic network in the highlands of central and southern Peru," Barbieri said. "This is where the Inca Empire and its predecessors originated, and their conquests, road networks and empire-building ended up homogenizing the genetic make-up here."
The team did not see close genetic ties between populations speaking the Quechua language in different geographic regions, suggesting individuals in this region may adopted the language without widespread population migration into the Chachapoyas.
"It seems that Quechua reached Chachapoyas without any big movement of people," senior author Paul Heggarty, a linguist at the Max Planck Institute for the Science of Human History, said in a statement. "This also doesn't fit with the idea that the Incas forced out the Chachapoyas population wholesale."