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Ancient Andean Genomes Reveal Genetic Substructure, Continuity of Populations

NEW YORK – An analysis of ancient genomes from the Andes Mountains has enabled researchers to trace the genetic history of populations in the region, finding both distinctions and continuity.

The Andes was home to the Incan Empire and other ancient civilizations, and while there have been numerous archaeological investigations of the region, there have been few genomic analyses.

An international team of researchers has analyzed genome-wide data from 89 individuals who lived between 500 and 9,000 years ago in the region. As they reported in Cell on Thursday, they were able to tease out genetic differences between populations living in the Andean highlands and those living along the coast that arose by 9,000 years ago, as well as between northern and southern populations in the region that emerged by about 5,800 years ago. Since about 2,000 years ago, there has been fairly consistent genetic continuity in the region, they found, with the exception of two cities.

"It represents the first detailed study of Andean population history informed by pre-Colonial genomes with wide-ranging temporal and geographic coverage," co-senior author Lars Fehren-Schmitz, associate professor at the University of California, Santa Cruz, said in a statement.

The researchers analyzed the ancient genomic data — which included data from 64 new individuals — alongside data from present-day individuals. Using principal components, the Admixture algorithm, and other analytical approaches, they began to uncover genetic structure within the region and teased out how it changed over time.

By about 9,000 years ago, genetic differences were already arising between individuals who lived in the Andean highlands and the coast. Later, by about 5,800 years ago or roughly when the Late Preceramic Period began, a split emerged between the northern and southern highland populations. This was also around the time when populations in the region began to rely more on plant cultivation, which has been thought to contribute to rapid population growth in some areas, the researchers noted.

After the establishment of these different population substructures, gene flow still continued, the researchers found. For instance, there appeared to be gene flow between populations in the highlands and on the North Coast of Peru, and between the Titicaca Basin and the South Peru Highlands and North Chile. Gene flow, though, dropped off after about 2,000 years ago. 

The researchers also detected evidence of long-range gene flow, not only between Andean populations but also between Andean and non-Andean populations. These shifts could be due to relocation policies that were in place during the Inca rule, but they noted additional research is needed to explore that idea.

Beginning about 2,000 years ago, the researchers observed, there was genetic continuity in a number of populations in the Andes, despite cultural upheavals. This, they noted, contrasts with findings in other parts of the world from this timeframe that instead experienced genetic shifts.

"To our surprise, we observed strong genetic continuity during the rise and fall of many of the large-scale Andean cultures, such as the Moche, Wari, and Nasca," first author Nathan Nakatsuka from Harvard Medical School said in a statement. "Our results suggest that the fall of these cultures was not due to massive migration into the region, [for example] from an invading military force, a scenario which had been documented in some other regions of the world." 

He and his colleagues noted a few exceptions to this observed genetic continuity, particularly in urban areas that were home to the capital regions of the Tiwananku and Inca cultures. These regions, they found, were cosmopolitan with people from a range of genetic backgrounds living there.

"It was interesting to start to see these glimpses of ancestral heterogeneity," Nakatsuka added. "These regions have some similarity to what we see now in places like New York City and other major cities where people of very different ancestries are living side by side."