Ancient DNA reveals the persistence of the first peoples of the Andes

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Machu Picchu was built by the Incas, one of the many cultures that have settled in the central Andes for thousands of years.

Matthew Butcher

By Elizabeth Pennisi

Some of the world’s most famous and examined archaeological sites dot the flanks of the central Andes, documenting an invention of agriculture and the rise and fall of powerful civilizations such as the Incas. Now, the largest study of ancient human genomes in South America has added a personal touch to the artifacts. New research reveals who lived there, when they lived, and how they moved and mixed. And although it is a very studied area, a big surprise appeared: the descendants of the first inhabitants persisted even as civilizations came and went.

“This document highlights a region that is home to some of the most studied ancient societies in the world during a particularly dynamic period in its history,” said Jennifer Raff, a geneticist and anthropologist at the University of Kansas, Lawrence, who was not involved in the work. “Now we are starting to understand biological history as well as archaeological history.

The central Andes, located mainly in present-day Peru, include coastal and mountainous regions. The Incas are the best known of the ancient civilizations to live there: during their reign of 1000 years, until the Spanish conquered them in the mid-1500s, they built a vast road network and built magnificent stone structures, such as Machu Picchu. And they were preceded by several other well-developed companies. The Moche lived there from 200 to 850 AD and are known to have built giant adobe mounds with murals inside. The Wari, which partially overlap in time, are known for their fine textiles and terraced farming. And there were also other groups, like the Nasca and Tiwanaku.

Eighty-nine skeletons from many archaeological sites in the Andes provided the study’s ancient DNA.

Guido Valverde

Researchers at Harvard University and other institutions had already sequenced DNA from 9,000-year-old human remains from the central highlands of the Andes as part of a large-scale investigation into dozens of ancient DNA samples from South America. For a more complete overview of the region’s genetic history, teams led by Harvard population geneticist David Reich and Lars Fehren-Schmitz, paleogenomist at the University of California at Santa Cruz, joined South American colleagues and worked with local authorities to obtain DNA from many key archaeological sites, sequencing 64 new old genomes. Using radiocarbon dating, they determined that the DNA belonged to people who lived between 9,000 and 500 years. The researchers compared these genomes with each other and 25 old samples already sequenced.

The people who lived in the highlands 9,000 years ago were genetically distinct from the ancient groups of people who inhabited the coastal region and the northern and southern regions, and still are today, according to graduate student Nathan Nakatsuka of Harvard and colleagues today Cell. The upland genomic group has even persisted despite several cultural upheavals as the Incas, Moche and others have come and gone over the past 2,000 years. This genetic stability contrasts with the tumultuous events in Eurasia during the same period; there, genetic studies have found evidence of repeated replacements of the local population by new arrivals, says Nakatsuka.

“These data confirm what I and other researchers have proposed,” said Francesca Giulietta Fernandini Parodi, an archaeologist at the Pontifical Catholic University of Peru (PUCP): repeated invasions have not resulted in the disappearance of the local population.

However, the inhabitants of the highlands were not isolated. In the major cities of Inca and Tiwanaku, DNA from the new study indicated that people from many different places lived side by side. “They looked like places like New York,” said PUCP archaeologist Luis Jaime Castillo.

More genomes could refine or even change this picture, warns Castillo, who hopes more DNA data will be available. Fernandini welcomes the new data. “It is important to integrate our [archaeological] studies with old DNA evidence to get a clearer scenario, “she said. The work “is a major advance in the study of the ancient Andean populations”.

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