Machu Picchu was built by the Incas, one of several cultures that settled in the Central Andes over thousands of years.

Matthew Butcher

Some of the world’s more famous and closely examined archaeological sites pepper the hillsides of the Central Andes, documenting an invention of farming and the rise and fall of powerful civilizations such as the Inca. Now, the largest study of ancient human genomes in South America has added a personal touch to the artifacts. The new research reveals who lived there, when they lived, and how they moved around and intermingled. And despite being a heavily studied area, a big surprise emerged: Descendants of early inhabitants persisted even as civilizations came and went.

“This paper sheds light on a region that’s home to some of the world’s most intensively studied ancient societies during a particularly dynamic period in its history,” says Jennifer Raff, an anthropological geneticist at the University of Kansas, Lawrence, who was not involved in the work. “Now, we are beginning to understand the biological history as well” as the archaeological history.

The Central Andes Mountains, located mostly in today’s Peru, includes coastal and highland regions. The Incas are the most well-known of the ancient civilizations to live there: During their 1000-year reign, until the Spanish conquered them in the mid-1500s, they built an extensive road system and constructed magnificent stone structures, such as Machu Picchu. And they were preceded by several other well-developed societies. The Moche lived there from 200 C.E. to 850 C.E. and are known for having built giant adobe mounds with murals inside. Overlapping partially in time were the Wari, known for fine textiles and terraced agriculture. And there were other groups as well, such as the Nasca and Tiwanaku.

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

Guido Valverde

Researchers from Harvard University and other institutions had already sequenced DNA from 9000-year-old human remains from the Central Andes highlands as part of a broad survey of dozens of South American ancient DNA samples. To get a more comprehensive look at the genetic history of the region, teams led by Harvard population geneticist David Reich and Lars Fehren-Schmitz, a paleogenomicist at the University of California, Santa Cruz, joined with South American colleagues and worked with local authorities to get DNA from many key archaeological sites, sequencing 64 new ancient genomes. Using radiocarbon dating, they determined the DNA belonged to people who lived between 9000 to 500 years ago. The researchers compared those genomes with each other and 25 already sequenced ancient samples.

The people who lived in the highlands 9000 years ago were genetically distinct from ancient groups of people who inhabited the coastal region and areas to the north and south, and have remained so even today, Harvard graduate student Nathan Nakatsuka and his colleagues report today in Cell. The highland genomic group even persisted despite several cultural upheavals as the Inca, Moche, and others came and went in the past 2000 years. Such genetic stability contrasts with tumultuous events in Eurasia during the same time; there, genetic studies have found evidence of repeated replacements of local people by newcomers, Nakatsuka says.

“These data confirm what I and other researchers have proposed,” says Francesca Giulietta Fernandini Parodi, an archaeologist at the Pontifical Catholic University of Peru (PUCP): Repeated invasions did not lead to the demise of local people.

Yet the highlands people were not isolated. In the large cities of both the Inca and the Tiwanaku, the DNA in the new study indicated that people from many different places lived side by side. “They were akin to places like New York City,” says PUCP archaeologist Luis Jaime Castillo.

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

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