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DNA Analysis Offers First Look at People of Ancient Andes

Despite millennia of cultural upheavals in some of the most famous ancient civilizations in South America, researchers have found a surprising amount of ancestral mixing and genetic continuity in DNA from the past.

(CN) — A wide-scale study of the genomic history of ancient civilizations in South America reveals ancient DNA data that can help scientists better understand the history of those who resided there long before Europeans colonized the continent.

The study, published Thursday in the journal Cell, discusses early genetic distinctions between groups in nearby regions, population mixing within and beyond the Andes, surprising genetic continuity amid cultural upheaval and ancestral mixing pots among some of the most widely known civilizations from the region.

The team was led by researchers at Harvard Medical School and the University of California, Santa Cruz. In their study, they looked at genome-wide data from 89 individuals who lived between 500 and 9,000 years ago, including some never before seen data.

Of the 89 individuals analyzed, 64 genomes, ranging from 500 to 4,500 years old, were newly sequenced, which more than doubled the number of ancient individuals with genome-wide data from South America.

"This was a fascinating and unique project," said Nathan Nakatsuka, first author of the paper and a doctoral student in the lab of David Reich in the Blavatnik Institute at Harvard Medical School.

The analysis included representatives of iconic civilizations in the Andes from whom scientists previously had no genome-wide data, including the Moche, Nasca, Wari, Tiwanaku and Inca.

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

"This study also takes a major step toward redressing the global imbalance in ancient DNA data," said Reich, professor of genetics at HMS and associate member of the Broad Institute of MIT and Harvard. "The great majority of published ancient DNA studies to date have focused on western Eurasia. This study in South America allows us to begin to discern at high resolution the detailed history of human movements in this extraordinarily important part of the world."

(Nakatsuka et al. / Cell)

The central Andes in present-day Peru is one of the rare locations in the world where farming was invented rather than being adopted from elsewhere. It is also home to the earliest known presence of complex civilizations in South America documented so far.

While the region has been a major focus of archaeological research, there had been no systematic characterization with genome-wide ancient DNA until now.

Geneticists on the team have previously done studies on the genetic history of South America as a whole, including analysis of several individuals from the Andean highlands from thousands of years ago.

Additionally, there have been analyses of present-day residents of the Andes, as well as a limited number of mitochondrial or Y-chromosome DNA analyses from individual ancient Andean sites.

This study, however, stands apart from these by expanding on the findings to provide a far more comprehensive portrait. Now, Nakatsuka said, researchers are "finally able to see how the genetic structure of the Andes evolved over time."

“By focusing on what is often called pre-Columbian history, the study demonstrates how large ancient DNA studies can reveal more about ancient cultures than studying present-day groups alone,” Reich said.

"In the Andes, reconstruction of population history based on DNA analysis of present-day people has been challenging because there has been so much demographic change since contact with Europeans," he added. "With ancient DNA data, we can carry out a detailed reconstruction of movements of people and how those relate to changes known from the archaeological record."

The findings reveal that 9,000 years ago, groups living in the Andean highlands became genetically distinct from those that eventually came to live along the Pacific Coast, and the effects of this early differentiation are still seen today.


The genetic fingerprints distinguishing people living in the highlands from those in nearby regions are "remarkably ancient," said Nakatsuka.

The team found that 5,800 years ago, the population of the north also developed distinct genetic signatures from populations that became prevalent in the south, which again can still be seen today. After this, gene flow continued to occur among all regions in the Andes, although it dramatically slowed about 2,000 years ago.

"It is exciting that we were actually able to determine relatively fine-grained population structure in the Andes, allowing us to differentiate between coastal, northern, southern and highland groups as well as individuals living in the Titicaca Basin," Fehren-Schmitz said.

"This is significant for the archaeology of the Andes and will now allow us to ask more specific questions with regards to local demographies and cultural networks," said study co-author Jose Capriles of Pennsylvania State University.

Additionally, the team discovered genetic exchanges both within the Andes and between Andean and non-Andean populations. They found that ancient people traveled between south Peru and the Argentine plains and between the north Peru coast and the Amazon, effectively bypassing the highlands.

The most interesting aspect of these findings to Fehren-Schmitz was uncovering signs of long-range mobility in the Inca period. He said he was pleasantly surprised to find that ancient North Coast ancestry was present not only around Cusco, Peru, but also in a child sacrifice from the Argentinian southern Andes.

"This could be seen as genetic evidence for relocations of individuals under Inca rule, a practice we know of from ethnohistorical, historical and archaeological sources," he said.

“Although the findings of genetic intermingling throughout the Andes correlate with known archaeological connections, they will likely prompt additional archaeological research to understand the cultural contexts underlying the migrations,” said Nakatsuka.

"Now we have more evidence demonstrating important migrations and some constraints on when they happened, but further work needs to be done to know why exactly these migrations occurred.”

The analysis also revealed that multiple regions maintained genetic continuity over the past 2,000 years despite clear cultural transformations. The finding contrasts with many other world regions, where ancient DNA studies often document substantial genetic turnover during this period, said Reich.

The authors explained that the early population structures persisted through major social changes and on into modern societies. They note that these discoveries offer new evidence that can be incorporated with archaeological and other records to inform theories on the ancient history of different groups in the region.

"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," Nakatsuka said. "Our results suggest that the fall of these cultures was not due to massive migration into the region, e.g., from an invading military force, a scenario which had been documented in some other regions of the world."

There were however two exceptions to this continuity trend, and those were the vast urban centers that were home to the Tiwanaku and Inca cultures. While other civilizations were relatively genetically homogeneous, the capital regions of these civilizations were cosmopolitan, hosting people from many genetic backgrounds.

"It was interesting to start to see these glimpses of ancestral heterogeneity," Nakatsuka said. "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."

Due to a severe lack of pre-Columbian written histories, archaeology has been the main source of information used to reconstruct the complex history of the continent, said study co-author Chiara Barbieri of the University of Zurich.

"With the study of ancient DNA, we can read the demographic history of ancient groups and understand how ancient and present-day groups are related," she said. "The link with the genetic study of living populations opens a direct dialogue with the past and an occasion to involve local communities."

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