Ancient DNA reveals the genetic portrait of Andes civilisations

  Last updated May 12, 2020 at 11:03 am

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A study of DNA belonging to ancient humans in South America has revealed a story of 9000 years of civilisations and surprising genetic continuity.


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Machu Picchu reveals the stories of past societies in South America. Credit: Shutterstock




Why This Matters: This is the first large-scale genomic portait of Andean civilisations.




Across the central Andes, remnants of ancient civilisations such as Machu Picchu attract archaeologists and tourists alike. The hillside settlements reveal fascinating stories of agriculture, complex societies, and the rise and fall of powerful empires.


Now, the first large-scale study of DNA belonging to the ancient inhabitants have revealed more details of those who lived there and how they moved and mixed with other groups across the continent. They also found a surprising level of genetic continuity – genetic differences between groups that arose millenia ago still continue today, even as other civilisations came and went around them.


In the study, published in the journal Cell, researchers analysed the DNA of 89 ancient humans who lived in the central Andes between 500 and 9,000 years ago. They then compared it with the genetic diversity of present day occupants, to shed light on the genetic changes over time.




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The ancient remains included 65 humans never before studied.


“We know from archeological research that the central Andes region is extremely rich in cultural heritage, however up until now the genomic makeup of the region before arrival of Europeans has never been studied,” says Associate Professor Bastien Llamas, from the University of Adelaide, who was involved in the study. The project was a collaboration between researchers from eight countries, including the University of Adelaide together with the others from Argentina, Bolivia, Chile, Germany, Peru, the UK and the US.


Ancient DNA reveals secrets of long-past civilisations


“While archaeological records play a role in connecting cultures, studying ancient DNA can provide a finer grain picture,” says Llamas


“For example, archaeological information may tell us about two or three cultures in the region, and eventually who was there first, but ancient DNA can inform about actual biological connections underlying expansion of cultural practices, languages or technologies.”


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Ancient Incan Fort in The Ruins of Pisac City in Sacred Valley, Cuzco, Peru. Credit: Alexandre Morin-Laprise


The central Andes, mostly found in today’s Peru, is a region rich in history. Over the span of several centuries several distinct groups arose and dissipated, vying for control of the region. Among the major players of the last 2000 years were the Moche, Wari, Nazca and Tiwanaku. The most known, however, are the Inca, who dominated a large portion of the Andes prior to the Spanish Invasion in the 1500’s and built extensive road networks and the formidable citadel of Machu Picchu.


However, there were other groups living in the region thousands of years beforehand.


The analysis revealed that by 9000 years ago, groups living in the Andean highlands became genetically distinct from those that eventually came to live along the Pacific coast. The effects of this early differentiation are still seen today.




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By 5800 years ago, the population of the north also developed distinct genetic signatures from populations that became prevalent in the south, the team found. Again, these differences can be observed today.


After that time, gene flow occurred among all regions in the Andes, although it dramatically slowed after 2000 years ago. From then until around 500 years ago, they found with minimal changes to the genetic structure of the central Andean region.


“This was quite surprising given this period saw the rise and fall of many large-scale Andean cultures such as Moche, Wari and Nazca, and suggests that these empires implemented a cultural domination without moving armies,” says Llamas.




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The team discovered genetic exchanges both within the Andes and between Andean and non-Andean populations. Ancient people moved between south Peru and the Argentine plains and between the north Peru coast and the Amazon, largely bypassing the highlands.


Incan cities were rather cosmopolitan


However the highlands areas weren’t completely isolated. The study found that in large cities of the Tiwanaku and Inca, people of diverse ancestries lived side-by-side.


“It was interesting to uncover signs of long-range mobility during the Inca period. Archaeology shows the Inca occupied thousands of kilometres from Ecuador through to northern Chile – which is why when Europeans arrived they discovered a massive Incan empire, but we found close genetic relationships between individuals at the extreme edges of the empire.”


Surprisingly however, multiple regions have maintained genetic continuity over the past 2000 years, despite transformations in society around them. This contrasts with many other world regions where ancient DNA studies often document substantial genetic turnover during this period.


“We hope this more detailed genetic picture of populations of the central Andean Highlands will allow archeologists to ask new questions about the history of the region and will lead to further cultural learnings and strengthen collaboration with local communities,” says Llamas.


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