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First ancient DNA from Indus Valley civilization links its people to modern South Asians

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IMAGE: This is a photograph of a red slipped ware globular pot placed near the head of the skeleton that yielded ancient DNA. There are lines as well as indentations on... view more 

Credit: Vasant Shinde / Deccan College Post Graduate and Research Institute

Researchers have successfully sequenced the first genome of an individual from the Harappan civilization, also called the Indus Valley Civilization (IVC). The DNA, which belongs to an individual who lived four to five millennia ago, suggests that modern people in India are likely to be largely descended from people of this ancient culture. It also offers a surprising insight into how farming began in South Asia, showing that it was not brought by large-scale movement of people from the Fertile Crescent where farming first arose. Instead, farming started in South Asia through local hunter-gatherers adopting farming. The findings appear September 5 in the journal Cell.

"The Harappans were one of the earliest civilizations of the ancient world and a major source of Indian culture and traditions, and yet it has been a mystery how they related both to later people as well as to their contemporaries," says Vasant Shinde, an archaeologist at Deccan College, Deemed University in Pune, India, and the chief excavator of the site of Rakhigarhi, who is first author of the study.

The IVC, which at its height from 2600 to 1900 BCE covered a large swath of northwestern South Asia, was one of the world's first large-scale urban societies. Roughly contemporary to ancient Egypt and the ancient civilizations of China and Mesopotamia, it traded across long distances and developed systematic town planning, elaborate drainage systems, granaries, and standardization of weights and measures.

Hot, fluctuating climates like those found in many parts of lowland South Asia are detrimental to the preservation of DNA. So despite the importance of the IVC, it has been impossible until now to sequence DNA of individuals recovered in archaeological sites located in the region. "Even though there has been success with ancient DNA from many other places, the difficult preservation conditions mean that studies in South Asia have been a challenge," says senior author David Reich, a geneticist at Harvard Medical School, the Broad Institute, and the Howard Hughes Medical Institute.

Answering questions about the ancient people of the Indus Valley was in fact the primary reason Reich founded his own ancient DNA laboratory in 2013.

In this study, Reich, post-doctoral scientist Vagheesh Narasimhan, and Niraj Rai, who established a new ancient DNA laboratory at the Birbal Sahni Institute of Palaeosciences in Lucknow, India, and led the preparation of the samples, screened 61 skeletal samples from a site in Rakhigarhi, the largest city of the IVC. A single sample showed promise: it contained a very small amount of authentic ancient DNA. The team made over 100 attempts to sequence the sample. Reich says: "While each of the individual datasets did not produce enough DNA, pooling them resulted in sufficient genetic data to learn about population history."

There were many theories about the genetic origins of the people of the IVC. "They could resemble Southeast Asian hunter-gatherers or they could resemble Iranians, or they could even resemble Steppe pastoralists--all were plausible prior to the ancient DNA findings," he says.

The individual sequenced here fits with a set of 11 individuals from sites across Iran and Central Asia known to be in cultural contact with the IVC, discovered in a manuscript being published simultaneously (also led by Reich and Narasimhan) in the journal Science. Those individuals were genetic outliers among the people at the sites in which they were found. They represent a unique mixture of ancestry related to ancient Iranians and ancestry related to Southeast Asian hunter-gatherers. Their genetic similarity to the Rakhigarhi individual makes it likely that these were migrants from the IVC.

It's a mix of ancestry that is also present in modern South Asians, leading the researchers to believe that people from the IVC like the Rakhigarhi individuals were the single largest source population for the modern-day people of India. "Ancestry like that in the IVC individuals is the primary ancestry source in South Asia today," says Reich. "This finding ties people in South Asia today directly to the Indus Valley Civilization."

The findings also offer a surprising insight into how agriculture reached South Asia. A mainstream view in archaeology has been that people from the Fertile Crescent of the Middle East--home to the earliest evidence of farming--spread across the Iranian plateau and from there into South Asia, bringing with them a new and transformative economic system.

Genetic studies to date seemed to add weight to this theory by showing that Iranian-related ancestry was the single biggest contributor to the ancestry in South Asians.

But this new study shows that the lineage of Iranian-related ancestry in modern South Asians split from ancient Iranian farmers, herders, and hunter-gatherers before they separated from each other--that is, even before the invention of farming in the Fertile Crescent. Thus, farming was either reinvented locally in South Asia or reached it through the cultural transmission of ideas rather than through substantial movement of western Iranian farmers.

For Reich, Shinde, and their team, these findings are just the beginning. "The Harappans built a complex and cosmopolitan ancient civilization, and there was undoubtedly variation in it that we cannot detect by analyzing a single individual," Shinde says. "The insights that emerge from just this single individual demonstrate the enormous promise of ancient DNA studies of South Asia. They make it clear that future studies of much larger numbers of individuals from a variety of archaeological sites and locations have the potential to transform our understanding of the deep history of the subcontinent."

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This work was supported by the NCP fund of the Council of Scientific and Industrial Research (CSIR), Government of India, Deccan College, Deemed University, Government of Haryana the National Science Foundation, the National Institutes of Health, an Allen Discovery Center grant, and the John Templeton Foundation.D.R. is an Investigator of the Howard Hughes Medical Institute. The authors declare no competing interests.

Cell, Shinde and Narasimhan et al.: "An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers" https://www.cell.com/cell/fulltext/S0092-8674(19)30967-5

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