Treasure Trove

Largest-ever ancient-DNA study illuminates millennia of South and Central Asian prehistory

Photo of gravesite taken from above shows a skeleton and pots with a measuring stick
The first sequenced genome from an archaeological site associated with the ancient Indus Valley Civilization came from this woman buried at the city of Rakhigarhi. Image: Vasant Shinde/Cell

The largest-ever study of ancient human DNA and the first genome of an individual from the ancient Indus Valley Civilization reveal in unprecedented detail the shifting ancestry of Central and South Asian populations over time.

The research, published online Sept. 5 in a pair of papers in Science and Cell, also answers longstanding questions about the origins of farming and the source of Indo-European languages in South and Central Asia.

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Geneticists, archaeologists and anthropologists from North America, Europe, Central Asia and South Asia analyzed the genomes of 524 never before-studied ancient individuals. The work increased the worldwide total of published ancient genomes by about 25 percent.

By comparing these genomes to one another and to previously sequenced genomes, and by putting the information into context alongside archaeological, linguistic and other records, the researchers filled in many of the key details about who lived in various parts of this region from the Mesolithic Era (about 12,000 years ago) to the Iron Age (until around 2,000 years ago) and how they relate to the people who live there today.

“With this many samples, we can detect subtle interactions between populations as well as outliers within populations, something that has only become possible in the last couple of years through technological advances,” said David Reich, co-senior author of both papers and professor of genetics in the Blavatnik Institute at Harvard Medical School.

“These studies speak to two of the most profound cultural transformations in ancient Eurasia—the transition from hunting and gathering to farming and the spread of Indo-European languages, which are spoken today from the British Isles to South Asia—along with the movement of people,” said Vagheesh Narasimhan, co-first author of both papers and a postdoctoral fellow in the Reich lab. “The studies are particularly significant because Central and South Asia are such understudied parts of the world.”

“One of the most exciting aspects of this study is the way it integrates genetics with archaeology and linguistics,” said Ron Pinhasi of the University of Vienna, co-senior author of the Science paper. “The new results emerged after combining data, methods and perspectives from diverse academic disciplines, an integrative approach that provides much more information about the past than any one of these disciplines could alone.”

“In addition, the introduction of new sampling methodologies allowed us to minimize damage to skeletons while maximizing the chance of obtaining genetic data from regions where DNA preservation is often poor,” Pinhasi added.

One of the most exciting aspects of this study is the way it integrates genetics with archaeology and linguistics.

Ron Pinhasi

University of Vienna

This problem has been in the air for 200 years or more and it’s now rapidly being sorted out.

Nick Patterson

Research fellow in genetics, HMS

The study directly ties present-day South Asians to the ancient peoples of South Asia’s first civilization. 

Vagheesh Narasimhan

Postdoctoral fellow, HMS