Largest Ever Study On Ancient DNA Sheds Light On Modern South Asians' Complex Ancestry


Rosie McCall

Staff Writer

clockSep 6 2019, 13:16 UTC

The team sequenced the DNA of a single female from the Indus Valley Civilization. Here she is lying in a grave containing typical IVC grave goods. Vasant Shinde/Deccan College Post Graduate and Research Institute

Recent advances in DNA analysis have enabled scientists to determine the ancestry of people living thousands of years ago – a feat that would not have been possible just a few years ago. Now, two papers have used genome analysis to unravel the history of people living in South and Central Asia.


The first, published in Science, involved decoding genomes harvested from 523 ancient people who lived in a region spanning Iran, Russia, and India between 3,000 and12,000 years ago, making it the largest study of ancient DNA published to date, the study authors say. The project has increased the number of published ancient genomes by 25 percent and shifted the focus of that data further eastwards, as previous analysis has almost entirely centered on Europe. These were then compared to the ancestry of modern South Asians.

The results show the bulk of DNA in modern South Asians is inherited from groups of early hunter-gatherers in Iran and Southeast Asia, Bronze Age pastoralists from the European Steppe, and people from the Indus Valley Civilization. The pastoralists (also called 'Yamnaya') were the same group of people who took over large swathes of Europe circa 4,000 years ago, and it is this connection that the study authors believe explains the linguistic similarities between Indo-Iranian and Balto-Slavic branches of Indo-European language.

"Our maps in this study illustrate how transcontinental gene flow evolved over vast territory and thousands of years, but one must be careful not to view these genetic arrows as colonial invasions – in fact, our data show that human mobility typically brought about gradual change over the span of centuries, and sometimes millennia," co-senior author Michael Frachetti of Washington University, said in a statement.

The second study, published in Cell, reports on the first-ever successfully sequenced genome of a member of the Indus Valley Civilization, a Bronze Age civilization that covered the northern part of South Asia, was once larger than Mesopotamia, and disappeared mysteriously 4,000 years ago. Researchers looked at the DNA of a single woman, who died nearly 5,000 years ago in the Indus Valley at a site called Rakhigarhi, approximately 150 kilometers northwest of Delhi. The team was (eventually) able to extract enough DNA from the skeleton's ear bone, but it was no easy task and took more than 100 attempts. The region's hot climate means skeletons like these are often found in poor condition – indeed, hundreds of skeletons from the Indus Valley have been found but she was the only one of 61 sampled that produced genetic material.


"There’s no doubt this is the most intensive effort we’ve ever made to get ancient DNA from a single sample," said David Reich, a geneticist at Harvard University, Science reports.

Map of the Indus Valley Civilization (aka the Harappan civilization). "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," Vasant Shinde, an archaeologist at Deccan College, said in a statement. It was at its height between 2600 and 1900 BCE. Vasant Shinde / Deccan College Post Graduate and Research Institute

Testing reveals the skeleton was most likely a woman who lived sometime between 2800 to 2300 BCE, and that her ancestry was a combination of South Asian hunter-gatherer and Iranian. Interestingly, the latter part of her DNA was found to predate the Fertile Crescent's farming revolution circa 10,000 years ago by approximately 2,000 years.

This contradicts assumptions that the farmers of the Fertile Crescent – an area that includes today's Iran – moved eastwards and mingled with South Asian hunter-gatherers, and suggests the Iranian hunter-gatherers who preceded them were already at it. It also suggests that farming wasn't introduced to South Asia by the migration of those in the Fertile Crescent but instead, agriculture developed in the two regions separately and independently – or through cultural contact.


This skeleton was not a one-off. Eleven others analyzed in the first study displayed similar genes, suggesting they were migrants (or descendants of) from the Indus Valley. Still, the team hopes to analyze more DNA from Indus Valley sites and create an even clearer picture of the mixing of people and cultures in ancient Asia.

"What we see in both in the isotopic information as well as the archaeological information is trade and exchange of agricultural material and production happening in both directions," Vagheesh Narasimhan, co-first author of the first study, said in a statement.

"Now with the ancient DNA, we're actually seeing that in the people," he explained. "It's giving us confidence to understand what happened in the past and how this process is happening."