Rare Ancient DNA Provides Window Into a 5,000-Year-Old South Asian Civilization

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Rare Ancient DNA Provides Window Into a 5,000-Year-Old South Asian Civilization

Two new genetic studies published shed light on the Indus Valley Civilization, one of the earliest human civilizations. The work sheds light on the origins of these people who built one of the cradles of civilization. Just as importantly, it also reveals where they went.

Rare Ancient DNA Provides Window Into a 5,000-Year-Old South Asian Civilization
The skeleton of an individual from the Indus Valley Civilization whose fragile, ancient DNA revealed links to modern-day South Asian populations.

The Indus Valley civilization is one of earliest civilizations in world history, rivaling Mesopotamia and Ancient Egypt in scale. Nestled along the fertile flood plain of the Indus River, the Indus Valley was home to an estimated one million people spread over a Texas-sized region in what is now India and Pakistan some 4,000 to 5,000 years ago. 

Located at the crossroads of historic trade routes, the region has been settled by a number of groups through time. But where the first civilization to arise there came from was a mystery.

New research suggests that it was a homegrown effort: nearby hunter-gatherer groups likely coalesced into a civilization that defined this early chapter in India’s history. And from there, the peoples of the Indus Valley would spread beyond India, leaving their mark on a wide swath of South Asia.

Unlocking Ancient DNA

One of the new papers out this week, published in Cell, offers the first-ever look at a genome from an individual from the Indus Valley Civilization. Finding DNA from this part of the world is extremely rare because hot and humid climates aren’t ideal for DNA preservation.


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However, after screening 61 skeleton samples excavated from an Indus burial site outside of New Delhi, the researchers stumbled on one with a small amount of DNA still preserved.

It belonged to a woman who lived around 4,000 years ago. After discovering the rare find, the researchers painstakingly sequenced the DNA sample to obtain a full genomic picture.

A map of the Indus Valley, or Harappan, Civilization. Rakhigarhi, the location of the burial that yielded ancient DNA for analysis, is highlighted in blue.

These findings offer clues into how farming began in South Asia. A long-held theory was that migrants from the Fertile Crescent — an area that includes southeastern Anatolia, Iran, Iraq, and Syria — spread across the Iranian plateau and then into South Asia, bringing their farming practices with them. And previous genetic studies into South Asian populations backed that theory up.

But the Indus woman’s genetic history told another story. Her ancestry was a mix of Southeast Asian and early Iranian hunter-gatherers. Missing was DNA from Fertile Crescent migrants or from another group called Steppe Pastoralists from Eurasia, also farmers. Because Iranian farmers and pastoralists didn’t arrive in the Indus region until later on, it’s an indication that the people of the Indus Civilization either figured out how to farm the land independently, or this practice was introduced to the region another way.

But the researchers also looked forward in time to see how the Indus woman was related to the people that inhabit South Asia today. In that analysis lay one of their most remarkable insights. There are strong genetic links between the Indus people and modern South Asians, which encompasses Afghanistan, Bangladesh, Bhutan, Maldives, Nepal, India, Pakistan and Sri Lanka, they found. Study author Vagheesh Narasimhan said this is evidence that all modern-day South Asians descend from people of the Indus Valley Civilization.

Moving and Mixing

The second study, which appeared in Science and was authored by many of the same researchers behind the Cell paper, offers more insights into the history of modern South Asians. Considered to be the largest study of ancient DNA ever published, it provides a closer look into the migrations and cultural transformations that shaped modern-day South Asian ancestry.

To chart this complex story of ancient movement and mixing, Narasimhan said the team analyzed 523 genomes from people excavated from around South and Central Asia who lived as early as 12,000 years ago (the Mesolithic Era) to 2,000 years ago (the Iron Age).

Similar to the companion study of the single genome, this analysis revealed that South Asians are closely related to the hunter-gatherers of Iran and Southeast Asia.

A red pot found near the head of the Indus Valley skeleton that yielded ancient DNA.

But, things get really interesting after the Indus Valley Civilization’s collapse in 1800 BCE. The society’s people — who were likely genetically similar to the ancient woman found outside of New Delhi —  mixed with ancestral groups from India’s peninsula. The researchers say the result of this mingling forms the backbone of modern-day South Indian ancestry.

Around the same time, others in the wake of the Indus Valley Civilization’s collapse were mixing with Steppe Pastoralists who migrated to the region — and who brought with them the early versions of Indo-European languages that are spoken in India today.

Illuminating the Past

Narasimhan said that these studies are testaments to the power of ancient DNA in bringing bygone civilizations to light. Expanding genome sequencing to larger numbers of people from a wider range of excavation sites in the Indus region could go a long way toward filling in more gaps in our knowledge.


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They hope to use their DNA decoding technique to unlock more secrets of the Indus Valley Civilization and learn about other ancient societies from underrepresented parts.


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