Genetic Study Reveals Shocking Details about Ancestry of Modern Indians

Featuring a rich and diverse mix of ethnicities and cultures, the people of South Asia have always been a source of fascination for scientists interested in studying human evolution and genetics. It was this interest that motivated what is so far the most extensive analysis ever undertaken of the genetic heritage of the people of India, which has revealed some eye-opening details about who these individuals really are and about how their ancestors arrived in the region.

In a study recently published in the journal bioRxiv, a multinational team of genetic scientists, led by University of California—Berkeley population geneticist Priya Moorjani, disclosed the findings of their study of the genomes of a broad sampling of residents of India, the second-most populous country in the world. This analysis revealed new details about India’s ancient connection to the lands of modern-day Iran (migrants from that region helped populate India), plus information about when the first hunter-gatherers arrived in India to stay.

But even beyond this data, the researchers discovered something quite fascinating. They learned that the Indian genomes contain a more diverse sampling of Neanderthal and Denisovan DNA than had previously been suspected. The fossilized remains of neither the Neanderthals nor their close relatives the Denisovans have ever been found in India, which leaves researchers no choice but to speculate on how all this genetic material from these extinct human cousins managed to infiltrate India’s collective gene pool.

Reconstructed face of a Siberian Denisovan (right) alongside the Hebrew University’s representation of a Sunda Denisovan (left). (Left © Hernandez/Cartwright/Collins; Right) © Maayan-Harel)

A Diverse People with Diverse Ancestors

The majority of Indians are related to three groups of ancient ancestors. This includes hunter-gatherers who settled the region tens of thousands of years ago, agriculturalists from the region of modern-day Iran who migrated to the Indian subcontinent in search of arable land between 4,700 and 3,000 BC, and wandering herders from the steppes of central Eurasia who invaded Indian territory in the early-to-mid second millennium BC.

Seeking to explore these relationships in a more in-depth manner, Priya Moorjani and her colleagues were able to fully sequence the genomes of approximately 2,700 modern Indians, working with data obtained from the Longitudinal Aging Study in India–Diagnostic Assessment of Dementia (LASI-DAD). This represented by far the biggest sampling of Indian DNA ever studied, and included representatives from every geographic region, language group, ethnic identity and social class.

The new study confirmed the first two of these relationships. However, the genetic signal was too weak from the final group to firmly establish a genetic connection.

 

Adding a comparative aspect to their studies, the researchers also studied DNA extracted from other people living in South and Central Asia, to see if any further relationships might be detected. They hit paydirt using this method, as they were able to genetically link modern Indians with a prehistoric farming-based community known as Sarazm, which is located in what is now Tajikistan in Central Asia, approximately 750 miles (1,200 kilometers) northeast of India. Farmers who lived at this thriving Neolithic settlement grew wheat and barley and also raised cattle, and were known to have formed extensive trading networks throughout the surrounding region.

Crowded street in New Delhi, India. (Marco Taliani/Adobe Stock)

Unveiling the Historical Ties Between Sarazm and India

Michael Frachetti, an archaeologist at Washington University in St. Louis who didn’t participate in the new study, was intrigued by the discovery of the connection between the people of ancient Sarazm and modern India. Based on his independent research he is convinced that Sarazm was an important regional crossroads and trading hub several thousand years ago, and he further believes that the people of Sarazm helped spread farming knowledge and technologies into northern India. 

“There’s a very significant story being told here,” he told an interviewer from Science. “Societies were far more connected in the past than most have given then credit for.”

Further evidence of this connection was revealed when the researchers looked more closely at the DNA sequences obtained from the skeletal remains of an ancient resident of Sarazm, and discovered that they contained traces of Indian DNA. Another skeleton excavated from a cemetery found at Sarazm was buried with ceramic bracelets that match similar pieces of jewelry known to have been manufactured in Neolithic period India.

“That really helped directly connect the two cultures, and it showed that it wasn’t just one-way mixing,” Moorjani explained.

Looking beyond the migrations that helped populate India 5,000 years ago, the genetic scientists were able to detect traces of DNA that came from the earliest hunter-gatherers who settled in India.

These people have sometimes been credited with making stone tools found at Indian archaeological sites that date back to 80,000 BC, although this claim has proven controversial because of the lack of skeletal discoveries at the same sites. Addressing this issue, the scientists were able to link the earliest hunter-gatherer DNA in the Indian population with a single migration of people who arrived from Africa about 50,000 years ago, which rules out the possibility that hunter-gatherer ancestors were responsible for the creation of the stone tools. This means modern Indians aren’t related to those ancient toolmakers, whoever they might have been.

The Surprisingly Deep Connection between Neanderthals and Modern Indians

Undoubtedly the biggest surprise to emerge from this new research is the discovery of a robust Neanderthal and Denisovan presence in the genomes of modern Indians, with the Neanderthal DNA fingerprint in particular standing out.

In total, between one and two percent of Indian DNA was inherited from these two extinct archaic human species. This is in line with what has been discovered in other human populations. But what is unique is the sheer diversity of the Neanderthal DNA that modern Indian genomes contain. Approximately 90% of all the Neanderthal DNA known to have existed is represented somewhere in the collective Indian gene pool, which is 50% more than was found in the genes of Icelanders who were analyzed in a similarly designed study.

Despite the fact that Neanderthal bones have never been excavated in India, they may still have resided in the region tens of thousands of years ago, encountering humans and mating with them before going extinct in approximately 40,000 BC. Different groups of Neanderthals carrying diverse sets of genes may have visited and/or lived in India during those times, which would explain the rich diversity of DNA they passed on to the ancestors of modern Indians. If they left no remains, it suggests those Neanderthal groups didn’t choose to remain in India for an extended period, perhaps because the animals they preferred to hunt were relatively scarce, or because they found the hot climate uncomfortable.

But it’s also possible that the richness of the Neanderthal DNA reflects the diversity of India’s people. The migrants who came to India from Iran, Sarazm, the steppes of Central Asia and elsewhere may have brought a wide sampling of Neanderthal genes with them, and the mixing and matching that took place over thousands of years may have ensured that an impressive collection of Neanderthal DNA would remain rooted in India’s genetic heritage.

The discovery of so much Neanderthal DNA in the people of India does raise one intriguing possibility, and that is that Neanderthals may have been the ones who made the 80,000-year-old tools that have been found at various archaeological sites. It is known that bones tend to decay much more rapidly in hot and humid climates, like that found in India, and that may explain why the Neanderthals left behind tools and DNA but no skeletal remains.

As of now this idea is only speculation, and will have to remain so until the day comes when Neanderthal bones are actually excavated in India, with stone tools buried right beside them—if such a day ever comes.

Top image: Indian family standing and smiling holding their kids in the park. Source: kristineldridge/Adobe Stock

By Nathan Falde