Where did India’s people come from? Massive genetic study reveals surprises

Analysis confirms Iranian influx, but also finds genes from Neanderthals and a mysterious human ancestor

South Asia is home to one of the most diverse assemblages of people in the world. A mélange of different ethnic identities, languages, religions, castes, and customs makes up the 1.5 billion humans who live here. Now, scientists have revealed the most detailed look yet of how this population took shape.

In the largest ever modern whole-genome analysis from South Asia—published as a preprint last month on bioRxiv—researchers reveal new details about the origin of India’s Iranian ancestry and when ancient hunter-gatherers settled the region. The study also turns up a surprise: an unexpectedly rich diversity of genes from Neanderthals and their close evolutionary cousins, the Denisovans. Because no fossils of these ancient human relatives have been found in India, researchers are speculating about how these genes got there—and why they stuck around.

Global genetic sequencing efforts have largely ignored India, says population geneticist Kelsey Witt of Clemson University, who wasn’t involved with the work. So, “We’re learning a lot about populations that we didn’t know much about.”

Most Indians are primarily a mixture of three ancestral populations: hunter-gatherers who lived on the land for tens of thousands of years, farmers with Iranian ancestry who arrived sometime between 4700 and 3000 B.C.E., and herders from the central Eurasian steppe region who swept into the region sometime after 3000 B.C.E., perhaps between 1900 and 1500 B.C.E.

In the new study, University of California, Berkeley population geneticist Priya Moorjani—who also co-led the previous work—and her colleagues confirm the identities of those ancestral groups. They also add fresh wrinkles by using a much larger sample of modern Indians than previous analyses. Working with data from the Longitudinal Aging Study in India–Diagnostic Assessment of Dementia (LASI-DAD), Moorjani’s team sequenced more than 2700 modern Indian genomes—hundreds more than in past studies—including people from nearly every geographic region, speakers of every major language group, and all tribes and castes.

To find out more about the identity of the Iranian-related farmers who entered the region thousands of years ago, the researchers analyzed previously extracted ancient DNA from groups with Iranian ancestry who predated the genetic pulse into India. They then played out simulations to see whose genes best matched the patterns seen in present-day Indians. The best fit came from farmers from an ancient agricultural center called Sarazm in the northwest of what today is Tajikistan. Farmers here grew wheat and barley and kept cattle, and traded extensively throughout Eurasia.

Interestingly, one ancient individual from Sarazm also carried traces of Indian ancestry; another was buried with ceramic bracelets similar to those made in ancient India. “That really helped directly connect the two cultures, and it showed that it wasn’t just one-way mixing,” Moorjani says.

Michael Frachetti, an archaeologist at Washington University in St. Louis, who wasn’t involved with the new work, says he is “highly compelled” by the finding. He has long argued that Sarazm would have been a key outpost for spreading farming and domestic animals—as well as human genes—south into Kashmir and northwestern India. “There’s a very significant story being told here,” he says. “Societies were far more connected in deep time than most have given then credit for.”

Still, other ancestral source populations, such as those from the steppe, remain somewhat “vague,” says biological anthropologist Gyaneshwer Chaubey at Banaras Hindu University. He says the relative paucity of ancient DNA samples from India means other, ancient source populations could be missing from the mix.

Even deeper in time, Moorjani and colleagues uncovered unexpected details about prehistoric migration and mingling. Scholars have debated over the years whether modern humans were responsible for stone tools found in India and dated to approximately 80,000 years ago, and if so, whether they left a genetic legacy in modern populations. But with no remains associated with these tools, researchers haven’t been able to pin down their makers.

The new study suggests those early toolmakers only left traces in living people. By estimating how much genetic mutation occurs between generations and calculating how long it would have taken India’s modern population to reach its current state of variation, Moorjani and her colleagues argue that the settlers who gave rise to contemporary Indians were part of a single migration out of Africa about 50,000 years ago.

In addition, the scientists found that the modern individuals sampled derive 1% to 2% of their ancestry from Neanderthals and their close cousins, the Denisovans—on par with Europeans. But Indians collectively carry a stunning variety of these archaic genes compared with other worldwide populations.

About 90% of all known Neanderthal genes that have made their way into human populations turned up in the 2700 Indian genomes. That’s about 50% more than was recovered in a similar study of Neanderthal DNA in Icelanders that analyzed more than 27,000 genomes. The researchers also identified several new candidates for Neanderthal- and Denisovan-inherited genes that may have given their descendants some evolutionary advantage, though it’s too early to say what those boons might have been.

Moorjani says ancient humans might have encountered and mated with a relatively large, genetically diverse population of our archaic cousins living on the subcontinent—although no fossils of those archaic cousins have been found. Another possibility is that India’s vast geographical boundaries and close kin–marrying traditions preserved different segments of Neanderthal DNA than on other continents.

Researchers need more genetic and archaeological studies to put those mysteries to rest, Witt says. “There are so many different possibilities, so many populations coming together. It’s a really complex problem to solve.”

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