South Asians are descended from a mix of farmers, herders, and hunter-gatherers, ancient DNA reveals

AUSTIN—Today, the population of South Asia is divided into dozens of ethnic, linguistic, and religious groups that live side by side—but not always in harmony. A contentious border separates India and Pakistan; political movements draw stark lines between India’s Muslim and Hindu populations. Groups don’t mix much, as people tend to marry those who share their ethnicity and tongue.

Now, a study of the first ancient DNA recovered from South Asia shows that populations there mingled repeatedly thousands of years ago. Nearly all of the Indian subcontinent’s ethnic and linguistic groups are the product of three ancient Eurasian populations who met and mixed: local hunter-gatherers, Middle Eastern farmers, and Central Asian herders. Three similar groups also mingled in ancient Europe, giving the two subcontinents surprisingly parallel histories.

The study, presented here last week at the meeting of the American Association of Physical Anthropologists and in a preprint on the bioRxiv server, sheds light on where these populations came from and when they arrived in South Asia. It also strengthens the claim that Proto-Indo-European (PIE)—the ancestral language that gave rise to modern languages from English to Russian to Hindi—originated on the steppes of Asia.

“It’s first-rate work,” says Partha Majumder, a geneticist at the National Institute of Biomedical Genomics in Kalyani, India. He found hints of similar genetic patterns in his previous studies, but the addition of ancient DNA makes the new conclusions stronger, he says. “It’s absolutely stunning.”

Priya Moorjani, a geneticist at the University of California, Berkeley, studies how South Asian populations relate to each other and to others around the world. In previous work, she analyzed the genomes of nearly 600 modern Indians and Pakistanis from 73 ethnolinguistic groups in South Asia. Her team found that almost all people living in India today carry ancestry from two ancient populations: Ancestral North Indians, who were more related to people from Central Asia, the Middle East, the Caucasus, and Europe; and Ancestral South Indians, who were more related to indigenous groups living in the subcontinent today. But without DNA from ancient people, Moorjani couldn’t be sure who gave rise to those ancestral populations, or when.

Moorjani, David Reich of Harvard University, and Kumarasamy Thangaraj of the Centre for Cellular and Molecular Biology in Hyderabad, India, spent years searching for ancient DNA in South Asia, where hot climates might degrade it. Finally, their team recovered and analyzed ancient genomes from 65 individuals who lived in northern Pakistan between 1200 B.C.E. and 1 C.E. They also analyzed 132 ancient genomes from Iran and southern Central Asia, and 165 from the steppes of Kazakhstan and Russia, and compared them with published ancient and modern genomes. These data allowed them to reconstruct when different populations arrived in South Asia and how they interacted.

Between 4700 and 3000 B.C.E., farmers from Iran mixed with hunter-gatherers indigenous to South Asia, Moorjani said. This combination of ancestries was found in the DNA of skeletal remains from sites in Turkmenistan and Iran known to have been in contact with the Indus Valley civilization, which thrived in Pakistan and northwest India starting around 3300 B.C.E. The researchers dub this population “Indus periphery.” The 65 ancient people from Pakistan also show this combination, although they all lived after the Indus civilization declined. The researchers suspect that “Indus periphery” people actually may have been the founders of Indus society, although without ancient DNA from Indus Valley burials, they can’t be sure.

Still, Moorjani’s team sees this ancient mixture of Iranian farmers and South Asian hunter-gatherers all over South Asia today. As the Indus Valley civilization declined after 1300 B.C.E., some Indus periphery individuals moved south to mix with indigenous populations there, forming the Ancestral South Indian population, which today is more prominent in people who speak Dravidian languages such as Tamil and Kannada, and in those belonging to lower castes.

Meanwhile, herders from the Eurasian steppe moved into the northern part of the subcontinent and mixed with Indus periphery people still there, forming the Ancestral North Indian population. Today, people who belong to higher castes and those who speak Indo-European languages such as Hindi and Urdu tend to have more of this ancestry. Shortly after, these two already mixed groups mixed with each other, giving rise to the populations living in India today.

“Strikingly, this is very similar to the pattern we see in Europe,” Moorjani said. Around 7000 B.C.E., agriculture spread into both Europe and South Asia with farmers from Anatolia and Iran, respectively, who each mixed with local hunter-gatherer populations. After about 3000 B.C.E., Yamnaya pastoralists from the Central Asian steppe swept both east and west, into Europe and South Asia, bringing the wheel and perhaps cannabis.

Earlier genetic work had linked the arrival of these herders to the spread of Indo-European languages in Europe. But other researchers, including archaeologist Colin Renfrew of the University of Cambridge in the United Kingdom, had argued that the earlier Anatolian farmers were the original PIE speakers. The new data “make a strong case” for the Yamnaya as carriers of Indo-European languages, Renfrew says. But he still thinks Anatolian farmers could have spoken the earliest language in that family.