India Genetic Study Reveals Surprising Threads of Modern Ancestry

India, the world's most populous nation, has historically been under-represented in genetic research. That omission has created a substantial blind spot in efforts to understand human origins and the genetic diversity of our species.

A new study examining the past 50,000 years through thousands of genomes aims to address this shortfall, uncovering several unexpected strands in the complex ancestry of present-day India.

India genetic study maps population diversity

Population geneticist Elise Kerdoncuff of the University of California, Berkeley, and her colleagues sequenced DNA from 2,762 people in India. The sample included people from most geographical regions, rural and urban communities, speakers of every major language, and tribal and caste groups, in an effort to reflect the country's exceptional diversity.

The team sought answers to major questions: when did modern humans first reach India from Africa? Did they arrive as part of the principal migration out of Africa, or did an earlier movement take place, possibly following a coastal route? They also investigated what genetic evidence remains in Indian populations from the extinct archaic humans Neanderthals and Denisovans.

"These analyses provide a detailed view of the population history of India and underscore the value of expanding genomic surveys to diverse groups outside Europe," Kerdoncuff and colleagues write in their preprint, which has been posted to bioRxiv ahead of peer review.

Earlier research has indicated that most Indians trace their ancestry to three ancestral populations: descendants of ancient Iranian farmers, who came to the Indian subcontinent at some point between 4700 and 3000 BCE; pastoralists from the Eurasian steppe, who entered India between 1900 and 1500 BCE; and indigenous South Asian hunter-gatherers, who had occupied the region far earlier.

Kerdoncuff and colleagues found considerable variation in the contribution from these three groups among modern Indian individuals, although distinct trends were apparent.

For instance, ancestry linked to Andamanese hunter-gatherers was greatest in southern India and lowest in the north, while also being more prevalent among particular language and caste groups.

"This highlights that the ancient admixture events are related to the spread of languages and the history of the traditional caste system in India," Kerdoncuff and colleagues write.

Ancient migration links between Sarazm and India

By modelling how previously recovered ancient DNA from Iranian-related groups may have produced the genomic sequences of the present-day Indians included in the research, the scientists concluded that the most probable explanation involved an arrival of farmers from Sarazm, an ancient farming centre in present-day Tajikistan.

Archaeological research had already suggested trading links between Sarazm and South Asia. However, the connection was not solely in one direction: among the ancient Iranian ancestors, Kerdoncuff and colleagues identified one individual who also carried signs of Indian genetic ancestry.

"Societies were far more connected in deep time than most have given them credit for," Michael Frachetti, an archaeologist at Washington University in St. Louis who was not involved in the research, told journalist Michael Price at Science.

Looking still further into the past, the researchers determined that modern Indians receive 1-2 percent of their ancestry from archaic hominins, Neanderthals and Denisovans, a level comparable with that in Europeans and Americans.

However, the genomes analysed in the study contained a much broader range of Neanderthal and Denisovan genetic material than those of other sampled populations.

"Strikingly, [about] 90.7 percent of worldwide Neanderthal sequences are seen in India" and "around 51 percent of Denisovan sequences are unique to India," Kerdoncuff and colleagues write.

Finally, regarding their central question about the origins of Indians, the team concluded that most genetic variation in India comes from one large migration out of Africa around 50,000 years ago. Earlier waves of migration appear to have contributed little genetic material to present-day Indian populations.

The study has not yet undergone peer review and is available on the bioRxiv preprint server.