Modern Indian People Have a Wide Range of Neanderthal DNA, Study Finds

The genomes of people in India today contain a wide range of Neanderthal DNA—with more diversity in gene sequences from our ancient relatives than any other modern population previously examined, new research finds.

The study, which was posted to the preprint server bioRxiv last month and has not yet been peer reviewed, also examined the Iranian ancestry of Indian people and found that a migration out of Africa around 50,000 years ago contributed most of India’s current genetic diversity.

India has been “underrepresented in whole genome sequencing studies,” the authors write. The researchers analyzed 2,762 genomes from India, both providing insight into the population history of the country and expanding the scope of such studies, which have usually been focused on people of European ancestry.

“We’re learning a lot about populations that we didn’t know much about,” Kelsey Witt, a population geneticist at Clemson University who did not contribute to the findings, tells Science’s Michael Price.

While some recent genomic studies have included Indian populations, they’ve typically sampled very few people or focused on Indian people living outside of India, thus representing only a narrow range of the genetic diversity seen within the country today, the authors write. As a result, researchers have only a limited understanding of India’s genetic history.

Very excited to share out recent work on Indian evolutionary history led by @e_kerdoncuff & @SkovLaurits. Many surprises (e.g., archaic ancestry in India) and some clarifications (e.g. source of Iranian-farmer ancestry related to Sarazm) and timing of OOA in India. More details https://t.co/kiANY4kJPH

— Priya Moorjani (@moorjani_priya) February 21, 2024

For the new study, the researchers looked at a nationally representative sample of genomes of people 60 years or older. The data included people from most geographic regions, speakers of all major languages in the country and people from all tribes and caste groups. The researchers studied the DNA of people from 18 states and included people from both rural and urban areas.

Scientists already understood that most Indians are descended from three groups: ancient Iranian farmers, Eurasian steppe herders and South Asian hunter-gatherers. But until now, they didn’t have a clear idea on how the Iranian farmers came to the region, study co-author Priya Moorjani, a population geneticist at the University of California, Berkeley, tells Live Science’s Emily Cooke.

By comparing modern Indian DNA to ancient DNA that had been collected from people with Iranian ancestry, they traced this genetic heritage to a group of farmers in Sarazm, located in modern-day Tajikistan.

The team also found that 1 to 2 percent of Indian ancestry comes from Neanderthals and Denisovans. Most other modern humans also have this percentage of Neanderthal and Denisovan DNA, except for African people, who on average get 0.5 percent of their DNA from Neanderthals, according to New Scientist’s James Woodford.

Neanderthals, the closest extinct human relative, lived in the same parts of western Asia as modern humans for 30,000 to 50,000 years. Denisovans were close relatives of both Neanderthals and modern humans that interbred with both species.

“By studying modern Indian DNA, we recovered about 50 percent of the Neanderthal genome and 20 percent of the Denisovan genome that entered the Indian gene pool long ago,” Moorjani tells the Times of India’s Neha Madaan. “Moreover, we discovered that Indians have the most unique Neanderthal segments compared to people worldwide.”

The DNA in the study contained more than 90 percent of known Neanderthal gene sequences, and almost 12 percent of the Neanderthal sequences found in India had never been seen before. The discovery suggests researchers might be able to reconstruct the Neanderthal genome from studying living humans, rather than having to extract DNA from ancient remains, writes New Scientist.

Most of the genetic variation observed in the study was attributed to a major migration out of Africa 50,000 years ago. The findings indicate that researchers should re-examine models of human origins to account for the genetic diversity of India, the study authors write.

Studying Indians’ genetic ancestry inherited from Neanderthals could provide insights into genetic health risks, as DNA from these human relatives may be linked to diseases, Niraj Rai, who studies ancient DNA at the Birbal Sahni Institute of Paleosciences in India and was not involved in the research, tells the Times of India.

While the researchers may have identified some genes from Neanderthals and Denisovans that confer evolutionary benefits on those who inherit them, it’s too early to say what the advantages might have been, writes Science.

Will Sullivan | | READ MORE

Will Sullivan is a science writer based in Washington, D.C. His work has appeared in Inside Science and NOVA Next.