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India Harbors Half the World’s Neanderthal DNA

Scientists analyzing the genomes of nearly 3,000 Indians have uncovered something unexpected: this single country preserves about half of all surviving Neanderthal genetic material—more ancient human DNA than any other population studied to date.

The finding emerged from the largest genetic survey of India ever conducted, published today in Cell. Researchers sequenced complete genomes from 2,762 individuals across 18 states, representing the subcontinent’s extraordinary diversity of languages, ethnicities, and geographic regions.

“One of the most striking and unexpected findings was that India harbors the highest variation in Neanderthal ancestry among non-Africans,” said co-lead author Laurits Skov, formerly of UC Berkeley. The team reconstructed roughly 50% of the Neanderthal genome and 20% of the Denisovan genome from Indian individuals alone.

A 50,000-Year Migration Story

The genetic analysis traces most Indian ancestry back to a single major migration out of Africa around 50,000 years ago. These early humans interbred with Neanderthals and Denisovans before spreading across Eurasia, carrying between 1% and 2% archaic human DNA in their genomes—similar to Europeans.

But India’s complex history created a unique genetic mosaic. Around 10,000 years ago, farmers from Iran and nomadic herders from Central Asia mixed with local hunter-gatherers. Then, about 5,000 years ago, many communities shifted toward endogamy—marriage within specific groups—creating genetic bottlenecks that preserved rare DNA variants.

“This complex history highlights how critical it is to incorporate ancestry and homozygosity in future medical and functional genomics research in India,” said senior author Priya Moorjani, a UC Berkeley molecular biologist.

Medical Implications Hidden in History

The study revealed important health connections tied to this genetic heritage:

  • A mutation causing dangerous reactions to anesthetics appears almost exclusively in Indian communities, particularly among the Vysya people of Andhra Pradesh and Telangana
  • Numerous rare disease variants exist at higher frequencies in specific populations due to founder effects
  • Some Neanderthal DNA segments appear linked to immune function and may influence disease susceptibility

The research identified one particularly intriguing genetic region: a stretch of Denisovan DNA in the BTNL2 gene, part of the immune system’s major histocompatibility complex. This sequence appears at unusually high frequency—about 10%—in Indians and East Asians but is rare in Europeans and absent in Oceanians.

Rewriting Human Migration Models

The sheer volume of archaic DNA preserved in India challenges existing models of human dispersal. “Did the range of Neanderthals and Denisovans extend to South Asia? Did modern humans encounter Neanderthals further east in Eurasia rather than the Middle East as widely believed?” the researchers ask.

Archaeological evidence from sites like Sarazm in Tajikistan supports the genetic findings. One ancient individual there was buried with shell bangles identical to those found at Neolithic sites in India and Pakistan, made from sea shells originating in the Indian Ocean.

The study also confirmed that Indians carry ancestry from three main sources: ancient Iranian farmers (27-68%), indigenous South Asian hunter-gatherers (19-69%), and Central Asian steppe pastoralists (0-45%). This complex mixing, followed by thousands of years of endogamous marriage practices, created the genetic landscape researchers see today.

A Living Library of Human Evolution

With around 5,000 distinct ethno-linguistic and religious groups, India represents one of humanity’s most genetically diverse regions. Yet until now, Indian populations remained underrepresented in global genomic studies.

The researchers found 24 million genetic variants never seen before, with the vast majority being rare variants specific to Indian populations. This previously hidden diversity offers crucial insights for understanding human evolution and developing precision medicine approaches.

“These findings fill a critical gap and reshape our understanding of how ancient migrations, archaic admixture and social structures have shaped genetic variation and risk of diseases,” Moorjani explained.

The team continues analyzing genomes from the larger LASI study, which has collected data from over 70,000 individuals, aiming to understand aging and age-related diseases across India’s diverse populations.

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