NRI PULSE STAFF REPORT
Landmark study uncovers deep ancestral roots, archaic DNA, and rare variants linked to disease in Indian population
A study mapping the entire genome of more than 2,700 individuals from across India has revealed that the country’s genetic diversity is among the richest and most complex in the world — and has a profound impact on health and disease susceptibility today.
Published in the prestigious journal Cell, the research, led by Dr. Priya Moorjani of UC Berkeley and a global team of scientists, is the most comprehensive genomic survey ever conducted in India. It uncovers a sweeping evolutionary history that stretches back 50,000 years — from the first human migration out of Africa to the more recent impacts of cultural practices such as endogamy.
Three Major Ancestral Groups
The study found that the majority of Indians today carry ancestry from three ancient populations:
- South Asian hunter-gatherers (AHG),
- Neolithic Iranian-related farmers and herders, and
- Eurasian Steppe pastoralists.
These ancestries began to mix thousands of years ago. For example, a major influx of Iranian farmer ancestry came from a group of 4th millennium BCE farmers and herders in Tajikistan, known archaeologically as Sarazm. Intriguingly, shell bangles worn by a Sarazm woman are identical to those found at ancient sites in Pakistan and Gujarat, suggesting active trade and cultural exchange with early Indus Valley civilizations.
Endogamy and Disease Risk
Over time, especially in the last few thousand years, India experienced a demographic shift toward endogamy — marrying within one’s community. This has led to unusually high levels of homozygosity (inherited identical copies of genes from both parents) and shared ancestry. On average, each participant in the study had at least one fourth-degree relative in the dataset — a level of genetic closeness not commonly seen in such studies.
This tight genetic structure increases the likelihood of inheriting rare, recessive genetic disorders. The team cataloged over 160,000 genetic variants never before documented, many of which are linked to congenital conditions, metabolic diseases, and neurological disorders such as dementia. Some variants, such as the one responsible for BCHE deficiency, were common in specific Indian communities but absent outside the country.
Neanderthal and Denisovan Legacy
Remarkably, the study also found that Indians possess more genetic variation from archaic humans — Neanderthals and Denisovans — than any other modern population. About 1–2% of Indian ancestry comes from these ancient cousins, but Indians retain a broader range of archaic variants.
Some of these variants may have helped ancient Indians adapt to their environments. For instance, immune-related genes inherited from Denisovans and Neanderthals may influence how modern Indians respond to infections, including COVID-19. One gene cluster on chromosome 3, inherited from Neanderthals, has already been linked to severe COVID symptoms.
The research also identified areas of the genome — called “ancestry deserts” — where no Neanderthal or Denisovan DNA remains. Notably, one of these regions includes the FOXP2 gene, which plays a key role in human language development.
A Call for India-Focused Medical Genomics
This extensive genetic mapping has major implications for public health. It highlights the urgent need to include Indian populations in global medical research. Disease studies and drug development often rely on genetic data from European or East Asian populations, which can miss critical variants unique to South Asians.
By understanding India’s unique genetic history, researchers and doctors could better diagnose inherited diseases, tailor treatments, and design more inclusive public health strategies.
Limitations and the Road Ahead
While this study sets a new benchmark, the researchers acknowledge limitations. Ancient DNA from India and Central Asia remains scarce, making it difficult to precisely pinpoint the origins of some ancestries. As more ancient genomes become available, scientists hope to refine these insights further.
Still, the findings provide a powerful reminder of how ancient migrations, social customs, and interbreeding with archaic humans continue to shape the health of millions of Indians today.
As Dr. Moorjani puts it, “Understanding our past is key to improving health outcomes in the future.”
