‘No genetic basis for Brahmin, dalit or OBC identities’: Niraj Rai

Dr Niraj Rai, group head, Ancient DNA Laboratory, Birbal Sahni Institute of Palaeosciences, Lucknow

Is a genetic map of India possible in one frame?

Very difficult. After Africa, India is probably the world’s most genetically diverse region—with distinct language groups, ethnicities and population structures. Present-day genomic data alone cannot fully reconstruct India’s demographic history; you would need sequencing data from millions of modern Indians just to understand the last 500-600 years. Ancient DNA changes that. It acts like a time machine, letting us reconstruct ancient migration patterns, mobility and adaptation going much further back.

Do genetic findings clash with oral histories?

Often. In India, we have repeatedly failed to validate them. The Kodavas of Karnataka claim Iranian ancestry—genetically, we couldn’t support that. Sinhalese communities assert distinct origins but are largely similar to neighbouring Tamil populations, with only minor north Indian gene flow detectable. In Ladakh’s so-called ‘Aryan villages’, we found no evidence of Alexander the Great’s lineage or any ancient Greek connection. Even caste-based origin narratives don’t hold up. Being a Brahmin myself, I can say I am not genetically distinct from neighbouring communities. Present-day Indians are highly mixed, and there is no strict genetic basis for caste divisions.

What did the Rakhigarhi DNA study actually reveal?

It is unfortunate that despite its importance, the findings are still widely misunderstood. The study had real limitations—a single female individual, and only partial genome data. But even that proved valuable. When we compared the Rakhigarhi genome against global ancient DNA databases, we found strong matches with ancient populations from Iran and Turkmenistan—populations that were themselves genetically unique, closely resembling neither modern nor most other ancient populations. We believe Harappan individuals had migrated to those regions, and used those datasets as proxy populations for modelling Harappan ancestry.

The analysis pointed to two major ancestral sources: ancient Iranian-related agriculturalist or hunter-gatherer lineages, and Andamanese-related (Onge) ancestry—the best available proxy for ancient south Asians who have been present in the region for roughly 60,000–70,000 years. Modelling suggested that these two lineages diverged around 10,000 years ago—one branch contributing to early Iranian agricultural populations, the other to Harappan ancestry—and did not significantly mix again for thousands of years. This implies agriculture in south Asia likely developed indigenously, rather than being introduced through large-scale migration from Iran or Anatolia.

The third key finding: present-day Indians carry steppe-related ancestry in varying proportions, but the Rakhigarhi individual had none. This confirms that Central Asian gene flow had not reached the Indus Valley Civilisation (IVC) by 2000 BC—steppe mixing came later.

In summary: indigenous agricultural development, no steppe ancestry in the Harappan period, and steppe integration occurring only after the IVC's decline.

The Harappans were among the ancient world’s most sophisticated people—Rakhigarhi, Mohenjo-daro, Lothal and Dholavira all demonstrate remarkable urban planning and maritime trade. And their genetic legacy endures across all of south Asia. Dravidian populations, north Indians, Kashmiris, Ladakhis, Sri Lankans—all carry Harappan-related ancestry to some degree. Whatever our linguistic or cultural differences, that shared Harappan ancestry remains a deep genetic bond connecting all south Asians.

What does this say about the Aryan theory?

Our findings strongly challenge the older Aryan invasion model. We have ancient DNA from roughly 1500–1200 BCE across different parts of India, and we simply don’t see strong steppe or Central Asian ancestry during that period. I will admit I once believed the traditional invasion narrative—I was taught that Brahmins were a superior group who migrated from Central Asia. The genetic evidence forced me to reconsider, and eventually I convinced my own family likewise.

What the data actually suggests is no sudden violent invasion. steppe-related admixture appears gradual, likely arriving much later—around 600–700 BCE in some regions. And having more or less steppe ancestry makes no population ‘superior’ or ‘pure’. There are no genetically pure populations anywhere on Earth. Every population is mixed.

A large-scale violent invasion would leave clear archaeological signatures—cultural replacement, new pottery, weapons, metallurgy, material culture tied to Central Asia. That evidence is not there. The IVC had already declined before significant steppe mixing occurred. Climatic stress and the collapse of trade networks pushed Harappan populations towards rural agricultural life, but it was not a sudden extinction. Population sizes actually continued growing, because agriculture and pastoralism were already well established. The Harappans did not disappear—their descendants spread across the subcontinent while later mixing occurred gradually.

Genetics cannot establish human superiority. Scientifically, ‘superior’ could only refer to better health outcomes, not race, caste or purity.

Why is the Sinauli excavation site important?

Sinauli yielded the first well-decorated war chariot from ancient India— almost certainly horse-drawn, even though horse remains have not been found yet. If horses existed in the upper Gangetic plains well before steppe integration or Central Asian arrival, it pushes back the timeline of indigenous horse use and potentially the chronology of the Rig Veda, which is full of horse references.

The site also connects with the Ochre Coloured Pottery (OCP) culture. As the Harappan civilisation declined and became localised, Harappan-descended groups moved into the Gangetic plains, mixed with OCP-associated populations and adopted local pottery traditions. It is a story of cultural amalgamation, not conflict, unlike parts of Europe and Africa where archaeology shows widespread skeletal trauma from organised warfare. Indian sites, by contrast, show relatively little such evidence.

What about genetically-based diseases in Indian populations?

Around 55 per cent of present-day Indians carry very high genetic disease risk. Previously, Ashkenazi Jews and Finns were considered the most extreme cases of genetic bottlenecking. But Indian populations now appear even more severely affected, largely because of long-term caste-based endogamy. Small ancestral groups expanded into large modern populations while remaining highly inbred, accumulating recessive mutations that cause serious disease.

We are already seeing the effects: roughly 5 per cent of some populations carry mutations linked to myosin-binding protein deletions, associated with sudden cardiac arrest and cardiomyopathy in young people. Other regions—Africa, east and southeast Asia, the west—do not show this burden at the same scale. India is uniquely affected.

What is the solution?

Long-term, the most effective solution is IVF with embryo screening— selecting the healthiest embryo before implantation. More immediately, genetic screening before marriage is critical. A test costing roughly ₹10,000–₹20,000 can identify whether both partners carry the same harmful recessive mutations. If they do, IVF becomes strongly advisable. Even without detected risk, IVF improves the chances of healthy offspring.

Marrying outside one’s caste or community helps, but is not sufficient on its own—both individuals may still carry harmful recessive genes. Genetic screening provides the clearest picture.

What does ancient DNA tell us about the origins of caste?

The rigid caste system is not deeply ancient. Genetically, we see no evidence of strict caste separation going back 4,000 years. My view is that rigidity set in around the 9th or 10th century, during periods of external invasion and instability, when smaller groups began restricting marriage within narrow social boundaries.

Is there a historical basis for India’s disease burden?

Even medieval samples from around 800 AD do not show this level of recessive gene load. The founder effect appears to have intensified over the last 1,200 years. It is particularly acute in some Muslim communities, where repeated marriage within the same extended family compounds the problem—there is no gotra-equivalent system to limit close inbreeding. Parsis show a similar pattern, with long-term endogamy contributing to population decline.

So match DNA instead of kundli?

I would say both. I am a believer in astrology—I think it offers a second layer of protection. Genetic screening and astrological calculation should both be followed seriously.

Is there an evidence-based case for ending the caste system?

Yes. There is no genetic basis for Brahmin, dalit or OBC identities—we are broadly the same. There is also no Vedic basis for the rigid caste hierarchy as it exists today. That said, if people continue to marry within their communities, genetic screening becomes even more important.

Can practices like yoga, pranayam or meditation influence our DNA?

The genetic blueprint itself doesn’t change. But gene expression can be regulated through epigenetic modification. Meditation appears to influence stress responses, hormonal systems and how certain genes behave, potentially reducing the expression of harmful genes. You are not changing your DNA, but you may be controlling how it expresses itself. That, to me, is the real power of meditation.