From Goa to Himalayas: How ancient DNA is rewriting Indian history

The Church of St Augustine in Goa held a mystery for nearly four centuries. It was one of the largest Augustinian churches in the world, but was abandoned in 1835 after the Portuguese expelled Augustinians from Goa and other parts of the empire. The mystery revolved around Portuguese and Georgian records which suggested that the remains of a queen who became a saint lay beneath the ruins of the church.

Her name was Ketevan, queen consort of David I of Kakheti in eastern Georgia. In 1614, more than a decade after the death of David, the Persian ruler Shah Abbas I invaded Kakheti and took the queen captive. She was executed in 1624 as she refused to convert to Islam. An Augustinian friar from Goa, it was believed, secretly recovered her remains and placed them in a black stone casket at the church in Goa.

As Georgians held onto the belief, officials from the Soviet state of Georgia approached India in 1980 to help locate the relics. In 2005, archaeologists accidentally uncovered three skeletal fragments near the chapel and labelled them QKT-1, QKT-2 and QKT-3. Could one of these bones belong to Queen Ketevan?

To find the answer, the Archaeological Survey of India turned to the fairly new Ancient DNA Laboratory at the Centre for Cellular and Molecular Biology in Hyderabad. Kumaraswamy Thangaraj, a CCMB geneticist, took up the case, later joined by research scholar Niraj Rai and geneticist Gyaneshwer Chaubey. “The Indian climate is not friendly to old bones,” said Thangaraj. “Heat, moisture, bacteria…, everything works against preservation.”

Mitochondrial DNA analysis showed that QKT-1 belonged to a woman, the other two to men from Goa. After analysing 30 samples brought from Georgia, the team concluded that QKT-1 was very likely Ketevan’s right-arm bone, lending strong support to the historical account of her remains.

The finding drew much excitement in Georgia. The relic was sent there for a six-month exhibition in 2017, and four years later, External Affairs Minister S. Jaishankar travelled to Tbilisi to formally hand it over. “The prime minister mentioned it in his Mann Ki Baat,” said Thangaraj, who received the Padma Shri in 2026. “That gives the satisfaction that what we do in the lab is helping society and governments.”

Analysis of ancient DNA has also helped explain a bit of a mystery regarding hundreds of skeletons found at Roopkund, a glacial lake at an altitude of 5,000m in Uttarakhand. It had puzzled researchers for decades. For long, it was assumed that the skeletons belonged to victims of a single catastrophic event. The DNA told a different story. “The skeletons belonged to two different periods, roughly a thousand years apart,” said Thangaraj.

The largest group of skeletons was of south Asian origin, which date to around 800 CE. Another group was of eastern Mediterranean origin, while one individual showed ancestry linked to southeast Asia. These two sets date to around 1800 CE.

“Our interpretation is that the south Asian group was on a pilgrimage to the Nanda Devi temple,” said Rai. “At some point they lost their way and reached the lake. Then a severe hailstorm [perhaps struck].” His team continues to study the skeletons through isotope analysis of teeth, which reveals where people lived and moved before death.

These old mysteries are being unravelled by a new generation of Indian geneticists using DNA to trace migrations, diets and population histories. The field has expanded rapidly over three decades with advances in sequencing technology. India, one of the world’s most genetically diverse regions, is an extraordinary laboratory for such work.

For much of the 20th century, archaeology belonged to the excavators, the people who dug through soil, cleaned pottery shards and decoded ancient scripts, a world glamorised on screen by the Indiana Jones franchise. That has changed. Some of the biggest breakthroughs now emerge from laboratories, where scientists in sterile suits read genetic signatures preserved in bone and teeth. The shovel now works with the sequencer.

Archaeologists identify where people lived and the material culture they left behind. Geneticists reveal where those people came from, how they moved, what they ate and how populations mixed over time. “It is like time travel,” said Rai. “Once we obtain ancient DNA data, we can effectively travel into the past. We conduct spatio-temporal analysis in the laboratory, and when we visualise the data, we can understand what was happening in a particular period.”

Thangaraj’s office on the leafy CCMB campus in Hyderabad is crowded with trophies, journals and a framed photograph with former president A.P.J. Abdul Kalam. He grew up in a farming family, where he learned the importance of preserving quality seed for better yield. After joining CCMB, he traced migrations within India, theorised on the origins of the caste system, studied the Onge of the Andaman Islands, who migrated from Africa around 65,000 years ago, and worked on genetic diseases that disproportionately affect Indians. Then came the discovery of the Rakhigarhi skeletons in 2015. The DNA analysis fuelled some of the most polarised debates in India and abroad.

For Rai, who had been preparing to study plant genomics, the Queen Ketevan case was a turning point, and he decided to study ancient DNA instead. Most geneticists have been working with existing genome data. In 2018 Rai moved to the Birbal Sahni Institute of Palaeosciences, Lucknow, and spent his first year building India’s first dedicated ancient DNA facility. The small lab, tucked into a corner of the Nehruvian-era building, is a clean room where controlled air pressure and UV lights prevent stray DNA from contaminating samples. Researchers work in gloves, masks and full-body suits, since a single touch of an ungloved hand deposits roughly a million skin cells, each carrying a complete human genome. “They stay in that suit for long periods,” said Rai.

The bone is cleaned mechanically, then chemically, then under UV light. A portion is powdered and dissolved in a solution that releases whatever genetic material remains, which is then filtered, concentrated and processed into a sequencing library. In colder climates, ancient DNA can survive in remarkable condition. In India, humidity accelerates decay. “We may have to repeat the extraction ten times for a single sample,” said Rai.

Two most useful parts of a skeleton are the teeth and the petrous bone, a dense wedge at the base of the skull near the inner ear. Its density keeps bacteria out long after death, so the cells inside decay more slowly. Whatever a child drank while her teeth were forming stays locked in the enamel for thousands of years, and since different regions carry different ratios of oxygen isotopes, each tooth holds a geographic signature that can provide clues about where a person grew up and, when combined with other evidence, how they moved during their lifetime.

Chaubey came to CCMB searching for answers about his own ancestry. He later completed his PhD at Tartu University in Estonia and now runs the Gyan Lab at the Banaras Hindu University, where one project examines whether genetic factors are associated with traits linked to ascetic behaviour.

His lab has also examined caste endogamy in the Gangetic plains, home to thousands of caste groups that marry strictly within their own community. “People may share food and festivals,” he said, “but they generally do not marry outside their community.”

That isolation leaves genetic signatures that can be read like historical documents. When Covid-19 struck, his team identified a gene variant that appeared to reduce viral entry into human cells, present in nearly 60 per cent of south Asians. That finding helped researchers zero in on small, isolated and endogamous tribal groups like the Onge who lacked the variant, making them the most vulnerable.

Equally interesting studies about Indian ancestry are being done at the University of California, Berkeley, by Priya Moorjani, associate professor at the university’s department of molecular and cell biology. Working with the largest modern whole-genome dataset ever assembled from south Asia, her team found evidence for the three-part ancestry model for Indian populations: ancient south Asian hunter-gatherers, Iranian-related farmers and steppe pastoralists.

One of Moorjani’s most striking findings concerns Neanderthals. No Neanderthal fossil has ever been found in India. Yet, analysis of 2,700 modern Indian genomes showed that about 90 per cent of all known Neanderthal genes were present in them, roughly 50 per cent more than what was found in a similar study of Neanderthal DNA in Icelanders that analysed 27,000 samples. Whether Neanderthals once lived in India and their fossils simply await discovery, or India’s patterns of endogamy have preserved different segments of Neanderthal DNA than elsewhere, remains an open question.

No study has tested India’s mixed ancestry more sharply than the one built around a 4,500-year-old skeleton found at Rakhigarhi in Haryana, 150km from Delhi. The individual carried no steppe ancestry, the genetic signature associated with pastoralists who swept into south Asia from central Asia in a migration now dated to roughly 2000-1500 BCE. “Our modelling suggested that around 10,000 years ago, a population split occurred,” said Rai. “One branch later contributed to early Iranian agriculturalists and another to the Harappan population. The steppe-related admixture entered south Asia later, after the mature Indus Valley period.”

One of the most contested ideas in Indian history is that a large migration of Indo-European-speaking peoples from the steppe fundamentally transformed the subcontinent’s population and culture. The Rakhigarhi data suggested something more nuanced. The Indus Valley people were largely indigenous at that time, tracing ancestry to ancient south Asian and Iranian hunter-gatherer lineages. The steppe pastoralists arrived later and mixed gradually with local populations. “There is no evidence of a violent invasion model,” said Rai. “Ancient DNA suggests that genetic mixing was gradual and happened much later, roughly around 600 BCE to 700 BCE in some regions.”

Archaeologists urge caution before drawing final conclusions. But Thangaraj and Rai return to the same point: almost every group in India carries both ancestral north Indian (ANI) and ancestral south Indian (ASI) heritage, in different proportions. North Indian populations carry some additional ancestry related to western Eurasian populations, while south Indian populations preserve a more distinct ancient south Asian component. Most of this mixing occurred between 4,000 and 2,000 years ago, blending and re-blending to create the genetic structure seen in Indians today. Linguistically and culturally, groups may differ. Genetically, they are connected.

That debate is one reason why Tamil Nadu pushed to build its own ancient DNA lab, to assess the lineage of the Tamils independently. G. Kumaresan, who heads the department of genetics at the Madurai Kamaraj University, has identified genetic continuity between populations who lived in the region for the past 3,000 years. His team, working with Liverpool John Moores University, has also reconstructed the face of an ancient south Indian person, an exercise Kumaresan calls “70 per cent science and 30 per cent art.”

At Mangalore University, M.S. Mustak and Jaison Sequeira, along with Ranajit Das and his team, have studied the Koraga, a small, isolated community on Karnataka’s west coast whose population has been declining steadily. Their work challenges long-standing claims linking the Koraga to the Africans, tracing them instead to ancient populations of the Iranian plateau, one branch of which remained hunter-gatherers while another turned to agriculture. “This is a highly inbred population, so we are also looking for exogamous clans within the community,” said Sequeira, who hopes the work could eventually inform genetic counselling and public health strategies for a community facing both demographic decline and social exclusion.

Chandana Basu, who runs the Genophen Lab at the Centre for Genetic Disorders, Banaras Hindu University, says ancient DNA explains why populations look and adapt differently, and why some are more susceptible to particular diseases. One of her key studies identified a gene, SLC24A5, linked through shared ancestry to west Eurasian populations, that plays a major role in determining skin colour variation among indigenous south Asians. Her more recent work on populations in Assam has challenged the old assumption that the northeast was genetically isolated, showing instead that the region acted as a major corridor connecting south Asia with east and southeast Asia.

The caste question sits at the intersection of all this. Can genetics identify when or how caste emerged? “From a genetic perspective, caste is not an ancient biological system,” said Rai. “It appears to have developed historically when populations began forming smaller endogamous groups. Even in the Rig Veda there is no genetic concept of caste.”

His lab has found similar patterns at nearly every site it has studied. Work on the Kodava community of Karnataka, whose oral traditions link them to Iran, found no genetic support for the claim. The Sinhalese of Sri Lanka turned out to be genetically close to populations in Tamil Nadu, with only a small contribution from north India. The oral histories may be vivid and specific. The genomes are indifferent to them.

For communities whose identities and social hierarchies are built on claims of purity or distinct origins, this is hardly a comfortable message. Chaubey has adopted an unusual approach to navigating these sensitivities: his lab shares draft papers with communities before publication and has abandoned at least ten studies after communities objected to the findings. “When we work with a community we explain exactly what we are studying. If they reject the findings entirely, we abandon the paper,” he said. To some scientists, this may seem like capitulation to social pressure; to others, it is a model for conducting ethical research in a deeply unequal society.

The bones hold the key to the whole puzzle. They tell us that we are all migrants, all mixed, all connected. And they tell us that the only honest answer to where we come from is a very long story, full of detours and surprises, with no clear beginning and no end in sight.

VALLEY VARIANTS

The Kashmir Valley has yielded complexities. The earliest inhabitants carried largely local maternal lineages, with faint traces of contact with the Iron Age Swat Valley. By the medieval period, though, the gene pool had shifted—showing clear links to both Swat Valley populations and Bronze Age Central Asia.

ROMA RIDDLE

The Roma, once called Gypsies, left the subcontinent a thousand years ago, drifting west through Persia into Europe. Their language keeps Indic roots; their music echoes north Indian folk forms. Ancient DNA points to a single origin—likely Punjab and Rajasthan—with markers traceable in Roma across Europe. It was no single event, but a slow drift.

PART AND PARSI

The Parsis of Mumbai and Gujarat, Zoroastrian refugees from Persia, arrived in India between the eighth and tenth centuries. Their genes carry a clear west Asian signature, layered with centuries of mixing with local populations. It confirms an old community saying: they blended in like sugar in milk.

MISSING MARKER

In 2003, Oxford geneticists Chris Tyler-Smith and Tatiana Zerjal found a Y-chromosome ‘star cluster’ in 16 Asian populations, from Mongolia to Iran to Pakistan’s Hazara, carried by 8 per cent of men—about 0.5 per cent of the world’s male population. It traced to about a thousand years ago, matching Genghis Khan’s empire. Yet, a screening of 12,000 mainland Indian samples found none. The mark of Genghis fades at the Indus.

Genome India Project

* Nearly 10,000 genomes sequenced

* 83 population groups studied

* Millions of previously undocumented genetic variants identified

* Aims to improve understanding of Indian genetic diversity and disease risk

* Enables population-specific medicine and better disease prediction for south Asian populations

Key ancient DNA insights

* Humans share most of their DNA

* Indian populations were shaped by repeated migration and admixture over tens of thousands of years

* Genetics does not map neatly on to caste, language or regional identity

* Ancient DNA evidence in India is still limited and evolving

* No mainland Indian population is genetically “pure”