A recent study on Sri Lankan populations, published in Current Biology (June 2025), goes beyond science: it challenges long-held assumptions about population origins and rewrites our understanding of Sri Lankan genetic history. Dr. Maanasa Raghavan led this research alongside Dr. Niraj Rai of the Birbal Sahni Institute of Paleosciences and Dr. Ruwandi Ranasinghe of the University of Colombo.
Dr. Maanasa Raghavan is the Neubauer Family Assistant Professor of Human Genetics at the University of Chicago, where she directs one of the world's most advanced ancient DNA laboratories. With a PhD in Paleogenomics from the University of Copenhagen and an MSc in Archaeological Sciences from Oxford, she represents a new generation of scientists who are literally excavating the molecular past to challenge long-held assumptions about human origins.
This is our exclusive interview with Dr. Maanasa Raghavan.
What first inspired you to study human migration and ancient DNA, and how did this project in Sri Lanka come about?
I am originally from India, though I have moved around the world and lived in different countries while growing up. This constant sense of “migration” in my own life perhaps sparked my interest in understanding how our ancestors moved across the world—and how those ancient journeys continue to shape our biology today. At the same time, I have always been deeply interested in the human past and archaeology. Population genetics and ancient DNA allow me to work at the intersection of these fields.
This particular project grew out of a collaboration between myself, Dr. Niraj Rai of the Birbal Sahni Institute of Paleosciences, and Dr. Ruwandi Ranasinghe of the University of Colombo. Without the contributions of local research teams, and above all, the generous participation of communities across Sri Lanka, this study would not have been possible. I extend my heartfelt thanks to them all.
Your team studied the DNA of 54 people, including 35 Sinhalese and 19 Adivasi individuals from Rathugala and Eachchilampattu. Why did you choose these specific locations, and how did you ensure that your study fairly represented the genetic and cultural diversity of these communities?
That’s an excellent question. Let me begin with the Adivasi. Today, these communities are generally small and scattered, and one of our first challenges was gaining their trust. We worked closely with our collaborators—Dr. Ruwandi Ranasinghe at the University of Colombo and Prof. Gamini Adikari at the University of Kelaniya—who had long-standing relationships with Adivasi leaders. Thanks to that trust, we were able to recruit participants from two distinct locations: Rathugala, an interior forest-dwelling group, and Eachchilampattu, a coastal group in the east. By selecting one inland and one coastal community, we could ask whether geography and lifestyle differences had led to any genetic divergence between them.
Within each clan, we randomly recruited consenting adult donors. An important criterion was to avoid sampling close relatives—siblings, parents, or cousins—since including too many family members could bias the results and fail to represent the wider population.
For the Sinhalese, we aimed to capture their diversity across the island. We collected samples from individuals originating from multiple cities: Galle, Anuradhapura, Kandy, Matale, Ratnapura, Kurunegala, Colombo, Kalutara, and Gampaha. This broad spread allowed us to build a representative snapshot rather than focusing on just one region.
It’s also worth noting that while we didn’t directly sample Sri Lankan Tamils in this study, we did have access to high-quality data on around 100 Tamil individuals through the 1000 Genomes Project, which had sampled people of Sri Lankan Tamil ancestry living in the UK. This enabled us to include them in our comparative analysis.
Now, you might wonder—can such a small number of participants really tell us much? The answer is yes. An individual’s genome carries the combined legacy of their parents, grandparents, and earlier generations. That means even a modest sample, if carefully chosen, can reveal a great deal about population history. Of course, there’s always the chance that some diversity is missed or that statistical power is limited—especially in smaller groups like the Adivasi. But our analyses provided a reassuring result: the Adivasi groups from Rathugala and Eachchilampattu, as well as the Sinhalese and Sri Lankan Tamils, are genetically most similar to one another, with only limited structure within each sampled community.
Dr. Niraj Rai
We know that the Adivasi community in Eachchilampattu speaks Tamil today and shares cultural similarities with nearby Tamil populations. How should we understand this language change in light of your findings about their unique genetic heritage?
Over time, the Adivasi clans have gradually assimilated with their neighboring populations—interacting with Tamils along the coast and Sinhalese in the interior. This is reflected in their language: the original Vedda tongue has absorbed many Tamil and Sinhala words, and in places such as Eachchilampattu, the Adivasi now predominantly speak Tamil.
Our genetic analyses offer a complementary perspective. They show that the Adivasi are genetically closest to Sri Lanka’s urban Sinhalese and Tamil populations, as well as to South Indian groups—an expected outcome given centuries of contact and exchange. At the same time, the Adivasi retain a slightly higher proportion of ancient hunter-gatherer ancestry compared to both Sinhalese and Tamils, and their genomes also reflect the demographic signatures of their historically small population sizes.
So what does this mean? It suggests that while their DNA still carries echoes of a deeper ancestry predating the arrival of agriculture and large-scale settlement in Sri Lanka, culturally, linguistically, and even biologically, the Adivasi have mixed extensively with their neighbors. In other words, their genetic heritage is not isolated from the rest of the island but forms part of a shared Sri Lankan and broader South Asian story—with the Adivasi preserving a distinctive connection to ancient hunter-gatherer lineages.
Your research reveals that both Sinhalese and Adivasi people have significant genetic contributions from ancient South Indian populations. Can you explain in simple terms what these ancestral genetic components are and how you identified them? What populations or genetic databases did you use as reference points to understand these ancestry patterns?
To put it simply, when we examine the DNA of present-day South Asian populations—including Sri Lankans—we find that it reflects a mixture of ancestries from very ancient sources. Previous large-scale studies of Indian populations have provided a model that helps us interpret these patterns.
One key component is what geneticists call “Ancestral South Indian” (ASI) ancestry. This ancestry itself is made up of two very old lineages:
- One is related to the Onge people of the Andaman Islands, who serve as a distant genetic proxy for an ancient hunter-gatherer ancestry that was once widespread across South Asia.
- The other is related to ancient populations from Iran, who contributed a distinctive ancestry that spread into South Asia several thousand years ago.
These two lineages mixed to form the ASI. Today, the highest proportions of ASI ancestry are seen in tribal groups in South India, but it was likely widespread across the subcontinent until about 2,000–4,000 years ago.
Later, a third ancestry entered the picture: groups from the Eurasian Steppe, who migrated south into the subcontinent. Their DNA combined with ASI to form what is known as “Ancestral North Indian” (ANI) ancestry. This ancestry is most common today in North India and Pakistan and is associated with Indo-European language speakers. Many South Indian groups also carry some Steppe-related ancestry due to subsequent mixing.
In our study, we used well-established proxy populations from previously published ancient and modern genetic data as reference points. We then modeled the genomes of the Sinhalese, Adivasi, and Sri Lankan Tamils against these sources. Our findings show that all three groups—Sinhalese, Adivasi, and Tamils—derive their primary ancestry from two ASI components: Onge-related and ancient Iranian-related, closely resembling South Indian populations. In addition, they all contain a small proportion—less than 10%—of Steppe-related ancestry, which is comparable to or lower than what is observed in most South Indian groups today.
In simple terms: the core ancestry of Sri Lankans is shared with ancient South Indians, originating from a blend of indigenous hunter-gatherer and Iranian-related groups, with a small, later contribution from Steppe populations.
Your study suggests two possible explanations for how the Sinhalese came to be: one is that they share very ancient roots with South Indian populations, and the other is that migrants from North India came long ago but then mixed extensively with South Indian groups. Based on your research, which explanation seems more likely? And is there any genetic evidence today—such as DNA passed down through mothers or fathers—that still shows traces of North Indian ancestry among the Sinhalese?
With the data we have now, it’s very hard to tell the difference between the two main scenarios. The truth is that most Indian and Sri Lankan populations already share very similar genetic backgrounds. When groups that are closely related mix with each other, it becomes almost impossible to separate their histories thousands of years later.
One way forward is through ancient DNA—genetic material taken directly from skeletons that lived before these possible migrations or mixing events. That would let us compare “before and after.” But this is extremely difficult in South Asia, where the hot, humid climate destroys DNA over time, and where suitable archaeological remains are rare.
Based only on DNA from living people, we cannot say for certain whether the Sinhalese came mainly from ancient South Indian roots or from a North Indian migration that later mixed in. What we can say is that, today, the Sinhalese are genetically closest to South Indian populations—just like the Tamils and the Adivasi.
When we look at maternal and paternal lines (mitochondrial DNA from mothers, and Y-chromosome DNA from fathers), the picture is mixed. These lineages are found across both North and South India. But it’s important to note that these are single markers—just one thread of DNA compared to the thousands of threads in the full genome. Because of a natural process called genetic drift, these single markers can change a lot over generations, sometimes giving a misleading picture. This doesn’t mean there was never a migration from the north—it just means that if such a movement happened, those people blended so completely with locals that the distinct “North Indian” signal is no longer visible.
Finally, it’s worth remembering: genetics and culture are not the same thing. Language, oral history, and identity are shaped by many forces beyond DNA. That contrast is fascinating, but it also reminds us that ancestry in our genes should not be confused with the way people understand and express who they are.
Based on your analyses, what does the DNA reveal about the level of genetic relatedness among the Sri Lankan populations?
We used several population genetics methods to measure how much genetic variation—known as “alleles”—different groups share. Some of these methods examine overall allele frequencies, others analyze longer stretches of shared DNA called “haplotypes,” and still others estimate how far back in time these haplotypes were inherited from a common ancestor.
Each method provides a slightly different perspective, but together they help us identify patterns of relatedness, changes in population size over time, and the points at which groups may have split from one another.
Our findings show that all four Sri Lankan populations in our study—the Sinhalese, the two Adivasi clans, and the Sri Lankan Tamils—are genetically very similar to one another overall. It is important to be precise here: we are not saying that the Adivasi are closer to the Sinhalese than to the Tamils. In fact, the Adivasi are about equally related to both groups.
What we did observe is that the two Adivasi clans are most closely related to each other, which reflects their more recent shared history before they became geographically separated.
Your research shows that Adivasi communities experienced significant population declines, with the interior group facing more severe challenges than the coastal group. How were you able to estimate when these population changes happened using genetic data? And how reliable are these dating methods?
The method we used is based on a concept called “coalescence,” which means tracing different genetic lineages back in time to find their common ancestor. The principle is straightforward: in smaller populations, people share ancestors more recently, so their genetic lineages coalesce more quickly. In larger populations, it takes much longer to reach the common ancestor, who lived further back in time.
An example may help. Imagine a small family reunion with just your parents, siblings, and a few cousins. Everyone can trace their lineage back to the same grandparents very quickly. But if you invite your entire extended family, the common ancestor might be a great-great-grandparent instead. The bigger the family, the further back you need to go before everyone connects.
Our analysis works on the same principle. In practice, we divide the genomes of multiple individuals into haplotypes (stretches of DNA) and use a method that traces the coalescence rate and timing of these lineages. If lineages take longer to coalesce, it indicates the population was larger in the past. If they coalesce quickly, it suggests the population size was smaller. By compiling many such events across multiple genomes, we can reconstruct how population sizes changed over time.
These methods are generally reliable and include statistical confidence intervals, but there are important caveats. What they estimate is the “effective” population size—that is, the number of individuals who actually passed on their genes to future generations. This may not match the actual census size, since not everyone leaves descendants. In addition, severe population crashes—what we call genetic bottlenecks—can sometimes distort the results. For this reason, the findings must always be interpreted with caution.
Your research challenges long-held beliefs about Sinhalese origins, particularly the idea of purely North Indian or "Aryan" ancestry. How do you think these scientific findings might influence how Sri Lankans understand their own history - whether in public discussions, school curricula, or political conversations?
We want to emphasize that we are not challenging anyone’s beliefs. Our work focuses on the genetic histories of populations, which represent only one aspect of a group’s or individual’s identity. Biological identity is not the same as self-identity or cultural identity—each has very different origins, and they should not be forced to reconcile.
For example, a population may have encountered another without mixing biologically, yet exchanged cultural traits such as language, diet, or technology—or the reverse. What we present here should be understood strictly as part of the biological history. In this context, we do not find any biological ancestry in present-day Sinhalese that can be directly traced to North Indian groups today.
That said, oral histories and chronicles do not always capture the underlying reasons for perceived connections with other communities. The shared linguistic affinity between the Sinhalese and North Indian groups—both belonging to the Indo-European language family—may reflect language similarity rather than biological exchange. It is also possible that cultural and genetic mixing occurred at different rates. Another scenario is that the populations described in the Sinhalese chronicles as originating in North or Northeast India may themselves have been genetically different at the time, or they may have mixed with South Indian groups along the way while still preserving their language.
There are, therefore, multiple scenarios consistent with our results. Based on genetic data alone, however, we cannot yet pinpoint the exact mechanism. Nevertheless, we hope our findings encourage communities to broaden their understanding of the many dimensions of their bio-cultural identities—and to actively participate in, and even lead, future scientific research in this field.
Looking ahead, what are the key questions that remain unanswered about Sri Lanka’s population history? How might emerging technologies in genetic research—particularly ancient DNA studies—help fill the gaps in our understanding of how different communities arrived on the island and evolved over time?
Some important questions still remain. One is the genetic origins of the Adivasi. They are often thought to descend from the region’s earliest hunter-gatherers, yet today they are genetically close to the Sinhalese, Sri Lankan Tamils, and South Indian populations. All of these groups carry not only ancestry from early hunter-gatherers but also a major component from ancient Iranian-related groups—ancestry not seen in other Asian hunter-gatherer populations such as the Andamanese. Ancient DNA, especially from periods before the migrations of the Sinhalese and Sri Lankan Tamils, could help uncover the genetic signatures of Sri Lanka’s pre-admixture hunter-gatherer inhabitants and trace subsequent migrations from India and beyond.
Another open question concerns the origins and migratory history of the Sinhalese, particularly in light of their distinct linguistic affiliation. Their story remains incomplete and invites further investigation.
As with ancient DNA studies more broadly, these questions can only be addressed through a multidisciplinary approach—bringing together anthropology, linguistics, archaeology, history, population genetics, and community knowledge to build a fuller and more nuanced narrative of Sri Lanka’s past.
