First ancient DNA from Indus Valley civilization links its people to modern South Asians
Researchers have successfully sequenced the first genome of an individual from the Harappan civilization, also called the Indus Valley Civilization (IVC). The DNA, which belongs to an individual who lived four to five millennia ago, suggests that modern people in India are likely to be largely descended from people of this ancient culture. It also offers a surprising insight into how farming began in South Asia, showing that it was not brought by large-scale movement of people from the Fertile Crescent where farming first arose. Instead, farming started in South Asia through local hunter-gatherers adopting farming. The findings appear September 5 in the journal Cell.
"The Harappans were one of the earliest civilizations of the ancient world and a major source of Indian culture and traditions, and yet it has been a mystery how they related both to later people as well as to their contemporaries," says Vasant Shinde, an archaeologist at Deccan College, Deemed University in Pune, India, and the chief excavator of the site of Rakhigarhi, who is first author of the study.
The IVC, which at its height from 2600 to 1900 BCE covered a large swath of northwestern South Asia, was one of the world's first large-scale urban societies. Roughly contemporary to ancient Egypt and the ancient civilizations of China and Mesopotamia, it traded across long distances and developed systematic town planning, elaborate drainage systems, granaries, and standardization of weights and measures.
Hot, fluctuating climates like those found in many parts of lowland South Asia are detrimental to the preservation of DNA. So despite the importance of the IVC, it has been impossible until now to sequence DNA of individuals recovered in archaeological sites located in the region. "Even though there has been success with ancient DNA from many other places, the difficult preservation conditions mean that studies in South Asia have been a challenge," says senior author David Reich, a geneticist at Harvard Medical School, the Broad Institute, and the Howard Hughes Medical Institute.
Answering questions about the ancient people of the Indus Valley was in fact the primary reason Reich founded his own ancient DNA laboratory in 2013.
In this study, Reich, post-doctoral scientist Vagheesh Narasimhan, and Niraj Rai, who established a new ancient DNA laboratory at the Birbal Sahni Institute of Palaeosciences in Lucknow, India, and led the preparation of the samples, screened 61 skeletal samples from a site in Rakhigarhi, the largest city of the IVC. A single sample showed promise: it contained a very small amount of authentic ancient DNA. The team made over 100 attempts to sequence the sample. Reich says: "While each of the individual datasets did not produce enough DNA, pooling them resulted in sufficient genetic data to learn about population history."
There were many theories about the genetic origins of the people of the IVC. "They could resemble Southeast Asian hunter-gatherers or they could resemble Iranians, or they could even resemble Steppe pastoralists--all were plausible prior to the ancient DNA findings," he says.
The individual sequenced here fits with a set of 11 individuals from sites across Iran and Central Asia known to be in cultural contact with the IVC, discovered in a manuscript being published simultaneously (also led by Reich and Narasimhan) in the journal Science. Those individuals were genetic outliers among the people at the sites in which they were found. They represent a unique mixture of ancestry related to ancient Iranians and ancestry related to Southeast Asian hunter-gatherers. Their genetic similarity to the Rakhigarhi individual makes it likely that these were migrants from the IVC.
It's a mix of ancestry that is also present in modern South Asians, leading the researchers to believe that people from the IVC like the Rakhigarhi individuals were the single largest source population for the modern-day people of India. "Ancestry like that in the IVC individuals is the primary ancestry source in South Asia today," says Reich. "This finding ties people in South Asia today directly to the Indus Valley Civilization."
The findings also offer a surprising insight into how agriculture reached South Asia. A mainstream view in archaeology has been that people from the Fertile Crescent of the Middle East--home to the earliest evidence of farming--spread across the Iranian plateau and from there into South Asia, bringing with them a new and transformative economic system.
Genetic studies to date seemed to add weight to this theory by showing that Iranian-related ancestry was the single biggest contributor to the ancestry in South Asians.
But this new study shows that the lineage of Iranian-related ancestry in modern South Asians split from ancient Iranian farmers, herders, and hunter-gatherers before they separated from each other--that is, even before the invention of farming in the Fertile Crescent. Thus, farming was either reinvented locally in South Asia or reached it through the cultural transmission of ideas rather than through substantial movement of western Iranian farmers.
For Reich, Shinde, and their team, these findings are just the beginning. "The Harappans built a complex and cosmopolitan ancient civilization, and there was undoubtedly variation in it that we cannot detect by analyzing a single individual," Shinde says. "The insights that emerge from just this single individual demonstrate the enormous promise of ancient DNA studies of South Asia. They make it clear that future studies of much larger numbers of individuals from a variety of archaeological sites and locations have the potential to transform our understanding of the deep history of the subcontinent."
Burial I6113 was the only one that yielded ancient DNA from the Indus Valley civilization.VASANT SHINDE
The climate of South Asia is not kind to ancient DNA. It is hot and it rains. In monsoon season, water seeps into ancient bones in the ground, degrading the old genetic material. So by the time archeologists and geneticists finally got DNA out of a tiny ear bone from a 4,000-plus-year-old skeleton, they had already tried dozens of samples—all from cemeteries of the mysterious Indus Valley civilization, all without any success.
The Indus Valley civilization, also known as the Harappan civilization, flourished 4,000 years ago in what is now India and Pakistan. It surpassed its contemporaries, Mesopotamia and ancient Egypt, in size. Its trade routes stretched thousands of miles. It had agriculture and planned cities and sewage systems. And then, it disappeared. “The Indus Valley civilization has been an enigma for South Asians. We read about it in our textbooks,” says Priya Moorjani, a computational biologist at the University of California at Berkeley. “The end of the civilization was quite mysterious.” No one alive today is sure who the people of the Indus Valley civilization were or where they went.
A pair of newly published papers use ancient DNA to shed light on the Indus Valley civilization and the entire history of people in South and Central Asia.Thefirst studyis a sweeping collection of 523 genomes—300 to 12,000 years old—from a region spanned by Iran, Russia, and India. By comparing the results with modern South Asians’ genomes, the study showed that South Asians today descended from a mix of local hunter-gatherers, Iranian-related groups, and steppe pastoralists who came by way of Central Asia. It’s the largest number of ancient genomes reported in a single paper, all made possible by an ancient DNA “factory” the geneticist David Reich has built at Harvard. (Moorjani completed her doctorate in Reich’s lab and is a co-author on this paper.)
The second study focuses on just a single genome from the Indus Valley civilization: I6113, a woman who died more than 4,000 years ago. Her skeleton was the only one—out of more than 100 samples the researchers tested from 10 different Indus Valley–civilization sites—that yielded ancient DNA, but even then it was contaminated and of poor quality. “We had to squeeze, squeeze, squeeze the sample really hard, more than we’ve done in any other sample we’ve ever tried,” says Reich, who is also a senior author of the second paper. The team ultimately tried to sequence DNA from I6113’s ear bone more than 100 times, each time yielding a tiny dribble of genetic data. That I6113 gets her own paper is a testament to both the technical difficulty of sequencing her DNA and the importance of the Indus Valley civilization. Even before publication, rumors were swirling in India about what the ancient DNA would show, and how it would play into the politics of the Hindu-nationalist ruling party.
What’s intriguing about I6113’s DNA is what she lacks: any of the steppe ancestry that is widespread in contemporary South Asians. Instead, she appeared to have a mix of Southeast Asian hunter-gatherer and Iranian-related ancestry.
The two studies piece together a history of how the people of the Indus Valley civilization are related to South Asians today. After the decline of the civilization 4,000 years ago, people with a genetic makeup similar to I6113 mixed with people of Southeast Asian hunter-gatherer ancestry to form what has been called Ancestral South Indians. From 4,000 to 3,000 years ago, other people descended from the Indus Valley civilization mixed with people of steppe-pastoralist ancestry, who likely brought horses and the Indo-European languages now spoken on the subcontinent, to form a group that has been called Ancestral North Indians. These two ancestral groups then mixed as well, giving rise to the great diversity of ethnic groups in South Asia. Go back far enough, and both sides trace to the Indus Valley civilization, which appears to be the single largest source of ancestry for modern South Asians.
The team studying I6113 noticed something intriguing about the Iranian-related portion of her ancestry, too. It appears to date to before the advent of farming in the Fertile Crescent. This suggests that farming did not, as many have thought, spread to South Asia through the migration of people from the Near East. It may have arisen independently in South Asia or spread through cultural contact.
Of course, this is a lot to rest on a single genome. “That would be like taking a single sample from Tokyo and trying to generalize about the whole ancestry of Japan,” Reich admits. But the team’s confidence in its results was bolstered when the researches found that I6113 was genetically similar to 11 people from the 523-genome paper who were buried not in South Asia, but in what is now Iran and Turkmenistan. These 11 people were also “outliers” in their own burial sites. The team thinks they may have been migrants or the children of migrants from the Indus Valley civilization. Archaeological evidence suggests people traveled between these regions as well.
The cities of the Indus Valley Civilization were cosmopolitan places, which also makes it harder to generalize from one genome. J. Mark Kenoyer, an anthropologist at the University of Wisconsin at Madison who was not an author of either study, cautions that only a small number of people who lived in these cities were buried in cemeteries—probably elites. The rest might have been cremated, or their bones simply left uncovered and thus scattered over time. “The cemeteries of the Indus civilization do not represent the people of the Indus civilization. They represent one community,” he says.
Still, more cemetery samples would be better than just one. The research team behind I6113 is trying to sequence more bones from the Indus Valley civilization. Vasant Shinde, an archeologist at Deccan College whose team excavated I6113, says the attempts to get ancient DNA from Indus Valley–civilization sites have been a years-long learning process. To prevent contamination with modern DNA, team members now wear gowns and masks even while excavating in the field. They do not reuse excavation instruments from burial to burial. Niraj Rai, a geneticist who was a visiting fellow in Reich’s lab, also set up an ancient-DNA lab at the Birbal Sahni Institute of Palaeosciences in Lucknow, India, where I6113’s DNA was extracted. “This is beginning,” Shinde says. “This is not the end.” He expects more ancient DNA to come.
In India, ancient DNA has generated intense interest, says Tony Joseph, the author of Early Indians: The Story of Our Ancestors and Where We Came From. He told me his book, published last December, is already in its seventh printing. After a preliminary version of the large Central and South Asian genomes study was posted on bioRxiv last March, it became the site’s most downloaded preprint of 2018. The preprint generated controversy, too, especially the finding that many Indians have ancestry from steppe pastoralists. Hindu nationalists, as Joseph has written, believe that Aryans—who originated in India and spread through Europe and Asia—are the source of Indian civilization. This is contradicted by ancient DNA that finds the population history in India itself contains far more mixing and migration. (Further complicating things, Nazis co-opted the term Aryans to mean something different, a master race of European origin.) A prominent MP even attacked Reich when the preprint came out, tweeting out an article titled, “There Are Lies, Damned Lies and (Harvard’s ‘Third’ Reich and Co’s) Statistics.” Reich, who has experienced how fraught talking about genetics and identity can be, acknowledged the political interest in his work, but declined to get into it.
Ancient DNA has captured the public imagination precisely because it promises an answer to questions like Where did we come from? and Who are we?—questions that also have deep political undercurrents. To sequence I6113’s DNA is to draw genetic connections between an ancient civilization and the people who live in the region today, to add fuel to arguments about who can lay claim to a cultural inheritance. All this, contained in a half-inch wisp of an ear bone.
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First DNA From This Ancient Civilization Reveals Ancestry of Modern South Asians
TESSA KOUMOUNDOUROS
5 SEP 2019
Long before climate change drove them to abandon their thriving cities, a group of hunter-gatherers settled in the Indus River Valley as farmers, leading to the creation of one of the world's first large-scale urban societies, complete with booming economies and long-distance trade.
The Harappan civilisation, which peaked around 2,600 to 1,900 BCE, boasted pioneering town planning, elaborate drainage systems and granaries. They were a multicultural society and even had their own standardised system of weights and measures. But what enticed these people to drastically change their roaming ways in the first place?
"A mainstream view is that farming came to South Asia through the large-scale westward movement of Iranian farmers," geneticist David Reich from Harvard University told ScienceAlert.
Hints of Iranian ancestry in modern South Asians led researchers to suspect that when these ancient Iranians migrated from the Fertile Crescent in the Middle East (where the earliest evidence of farming has been found), they took their new agricultural way of life with them.
But a team of researchers led by archaeologist Vasant Shinde from Deccan College in India has just up-ended that scenario's timeline.
For the first time, the team successfully sequenced a genome from an individual found buried in this ancient civilisation's remains, in a cemetery at the site of Rakhigarhi in Haryana, India.
(Vasant Shinde/Deccan College Post Graduate Research Institute)
Above: Globular pot found near the head of the skeleton that yielded ancient DNA.
While this site has long been of interest, the hot South Asian climate provides the perfect conditions for degrading biological material, leaving little intact DNA to extract. But the team managed to find enough DNA from the 4,000 to 5,000 year old remains by re-sampling the skeleton over 100 times and pooling the results.
Their analysis showed that the genes associated with this individual's Iranian ancestry came from before the time when farmers and hunter-gatherers in the area separated from each other. This individual's Iranian ancestors left before farming spread through Iran, explained Reich.
"Our study says that farming arose in South Asia either through local invention or adoption of ideas from western neighbours (cultural communication) or some combination," he said.
Comparing this individual's genome with those from another study about to be published in Science, the team also provided some insights into the trade and movements between these ancient civilisations.
Eleven individuals out of 523 genetically sampled from Gonur in Turkmenistan and Shahr-i-Sokhta in Iran belonged to the same genetic group as the South Asian individual.
"This suggests that these 11 individuals were migrants or recent descendants of migrants from the Indus Valley Civilisation," Reich said, which is supported by the cultural connections seen between the sites.
Map of the Indus Valley Civilisation and other significant Harappan sites. (Shinde et al. Cell, 2019)
"The Harappans were one of the earliest civilisations of the ancient world and a major source of Indian culture and traditions, and yet it has been a mystery how they related both to later people as well as to their contemporaries," Shinde explained.
While we now know them through their urban remains and 4,000 year old relics, this newly sequenced genome revealed the ancient Harappan civilisation has a much greater legacy.
"This individual buried in an Indus Valley Civilisation cemetery, was part of a population that is the single largest source of ancestry in nearly all South Asians today," explained Reich.
Of course there's only so much that can be learnt from one individual's genome, so the researchers hope the technique they used will allow them to study the genomes of many other individuals from the Harappa civilisation to create a bigger picture of this rich history.
"We also want to study individuals from other time periods and geographic locations in South Asia," Reich said, "particularly just before and after the advent of farming in order to understand the extent to which genetic change accompanied these economic transformations."
Skeletal remains analysed in the study. Image credits: Vasant Shinde
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We have all heard of the Indus Valley Civilisation, an ancient Bronze Age civilisation that thrived in the northwestern regions of South Asia in the third millennium BCE. It is well known for its granaries, drainage systems and systematically planned cities like Harappa and Mohenjodaro. However, not much is known about its rise and fall; although there are various theories. Historians have not reached consensus on many aspects of this period as its script remains undeciphered, hiding the facts. The lives of the antecedents and successors of the Indus people also remain shrouded in mystery.
In a pair of new studies published in the journals Science and Cell, a consortium of international researchers, including those from India, have tried to decipher the origins of present-day Central and South Asian people. They have used recent advances in genetics to extract and analyse genetic material (DNA) from the remains of several ancient populations, including people from the Indus Valley Civilisation.
Figure 1: Geographical span of the Indus Valley Civilisation. [Image credits: Vasant Shinde]
In the study titled The formation of human populations in South and Central Asia, the researchers investigate where the people of the Indus Valley Civilisation came from, and the ancestry of the present-day Indians. The researchers used genetic data from 523 ancient humans from sites across South and Central Asia to piece together a comprehensive picture of the origins of the present-day population of South Asia.
The study found that the people of the Indus Valley Civilisation did not descend from the early farmers of the Fertile Crescent. However, they still had ancestry in another Iranian-related hunter-gatherer population.
"We 'don't know where that population lived. It could have been in South Asia or some unsampled location in the Iranian plateau," says Dr Vagheesh Narasimhan in an interview with Research Matters. He is a researcher at the Department of Genetics, Harvard Medical School, USA and the lead author of the two studies.
If we look at the present-day South Asians, a majority of their ancestors are the people of the Indus Valley Civilisation. Following the decline of the Indus Valley Civilisation, around 2000 BCE, two distinct populations were formed when the Indus Valley people mixed with others.
Firstly, the Ancestral South Indian (ASI) population, which was formed by a mixture of the Indus Valley and the ancient ancestral South Indian population. On the other hand, the Ancestral North Indian (ANI) population was formed by a mixture of Indus Valley people with the Steppe pastoralists from the Eurasian Steppes. The Steppe pastoralists were nomads from the steppes, a temperate zone stretching from modern-day Bulgaria in the west through Manchuria in the east. Steppe ancestry arrived in South Asia between 1900 and 1500 BCE. The present-day Indian population is a mixture of these two source populations - Ancestral South Indian (ASI) and Ancestral North Indian (ANI).
The study also throws some insights into how the Steppe pastoralists made their way into South Asia. The researchers looked at the inheritance of the Y chromosome—a sex chromosome found only in males and passed on from father to son. They combined information from the Y chromosome and non-sex chromosomes to see that the Steppe ancestry was introduced into South Asia predominantly by males.
A significant implication of the findings is the understanding of the spread of the Indo-European language family. This family includes Latin-derived languages like Spanish, Sanskrit-derived languages like Hindi and English among several others.
"Our results provide evidence for a significant movement of people into Europe and South Asia in the Bronze Age in a manner that mirrors the shared features of certain Indo-European languages with others. Steppe pastoralist related ancestry spread across Eurasia in the Bronze Age in a manner that parallels specific shared features between different Indo-European language families", explains Dr Narasimhan.
Interestingly, the Steppe ancestry is very high among Brahmin and Bhumihar groups. Since Brahmins were the traditional custodians of liturgy in Sanskrit, the high Steppe ancestry indicates a Bronze Age Steppe origin for South Asia's Indo-European languages.
Figure 2: A Red Slipped ware globular pot placed near the head of the skeleton that yielded ancient DNA. [Image Credit: Vasant Shinde]
The two studies provide a reasonably precise chronology thanks to radiocarbon dating. It is a technique of determining the age of an object by looking at the radioactive carbon isotopes. The proportion of radioactive carbon (C-14) to ordinary carbon (C-12) in organic matter tells us how long it has been dead. Because, once it is dead, it would have stopped exchanging carbon with the environment.
"One of the major results of our study is the reporting of 269 new radiocarbon dates directly on human bone, for which ancient DNA data and the archaeological context of the samples are available," remarks Dr Narasimhan.
The study is the first-of-its-kind to use ancient DNA samples to paint the history of today's Indians.
"In this part of the world, where there has been a paucity of such dates, this new information helps us to synchronise the chronology of different parts of this broad region and describe the interaction, archaeologically and genetically," opines Prof. Narasimhan.
In a companion study titled An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers, the researchers analysed DNA from the skeletal remains of an individual found in Rakhigarhi cemetery, situated in present-day Haryana. Rakhigarhi was one of the largest cities of the Indus Valley Civilization. Their findings provide insights into the origin of farming in South Asia.
One of the most definitive milestones in human history is our transition from nomadic hunter-gatherers to settled agriculturists. This change depended not only on technological advances but also how people lived and related to each other. Farming is known to have originated in the Fertile Crescent—a semicircular region in the Middle East from the Meditteranean Sea to the Persian Gulf. Historians have long wondered how it then spread to other parts of the world. Was it through large scale human migrations, or did it develop independently?
The DNA analysis of the Indus Valley individual indicates no ancestral relationship with the farmers in the Fertile Crescent.
"Our results suggest that the advent of farming in South Asia was not mediated by significant movements of people from the Near East or Western Iran," says Prof. Narasimhan. The study also does not show any evidence of Steppe pastoralist ancestry, providing further evidence that the Steppe pastoralists only arrived much later in South Asia.
Does this mean farming was independently invented in South Asia?
"While our data could be consistent with this scenario, they are also entirely consistent with people copying farming technology from their neighbours through a process of cultural diffusion," explains Prof Narasimhan.
He suggests the need for additional DNA analysis of humans and domesticated crops from these regions to conclusively prove how agriculture developed in the Indus Valley.
This article has been run past the researchers, whose work is covered, to ensure accuracy.
At roughly the same time that ancient Egyptians were constructing their first great pyramids and Mesopotamians were building monumental temples and ziggurats, the Harappans of South Asia—also known as the Indus Valley Civilization—were erecting massive baked brick housing complexes and cutting elaborate canal systems. The civilization’s abrupt downfall remains one of the great mysteries of the ancient world. Now, for the first time, scientists have analyzed the genome of an ancient Harappan. The findings reveal little about why the society collapsed, but they illuminate both its past and its continuing genetic legacy in modern Indians.
“The Indus Valley Civilization has been an enigma for a long time,” says Priya Moorjani, a population geneticist at the University of California, Berkeley, who wasn’t involved with the study. “So it’s very exciting to … learn about [its] ancestry and history.”
The Indus Valley Civilization emerged sometime around 3000 B.C.E. and had collapsed by about 1700 B.C.E. During its height, it stretched across much of what is today northwestern India and parts of eastern Pakistan. It is alternatively known as the Harappan civilization, after the first of its sites to be excavated in Punjab province in Pakistan beginning in the 1820s. Along with ancient Egypt and Mesopotamia, it was among the world’s first large-scale urban agricultural societies, boasting somewhere between 1 million and 5 million inhabitants across five central cities.
Although hundreds of skeletons from the Indus Valley have been uncovered, the region’s hot climate rapidly destroys the genetic material that has been instrumental in tracing the history of other early civilizations.
In recent years, however, scientists have learned that the petrous bone of the inner ear contains an unusually high quantity of DNA, allowing them to locate usable genetic material even in otherwise degraded skeletons. A team led by geneticist David Reich at Harvard University and archaeologist Vasant Shinde at Deccan College in Pune, India, decided to try the promising technique with Indus specimens. They sampled more than 60 skeletal pieces, including numerous petrous bones, before they were able to extract ancient DNA from one. Then they had to sequence the sample more than 100 times to piece together a relatively complete genome.
“There’s no doubt this is the most intensive effort we’ve ever made to get ancient DNA from a single sample,” Reich says.
The sampled individual, most likely a woman based on her DNA, was buried among dozens of ceramic bowls and vases in an Indus site known as Rakhigarhi, about 150 kilometers northwest of modern-day Delhi. Archaeological evidence suggests she lived sometime between 2800 and 2300 B.C.E. Her genome closely matched DNA from 11 other individuals who had been found at sites in Iran and Turkmenistan, where conditions favor better DNA preservation. (Those individuals belong to a set of 523 ancient DNA sequences used to chart the population history of South Asians and published today in Science.)
Knowing that the Indus civilization traded with those regions, and that those 11 individuals had little in common genetically with others buried in their regions, Reich and colleagues concluded they were likely Harappan migrants.
Now working with a bank of Indus genomes presumed to be 12 individuals strong, the researchers compared their genetic signatures to DNA from other ancient civilizations in Eurasia as well as modern populations. A resulting Indus family tree revealed that although the civilization collapsed nearly 4000 years ago, its genetic stock forms the basis of most people living in India today, the team reports today in Cell.
The Science paper, also led by Reich, notes that modern people from North India also bear the genetic marks of ancient interbreeding with herders from the Eurasian steppe, a vast grassland that stretches across northern Asia, moving southward around 2000 B.C.E. Those steppe herders carried European DNA from previous interbreeding events, the authors note, explaining the once-perplexing genetic link between Europeans and South Asians. Over the next few thousand years, the groups in north and south India intermixed, leading to the modern population’s complex ancestral mix.
One surprise concerns DNA related to ancient Iranians, which was previously found to be prevalent in modern South Asians. The finding seemed to back a popular belief among anthropologists that migrants from the Fertile Crescent—which comprises modern-day Iran and gave rise to the world’s first farmers who began to rove about 10,000 years ago—moved east at some point and mixed with South Asian hunter-gatherers, introducing agriculture to the Indian subcontinent. Yet the new study suggests the Iranian-related DNA in both the Indus individuals and modern Indians actually predates the rise of agriculture in Iran by some 2000 years. In other words, that Iranian-related DNA came from interbreeding with 12,000-year-old hunter-gatherers, not more recent farmers, Reich explains.
“It seems likely there were independent advents of farming,” says biological anthropologist Gyaneshwer Chaubey at Banaras Hindu University in Varanasi, India, who wasn’t involved with the study. One explanation, he notes, might be that ancient South Asians learned farming practices from their neighbors without interbreeding with them.
Figuring out exactly what happened will require more archaeological work and more ancient DNA samples from across the region, Chaubey says. “The findings from the study are extremely exciting, but this is just the beginning of the story.”