Lady I6113’s DNA
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தேமொழி
Sep 6, 2019, 5:31:40 AM9/6/19
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source:The Atlantic https://www.theatlantic.com/science/archive/2019/09/indus-valley-civilization-dna-has-long-eluded-researchers/597481/
A Burst of Clues to South Asians’ Genetic Ancestry
A tiny ear bone from more than 4,000 years ago is shaping the story of migration and heritage in India.
SARAH ZHANG
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. The first study is 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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தேமொழி
Sep 18, 2019, 11:56:47 PM9/18/19
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MIGRATIONS | HISTORY & CULTURE
New reports clearly confirm ‘Arya’ migration into India
Tony Joseph
SEPTEMBER 13, 2019
The Arya were central Asian Steppe pastoralists who arrived in India between roughly 2000 BCE and 1500 BCE, and brought Indo-European languages to the subcontinent
The last time a paper titled ‘The Genomic Formation of South and Central Asia’ was released online, in March 2018, it created a sensation in India and around the world. Mostly because the paper, co-authored by 92 scientists, many of them doyens of different disciplines, said that between 2000 BCE and 1000 BCE, there were significant migrations from the Central Asian Steppe that most likely brought Indo-European languages into India — just as Steppe migrations into Europe a thousand years earlier, beginning around 3000 BCE, had spread Indo-European languages to that continent as well. In other words, the paper supported the long-held idea of an ‘Arya’ migration into India — or, to put it more accurately, a migration of Indo-European language speaking people who called themselves ‘Arya’.
There were many who did not like that finding, and the most important counter-argument they made was that the paper was not peer-reviewed and was merely released in a pre-print server and, therefore, one had to withhold judgement until the paper was published in a scientific journal with peer review. That the paper was co-authored by 92 scientists of high reputation, including many from India, did not matter in their opinion. The lead author of the paper was Vagheesh Narasimhan of Harvard Medical School, while Kumarasamy Thangaraj of the Centre for Cellular and Molecular Biology was a co-director, along with David Reich of Harvard Medical School. Other Indian co-authors included Niraj Rai of the Birbal Sahni Institute for Palaeosciences and Vasant Shinde, then Director of Deccan College.
Even more evidence
Well, that paper has now been peer-reviewed and published in the most reputed of journals, Science. It has 117 scientists as co-authors, significantly up from the 92 last year. The paper is now titled ‘The Formation of Human Populations in South and Central Asia’. And what does it say on the question of Steppe migrations? The same thing, but with even more evidence and detail. Here is a direct quote, and not just any quote, but the very essence of the paper:
“By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization’s decline, its people mixed with individuals in the southeast [i.e, southeast of northwestern India where the Indus Valley Civilization flourished: editor] to form one of the two main ancestral populations of South Asia [called Ancestral South Indians or ASI: editor], whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population [or Ancestral North Indians, ANI: editor]. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.”
The First Indians
Shorn of scientific jargon, here is what that means: The reference to the early hunter-gatherers of Southeast Asia is a reference to the Andamanese, whom the rest of the paper abbreviates as AHG or Andamanese Hunter Gatherers. This is the same as the Ancient Ancestral South Indians (AASI) that the earlier paper talked about, or First Indians, which is the term used in my book, Early Indians. No matter which name you use — hunter-gatherers of Southeast Asia, AHG or First Indians — they all refer to the descendants of the Out of Africa migrants who reached India around 65,000 years ago and then moved on to Southeast Asia, East Asia and further on.
So this is what the abstract means in full: The primary source of ancestry for today’s South Asians is a mixture of First Indians and a people related to the hunter-gatherers of Iran. This mixed population created the agricultural revolution in northwestern India and built the Harappan Civilisation that followed. When the Harappan Civilisation declined after 2000 BCE due to a long drought, the Harappans moved south-eastwards (from northwestern India) to mix with other First Indians to form the Ancestral South Indian (ASI) population whose descendants live in south India today.
Around the same time, the Harappans also mixed with Steppe pastoralists who had by then migrated to north India through Central Asia, to form the Ancestral North Indian (ANI) population. The Steppe ancestry of the people of both South Asia and Eastern Europe in the Bronze Age explains how the movements of the Central Asians between the two regions caused the well-known similarities between the Indo-Iranian and Balto-Slavic languages.
The study goes on to further elaborate on the Steppe migration. Here is another quote from the same paper: “Between around 2000 and 1000 BCE, people of largely Central Steppe - MLBA (or Middle to Late Bronze Age) ancestry expanded toward South Asia, mixing with people along the Indus Periphery Cline to form the Steppe Cline.”
If these quotes surprise you because you thought the recent genetic studies had disproved Arya migration, then you have a bone to pick with some voices in Indian mass media for utterly misleading you. The Science study substantiated its earlier findings about Steppe migrations into India with even more evidence, but many newspapers and websites chose to go to town with headlines such as this: ‘New genetic studies dent Arya migration theory.’
So how did Indian media twist a straight story into something diametrically opposite? To answer that, we have to look at a second study that was released at the same time. This study, based on the ancient DNA of a woman who lived in the Harappan site of Rakhigarhi about 4,600 years ago, was published in Cell, co-authored by 28 scientists including some co-authors of the Science report, such as Thangaraj, Reich, Narasimhan and Rai, with Shinde being the lead author. The study’s title seemed straightforward: ‘An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers.’ But this made many journalists jump to the conclusion that it meant there was no Arya migration either.
The journalists would not have reached this hasty conclusion had they read at least the summary of the Cell paper. Here is a direct quote from the summary: “These individuals had little if any Steppe pastoralist related ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today.” Pay particular attention to the last four words: “as it is today”. The meaning is clear. Today, Steppe pastoralist ancestry is ubiquitous, but it was not so during the period of the Indus Valley Civilisation. (How ubiquitous is it today? The new studies have that figure too: it could be up to 30% in some population groups in India.)
The only possible conclusion from this, therefore, is that the Steppe migrations to India happened after the decline of the Harappan Civilisation. That is no surprise. It has always been understood that the Arya migration from the Steppe happened after 2000 BCE. So to anyone who applies their mind, the absence of Steppe ancestry in a skeleton in Rakhigarhi from 2600 BCE is clear confirmation that the earlier understanding was correct, that the Arya were not present during the Harappan Civilisation, and that they arrived later. In other words, the Harappan Civilisation was pre-Arya, and so was the language they spoke.
So what’s new?
The Cell paper, in fact, goes on to talk about Indo-European languages arriving with the Steppe pastoralists after 2000 BCE. Here is a quote from the paper that minces no words about migrations from the Central Asian Steppe bringing Indo-European languages to India between 2000 BCE and 1500 BCE: “However, a natural route for Indo-European languages to have spread into South Asia is from Eastern Europe via Central Asia in the first half of the 2nd millennium BCE, a chain of transmission that did occur as has been documented in detail with ancient DNA. The fact that Steppe pastoralist ancestry in South Asia matches that in Bronze Age Eastern Europe (but not Western Europe) provides additional evidence for this theory, as it elegantly explains the shared distinctive features of Balto-Slavic and Indo-Iranian languages.”
On the two key issues: who were the Harappans and who were the Arya, the new studies thus arrive at the exact same conclusions. The Harappans who created the agricultural revolution in northwestern India and then built the Harappan civilisation were a mix of First Indians and Iranians who spoke a pre-Arya language. The Arya were central Asian Steppe pastoralists who arrived in India between roughly 2000 BCE and 1500 BCE, and brought Indo-European languages to the subcontinent. Is there anything on which the two papers differ? No. They have the same conclusions — not surprising considering that the simultaneously published papers have many authors in common many authors are common between the two papers published simultaneously.
But is there anything new in these two studies, which we didn’t know earlier? Yes, a few details. For example, the earlier study on Genomic Formation of South and Central Asia said the migrants from Iran who mixed with First Indians were herders. The new study says the Iranians arrived in India before agriculture or even herding had begun anywhere in the world. In other words, these migrants were likely to have been hunter-gatherers, which means they did not bring a knowledge of agriculture. In Early Indians, I have made a strong case for agricultural experiments to have begun in India independently and have pointed out, in support, that critical domestications of animals such as zebu cattle and water buffalo had happened in India independently of elsewhere.
A few other details provide greater clarity to these prehistoric migrations that shaped Indian demography. For example, previous studies had described the Steppe migrations as happening between 2000 BCE and 1000 BCE. The new Science paper narrows it to between 2000 BCE and 1500 BCE or to the first half of the second millennium. This is because after 1500 BCE the populations of Central Asia begin to show a higher level of East Asian ancestry of a kind that is not noticeable in India.
Another spin around the new studies suggests an ‘Out of India’ migration. This is also misleading. If by ‘Out of India’ migration we are referring to the fact that some Harappans visited neighbouring civilisations or cultures such as the Bactria-Margiana Archaeological Complex (BMAC) or Shahr-i-Sokhta, with whom they had trade and cultural links, these are well-known and unsurprising facts.
But if by ‘Out of India’ migration we mean large-scale migration of prehistoric Indians towards the West, spreading culture and language all the way from, say, Harappa to Iceland, then there is not a shred of evidence, genetic or otherwise, to suggest that. It also contradicts the studies’ position that migrations from the Central Asian Steppe brought Indo-European languages to India after 2000 BCE.
The DNA clincher
One question often raised is: how robust can ancient DNA studies based on a few samples be? The answer is that it would be a mistake to look at one genome as something akin to say, a person in a survey answering a question as Yes or No. A single genome carries within itself the genetic track record of a person’s ancestors going back thousands or tens of thousands of years. So when you sequence a genome, say the one belonging to the woman from Rakhigarhi, you are getting a peek into the genomes of thousands of people ancestral to her. That is why in population genetics studies, even a few samples can provide huge insights.
Importantly, the two recent studies are based on 12 ancient DNA samples: one from Rakhigarhi, 8 from Shahr-i-Sokhta in eastern Iran and three from Gonur in BMAC. The study published last year was based on just three samples from Shahr-i-Sokhta and Gonur. The number of samples has now trebled.
The reason why the three samples studied last year were considered as proxy for Harappan people was because they stood out (or were outliers) from the rest of the population of that time; they carried a significant amount of First Indian ancestry unlike the others around them. This suggested they were migrants from the Harappan Civilisation. The new Cell study validates the assumption that these outliers were indeed migrants from Harappan cities because the Rakhigarhi DNA sample matches exactly the 11 samples from Shahr-i-Sokhta and Gonur. It has reconfirmed the earlier findings with even more robust data.
On the question of the language of the Harappans, the 2018 study had mentioned the possibility of it being Dravidian. The new paper goes into greater detail to suggest that Dravidian was likely to have been the language of the Ancestral South Indians (ASI) formed as a result of the mixing of the Harappan population with First Indians. The study says: “A possible scenario combining genetic data with archaeology and linguistics is that proto-Dravidian was spread by peoples of the Indus Valley Civilisation along with the Indus Periphery Cline ancestry component of the ASI.” The study also points out that of the 11 ancient DNA samples of Harappan migrants recovered from Shahr-i-Sokhta and Gonur, two carried the Y chromosome haplogroup H1a1d2, which is today primarily found in southern India.
There is a lesson here for both readers and the media. When reporting on science, it is important to go by what is written in the papers rather than by statements made outside them. Peer-reviewed papers published in reputed journals by well-known scientists are robust and durable; fleeting statements made at press conferences are ephemeral and prone to being misheard or misreported, and could sometimes run contrary to the evidence on hand.
What we know today, based on these two papers, is mostly what we knew last year, but with far greater supporting evidence. Which is that we are a multi-source civilisation, not a single-source one, drawing our cultural impulses, traditions and practices from a variety of heredities and migration histories. We are all Indians. We are all migrants. And we are all mixed.
The writer is the author of Early Indians: The Story of Our Ancestors and Where We Came From.
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On Friday, September 6, 2019 at 2:31:40 AM UTC-7, தேமொழி wrote:
A Burst of Clues to South Asians’ Genetic Ancestry
A tiny ear bone from more than 4,000 years ago is shaping the story of migration and heritage in India.
SARAH ZHANGSEP 5, 2019
தேமொழி
Sep 20, 2019, 10:21:54 PM9/20/19
to mint...@googlegroups.com
17791From 'Ancient Ancestral South Indians (AASI)' to 'Andamanese Hunter Gatherers (AHG)': Political Pressure on Peer-Reviewed Science Papers?
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