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print versionbioRxiv - March 31, 2018
The Genomic Formation of South and Central Asia
Vagheesh M Narasimhan, Nick J Patterson, Priya Moorjani, Iosif Lazaridis, Lipson Mark, Swapan Mallick, Nadin Rohland, Rebecca Bernardos, Alexander M Kim, Nathan Nakatsuka, Inigo Olalde, Alfredo Coppa, James Mallory, Vyacheslav Moiseyev, Janet Monge, Luca M Olivieri, Nicole Adamski, Nasreen Broomandkhoshbacht, Francesca Candilio, Olivia Cheronet, Brendan J Culleton, Matthew Ferry, Daniel Fernandes, Beatriz Gamarra, Daniel Gaudio, Mateja Hajdinjak, Eadaoin Harney, Thomas K Harper, Denise Keating, Ann-Marie Lawson, Megan Michel, Mario Novak, Jonas Oppenheimer, Niraj Rai, Kendra Sirak, Viviane Slon, Kristin Stewardson, Zhao Zhang, Gaziz Akhatov, Anatoly N Bagashev, Baurzhan Baitanayev, Gian Luca Bonora, Tatiana Chikisheva, Anatoly Derevianko, Enshin Dmitry, Katerina Douka, Nadezhda Dubova, Andrey Epimakhov, Suzanne Freilich, Dorian Fuller, Alexander Goryachev, Andrey Gromov, Bryan Hanks, Margaret Judd, Erlan Kazizov, Aleksander Khokhlov, Egor Kitov, Elena Kupriyanova, Pavel Kuznetsov, Donata Luiselli, Farhad Maksudov, Chris Meiklejohn, Deborah C Merrett, Roberto Micheli, Oleg Mochalov, Zahir Muhammed, Samridin Mustafakulov, Ayushi Nayak, Rykun M Petrovna, Davide Pettner, Richard Potts, Dmitry Razhev, Stefania Sarno, Kulyan Sikhymbaevae, Sergey M Slepchenko, Nadezhda Stepanova, Svetlana Svyatko, Sergey Vasilyev, Massimo Vidale, Dima Voyakin, Antonina Yermolayeva, Alisa Zubova, Vasant S Shinde, Carles Lalueza-Fox, Matthias Meyer, David Anthony, Nicole Boivin, Kumarasmy Thangaraj, Douglas Kennett, Michael Frachetti, Ron Pinhasi, David Reich
doi: https://doi.org/10.1101/292581
Abstract
The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.
https://www.biorxiv.org/content/early/2018/03/31/292581.full.pdf
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How We, The Indians, Came to Be by Tony Joseph
https://www.thequint.com/voices/opinion/genomic-study-vedic-aryan-migration-dravidian-languages-sanskrit
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Articles by David Reich on use and abuse of ancient DNA
New York Times, March 25, 2018
How Genetics Is Changing Our Understanding of ‘Race’
By David Reich
In 1942, the anthropologist Ashley Montagu published “Man’s Most Dangerous Myth: The Fallacy of Race,†an influential book that argued that race is a social concept with no genetic basis. A classic example often cited is the inconsistent definition of “black.†In the United States, historically, a person is “black†if he has any sub-Saharan African ancestry; in Brazil, a person is not “black†if he is known to have any European ancestry. If “black†refers to different people in different contexts, how can there be any genetic basis to it?
Beginning in 1972, genetic findings began to be incorporated into this argument. That year, the geneticist Richard Lewontin published an important study of variation in protein types in blood. He grouped the human populations he analyzed into seven “races†— West Eurasians, Africans, East Asians, South Asians, Native Americans, Oceanians and Australians — and found that around 85 percent of variation in the protein types could be accounted for by variation within populations and “races,†and only 15 percent by variation across them. To the extent that there was variation among humans, he concluded, most of it was because of “differences between individuals.â€
In this way, a consensus was established that among human populations there are no differences large enough to support the concept of “biological race.†Instead, it was argued, race is a “social construct,†a way of categorizing people that changes over time and across countries.
It is true that race is a social construct. It is also true, as Dr. Lewontin wrote, that human populations “are remarkably similar to each other†from a genetic point of view.
But over the years this consensus has morphed, seemingly without questioning, into an orthodoxy. The orthodoxy maintains that the average genetic differences among people grouped according to today’s racial terms are so trivial when it comes to any meaningful biological traits that those differences can be ignored.
The orthodoxy goes further, holding that we should be anxious about any research into genetic differences among populations. The concern is that such research, no matter how well-intentioned, is located on a slippery slope that leads to the kinds of pseudoscientific arguments about biological difference that were used in the past to try to justify the slave trade, the eugenics movement and the Nazis’ murder of six million Jews.
I have deep sympathy for the concern that genetic discoveries could be misused to justify racism. But as a geneticist I also know that it is simply no longer possible to ignore average genetic differences among “races.â€
Groundbreaking advances in DNA sequencing technology have been made over the last two decades. These advances enable us to measure with exquisite accuracy what fraction of an individual’s genetic ancestry traces back to, say, West Africa 500 years ago — before the mixing in the Americas of the West African and European gene pools that were almost completely isolated for the last 70,000 years. With the help of these tools, we are learning that while race may be a social construct, differences in genetic ancestry that happen to correlate to many of today’s racial constructs are real.
Recent genetic studies have demonstrated differences across populations not just in the genetic determinants of simple traits such as skin color, but also in more complex traits like bodily dimensions and susceptibility to diseases. For example, we now know that genetic factors help explain why northern Europeans are taller on average than southern Europeans, why multiple sclerosis is more common in European-Americans than in African-Americans, and why the reverse is true for end-stage kidney disease.
I am worried that well-meaning people who deny the possibility of substantial biological differences among human populations are digging themselves into an indefensible position, one that will not survive the onslaught of science. I am also worried that whatever discoveries are made — and we truly have no idea yet what they will be — will be cited as “scientific proof†that racist prejudices and agendas have been correct all along, and that those well-meaning people will not understand the science well enough to push back against these claims.
This is why it is important, even urgent, that we develop a candid and scientifically up-to-date way of discussing any such differences, instead of sticking our heads in the sand and being caught unprepared when they are found.
To get a sense of what modern genetic research into average biological differences across populations looks like, consider an example from my own work. Beginning around 2003, I began exploring whether the population mixture that has occurred in the last few hundred years in the Americas could be leveraged to find risk factors for prostate cancer, a disease that occurs 1.7 times more often in self-identified African-Americans than in self-identified European-Americans. This disparity had not been possible to explain based on dietary and environmental differences, suggesting that genetic factors might play a role.
Self-identified African-Americans turn out to derive, on average, about 80 percent of their genetic ancestry from enslaved Africans brought to America between the 16th and 19th centuries. My colleagues and I searched, in 1,597 African-American men with prostate cancer, for locations in the genome where the fraction of genes contributed by West African ancestors was larger than it was elsewhere in the genome. In 2006, we found exactly what we were looking for: a location in the genome with about 2.8 percent more African ancestry than the average.
When we looked in more detail, we found that this region contained at least seven independent risk factors for prostate cancer, all more common in West Africans. Our findings could fully account for the higher rate of prostate cancer in African-Americans than in European-Americans. We could conclude this because African-Americans who happen to have entirely European ancestry in this small section of their genomes had about the same risk for prostate cancer as random Europeans.
Did this research rely on terms like “African-American†and “European-American†that are socially constructed, and did it label segments of the genome as being probably “West African†or “European†in origin? Yes. Did this research identify real risk factors for disease that differ in frequency across those populations, leading to discoveries with the potential to improve health and save lives? Yes.
While most people will agree that finding a genetic explanation for an elevated rate of disease is important, they often draw the line there. Finding genetic influences on a propensity for disease is one thing, they argue, but looking for such influences on behavior and cognition is another.
But whether we like it or not, that line has already been crossed. A recent study led by the economist Daniel Benjamin compiled information on the number of years of education from more than 400,000 people, almost all of whom were of European ancestry. After controlling for differences in socioeconomic background, he and his colleagues identified 74 genetic variations that are over-represented in genes known to be important in neurological development, each of which is incontrovertibly more common in Europeans with more years of education than in Europeans with fewer years of education.
It is not yet clear how these genetic variations operate. A follow-up study of Icelanders led by the geneticist Augustine Kong showed that these genetic variations also nudge people who carry them to delay having children. So these variations may be explaining longer times at school by affecting a behavior that has nothing to do with intelligence.
This study has been joined by others finding genetic predictors of behavior. One of these, led by the geneticist Danielle Posthuma, studied more than 70,000 people and found genetic variations in more than 20 genes that were predictive of performance on intelligence tests.
Is performance on an intelligence test or the number of years of school a person attends shaped by the way a person is brought up? Of course. But does it measure something having to do with some aspect of behavior or cognition? Almost certainly. And since all traits influenced by genetics are expected to differ across populations (because the frequencies of genetic variations are rarely exactly the same across populations), the genetic influences on behavior and cognition will differ across populations, too.
You will sometimes hear that any biological differences among populations are likely to be small, because humans have diverged too recently from common ancestors for substantial differences to have arisen under the pressure of natural selection. This is not true. The ancestors of East Asians, Europeans, West Africans and Australians were, until recently, almost completely isolated from one another for 40,000 years or longer, which is more than sufficient time for the forces of evolution to work. Indeed, the study led by Dr. Kong showed that in Iceland, there has been measurable genetic selection against the genetic variations that predict more years of education in that population just within the last century.
To understand why it is so dangerous for geneticists and anthropologists to simply repeat the old consensus about human population differences, consider what kinds of voices are filling the void that our silence is creating. Nicholas Wade, a longtime science journalist for The New York Times, rightly notes in his 2014 book, “A Troublesome Inheritance: Genes, Race and Human History,†that modern research is challenging our thinking about the nature of human population differences. But he goes on to make the unfounded and irresponsible claim that this research is suggesting that genetic factors explain traditional stereotypes.
One of Mr. Wade’s key sources, for example, is the anthropologist Henry Harpending, who has asserted that people of sub-Saharan African ancestry have no propensity to work when they don’t have to because, he claims, they did not go through the type of natural selection for hard work in the last thousands of years that some Eurasians did. There is simply no scientific evidence to support this statement. Indeed, as 139 geneticists (including myself) pointed out in a letter to The New York Times about Mr. Wade’s book, there is no genetic evidence to back up any of the racist stereotypes he promotes.
Another high-profile example is James Watson, the scientist who in 1953 co-discovered the structure of DNA, and who was forced to retire as head of the Cold Spring Harbor Laboratories in 2007 after he stated in an interview — without any scientific evidence — that research has suggested that genetic factors contribute to lower intelligence in Africans than in Europeans.
At a meeting a few years later, Dr. Watson said to me and my fellow geneticist Beth Shapiro something to the effect of “When are you guys going to figure out why it is that you Jews are so much smarter than everyone else?†He asserted that Jews were high achievers because of genetic advantages conferred by thousands of years of natural selection to be scholars, and that East Asian students tended to be conformist because of selection for conformity in ancient Chinese society. (Contacted recently, Dr. Watson denied having made these statements, maintaining that they do not represent his views; Dr. Shapiro said that her recollection matched mine.)
What makes Dr. Watson’s and Mr. Wade’s statements so insidious is that they start with the accurate observation that many academics are implausibly denying the possibility of average genetic differences among human populations, and then end with a claim — backed by no evidence — that they know what those differences are and that they correspond to racist stereotypes. They use the reluctance of the academic community to openly discuss these fraught issues to provide rhetorical cover for hateful ideas and old racist canards.
This is why knowledgeable scientists must speak out. If we abstain from laying out a rational framework for discussing differences among populations, we risk losing the trust of the public and we actively contribute to the distrust of expertise that is now so prevalent. We leave a vacuum that gets filled by pseudoscience, an outcome that is far worse than anything we could achieve by talking openly.
If scientists can be confident of anything, it is that whatever we currently believe about the genetic nature of differences among populations is most likely wrong. For example, my laboratory discovered in 2016, based on our sequencing of ancient human genomes, that “whites†are not derived from a population that existed from time immemorial, as some people believe. Instead, “whites†represent a mixture of four ancient populations that lived 10,000 years ago and were each as different from one another as Europeans and East Asians are today.
So how should we prepare for the likelihood that in the coming years, genetic studies will show that many traits are influenced by genetic variations, and that these traits will differ on average across human populations? It will be impossible — indeed, anti-scientific, foolish and absurd — to deny those differences.
For me, a natural response to the challenge is to learn from the example of the biological differences that exist between males and females. The differences between the sexes are far more profound than those that exist among human populations, reflecting more than 100 million years of evolution and adaptation. Males and females differ by huge tracts of genetic material — a Y chromosome that males have and that females don’t, and a second X chromosome that females have and males don’t.
Most everyone accepts that the biological differences between males and females are profound. In addition to anatomical differences, men and women exhibit average differences in size and physical strength. (There are also average differences in temperament and behavior, though there are important unresolved questions about the extent to which these differences are influenced by social expectations and upbringing.)
How do we accommodate the biological differences between men and women? I think the answer is obvious: We should both recognize that genetic differences between males and females exist and we should accord each sex the same freedoms and opportunities regardless of those differences.
It is clear from the inequities that persist between women and men in our society that fulfilling these aspirations in practice is a challenge. Yet conceptually it is straightforward. And if this is the case with men and women, then it is surely the case with whatever differences we may find among human populations, the great majority of which will be far less profound.
An abiding challenge for our civilization is to treat each human being as an individual and to empower all people, regardless of what hand they are dealt from the deck of life. Compared with the enormous differences that exist among individuals, differences among populations are on average many times smaller, so it should be only a modest challenge to accommodate a reality in which the average genetic contributions to human traits differ.
It is important to face whatever science will reveal without prejudging the outcome and with the confidence that we can be mature enough to handle any findings. Arguing that no substantial differences among human populations are possible will only invite the racist misuse of genetics that we wish to avoid.
David Reich is a professor of genetics at Harvard and the author of the forthcoming book “Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past,†from which this article is adapted.
The New York Times. March 31, 2018
How to Talk About ‘Race’ and Genetics
By David Reich
In a Sunday Review essay last weekend, David Reich, a geneticist at Harvard, argued that science is changing how we think about “race†and urged a candid discussion of the findings, whatever they may be. Hundreds of readers left comments, many expressing worry about the possibility that the results could be misinterpreted or nefariously applied. Here are Dr. Reich’s responses to some of the comments. — The Editors
Unfortunately, science has always been misused. From slavery, to eugenics, to economic Darwinism, to anti-abortion politics, the latest scientific knowledge has been employed in the service of evil. The idea of forestalling such efforts is valiant but fruitless. Science must continue its pursuit of truth, and scientists, as always, must speak out when their discoveries are exploited for harmful purposes. — Syfredrick, Providence, R.I.
We scientists always need to keep in mind our social responsibilities and to think about whether what we are doing has positive or negative effects on our world.
With respect to today’s study of human variation, I am optimistic — I believe that it has been socially positive. It is making every racist view of the world untenable. In my just-published book, I explain how the ancient DNA revolution — which has provided far greater power to reveal what happened in our deep past than what was available before — has done far more to undermine racist beliefs than to support them. As I wrote in the final paragraph of my book:
The study of human variation has not always been a force for good. In Nazi Germany, someone with my expertise at interpreting genetic data would have been tasked with categorizing people by ancestry had that been possible with the science of the 1930s. But in our time, the findings from ancient DNA leave little solace for racist or nationalistic misinterpretation. In this field, the pursuit of truth for its own sake has overwhelmingly had the effect of exploding stereotypes, undercutting prejudice, and highlighting the connections among peoples not previously known to be related. I am optimistic that the direction of my work and that of my colleagues is to promote understanding, and I welcome our opportunity to do our best by the people, ancient and modern, whom we have been given the privilege to study.
My book also gives concrete examples of how it is no longer so easy to twist science to support long-cherished stereotypes because ancient DNA is now debunking the stories that used to be made up about the nature of human variation. As I wrote there:
The Nazi ideology of a “pure†Indo-European-speaking Aryan race with deep roots in Germany, traceable through artifacts of the Corded Ware culture, has been shattered by the finding that the people who used these artifacts came from a mass migration from the Russian steppe, a place that German nationalists would have despised as a source. The Hindutva ideology that there was no major contribution to Indian culture from migrants from outside South Asia is undermined by the fact that approximately half of the ancestry of Indians today is derived from multiple waves of mass migration from Iran and the Eurasian steppe within the last five thousand years. Similarly, the idea that the Tutsis in Rwanda and Burundi have ancestry from West Eurasian farmers that Hutus do not — an idea that has been incorporated into arguments for genocide — is nonsense. We now know that nearly every group living today is the product of repeated population mixtures that have occurred over thousands and tens of thousands of years. Mixing is in human nature, and no one population is — or could be — pure.
Having been immersed in the ancient DNA revolution for the past 10 years, I am confident that anyone who pays attention to what it is finding cannot come away feeling affirmed in racist beliefs. My childhood guesses about who we are and how we’re related to one another — and about the nature of differences among people — have been shown to be wrong again and again.
As Hamlet says to his friend in Shakespeare’s play, “There are more things in heaven and earth, Horatio/Than are dreamt of in your philosophy.†And that’s what the ancient DNA revolution is reminding us repeatedly. Anyone who thinks they can guess what the nature of human variation is based on the data we had available to us before these breakthroughs is wrong.
I think the most important point in the article, that could’ve been emphasized a bit more, is that differences in individuals are far greater than that of populations.
When those who use the stats of the average I.Q. justify that for racist ideologies, they seem to fail to recognize the fact that there is massive variance from the average of all races. As well as the fact that institutional discrimination also has a negative impact on I.Q. of populations, which when those factors are controlled (education, economic upbringing, even being adopted and raised by parents who are of a different race), leads to even less substantial difference in even the average I.Q. of populations.
Differences in individuals vary far more widely than populations. Especially with intelligence. — Brian, Washington
Indeed, we have known for almost a half-century that for the great majority of human traits shaped by genetics, there is far greater variation among individuals than populations.
This means that when a teacher looks around a classroom of students of diverse “races,†she or he shouldn’t see them as members of fundamentally different groups of people. “Race†has trivial predictive power about an individual person’s biological capabilities. Even if there are slight average differences among groups of humans, individuals from any group are capable of excelling in any realm.
“It is important to face whatever science will reveal without prejudging the outcome and with the confidence that we can be mature enough to handle any findings.†Fat chance. What if many stereotypes are, in fact, confirmed by genetic research? What is the likelihood that ideologues of the left and right will have the maturity to handle it? Nonexistent. — BarrowK, North Carolina
It is likely that a few stereotypes will be validated by findings from genetics — even if it is also certain that a great majority will be disproved. When this happens, the findings will certainly be used in sound bites by people who, for whatever reason, need to believe that racist views of the world have been correct all along. Well-meaning people need to prepare for this possibility, which is exactly the issue I tried to grapple with in my article.
So how should we handle the eventuality that for a few traits, average differences among populations arising from genetics will be discovered? I do not think that the right approach is to pretend that scientific research has shown there can be no meaningful average genetic differences among human populations, because that message is contradicted by scientific facts.
The key point is that whatever science finds should not affect the way we behave toward one another. Whatever small average differences across groups might exist (and genetic studies have already made it clear that average differences across populations are much less than those between individuals), we are members of a single species, all of whom must be given every opportunity to flourish in every realm.
I agree with the gist of what is being said here. I’m not sure, though, that we are prepared to have this conversation. For several years I taught a segment of a course on “intelligence.†It was challenging and interesting. We explored controversies, and we raised all the questions about population differences. We read not only scientific treatments of the notion, but we also read poetry and fiction that explored the nature and value of “intelligence.†I stopped teaching it recently. It’s just too risky given the current environment in the universities.
I appreciate the courage here, and I hope the intellectual environment shifts so that we can properly prepare ourselves for this discussion. — Nathan, San Marcos, Calif.
From my point of view, it should be possible for everyone to hold in their heads the following six truths:
1. “Race†is fundamentally a social category — not a biological one — as anthropologists have shown.
2. There are clear genetic contributors to many traits, including behavior.
3. Present-day human populations, which often but not always are correlated to today’s “race†categories, have in a number of instances been largely isolated from one another for tens of thousands of years. These long separations have provided adequate opportunity for the frequencies of genetic variations to change.
4. Genetic variations are likely to affect behavior and cognition just as they affect other traits, even though we know that the average genetic influences on behavior and cognition are strongly affected by upbringing and are likely to be more modest than genetic influences on bodily traits or disease.
5. The genetic variations that influence behavior in one population will almost certainly have an effect on behavior in others populations, even if the ways those genetic variations manifest in each population may be very different. Given that all genetically determined traits differ somewhat among populations, we should expect that there will be differences in the average effects, including in traits like behavior.
6. To insist that no meaningful average differences among human populations are possible is harmful. It is perceived as misleading, even patronizing, by the general public. And it encourages people not to trust the honesty of scholars and instead to embrace theories that are not scientifically grounded and often racist.
In short, I think everyone can understand that very modest differences across human population in the genetic influences on behavior and cognition are to be expected. And I think everyone can understand that even if we do not yet have any idea about what the difference are, we do not need to be worried about what we will find because we can already be sure that any differences will be small (far smaller than those among individuals).
As a society, we are already committed to giving everyone a full opportunity for self-realization — regardless of the particular hand each person is dealt from the deck of life. Since we are already committed to this, accommodating any slight differences in the average genetic influences on traits that might eventually be found should only be a little extra work to handle.
David Reich is a professor of genetics at Harvard and the author of the book “Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past.â€
