by David Reich
Not all the findings reported by the personal ancestry companies are inaccurate, and many people have obtained what for them is satisfying information from such testing, especially when it comes to tracing genealogies where the paper trail runs cold. One example is adoptees seeking their biological parents. Another is tracking down extended families.
From my own perspective, though, I do not find this approach to be satisfying. In preparing to write this book, I considered whether I should send my DNA to a personal testing company or study it in my own lab, and then describe the results, in imitation of the approach taken by many journalists covering the field of personal ancestry testing. But honestly, I am not interested. My own group—Ashkenazi Jews—is already overstudied. I am confident that my genome will be much like that of anyone else from this population. I would much rather use any resources I have to sequence the genomes of people who are understudied. I am also worried about the intellectual pitfall of self-study. I am innately suspicious of scientists who are hyper-interested in their own family or culture. They simply care too much. In my own laboratory, there are researchers from all over the world, and I encourage them, not always successfully, to choose projects on peoples not their own. For me, the approach of using the genome as a tool to connect myself to the world around me through personal links of family and tribe seems parochial and unfulfilling.
What the genome revolution has given us, though, is an even more important way to come to grips with who we are—a way to hold in our minds the extraordinary human diversity that exists today and has existed in our past. The problem of understanding the connections between self and the world is a central one for me, and has driven my lifelong interest in geography, history, and biology. Ironically for a person like myself, who is not at all religious, it is an example from the Bible that provides me with insight into how the genome revolution might be able to help solve this existential problem.
Every year on the holiday of Passover, Jews sit around the dinner table and recount the story of the Exodus from Egypt. The Passover holiday is important to Jews because it reminds them of their place in the world and encourages them to draw lessons about how they should behave. This narrative has been extraordinarily successful, as measured by the fact that it has sustained Jews in their identity for thousands of years as a minority living in foreign lands.
The Passover story begins with the myth of the patriarchs in ancient Israel: the first generation of Abraham and Sarah; the second of Isaac and Rebecca; the third of Jacob, Leah, Rachel, Bilhah, and Zilpah; and the fourth generation of twelve male children (the forefathers of the tribes of Israel) and a daughter, Dinah. These people are too removed from the huge populations of today to seem meaningfully connected to the present. The literary device that connects this ancient family to the multitudes that follow is Joseph, one of the sons of Jacob, who is sold by his brothers into slavery in Egypt, and who rises to a position of great power. When a famine strikes the land, the rest of the family also migrates to Egypt, where they are welcomed by Joseph despite the earlier crime they had committed against him. Four hundred years pass, and their descendants exponentially multiply into a nation numbering more than six hundred thousand military-age men and an even larger number of women and children. Under the leadership of Moses, they break their bonds of oppression, wander for dozens of years, and work out their code of laws. They then return to the Promised Land of their ancestors.
After reading the Passover story, Jews intuitively understand how within their population, numbering millions of people, they are related to each other and the past. The story allows Jews to think of those millions of coreligionists as direct relations—and to treat them with equal respect and seriousness even if they do not understand their exact relationships—to break out from the trap of thinking of the world from the perspective of the relatively small families we were raised in.
For me, the multitude of interconnected populations that have contributed to each of our genomes provide a similar narrative that helps me to understand my own place in the world and to avoid being daunted by the vast number of people in our species—the immensity of the human population numbering in the billions. The centrality of mixture in the history of our species, as revealed in just the last few years by the genome revolution, means that we are all interconnected and that we will all keep connecting with one another in the future. This narrative of connection allows me to feel Jewish even if I may not be descended from the matriarchs and patriarchs of the Bible. I feel American, even if I am not descended from indigenous Americans or the first European or African settlers. I speak English, a language not spoken by my ancestors a hundred years ago. I come from an intellectual tradition, the European Enlightenment, which is not that of my direct ancestors. I claim these as my own, even if they were not invented by my ancestors, even if I have no close genetic relationship to them. Our particular ancestors are not the point. The genome revolution provides us with a shared history that, if we pay proper attention, should give us an alternative to the evils of racism and nationalism, and make us realize that we are all entitled equally to our human heritage.
12
The Future of Ancient DNA
The Second Scientific Revolution in Archaeology
The first scientific revolution in archaeology began in 1949, when the chemist Willard Libby made a discovery that would transform the field forever and win him the Nobel Prize eleven years later.1 He showed that by measuring the fraction of carbon atoms in ancient organic remains that carry fourteen nucleons instead of the more common twelve or thirteen, he could determine the date when the carbon first entered the food chain. On earth, the radioactive isotope carbon-14 is mostly formed through the bombardment of the atmosphere by cosmic rays, maintaining the proportion of all carbon atoms of this type at a level of about one part per trillion. During photosynthesis, plants pull carbon out of the atmosphere and change it into sugar. From there, it gets integrated into all the other molecules of life. After a living thing dies, half the carbon-14 atoms decay into nitrogen-14 within 5,730 years. This means the fraction of all carbon atoms in ancient remains that have fourteen nucleons decreases in a known way, enabling scientists to determine a date for when the carbon entered a living thing as long as the date is less than about fifty thousand years ago (beyond that, the fraction of carbon-14 is too low to make a measurement).
Radiocarbon dating transformed archaeology, making it possible to determine the true age of materials, going beyond what was possible by studying the layering of remains. The discoveries that archaeologists made were profound. In Before Civilization: The Radiocarbon Revolution and Prehistoric Europe, Colin Renfrew described how radiocarbon dating showed that human prehistory extended much further back in time than had previously been thought, and described how the radiocarbon revolution overturned the assumption that all major innovations in European prehistory were imports from the Near East.2 While farming and writing were indeed of Near Eastern origin, innovations in metalworking and monumental constructions such as the building of megaliths like those at Stonehenge were not derived from ancient Egypt or Greece. These findings and many other discoveries about the true age of ancient remains sparked a new appreciation for indigenous cultures everywhere.
The penetration of radiocarbon dating into every aspect of archaeology is evident from the more than one hundred radiocarbon laboratories that provide dating to archaeologists as a service, and also from the fact that one of the basic skills serious archaeologists learn in graduate school is how to critically interpret radiocarbon dates. Radiocarbon dating has even changed archaeologists’ yardstick for time. The ancient Chinese measured years since emperors ascended the throne; the Romans since the mythical foundation of their city; and the Jews since the date of the creation of the world according to the Bible. Almost everyone today denominates years before or after the supposed birth date of Jesus. For archaeologists, time is now measured as the number of radiocarbon decay years Before Present (BP), def
ined as 1950, the approximate year when Willard Libby discovered radiocarbon dating.
The radiocarbon revolution transformed the discipline of archaeology into one that by the 1960s was no longer only a branch of the humanities, and instead now had equally strong roots in the sciences, with a high standard of evidence now required to support claims.3 Many additional scientific techniques were adopted by archaeologists in the period that followed, including flotation to identify ancient plant remains, and study of ratios of atomic isotopes beyond those of carbon to determine the types of foods peoples and animals ate and whether they moved across the landscape in their lifetimes. The rich new suite of scientific tools that archaeologists now had at their disposal made it possible for them to analyze the sites they excavated in ways that had not been possible for earlier generations of archaeologists, and to arrive at insights that were more reliable.
It is tempting to view ancient DNA as just one more new scientific technology that became available to archaeologists after the radiocarbon revolution, but that would be underestimating it. Prior to ancient DNA, archaeologists had hints of population movements based on the changes in the shapes of ancient skeletons and the types of artifacts people made, but these data were hard to interpret. But by sequencing whole genomes from ancient people, it is now possible to understand in exquisite detail how everyone is related.
The measure of a revolutionary technology is the rate at which it reveals surprises, and in this sense, ancient DNA is more revolutionary than any previous scientific technology for studying the past, including radiocarbon dating. A more apt analogy is the seventeenth-century invention of the light microscope, which made it possible to visualize the world of microbes and cells that no one before had even imagined. When a new instrument opens up vistas onto a world that has not previously been explored, everything it shows is new, and everything is a surprise. This is what is happening now with ancient DNA. It is providing definitive answers to questions about whether changes in the archaeological record reflect movements of people or cultural communication. Again and again, it is revealing findings that almost no one expected.
An Ancient DNA Atlas of Humanity
So far, the ancient DNA revolution has been highly Eurocentric. Of 551 published samples with genome-wide ancient DNA data as of late 2017, almost 90 percent are from West Eurasia. The focus on West Eurasia is a reflection of the fact that it is in Europe that most of the technology for ancient DNA analysis was developed, and it is in Europe that archaeologists have been studying their own backyards and collecting remains for the longest period of time. But the ancient DNA revolution is spreading, and has already produced several startling discoveries about human history outside of West Eurasia, most notably about the peopling of the Americas4 and of the remote Pacific islands.5 As technical improvements6 have now made it possible to get ancient DNA from warm and even tropical places, I have no doubt that within the next decade, ancient DNA from central Asia, South Asia, East Asia, and Africa will reveal equally great surprises. The product of this effort will be an ancient DNA atlas of humanity, sampled densely through time and space. This will be a resource that I think will rival the first maps of the globe made between the fifteenth and nineteenth centuries in terms of its contribution to human knowledge. The atlas will not answer every question about population history, but it will provide a framework, a baseline to which we will always return when studying new archaeological sites.
There is every reason to expect an avalanche of major discoveries from ancient DNA over the coming years as this atlas is built. One of the key frontiers that has hardly been touched by ancient DNA is the period between four thousand years ago and the present. The great majority of samples studied so far have been older, but of course we know from the written record as well as from archaeological evidence that more recent times—the period of the development of writing, complex stratified societies, and empires—have been extraordinarily eventful. The corpus of ancient DNA data even in West Eurasia is like a highway overpass still under construction and ending in midair, not quite connecting the populations of the past to those of the present. Using DNA to address what happened in this period will surely add to what we know from other disciplines.
To bridge the last four thousand years, to connect the past to the present, it is not sufficient to simply collect ancient DNA data from recent periods. The statistical methods that have worked so well for studying the earlier periods break down when examining data from more recent times. In particular, the methods based on Four Population Tests owe their power to measuring the proportions of ancestry from populations that are highly differentiated—the very different ancestries act like tracer dyes whose changing proportions can be tracked. However, in Europe, where we have made most progress in the ancient DNA revolution so far, we know that by four thousand years ago, many populations were already highly similar in their ancestry composition to those of today.7 For example, in Britain, we know that beginning after forty-five hundred years ago with people who buried their dead in association with wide-mouthed Bell Beaker pots, ancient Britons harbored a blend of ancestries very similar to that of present-day Britons.8 Yet it would be a mistake to conclude from this that the people of Britain today are descended without mixture from the “Beaker folk.” In fact, Britain’s population has been transformed by multiple subsequent waves of migration of continental people who were genetically similar to the people associated with Beaker burials. New, more sensitive methods are needed to determine how much ancestry in Britain derives from later waves.
To address this challenge, statistical geneticists are developing a new class of methods that make it possible to track mixtures and migrations even of populations that are highly similar in their deep ancestral composition. The secret is to focus on the recent shared history of the analyzed populations instead of the ancient shared history. When a sufficiently large number of samples are analyzed together, it is possible to find segments of the genome in which pairs of individuals share close ancestors over the last approximately forty generations, and by focusing on these segments of the genome, we can learn what happened in human history over this time frame (roughly one thousand years).9 With the small numbers of samples that have been available in ancient DNA studies so far, these methods have not been particularly useful because it is only the rare pair of individuals who are closely enough related to share identical long stretches of DNA. But as the number of individuals for whom we have ancient DNA increases, the number of pairs that we can analyze in order to detect relatedness increases according to the square of the number of samples. At the rate at which ancient DNA data are now being produced, it is reasonable to expect that within a few years, a single laboratory like mine will be producing genome-wide data from thousands of ancient people a year. This will make it possible to provide a detailed chronicle of how human populations have changed over recent millennia.
The power of this approach can already be seen in the 2015 study “The People of the British Isles,” which sampled more than two thousand present-day individuals from the United Kingdom whose four grandparents were all born within eighty kilometers of one another.10 The study found that the British population was very homogeneous by conventional measures. For example, the classic measure of genetic differentiation between two British populations is about one hundred times smaller than the same measurement of population differentiation comparing Europeans to East Asians. Despite the homogeneity, however, the authors were able to cluster the British population into seventeen crisply defined groups by searching for groups in which all pairs of individuals have elevated rates of recently shared genetic ancestors. Plotting the positions onto a map, they observed extraordinary genetic structuring, which has persisted despite the fact that people have moved back and forth continually over the British countryside over the past millennium, a process that would have been expected to homogenize the population. The boundaries of the clusters mark out the border between the southwestern counties of Devon a
nd Cornwall; the Orkney Islands off the north coast of Scotland; a largely undifferentiated cluster crossing the Irish Sea reflecting the migration of Scottish Protestants to Northern Ireland within the last few centuries; and within Northern Ireland, two distinctive and barely mixing clusters, which surely correspond to the Protestant and Catholic populations, divided by religion and hundreds of years of enmity under British rule. The success of this analysis, performed only on present-day people, gives hope for extending the approach to samples that are more ancient. In my laboratory, we already have generated genome-wide data on more than three hundred ancient Britons. Coanalyzing them with present-day Britons, including those from the “People of the British Isles” study, we expect to be able to connect the dots between the past and the present in this one small part of the world.
