Who We Are and How We Got Here

by David Reich

  A tempting idea is that the Basal Eurasians represent the descendants of a second wave of migration of modern humans north of the Sahara Desert, well after the dispersal of the population that interbred with Neanderthals. However, this is not correct, as the Basal Eurasian lineage shares much of the history of other non-Africans, including descent from the same relatively small population that founded all non-African lineages more than fifty thousand years ago. The ancient presence of the Basal Eurasians in Eurasia becomes even clearer when one considers that peoples who lived ten thousand years ago or more in what are now Iran and Israel each had around 50 percent Basal Eurasian ancestry,11 despite the clear genetic evidence that these two populations had been isolated from one another for tens of thousands of years.12 This suggests the possibility that there were multiple highly divergent Basal Eurasian lineages coexisting in the ancient Near East, not exchanging many migrants until farming expanded. The Basal Eurasians were a major and distinctive source of human genetic variation, with multiple subpopulations persisting for a long period of time.

  Where could the Basal Eurasians have lived, isolated as they seem to have been for tens of thousands of years from other non-African lineages? In the absence of ancient DNA, we can only speculate. It is possible that they may have sojourned in North Africa, which is difficult to reach from southern parts of the African continent because of the barrier of the Sahara Desert, and which is more ecologically linked to West Eurasia. Today, the peoples of North Africa owe most of their ancestry to West Eurasian migrants, making the deep genetic past in that region difficult to discern.13 However, archaeological studies have revealed ancient cultures there that could potentially have corresponded to the Basal Eurasians. The Nile Valley, for example, has been occupied by humans for the entire period since present-day Eurasians diverged from their closest relatives in sub-Saharan Africa.

  A hint about the possible homeland of the Basal Eurasians comes from the Natufians, hunter-gatherers who lived after around fourteen thousand years ago in the southwestern parts of the Near East.14 They were the first people known to have lived in permanent dwellings—they did not migrate from place to place searching for food despite being hunter-gatherers. They built large stone structures and actively managed local wild plants before their successors became full-fledged farmers. Their skulls as well as the stone tools they made are similar in shape to those of North Africans who lived around the same time, and it has been suggested on this basis that the Natufians migrated to the Near East from North Africa.15 In 2016, my laboratory published ancient DNA from six Natufians from Israel, and we found that they share with early Iranian hunter-gatherers the highest proportions of Basal Eurasian ancestry in the Near East.16 However, our ancient DNA data cannot determine where the ancestors of the Natufians lived, as we do not yet have comparable ancient DNA data from any other populations that lived at this time or earlier in North Africa, Arabia, or the southwestern Near East. And even if a genetic connection between Natufians and North Africa is established, it will not be the whole story, as it cannot explain the equally high proportions of Basal Eurasian ancestry in the ancient hunter-gatherers and farmers of Iran and the Caucasus.

  The Ghosts of Early Europeans

  The discovery of one major ghost population after another—Ancient North Eurasians and Basal Eurasians—might make it seem as if ancient DNA is unnecessary, since the existence of ghosts can be predicted from modern populations. But statistical reconstruction can only go so far. With data from present-day people, it is difficult to probe further back in time than the most recent mixture event. Moreover, because humans are so mobile, it is impossible to determine with any confidence where ancestral populations lived based on analyses of the genomes of their descendants. With ancient DNA directly extracted from the ghosts, however, it is possible to project further back in time, revealing even more ancient ghosts than can be recovered from modern data alone. So it was when the Mal’ta genome was sequenced. We discovered the Mal’ta genome statistically, but once we had access to the sequence, we were able to discover the even more distant Basal Eurasians.17

  In 2016, the lid of Pandora’s box opened wide, and a whole mob of ancient ghosts whirled out. My laboratory assembled genome-wide data from fifty-one ancient modern humans in Eurasia, most of them from Europe, who lived between forty-five thousand and seven thousand years ago.18 These samples spanned the entire period of the Last Glacial Maximum—which occurred between twenty-five thousand and nineteen thousand years ago—when glaciers covered the northern and middle latitudes of Europe so that all humans there lived in refuges in its southern peninsulas. Prior to our work, just a few remains provided genetic data from this period, and the picture that emerged from their analysis was static and monochromatic. But with all our new data, we could show that repeated population transformations, replacements, migrations, and mixtures had taken place over this vast stretch of time.

  When analyzing ancient DNA data, the usual approach is to compare ancient individuals to present-day ones, trying to get bearings on the past from the perspective of the present. But when this was done by Qiaomei Fu in my laboratory, her results shed little light on these ancient hunter-gatherers. The differences among humans today are hardly relevant to those that existed in Europe at the time depths she was studying. Fu needed to confront the data on their own terms. To do this, she began by comparing the ancient individuals to one another. She grouped them in four clusters that contained many samples that were similar both genetically and with respect to their archaeologically determined dates. Now she only needed to understand the relationships among the clusters. There were also some individuals who did not cluster with any others, especially among the oldest individuals.

  With her samples organized in this way, Fu was able to break down the story of the first thirty-five thousand years of modern humans in West Eurasia into at least five key events.

  Figure 13. Having migrated out of Africa and the Near East, modern human pioneer populations spread throughout Eurasia (1). By at least thirty-nine thousand years ago, one group founded a lineage of European hunter-gatherers that persisted largely uninterrupted for more than twenty thousand years (2). Eventually, groups derived from an eastern branch of this founding population of European hunter-gatherers spread west (3), displaced previous groups, and were eventually themselves pushed out of northern Europe by the spread of glacial ice, shown at its maximum extent (top right). As the glaciers receded, western Europe was repeopled from the southwest (4) by a population that had managed to persist for tens of thousands of years and was related to an approximately thirty-five-thousand-year-old individual from far western Europe. A later human migration, following the first strong warming period, had an even larger impact, with a spread from the southeast (5) that not only transformed the population of western Europe but also homogenized the populations of Europe and the Near East. At a single site—Goyet Caves in Belgium—ancient DNA from individuals spread over twenty thousand years reflects these transformations, with representatives from the Aurignacian, Gravettian, and Magdalenian periods.

  Event One was the spread of modern humans into western Eurasia and is evident in the two most ancient samples, an approximately forty-five-thousand-year-old individual whose leg bone had been found eroding out of a riverbank in western Siberia,19 and an approximately forty-thousand-year-old individual whose lower jaw was found in a cave in Romania.20 Both individuals were no more closely related to later European hunter-gatherers than they were to present-day East Asians. This finding showed that they were members of pioneer modern human populations that initially flourished but whose descendants largely disappeared. The existence of these pioneer populations makes it clear that the past is not an inevitable march toward the present. Human history is full of dead ends, and we should not expect the people who lived in any one place in the past to be the direct ancestors of those who live there today. Around thirty-nine thousand years ago, a supervolcano near present-day Naples in Italy dropped
an estimated three hundred cubic kilometers of ash across Europe, separating archaeological layers preceding it from those that succeeded it.21 Almost no Neanderthal remains or tools are found above this layer, suggesting that the climate disruption produced by the volcano, which could have produced multiyear winters, may have compounded competition with modern humans to create a crisis that drove Neanderthals to extinction. But the Neanderthals were not the only ones in crisis. Most modern human archaeological cultures that left remains below the ash layer left none above it. Many modern humans disappeared as dramatically as their Neanderthal contemporaries.22

  Event Two was the spread of the lineage that gave rise to all later hunter-gatherers in Europe. Fu’s Four Population Tests showed that both an approximately thirty-seven-thousand-year-old individual from eastern Europe (present-day European Russia)23 and an approximately thirty-five-thousand-year-old individual from western Europe (present-day Belgium) were part of a population that contributed to all later Europeans, including today’s.24 Fu also used Four Population Tests to show that during the entire period from around thirty-seven thousand to around fourteen thousand years ago, almost all the individuals she analyzed from Europe could be rather well described as descending from a single common ancestral population that had not experienced mixture with non-European populations. Archaeologists have shown that after the volcanic eruption around thirty-nine thousand years ago, a modern human culture spread across Europe making stone tools of a type known as Aurignacian, and that this replaced the diverse stone toolmaking styles that existed before. Thus genetic and archaeological evidence both point to multiple independent migrations of early modern human pioneers into Europe, some of which went extinct and were replaced by a more homogeneous population and culture.

  Event Three was the coming of the people who made Gravettian tools, who dominated most of Europe between around thirty-three thousand and twenty-two thousand years ago. The material remains they left behind include voluptuous female statuettes, as well as musical instruments and dazzling cave art. Compared to the people who made Aurignacian tools who came before them, the people who made Gravettian tools were much more deliberate about burying their dead, and as a result we have many more skeletons from this period than we do from the Aurignacian period. We extracted DNA from Gravettian-era individuals buried in present-day Belgium, Italy, France, Germany, and the Czech Republic. They were all genetically very similar despite their extraordinary geographic dispersal. Fu’s analysis indicated that most of their ancestry derived from the same sublineage of European hunter-gatherers as the thirty-seven-thousand-year-old individual from far eastern Europe, and that they then spread west, displacing the sublineage associated with Aurignacian tools and represented in the thirty-five-thousand-year-old Belgian individual. The changes in artifact styles associated with the rise of the Gravettian culture were thus driven by the spread of new people.

  Event Four was heralded by a skeleton from present-day Spain dating to around nineteen thousand years ago—one of the first individuals known to be associated with the Magdalenian culture, whose members over the next five thousand years migrated to the northeast out of their warm-weather refuge, chasing the retreating ice sheets into present-day France and Germany. The data once again showed a correspondence between the archaeological culture and genetic discoveries, documenting the spread of people into central Europe who were not directly descended from the Gravettians who had preceded them. There was also a surprise: most of the ancestry of individuals associated with the Magdalenian culture came from the sublineage represented by the thirty-five-thousand-year-old individual from Belgium who was associated with Aurignacian tools but who was later succeeded at the same site by people who used Gravettian tools and carried DNA similar to others in Europe associated with that culture of eastern European origin. Here was yet another ghost population that contributed to later groups in mixed form. The Aurignacian lineage had not died out, but instead had persisted in some geographic pocket, possibly in western Europe, before its resurgence at the end of the ice age.

  Event Five happened around fourteen thousand years ago, during the first strong warming period after the last ice age, a major climatic change known as the Bølling-Allerød. Geological reconstructions reveal that at this time, the Alpine glacial wall that extended down to the Mediterranean Sea near present-day Nice finally melted after about ten thousand years of dividing the west and east of Europe. Plants and animals from southeastern Europe (the Italian and Balkan peninsulas) migrated in abundance into southwestern Europe.25 Our Four Population Tests on our ancient DNA data showed that something similar happened with humans. After around fourteen thousand years ago, a group of hunter-gatherers spread across Europe with ancestry quite different from that of the people associated with the preceding Magdalenian culture, whom they largely displaced. Individuals living in Europe between thirty-seven thousand and fourteen thousand years ago were all plausibly descended from a common ancestral population that separated earlier from the ancestors of lineages represented in the Near East today. But after around fourteen thousand years ago, western European hunter-gatherers became much more closely related to present-day Near Easterners. This proved that new migration occurred between the Near East and Europe around this time.

  We do not yet have ancient DNA from the period before fourteen thousand years ago from southeastern Europe and the Near East. We can therefore only surmise population movements around this time. The people who had waited out the ice age in southern Europe became dominant across the entire European continent following the melting of the Alpine glacial wall.26 Perhaps these same people also expanded east into Anatolia, and their descendants spread farther to the Near East, bringing together the genetic heritages of Europe and the Near East more than five thousand years before farmers spread Near Eastern ancestry back into Europe by migrating in the opposite direction.

  The Genetic Formation of Present-Day West Eurasians

  Today, the peoples of West Eurasia—the vast region spanning Europe, the Near East, and much of central Asia—are genetically highly similar. The physical similarity of West Eurasian populations was recognized in the eighteenth century by scholars who classified the people of West Eurasia as “Caucasoids” to differentiate them from East Asian “Mongoloids,” sub-Saharan African “Negroids,” and “Australoids” of Australia and New Guinea. In the 2000s, whole-genome data emerged as a more powerful way to cluster present-day human populations than physical features.

  The whole-genome data at first seem to validate some of the old categories. The most common way to measure the genetic similarity between two populations is by taking the square of the difference in mutation frequencies between them, and then averaging across thousands of independent mutations across the genome to get a precisely determined number. Measured in this way, populations within West Eurasia are typically around seven times more similar to one another than West Eurasians are to East Asians. When frequencies of mutations are plotted on a map, West Eurasia appears homogeneous, from the Atlantic façade of Europe to the steppes of central Asia. There is a sharp gradient of change in central Asia before another region of homogeneity is reached in East Asia.27

  How did the present-day population structure emerge from the one that existed in the deep past? We and other ancient DNA laboratories found in 2016 that the formation of the present-day West Eurasian population was propelled by the spread of food producers. Farming began between twelve and eleven thousand years ago in southeastern Turkey and northern Syria, where local hunter-gatherers began domesticating most of the plants and animals many West Eurasians still depend upon today, including wheat, barley, rye, peas, cows, pigs, and sheep. After around nine thousand years ago, farming began spreading west to present-day Greece and roughly at the same time began spreading east, reaching the Indus Valley in present-day Pakistan. Within Europe, farming spread west along the Mediterranean coast to Spain, and northwest to Germany through the Danube River valley, until it reached Scandin
avia in the north and the British Isles in the west—the most extreme places where this type of economy was practical.

  Until 2016, getting genome-wide ancient DNA from the Near East to assess the extent to which these changes in the archaeological record were propelled by movements of people had failed, as the warm climate of the Near East quickens chemical reactions, accelerating the rate of breakdown of DNA. However, two technical breakthroughs changed this. One came from a method developed by Matthias Meyer, which involved enriching DNA extracted from ancient bones for human sequences of interest.28 This approach makes ancient DNA analysis up to one thousand times more cost-effective and gives access to samples that would otherwise provide too little DNA to study. Working together with Meyer, we adapted this method to make possible genome-wide analysis of large numbers of samples.29 The second breakthrough was the recognition that the inner-ear part of the skull—known as the petrous bone—preserves a far higher density of DNA than most other skeletal parts, up to one hundred times more for each milligram of bone powder. Within the petrous bone, the anthropologist Ron Pinhasi, working in Dublin, showed that the mother lode of DNA is found in the cochlea, the snail-shaped organ of hearing.30 Ancient DNA analysis of petrous bones in 2015 and 2016 broke through one barrier after another and made it possible for the first time to get ancient DNA from the warm Near East.

  Working with Pinhasi, we obtained ancient DNA from forty-four ancient Near Easterners across much of the geographic cradle of farming.31 The results revealed that around ten thousand years ago, at the time that farming was beginning to spread, the population structure of West Eurasia was far from the genetic monoculture we observe today. The farmers of the western mountains of Iran, who may have been the first to domesticate goats, were genetically directly derived from the hunter-gatherers who preceded them. Similarly, the first farmers of present-day Israel and Jordan were descended largely from the Natufian hunter-gatherers who preceded them. But these two populations were also very genetically different from each other. We and another research group32 found that the degree of genetic differentiation between the first farmers of the western part of the Near East (the Fertile Crescent, including Anatolia and the Levant) and the first farmers of the eastern part (Iran) was about as great as the differentiation between Europeans and East Asians today. In the Near East, the expansion of farming was accomplished not just by the movement of people, as happened in Europe, but also by the spread of common ideas across genetically very different groups.