Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past

by David Reich

fact, they had less hunter-gatherer ancestry than is present in diverse European populations today. The highest proportion of early farmer ancestry in Europe is today not in Southeast Europe, the place where Cavalli-Sforza thought it was most common based on the blood group data, but instead is in the Mediterranean island of Sardinia to the west of Italy.8

the people who live in a particular place today almost never exclusively descend from the people who lived in the same place far in the past.9 Under these circumstances, the power of any study that attempts to reconstruct past population movements from present-day populations is limited.

Modern genome-wide data shows that the primary gradient of farmer ancestry in Europe does not flow southeast-to-northwest but instead in an almost perpendicular direction, a result of a major migration of pastoralists from the east that displaced much of the ancestry of the first farmers.

We discovered that the population of northern Europe was largely replaced by a mass migration from the eastern European steppe after five thousand years ago

Vaesto aina joskus vaihtuu. Tavallisempaa tietysti etta vain Y-kromosomit.

great surprise that emerges from the genome revolution is that in the relatively recent past, human populations were just as different from each other as they are today, but that the fault lines across populations were almost unrecognizably different from today. DNA extracted from remains of people who lived, say, ten thousand years ago shows that the structure of human populations at that time was qualitatively different.

“The Collision That Formed India,” explains how the formation of South Asian populations parallels that of Europeans. In both cases, a mass migration of farmers from the Near East after nine thousand years ago mixed with previously established hunter-gatherers, and then a second mass migration from the Eurasian steppe after five thousand years ago brought a different kind of ancestry and probably Indo-European languages as well.

“The Genomics of Race and Identity,” argues that the orthodoxy that has emerged over the last century—the idea that human populations are all too closely related to each other for there to be substantial average biological differences among them—is no longer sustainable, while also showing that racist pictures of the world that have long been offered as alternatives are even more in conflict with the lessons of the genetic data.

The intensification of evidence for modern human behavior after fifty thousand years ago is undeniable, and raises the question of whether biological change contributed to it.

In 2002, Pääbo and his colleagues discovered two mutations in the gene FOXP2 that seemed to be candidates for propelling the great changes that occurred after around fifty thousand years ago. The previous year, medical geneticists had identified FOXP2 as a gene that, when mutated, produces an extraordinary syndrome whose sufferers have normal-range cognitive capabilities, but cannot use complex language, including most grammar.

These two mutations at FOXP2 cannot have contributed to the changes after fifty thousand years ago, since Neanderthals shared them,15 but Pääbo and his colleagues later identified a third mutation that is found in almost all present-day humans and that affects when and in what cells FOXP2 gets turned into protein.

is expected that only about 1,751 of her 16,777,216 twenty-fourth-degree genealogical ancestors contributed any DNA to her.

The number of ancestors you have doubles every generation back in time. However, the number of stretches of DNA that contributed to you increases by only around seventy-one per generation. This means that if you go back eight or more generations, it is almost certain that you will have some ancestors whose DNA did not get passed down to you. Go back fifteen generations and the probability that any one ancestor contributed directly to your DNA becomes exceedingly small.

San hunter-gatherers of southern Africa. Our study,27 like most others,28 found that the separation had begun by around two hundred thousand years ago and was mostly complete by more than one hundred thousand years ago.

The extremely ancient isolation of some pairs of human populations from each other conflicts with the idea that a single mutation essential to distinctively modern human behavior occurred shortly before the Upper Paleolithic and Later Stone Age. A key change essential to modern human behavior in this time frame would be expected to be at high frequency in some human populations today—those that descend from the population in which the mutation occurred—and absent or very rare in others. But this seems hard to reconcile with the fact that all people today are capable of mastering conceptual language and innovating their culture in a way that is a hallmark of modern humans.

Expanding our analysis to the whole genome, we could not find any location—apart from mitochondrial DNA and the Y chromosome—where all people living today share a common ancestor less than about 320,000 years ago.

A study she led in 2011 then showed that only a small fraction of evolution in humans has likely involved intense natural selection for advantageous mutations that had not previously been present in the population.32 Thus, intense and easily detectable episodes of natural selection such as those that have facilitated the digestion of cow’s milk into adulthood are an exception.

As genome-wide association studies proceed, they are beginning to investigate human variation in cognitive and behavioral traits,39 and studies like these—such as the ones for height—will make it possible to explore whether the shift to behavioral modernity among our ancestors was driven by natural selection. This means that there is new hope for providing genetic insight into the mystery that puzzled Klein—the great change in human behavior suggested by the archaeological records of the Upper Paleolithic and Later Stone Age.

The mutations necessary to facilitate modern human behavior were already in place, and many alternative combinations of these mutations could have increased in frequency together due to natural selection in response to changing needs imposed by the development of conceptual language or new environmental conditions.

We could see as much because

The test we developed is now called the “Four Population Test,” and it has become a workhorse for comparing populations. The test takes as its input the DNA letters seen at the same position in four genomes: for example, two modern human genomes, the Neanderthal, and a chimpanzee. It examines whether, at positions where there is a mutation distinguishing the two modern human genomes that is also observed in the Neanderthal genome—which must reflect a mutation that occurred prior to the final separation of Neanderthals and modern humans—the Neanderthal matches the second human population at a different rate from the first. If the two modern humans descend from a common ancestral population that separated earlier from the ancestors of Neanderthals, there is no reason why the mutation is more likely to have been passed down one modern human line than another, and thus the rate of matching of each of the two modern human genomes to Neanderthal is expected to be equal.

We have since refined this date by analyzing ancient DNA from a modern human from Siberia who, radiocarbon dating studies show, lived around forty-five thousand years ago. The stretches of Neanderthal-derived DNA in this individual are on average seven times larger than the stretches of Neanderthal-derived DNA in modern humans today, confirming that he lived much closer to the time of Neanderthal mixture.

There is genetic confirmation for smaller Neanderthal than modern human population sizes from the fact that the diversity of their genomes was about four times smaller. A history of small size is problematic for the genetic health of a population, because the fluctuations in mutation frequency that occur every generation are substantial enough to allow some mutations to spread through the population even in the face of the prevailing wind of natural selection that tends to reduce their frequencies.42 So in the half million years since Neanderthals and modern humans separated, Neanderthal genomes accumulated mutations that would prove detrimental when later, Neanderthal/modern human interbreeding occurred.

By measuring how much stronger the genetic evidence of archaic ancestry is in New Guineans compared to other non-Africans, we estimated that about 3 to 6 percent of New Guinean ancestry derives from Denisovans. That is above and beyond the approximately 2 percent from Neanderthals. Thus in total, 5 to 8 percent of New Guinean ancestry comes from archaic humans. This is the largest known contribution of archaic humans to any present-day human population.

Our first guess was mainland Asia, perhaps India or central Asia, on a plausible human migratory path from Africa to New Guinea. If this had been the case, the lack of much Denisovan-related ancestry in mainland East or South Asia could be explained by later waves of expansion on the part of modern humans without Denisovan-related ancestry, who replaced populations having Denisovan-related ancestry.

the archaic people who interbred with the ancestors of New Guineans were not close relatives of the Siberian Denisovans. When we examined the genomes of present-day New Guineans and Australians, and counted the number of DNA letter differences between them and the Siberian Denisovans to estimate when their ancestors separated from a common parent population, we discovered that everywhere in the genome, the number of differences was at least what would be expected for a population split that occurred 400,000 to 280,000 years ago.13 This meant that the ancestors of the Siberian Denisovans separated from the Denisovan lineage that contributed ancestry to New Guineans two-thirds of the way back to the separation of the ancestors of Denisovans from Neanderthals. In light of the remote relationship, the two groups probably had different adaptations, which would explain how they were able to thrive in such different climates. Given the extraordinary diversity of Denisovans—with much more time separation among their populations than exists among present-day groups—it makes sense to think of them as a broad category of humans, one branch of which became the ancestors of the archaic population that interbred with New Guineans and another that became Siberian Denisovans.

By examining mutations that occur at 100 percent frequency in present-day Africans, and measuring the excess rate at which they matched the Neanderthal over the Denisovan genome, we estimated that the unknown archaic population that interbred into Denisovans first split off from the lineage leading to modern humans 1.4 to 0.9 million years ago and that this unknown archaic population contributed at least 3 to 6 percent of Denisovan-related ancestry.

But another possibility suggests itself, which is that the ancestral population of modern humans, Neanderthals, and Denisovans actually lived in Eurasia, descending from the original Homo erectus spread out of Africa. In this scenario, there was later migration back from Eurasia to Africa, providing the primary founders of the population that later evolved into modern humans.

My laboratory’s first major discovery using the Four Population Test came when we tested the widely held view that Native Americans and East Asians are “sister populations” that descend from a common ancestral branch that separated earlier from the ancestors of Europeans and sub-Saharan Africans. To our surprise, we found that at mutations not shared with sub-Saharan Africans, Europeans are more closely related to Native Americans than they are to East Asians. It would be tempting to argue that this observation has a trivial explanation, such as Native Americans having some ancestry from European migrants over the last five hundred years. But we found the same pattern in every Native American population we studied, including those we could prove had no European admixture. The scenario of Native Americans and Europeans descending from a common population that split earlier from East Asians was also contradicted by the data. Something was deeply wrong with the standard tree model of population relationships.

We proposed that more than fifteen thousand years ago, there was a population living in northern Eurasia that was not the primary ancestral population of the present-day inhabitants of the region. Some people from this population migrated east across Siberia and contributed to the population that crossed the Bering land bridge and gave rise to Native Americans. Others migrated west and contributed to Europeans. This would explain why today, the evidence of mixture in Europeans is strong when using Native Americans as a surrogate for the ancestral population and not as strong in indigenous Siberians, who plausibly descend from more recent, post–ice age migrations into Siberia from more southern parts of East Asia. We called this proposed new population the “Ancient North Eurasians.”

The finding that several of the great populations outside of Africa today are profoundly mixed was at odds with what most scientists expected. Prior to the genome revolution, I, like most others, had assumed that the big genetic clusters of populations we see today reflect the deep splits of the past. But in fact the big clusters today are themselves the result of mixtures of very different populations that existed earlier.

Present-day Europeans and Near Easterners are mixed: they carry within them ancestry from a divergent Eurasian lineage that branched from Mal’ta, European hunter-gatherers, and East Asians before those three lineages separated from one another.

Lazaridis called this lineage “Basal Eurasian” to denote its position as the deepest split in the radiation of lineages contributing to non-Africans.

The profound transformation in culture that began with the Yamnaya is obvious to many archaeologists of the steppe. The increase in the intensity of the human use of the steppe lands coincided with a nearly complete disappearance of permanent settlements—almost all the structures that the Yamnaya left behind were graves, huge mounds of earth called kurgans. Sometimes people were buried in kurgans with wagons and horses, highlighting the importance of horses to their lifestyle. The wheel and horse so profoundly altered the economy that they led to the abandonment of village life. People lived on the move, in ancient versions of mobile homes.

Prior to the explosion of ancient DNA data in 2015, most archaeologists found it inconceivable that the genetic changes associated with the spread of the Yamnaya culture could be as dramatic as the archaeological changes. Even the archaeologist David Anthony, a leading proponent of the idea that the spread of Yamnaya culture was transformative in the history of Eurasia, could not bring himself to suggest that its spread was driven by mass migration. Instead, he proposed that most aspects of Yamnaya culture spread through imitation and proselytization.

Nick Patterson, Iosif Lazaridis, and I developed new statistical methods that allowed us to estimate that in Germany, people buried with Corded Ware pots derive about three-quarters of their ancestry from groups related to the Yamnaya and the rest from people related to the farmers who had been the previous inhabitants of that region. Steppe ancestry has endured, as we also found it in all subsequent archaeological cultures of northern Europe as well as in all present-day northern Europeans.

The discovery that the Corded Ware culture reflected a mass migration of people into central Europe from the steppe was not just a sterile academic finding. It had political and historical resonance. At the beginning of the twentieth century, the German archaeologist Gustaf

Kossinna was among the first to articulate the idea that cultures of the past that were spread across large geographic regions could be recognized through similarities in style of the artifacts they left behind. He also went further in viewing archaeologically identified cultures as synonymous with peoples, and he originated the idea that the spread of material culture could be used to trace ancient migrations, an approach he called the siedlungsarchäologische Methode, or “Settlement Archaeology.” Based on the overlap of the geographic distribution of the Corded Ware culture with the places where German is spoken, Kossinna suggested that the cultural roots of the Germans and of Germanic languages today lay in the Corded Ware culture. In his essay “The Borderland of Eastern Germany: Home Territory of the Germans,” he argued that because the Corded Ware culture included the territories of Poland, Czechoslovakia, and western Russia of his day, it gave Germans the moral birthright to claim those regions as their own.26 Kossinna’s ideas were embraced by the Nazis, and although he died in 1931, before they came to power, his scholarship was used as a basis for their propaganda and a justification for their claims to territories to the east.27 Kossinna’s suggestion that migration was the primary explanation for changes in the archaeological record was also attractive to the Nazis because it played into their racist worldview, as it was easy to imagine that migrations had been pro...

The correct theory that the Corded Ware culture spread through a migration from the east had already been proposed in the 1920s by Kossinna’s contemporary, the archaeologist V. Gordon Childe,30 although this idea too fell out of favor in the wake of the Second World War and the reaction to the abuse of archaeology by the Naz...

Our finding about the genetic link between the Yamnaya and the Corded Ware culture demonstrates the disruptive power of ancient DNA. It can prove past movements of people, and in this case has documented a magnitude of population replacement that no modern archaeologist, even the most ardent supporter of migrations, had dared to propose.

When the Corded Ware culture arrived, many tilled fields in central Europe were surrounded by virgin forests. But studies of pollen records in Denmark and elsewhere show that around this time, large parts of northern Europe were transformed from partial forest to grasslands, suggesting that the Corded Ware newcomers may have cut down forests, reengineered parts of the landscape to be more like the steppe, and carved out a niche for themselves that previous peoples of the region had never fully claimed.

One of the most important reasons for the collapse of Native American populations after 1492 was infectious diseases spread by Europeans who plausibly had built up some immunity to these diseases after thousands of years of exposure as a result of living in close proximity to their farm animals. But Native Americans, who by and large lacked domesticated animals, likely had much less resistance to them. Was it possible that, in a similar way, northern European farmers after five thousand years ago were decimated by plagues brought from the east, paving the way for the spread of steppe ancestry through Europe?

So, in contrast to what happened with the spread of the Corded Ware culture from the east, the initial spread of the Bell Beaker culture across Europe was mediated by the movement of ideas, not by migration.

The genetic impact of the spread of peoples from the continent into the British Isles in this period was permanent. British and Irish38 skeletons from the Bronze Age that followed the Beaker period had at most around 10 percent ancestry from the first farmers of these islands, with the other 90 percent from people like those associated with the Bell Beaker culture in the Netherlands. This was a population replacement at least as dramatic as the one that accompanied the spread of the Corded Ware culture. It turns out that the discredited idea of the “Beaker Folk” was right for Britain, although wrong as an explanation for the spread of the Bell Beaker culture over the European continent as a whole.

Prompted by the ancient DNA results, several archaeologists have speculated to me that the Bell Beaker culture could be viewed as a kind of ancient religion that converted peoples of different backgrounds to a new way of viewing the world, thus serving as an ideological solvent that facilitated the integration and spread of steppe ancestry and culture into central and western Europe. At a Hungarian Bell Beaker site, we found direct evidence that this culture was open to people of diverse ancestries, with individuals buried in a Bell Beaker cultural context having the full range of steppe ancestry from zero to 75 percent

By tracing possible migration paths and ruling out others, ancient DNA has ended a decades-old stalemate in the controversy regarding the origins of Indo-European languages. The Anatolian hypothesis has lost its best evidence, and the most common version of the steppe hypothesis—which suggests that the ultimate origin of all Indo-European languages including ancient Anatolian languages was in the steppe—has to be modified too.

However, there so far seems to be little archaeological evidence for destruction of Roman cities in this time, and if not for the detailed historical accounts, we might not know these pivotal events occurred.12 It is possible that in the apparent depopulation of the Indus Valley, too, we might be limited by the difficulty archaeologists have in detecting sudden change. The patterns evident from archaeology may be obscuring more sudden triggering events.

What can genetics add? It cannot tell us what happened at the end of the Indus Valley Civilization, but it can tell us if there was a collision of peoples with very different ancestries. Although mixture is not by itself proof of migration, the genetic evidence of mixture proves that dramatic demographic change and thus opportunity for cultural exchange occurred close to the time of the fall of Harappa.

The first genetic work in India gave seemingly contradictory results. Researchers studying mitochondrial DNA, always passed down from mothers, found that the vast majority of mitochondrial DNA in Indians was unique to the subcontinent, and they estimated that the Indian mitochondrial DNA types only shared common ancestry with ones predominant outside South Asia many tens of thousands of years ago.

In contrast, a good fraction of Y chromosomes in India, passed from father to son, showed closer relatedness to West Eurasians—Europeans, central Asians, and Near Easterners—suggesting mixture.

We found that the frequencies of the genetic mutations seen in all Indians are, on average, intermediate between those in Europeans and East Asians. The only way that this pattern could arise was through mixture of ancient populations—one related to Europeans, central Asians, and Near Easterners, and another related distantly to East Asians.