Neanderthals, Denisovans and Modern Humans

A scientific​ revolution is underway in the way we investigate and understand the past. The extraction and analysis of ancient DNA from human skeletal remains, the field in which David Reich is a leading researcher, is a technical advance that eclipses the advent of radiocarbon dating in the 1950s, and is already transforming our knowledge, not only of human biological evolution, but also of human history and culture.

The potential value of genetic insights into the past became clear in 1987 when Allan Wilson and his colleagues at Berkeley sampled mitochondrial DNA (mtDNA) – a mere 0.0005 per cent of the genome, inherited solely along the maternal line – from living populations and analysed it to show that Homo sapiens, rather than having a multi-regional origin, evolved in Africa 200,000 years ago or later, then dispersed throughout the world, displacing existing populations. Seizing the moment, the geneticist Luigi Luca Cavalli-Sforza produced The History and Geography of Human Genes (1994), in which he sought to synthesise archaeology, history, linguistics and genetics to tell the story of human migration and describe the way the world’s populations became established. Reich thinks this was a visionary work but flawed, not just because of the paucity of genetic evidence available at the time but also because Cavalli-Sforza didn’t sufficiently appreciate the sheer complexity of past population movements. These could only be revealed by ancient, not modern, DNA.

It was Svante Pääbo and his colleagues at the Max Planck Institute for Evolutionary Anthropology in Leipzig who developed much of the technology for extracting DNA from ancient skeletal remains. Pääbo’s group were primarily concerned with the Neanderthals. At first they focused on extracting mtDNA, partly because its relative abundance increased the chances of successful extraction, and partly because of the frequency of mutations in this part of the genome, all the better to establish the point of separation of the Neanderthals from the modern human lineage. The problem with mtDNA is that since it tracks just a single female lineage, it provides only an extremely narrow window through which to view the past: the evidence is incomplete, and potentially misleading. The real prize was to extract the complete Neanderthal genome. By 2007, armed with dramatically increased computing power and bones containing organic material with well-preserved DNA, Pääbo was in a position to begin developing a method for whole-genome extraction. He brought together an international team, which included David Reich.

Reich worked with Pääbo until 2013, then left for Harvard to set up, with Nadin Rohland, the first laboratory in the US focused on whole-genome ancient DNA. They industrialised the process of DNA extraction and analysis, and the result has been an exponential increase in data. In 2010 just five ancient human genomes were published; in 2014, the number was 38. But by August 2017 Reich’s laboratory had published genome-wide data from more than three thousand individuals. New data is now being generated at a pace that far outstrips publication.

It was the assumption of many that this work would make it possible for us to identify the genetic differences between early and modern types of humans, say between Homo neanderthalensis and Homo sapiens. What was the genetic basis of the evident differences in their behaviour and thought? What was the genetic mutation that occurred about a hundred thousand years ago to produce those Homo sapiens we refer to as modern humans, resulting in the origin of art, language, human global dispersal and the replacement of all other human types? That we would be able to answer these questions was, it turns out, something of a pipe-dream. We now know that there are about a hundred thousand places in the genome where modern humans are genetically different from Neanderthals, but we aren’t much further along in understanding the biological consequences (if any) of those differences. In any case, the notion of finding a ‘golden gene’ misunderstands the way human traits derive from the complex interactions of multiple genes with natural and cultural environments; it has been just as difficult to pinpoint the significant genetic differences between humans and our closest living relatives, the great apes.

So what is the revolution, if it is not in our understanding of the genetic basis of cognitive and behavioural differences between modern humans and our ancestors and relatives? It is in our ability to write the history of human populations, their movements and their mixing, throughout time and across the world, which in turn gives us insights into past population sizes, patterns of social interaction and political structures. All this from DNA. It is a bold insurgency into the territories of archaeology, anthropology and history, against which those disciplines have no defence.

Throughout my career studying prehistory, and for generations before that, archaeologists have argued over whether the spread of technology and cultures was caused by the spread of people (migration) or of ideas (acculturation). When the evidence takes the form of artefacts such as ceramic vessels with particular shapes and decorations, or lifestyles such as farming or metalworking, which appear to have originated in one place and are now found in another, it is virtually impossible to tell the difference between migration and acculturation. The spread of Neolithic farming from Anatolia into Europe is the classic case: did this happen because indigenous hunter-gatherers in Europe gradually adopted wheat and barley, sheep and cattle, along with all the accompanying technology, from farmers they encountered or heard about at the boundaries of their territories? Or was the spread of the Neolithic across Europe also caused by the migration of people, which gradually forced indigenous hunter-gatherers into marginal areas, and ultimately led to their extinction? The same debate has been had over and over, not just about Neolithic Europe but about different geographic regions, different transitions and different time periods throughout human history.

To generalise a little crudely, migration was the more favoured explanation in the earlier 20th century; for Vere Gordon Childe, to speak of a ‘culture’ was to speak of a ‘people’. Acculturation became more fashionable following the advent of the New Archaeology of the 1960s, when archaeologists’ attention was taken up with processes of cultural change, adaptation and social competition. The study of ancient DNA has restored the primacy of migration, but this time, dare one say, as the definitive explanation for a huge proportion of prehistoric change. Why is the evidence supplied by ancient DNA so decisive? Because it can be compared with DNA from individuals (living or dead) from known geographical areas or ancestry with a view to identifying similarities that reflect an inherited pattern of past mutation. No longer does the study of genealogical relationships depend on metrical comparisons of facial and post-cranial morphology from well-preserved skeletal remains. Indeed, our sense of what it means for evidence to be ‘well preserved’ has itself been transformed. Once the term referred to the proportion of the skeleton that survived either as bone or fossil, but now we can speak of ‘well-preserved’ tiny fragments of bone, because it is the survival of the DNA inside the fragments that is key. Our stories of the past are now being written not by the skulls that appear on the cover of Nature or Science, but by toe and finger bones, by locks of hair and the tiny bones of the inner ear (which, it turns out, preserve an especially high density of DNA).

The particular toe bone I have in mind belonged to a Neanderthal from southern Siberia, at least fifty thousand years ago, and had the best-preserved DNA yet recovered. Pääbo’s laboratory sequenced its genome in 2013. By then, Reich had analysed less well-preserved Neanderthal genomes and, by comparing them with modern human DNA, had begun to suspect that Neanderthals interbred with the earliest modern humans, who left Africa less than fifty thousand years ago. At the time that idea went wholly against the scientific consensus. But it was confirmed by Pääbo’s Siberian toe bone, consigning years of archaeological debates about the interrelation between Neanderthals and modern humans to history. The evidence is that at least some Neanderthals copulated with some modern humans to produce fertile offspring: as a result, their status as separate species is questionable. Further research has shown that non-Africans typically have between 1.5 and 2.1 per cent Neanderthal DNA. The higher frequencies are found in East Asians rather than in Europeans, even though Europe was the Neanderthals’ homeland. Surprise follows surprise in the new science, as it does in the pages of Reich’s book.

Sometimes​ the surprise is in discovering just how much we don’t know. In 2008 a bone from a child’s little finger was found in Denisova Cave in the Atlai Mountains of Siberia. Few other bones were found and it was therefore unclear whether the finger bone came from a modern human or from a Neanderthal; what’s more, the deposits were mixed up, and it wasn’t clear how, or if, the bones were associated with the stone artefacts also found in the cave. In the days before DNA analysis, Denisova Cave would have been just another archaeological site, with little new to tell us. But in the event part of the finger bone was sent to Pääbo’s laboratory, and our knowledge of human evolution changed for ever.

Pääbo extracted the mtDNA and then the whole genome from the finger bone. It was one of the best samples of ancient DNA ever discovered. Reich was asked to help with the analysis. It was found that the bone had a genome different from both Neanderthal and modern human DNA. It represented a previously unknown type of human, soon given the name ‘Denisovans’. (The name was chosen deliberately to avoid designating a new species, in recognition that the notion of distinct human species had been confounded by the interbreeding of Neanderthals and modern humans.) The Denisovans weren’t just genetically distinct; on the evidence of huge molar teeth also found in the cave, they would also have looked and behaved quite differently. By considering the number of mutations that differentiated Neanderthals, Denisovans and modern humans, and estimating the rate at which such mutations occurred, Reich and his colleagues concluded that the modern human lineage had split off between 770,000 and 550,000 years ago, and then the remaining lineage had split into Neanderthals and Denisovans between 470,000 and 380,000 years ago.

Then came another surprise: the Denisovans known from Siberia were found to be genetically closer to people from New Guinea than to anyone from mainland Eurasia. New Guinea! Nine thousand kilometres away and with a tropical climate. Reich weaves an explanation according to which the Denisovans separated into two lineages between 400,000 and 280,000 years ago, after which one branch – the Australo-Denisovans – interbred with the modern humans who were the direct ancestors of present-day New Guineans. The Australo-Denisovans are what Reich describes as a ‘ghost population’ – known only from genetics, since there are no identifiable skeletal remains. When in 2016 his laboratory assembled genome data from 51 ancient modern humans who lived in Europe between 47,000 and 7000 years ago, ‘a whole mob of ancient ghosts whirled out.’ These tell a story of successive populations arising, dispersing and mixing up their genomes. Some of them appear to be associated with Ice Age cultures defined by tool types, confirming Childe’s notion that such cultures equate to a ‘people’. The story culminates in a population dispersal from the south-east about 14,000 years ago that spread a relatively homogenous population across Europe and the Near East.

With further arrivals, the population of Europe continued to develop. About 8800 years ago the first farmers spread into Europe from Anatolia; it wasn’t until at least two thousand years later that they mixed with indigenous hunter-gatherers, who then fast disappeared. Those Anatolian farmers were once thought to be both the ancestors of modern Europeans and the speakers of proto-Indo-European – the language from which all Indo-European languages derive. Both these things turn out to be wrong. One of the most startling facts to come out of ancient DNA research is that soon after five thousand years ago people of the Yamnaya culture originating in the steppes of central Asia swept across central and western Europe, replacing existing populations. In Europe the skeletal remains of these people are associated with what Childe described in the 1930s as the ‘Corded Ware culture’, named after a distinctive decorative pattern on their pottery. So here too Childe was correct: the spread of this culture was also the spread of a people, whose genetic roots were in central Asia and who are most likely to have been the speakers of proto-Indo-European. Their success may have been owed to an efficient economic system involving wheeled vehicles, horses and oxen, and the extensive felling of forests to turn Europe into a steppe-like environment. They may also have brought the plague into Europe; they were immune, the plague having been endemic to their central Asian homeland, but it did for many of the indigenous Europeans.

Reich’s account of Europe between fifty thousand and five thousand years ago is just the start of a European story that continues with the origin and spread of the Bell Beaker culture, also defined on the basis of the particular shape and decoration of its ceramic vessels. This has validated the notion of the ‘Beaker folk’, which I used to think was one of the most absurd hypotheses about British prehistory. It now seems that a mere 10 per cent of the ancestry of Bronze Age people in Britain was from the local Neolithic population, and the remaining 90 per cent from people in the Netherlands associated with the Bell Beaker culture.

From Europe, Reich takes a global tour: India, the Americas, East Asia, the Pacific islands and finally back to Africa, where the human story began. On each continent there are stories to tell based on the analysis of ancient DNA from skeletal remains, some of which fit with established theories, some of which aren’t merely new but would otherwise have been unimaginable. Ghost populations proliferate. In one case, the genome of a 24,000-year-old boy, extracted from a skeleton found in Mal’ta in central Siberia, showed a stronger affinity to Native Americans and Europeans than to Siberians, indicating that he belonged to what had previously been identified as the entirely ghostly ‘Ancient North Eurasians’. The Asian, American and African stories are not as detailed as the ones about Europe because only about 10 per cent of the ancient human DNA data so far collected comes from outside Europe. This will surely be reversed before long as ancient DNA labs proliferate, probably becoming a scientific service industry, and the abundant skeletal remains in regions such as the Yellow and Yangtze Rivers in China – one of the places farming originated – are analysed.

Reich’s book isn’t just a collection of stories about the histories of human populations. It is a fascinating case study of scientific revolution: the role of colleagues, of conferences, chance meetings, discoveries, technological innovations; what we do not yet sufficiently understand (notably, the rate of mutation); what new methods are required, and so on. Reich also has interesting things to say about the way his discipline has over the years been caught up in politics. To take one example, Childe was not the first to associate the expansion of the Corded Ware culture with a ‘people’. Gustaf Kossinna, writing in 1919, proposed that the roots of the Germanic and German-speaking people lay in the Corded Ware culture. The Nazis cited his ideas to claim legitimacy for their annexation of territories where the Corded Ware culture had been found. They also found the notion that culture spreads by migration useful in making the case for the biological superiority of some peoples over others. When Reich and his colleagues were preparing their publication about a genetic link between the Yamnaya of central Asia and the Corded Ware culture, several of the co-authors, including a German archaeologist, resigned for fear of being seen (quite erroneously) as validating Kossinna’s ideas.

In another case, there were concerns when ancient DNA data indicated that an influx of people described initially by Reich as ‘West Eurasians’ into South Asia had made a major contribution to historical and present-day Indian populations. The suggestion that the cultural achievements of South Asia might be partly attributable to western Eurasians was considered politically unacceptable by Indian archaeologists. A potential crisis was averted when all parties agreed on the term ‘Ancestral North Indians’ rather than ‘Western Eurasians’ for the incoming population, which then mixed with the people now labelled ‘Ancestral South Indians’, who had a much longer presence in South Asia.

Unsurprisingly, North America is one of the most politically charged arenas for ancient DNA studies. Some indigenous Americans see genetic research as the latest attempt on the part of Europeans to enlighten them, having already taken their ancestors’ bones and artefacts to display in museums. The Navajo have forbidden the participation of tribe members in genetic studies, explaining in a document prepared for academic researchers that ‘human genome testing is strictly prohibited by the Tribe. Navajos were created by Changing Woman; therefore they know where they came from.’ In other cases, academics have found ways of working positively with Native Americans, showing them for example how DNA studies can demonstrate ancestral tribal links to skeletal remains.

The outcomes of ancient DNA studies can have implications for the politics of the present as well as the past. By comparing the ancestries of the Y chromosome (inherited on the male line) and of mitochondrial DNA (inherited on the female line), Reich and his colleagues have demonstrated a persistent historical pattern according to which dominant migratory populations mix with indigenous populations through the breeding of incoming males with native females. In the Antioquia region of Colombia, for instance, 94 per cent of the Y chromosomes are European in origin – deriving from the Spanish conquistadors – while 90 per cent of the mtDNA is native. The contribution of European-American men to the genetic make-up of today’s African-American population is about four times that of European-American women.

Characteristic​ Y-chromosome sequences can indicate the sexual dominance of particular powerful men. The most notable example is a male of the Mongol empire who lived between 1300 and 700 years ago and left many millions of direct male-line descendants across the territory the Mongols once occupied. Presumably, this was Genghis Khan. He was not alone in his sexual habits: single males who made a strikingly large genetic contribution to later populations are known in all regions of the Old World, especially from around five thousand years ago. That coincides roughly with the Bronze Age, a period when secondary products such as wool and dairy became important, trade in metal ores proliferated and signs of inequality became manifest – in imposing burial mounds, for instance. When the archaeological and the ancient DNA evidence are combined, it appears that the concentration of power in the hands of a small number of males has always been matched by increased reproductive opportunity. Should we simply accept that the tendency to inequality and the sexual dominance of powerful men is ingrained in human nature and will always determine the course of events? Reich believes not. The ‘constant effort to struggle against our demons – against the social and behavioural habits that are built into our biology – is one of the ennobling behaviours of which we humans as a species are capable,’ he writes. ‘Evidence of the antiquity of inequality should motivate us to deal with it in a more sophisticated way today, and to behave a little better in our own time.’

Prior to the genomic revolution, our knowledge of the genetic variation between populations had been sufficiently limited that we could rest easy in the consensus that the genetic variation within a single population was always greater than the variation between populations. There were no grounds for proposing a biological basis for racial differences – however those might be defined. But now that there is substantial evidence for population-level genetic variation, the situation has changed. Reich posits, for instance, that African Americans have a higher rate of prostate cancer than European Americans because the risk factors for prostate cancer are predominantly found in regions of their genome that have a high frequency of African ancestry. Earlier this year, Buzzfeed published an open letter signed by 67 scientists and scholars in the social sciences, law and humanities about Reich’s treatment of race. Responding to his claim about the comparative rates of prostate cancer, they point out that ‘lots of people not from West Africa also have this same gene. We don’t call these other people a “race” or say their “race” is relevant to their condition.’ The signatories recognise ‘the existence of geographically based genetic variations in our species’, but argue that ‘such variation is not consistent with biological definitions of race.’ Their position is not that human populations ‘have no biological attributes in common’, but that ‘the meaning and significance of the groups is produced through social interventions.’

The genomic revolution is providing hard evidence for substantial biological variation between populations. As it moves forward, Reich argues, we will increasingly be able to translate that variation into behavioural and cognitive differences, while fully recognising that any given trait is produced by the interaction of multiple genes and environmental factors. The indications are that these biological differences will not square with traditional racial stereotypes. The truth is that the language and modes of thinking we have all inherited are simply unsuited to handling the avalanche of genetic data that will shortly be available. Reich’s view, which he reiterated in the New York Times in March, is that ‘if we abstain from laying out a rational framework for discussing differences among populations, we risk losing the trust of the public … We leave a vacuum that gets filled by pseudoscience.’

The good news is that although we are all too aware of the way science can be misused for racist ends, the genome revolution has already thoroughly undermined biologically based nationalism. The big message of Reich’s book is that through our evolution and, even more important, our history, populations have continually mixed with each other. Tiny pockets of persistent endogamy apart, we are blends of past populations, which were themselves blends of those who went before. And that trend continues today with the great 20th and 21st-century migrations. The study of ancient DNA really does tell us ‘how we got here’. Whether it tells us ‘who we are’ is a far more difficult matter. That is as much about our culture and beliefs as it is our biology. Reich describes himself as an Ashkenazi Jew, who feels American, speaks English, and whose mind is a product of the European Enlightenment, an intellectual tradition quite different from that of his biological ancestors. He has not had his own DNA tested, but if he did it wouldn’t tell him ‘who he is’. There remains a place after all for archaeology, anthropology and history in telling us who we are, and who we would like to be.