Figure 2.5

Cluster diagram with K = 15. Dienekes Pontikos, “Human Genetic Variation: The First ? Components,” Diekenes’ Anthropology Blog, December 15, 2010, http://dienekes.blogspot.com/2010/12/human-genetic-variation-first.html.

Figure 2.6

Dendrogram of hierarchical clustering of the fifteen components. Dienekes Pontikos, “Human Genetic Variation: The First ? Components,” Diekenes’ Anthropology Blog, December 15, 2010, http://dienekes.blogspot.com/2010/12/human-genetic-variation-first.html.

Figure 2.7

Clustering analyses of modern DNA (left) and aDNA (right).³⁶ Mário Vicente and Carina M. Schlebusch, “African Population History: An Ancient DNA Perspective,” Current Opinion in Genetics & Development 62 (2020): 10.

Figure 2.8

“A possible model for gene flow events in the late Pleistocene.” Kay Prüfer et al., “The Complete Genome Sequence of a Neanderthal from the Altai Mountains,” Nature 505, no. 7481 (2014): 48. Reproduced with permission from SNCSC.

Figure 2.9

“Refined demography of archaic and modern humans.” Martin Kuhlwilm et al., “Ancient Gene Flow from Early Modern Humans into Eastern Neanderthals,” Nature 530, no. 7591 (2016): 432. Reproduced with permission from SNCSC.

Figure 2.10

“Separation of modern human and archaic ancestries in the past one million years.” Anders Bergström et al., “Origins of Modern Human Ancestry,” Nature 590, no. 7845 (2021): 234. Reproduced with permission from SNCSC.

Figure 2.11

(Left): The inferred maximum likelihood tree of human phylogeny relating modern and archaic humans without considering gene flow between them. (Right): The same tree allowing for ten admixture events between continental groups of modern humans on the basis of TREEMIX. Joseph K. Pickrell and Jonathan K. Pritchard, “Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data,” PLoS Genetics 8, no. 11 (2012): 8, 10.

Figure 5.1

Author studying the Neanderthal reconstructions in the Musée National de Préhistoire, Les Eyzies, France.

Figure 5.2

Mr. 4% at the Neanderthal Museum in Mettmann, Germany.

Figure 5.3

The Neanderthal as depicted (a) by German paleoanthropologist Hermann Schaaffhausen in 1876/1888, and (b) by Czech artist Frank Kupta in 1909.

Figure 5.4

“Werde Teil der Menschenfamilie.” Image/postcard on the website of the Neanderthal Museum in Mettmann, Germany.

Figure 5.5

Lucy as depicted at the Neanderthal Museum in Mettmann (left) and at the Musée National de Préhistoire, Les Eyzies (right).

Figure 5.6

Turkana boy as depicted at the Neanderthal Museum in Mettmann (left) and at the Musée National de Préhistoire, Les Eyzies (right).

Critical Perspectives on Ancient DNA: An Introduction

Daniel Strand and Anna Källén

In recent years, an intense focus on DNA has had a major impact on archaeology and our general knowledge about the ancient past.¹ While ancient DNA, or aDNA, has been extracted and analyzed since the late 1980s, the use of bioinformatics and innovations such as next-generation sequencing has from 2015 onward resulted in a dramatic increase in the number of analyzed samples. Although high-profile research papers on female Viking warriors and black Neolithic Europeans have made archaeogenetics famous beyond the corridors of academia, the field can be said to have got its definite public breakthrough in the fall of 2022, when the Nobel Prize in Medicine was awarded to Swedish paleogeneticist Svante Pääbo.

The hard-science muscle of archaeogenetics has certainly brought new resources, much attention, and a renewed confidence to research and knowledge claims within archaeology. Conversely, one might argue that the allure of archaeology has endowed genetic research with a profitable aura of adventure and mystique. In this sense, the rapid development of the field has been a win-win enterprise for archaeology and genetics. But what are the broader consequences of this development when it comes to our understanding of the ancient past? What are the social and political effects of a genetic conceptualization of past people’s identities and our present relations to them? What qualitative changes have the recent methodological developments in genomics brought to our knowledge of prehistory?

In Critical Perspectives on Ancient DNA, we dive deep into these issues, interrogating the practices, communications, and broader consequences of archaeogenetics. The seven chapters in this book present a critical perspective on this research field, exploring how, rather than simply revealing all-encompassing objective truths, it not only reifies old categories of identity and belonging but also creates new ones. The chapters assess to what extent archaeogenetics has contributed to a new and better version of historical knowledge, and they scrutinize the validity of bold claims about finding the real answers to questions of prehistoric events and ancient people’s identities. Do these claims have any foundation, or are they, rather, reflections of an ambitious—but ultimately impossible—positivist effort to uncover historical truths by employing the methods of natural science?

The Study of DNA

DNA is a molecule, of which long strands—chromosomes—exist in the nucleus of human cells. Parts of the chromosomes (usually considered to be less than 2 percent in humans) contain coded instructions for the production of various proteins and thus influence the physical functions and appearance of the human body. These units are called genes. A human genome contains the chromosomes for an individual in their cell nuclei, as well as a separate, smaller body of maternally inherited DNA found in the mitochondria, the cell’s “powerhouses.” By extracting and analyzing DNA from the cell nucleus and the mitochondria, and comparing the DNA of different individuals, it is possible to detect close biological family relationships and estimate distant ones. It is also possible to diagnose some diseases (such as Huntington’s disease and sickle-cell anemia) and trace some physical characteristics (such as waxy ears).

The iconic helix shape of the DNA molecule was officially presented by Francis Crick and James Watson in the early 1950s, a time of postwar optimism, when science and technological innovation were seen as leading the way to a prosperous future.² Crick and Watson became media celebrities, and DNA became publicly known as an objectively detectable code of life. It inspired widespread phantasms of DNA as a complete “blueprint” of an organism with the potential to bring the long-dead past back to real life, spicing up adventure fiction and archaeohorror films such as The Mummy.³ In the 1980s, when DNA profiling was developed for forensic science, DNA became widely known as hard evidence of individual identity, valid in a judicial sense. Altogether, this created a solid, popular confidence in DNA as a source of indisputable truth providing a complete map of an individual’s characteristics.

While it is easy to be seduced by the metaphor of DNA as a blueprint, this is not quite how genes works. As molecular anthropologist K. Ann Horsburgh puts it, “Blueprints share a one-to-one correspondence with the object they specify; they always produce the same results. This is certainly not the case with DNA.”⁴ In reality, the relation between DNA (the so-called genotype) and the actual outcome (the so-called phenotype) is much more complicated than suggested by the blueprint metaphor. Human identity and family relations are, moreover, defined by so many factors other than biology. Hence, there is little congruence between the great popular trust in DNA and what DNA can actually say in a scientific analysis—especially when it comes to aDNA. While this divergence between DNA as popular image and genetics as science is well known, it has rarely been brought into serious conversation by researchers working in the field. When it has, the focus has tended to be on the risks of false claims, which are said to diminish the public’s trust in science.⁵

In this volume, we offer a slightly different perspective on this problem. Rather than dismissing the inflated public trust in DNA as unimportant just because it may be false or trivial, we point to its great importance for archaeogenetics.⁶ In this vein, we recognize that knowledge about aDNA is not only created in science laboratories and at universities, but through complex meaning-making interactions between research and society at large. Throughout the volume, we maintain that the scientific discourse and practice of archaeogenetics have been formed in close, and continuous, interaction with popular imagination. Indeed, as Amade M’charek points out in her chapter in this book, archaeogenetics “invites a wide audience to project different kinds of aspirations, feelings, and vested ideas” on its subject. Popular phantasms and public expectations have played, and continue to play, prominent roles in the development of the field.

Ancient DNA, Archaeogenetics, and Archaeogenomics

Ancient DNA refers to the DNA of organic remains from the past. Since DNA molecules start to degrade as soon as the organism is dead—unless soft tissues are preserved as, for example, in the case of bog bodies or permafrost mummies—ancient DNA is in nearly every case more fragmentary than that of a living organism. Most attempts to extract and analyze aDNA are therefore ridden with problems of degradation. In analyses of ancient human DNA, there is also the risk of contamination from the abundance of DNA from living humans swirling around at archaeological excavations, in museums, and in the laboratory. For a long time, these problems seemed insurmountable, and it was not until the 1980s that the first studies of aDNA were published. In terms of knowledge structure and research questions, these studies built on earlier work in molecular anthropology, population genetics, and forensic science, but added the specific methodological challenges of working with degraded and potentially contaminated DNA, as well as questions and problems relating to archaeological and historical discourses.

The development of aDNA studies, or archaeogenetics, can be roughly divided into two phases. The first began in earnest in 1984, when scientists at a laboratory in Berkeley, California managed to sequence mitochondrial DNA from a stuffed quagga in a museum in Germany.⁷ Around the same time, biologists in Silicon Valley developed a new technology for replicating fragments of DNA from different types of samples in order to visualize genetic diversity. Geneticists had previously been forced to sequence particular strands of interest by hand, involving a heavy investment of time and money, but polymerase chain reaction (PCR) made it possible to amplify small fragments of genetic material and visualize them far more easily. By the beginning of the 1990s, scientists had successfully applied PCR to amplify aDNA fragments not only from preserved soft tissue, but also from dry bones and fossilized remains of ancient plants and insects.⁸

The field of human archaeogenetics—with which this book is primarily concerned—grew rapidly in the following years. As geneticists and molecular anthropologists turned from skin and mummies to more common ancient human remains in the form of bone and teeth, they could start addressing questions about genetic relations between tentative ancient population groups, such as the Pacific Islanders and Native Americans, as well as investigating prehistoric “celebrities” such as Ötzi, the 5,000-year-old man found in a melting glacier in the Tyrolean Alps in 1991.⁹ One particularly noted study during this period was a 1997 article in which geneticists in Germany presented the sequencing of mitochondrial DNA from the remains of an approximately 30,000-year-old Neanderthal individual. By demonstrating that the resulting sequence fell outside the variation of modern humans, the study indicated that Neanderthals went extinct without interbreeding with modern humans.¹⁰

In this first phase of archaeogenetics, the introduction of DNA to the toolkit of archaeological science also inspired discussions among archaeologists and molecular anthropologists regarding the methodological and epistemological challenges, and potential ethical issues, pertaining to this new line of research.¹¹

The second phase of archaeogenetics came with the introduction of the technology known as next-generation sequencing.¹² Developed in the first decade of the new millennium, this technology made it possible for scientists to sequence multiple small fragments of DNA in parallel, with bioinformatic technology piecing together the fragments by mapping “reads” to a reference genome. In practical terms, this meant that the whole breadth of a human genome could be sequenced in a single day, in contrast to the technology used in the 1990s, with which it could take over a year.¹³

The possibility of sequencing larger parts of ancient human genomes allowed archaeogenetics to develop into archaeogenomics.¹⁴ Published in 2010, the first genome-wide DNA studies of ancient humans included sequences from a 4,000-year-old individual from present-day Greenland and an archaic hominin individual from a Russian cave.¹⁵ The same year, a paper presenting the first sequencing of a Neanderthal genome showed that modern humans indeed have traces of DNA shared with Neanderthals in their genomes.¹⁶ This finding suggested that the two human subspecies, contrary to previous claims, not only lived at the same time but also interbred.

With next-generation sequencing, the number of sequenced samples from ancient human remains grew exponentially. While a handful of ancient genomes were sequenced in 2010, more than a hundred samples were sequenced every year between 2015 and 2018. By 2018, over 1,300 genome sequences had been produced from ancient human remains.¹⁷ Meanwhile, the publications on ancient human DNA—from scientific papers in Science and Nature to popular science books and journalistic reports—skyrocketed. As noted by scholars covering the development of archaeogenetics, the field has become a “hype” buttressed by a steady stream of interviews, television documentaries, TED talks, and newspaper profiles featuring the leading scientists in the discipline.¹⁸ According to philosopher of science Joyce Havstad, the unwavering media interest has turned archaeogenetics into a “sensational science” whose practitioners “can foreseeably expect to capture and sustain public interest … in a way that is likely to foster its development, and to amplify the publication and prestige of its results.”¹⁹ As Andreas Nyblom puts it in his contribution to this volume, archaeogenetics thrives in the media limelight.

The “aDNA Revolution”

The hype around archaeogenetics has not gone unnoticed by the scientists themselves. In the wake of next-generation sequencing and the steep publication curve of aDNA data and papers, researchers in the field have begun claiming that archaeogenetics constitutes a “revolution,” and that the application of new molecular technologies marks a “paradigm shift” in the history of archaeology and anthropology.²⁰ The revolution trope has been reproduced not merely in academic settings but also in popular science, news media, and interviews with scientists involved in the field.²¹

While many have been eager to announce this “aDNA revolution,” however, it is worth noting that few have sought to clarify why this is a revolution and against what or whom it is directed. In his classic 1962 book The Structure of Scientific Revolutions, historian of science Thomas Kuhn argues that a “scientific revolution” takes place when a discipline is confronted by a fundamental problem which threatens to devastate the entire scientific pursuit. With the establishment of a new “paradigm” designed to resolve the problem, Kuhn suggests, the discipline is saved, but at the expense of vast amounts of previously accepted knowledge, methodology, and terminology. As with a political revolution, Kuhn notes that the scientific revolution means that “the world itself changes.”²²

A critical question, however, is how all of this applies to aDNA research. What is the problem that threatens to undermine archaeology and anthropology, and to which genetic analysis promises a solution? What is the new paradigm established by archaeogenetics, and in what way(s) has it fundamentally transformed archaeological or anthropological research? What previously established archaeological knowledge has been ground by the mills of next-generation sequencing? And against whom or what is the revolution staged?

Since none of the proponents of the “aDNA revolution” have addressed any of these questions, it seems reasonable to suggest that the term does not purport to represent a scientific revolution in the traditional Kuhnian sense of the word. Rather, the “aDNA revolution” seems to be a somewhat hyperbolic euphemism for the past years’ increasing number of sequenced ancient genomes and published scientific papers. Seen from this perspective, it is revealing that Harvard-based geneticist David Reich, who is perhaps the person most closely associated with the term “aDNA revolution,” has described his main contribution to archaeogenetics as “to make ancient DNA industrial—to build an American-style genomics factory.”²³ As Reich boasts, his laboratory is “producing data so fast that the time lag between data production and publication is longer than the time it takes to double the data in the field.”²⁴

The most striking feature of this kind of rhetoric is the focus on numbers: more samples, more data, more papers. For Reich and his fellow aDNA revolutionaries, the revolution does not primarily seem to concern the quality of scientific results, but the quantitative leap in numbers of resources (ancient human genomes, next-generation sequencing technology, big data) and products (databases, scientific papers, books, conferences). While it is of course true that archaeogenetics has experienced a boom in the number of samples and publications, however, it is not apparent that this boom itself constitutes a “revolution” of archaeological or anthropological knowledge. Indeed, one could go as far as K. Ann Horsburgh in her concluding commentary to this volume and say that “despite grandiose claims to the contrary, aDNA data have not, and will not, revolutionize reconstructions of the past.”