Boots on the Ground in Africa's Ancient DNA 'Revolution': Archaeological

Home , African archaeology, Ancient DNA, Archaeogenetics, Human genome

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Debate Mary E. Prendergast & Elizabeth Sawchuk by cheaper sequencing, more efficient DNA-extraction and -preparation techniques, and new enrichment methods that restrict analysis to informative parts of the genome (Meyer & Kircher 2010; Meyer et al. 2012; Dabney et al. 2013;Fuet al. 2013, 2015). The best- known discovery, however, is that the petrous portion of the human temporal bone (often called the petrous pyramid) is richer in endogenous aDNA than any other skeletal element, and can yield sequences from poorly preserved material (Pinhasi et al. 2015). Humans possess two petrous pyramids—one on each side of the skull—that house the inner ear structures and reinforce the cranial base. The petrous region contains some of the densest bone in the body, and thus often preserves well archaeologically. Although new techniques minimise the amount of petrous pyramid used in aDNA analyses (Sirak et al. 2017), human remains are a non-renewable, yet intensively sought, resource. This raises concerns about the sustainability and ethics of current practices (Makarewicz et al. 2017). In the absence of discipline-wide protocols, individual research teams are often left to navigate sampling on a case-by-case basis, thereby contributing to widely varying and minimally documented practices. Archaeologists and curators are the ‘boots on the ground’ in this aDNA revolution, as they work with collections and ultimately make the most difficult decision of all: when is it acceptable to destroy human remains? Here we examine this question, alongside ethical issues particularly relating to African biomolecular research, with the goal of creating a more formal and public dialogue than the private discussions currently taking place via emails and across dining tables. While documents such as the Vermillion Accord (WAC 1989) outline the ethical treatment of human remains, tailoring these ideals to diverse research contexts is complex. Regional and indigenous-driven policies, such as the San Code of Ethics (SASI 2017), are still rare and call for respect from genomics researchers without providing specific directives. A new code of ethics for African genomics research (Yakubu et al. 2018) addresses many of the concerns we raise here, but applies to modern samples. Such documents rarely address destruction of ancient human tissue, nor how ethical principles, such as respect and care, translate into archaeological sampling protocols. In this paper, while recognising that ethics are subjective, we focus on three core issues within aDNA research: the dignified treatment of human remains; respect for and protection of cultural heritage; and the long-term preservation of future research opportunities. We outline a specific set of suggested protocols, drawing upon our experience in an ongoing project that examines ancient population structures and dynamics during the spread of food production in Holocene Africa. Since 2016, we have written seven proposals to sample African archaeological skeletons curated at African, European and North American institutions, and we have worked intensively in three African national museums to make inventories of human remains and choose samples for aDNA analysis. We reflect upon lessons learned and suggest best practices to develop, execute and follow through on collaborations focused on aDNA; many of these may be extended to other destructive analyses. We aim to stimulate exchanges amongst multiple stakeholders: not only curators, archaeologists and geneticists, but also descendant communities and the broader public, who do not always have a voice in the scramble for African human remains. Ultimately, we hope such discussion will lead to the development of a professional code of ethics for African aDNA research. © Antiquity Publications Ltd, 2018

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Debate Mary E. Prendergast & Elizabeth Sawchuk aDNA from increasingly early skeletons may have helped spur the current race to sample widely in museums—at a pace exacerbated by inter-laboratory competition. An analogy to the Scramble for Africa is regrettably apt, and makes it particularly important to consider how Africa’s colonial history affects multiple aspects of research on human remains. Recent calls have been made for ethical and regulated archaeogenetic research, in an age in which a few laboratories dominate access to samples worldwide (Makarewicz et al. 2017). While the Nagoya Protocol (CBD 2011) provides guidelines for fair access to samples and data, this was written with modern genetic resources in mind; additional consideration must be given to archaeogenetic samples. Morris (2017) identiﬁes pertinent issues in Africa and beyond, including competition without question-driven research; ‘parachute’ research, where samples are taken out of the country without engaging in long-term collaborations and capacity-building; geneticists’ ignorance (or dismissal) of bioarchaeological evidence; and lack of data comparability due to differing sample-processing methods among laboratories. Here, we highlight additional concerns that intertwine with Africa’s colonial history, and which are relevant to destructive analyses beyond aDNA.

Who ‘owns’ human remains? Who gives sampling permission? Colonial legacies become apparent in any search for African human skeletal collections. As these are often fragmented across continents, the logical cultural, chronological or geographic groupings of sites are torn apart, as are populations of individuals within sites, and even individual skeletons—depending on when and by whom they were excavated. A colonial-era penchant for exporting archaeological skulls, for example (see Hrdlicka 1918), led to the isolation of many individuals’ heads from their bodies, an issue that remains largely unaddressed. While there have been efforts, led by African and European civic groups and governments, and by intergovernmental organisations (such as the UN) to repatriate historical human remains, for example from Germany to Namibia, and from Spain to Botswana (Parsons & Segobye 2002; Wittwer-Backofen et al. 2014), public calls for repatriation of archaeological skeletons are rare (e.g. Musonda 2013). This issue is not limited to European and North American institutions. Within Africa, skeletal collections were moved widely across colonies controlled by a single power, leading to fragmentation across post-colonial states. Additionally, material often travelled to nearby countries where relevant expertise or facilities could be found, leading to the long-term curation of human remains outside their country of origin (e.g. Steyn et al. 2013). While repatriation is complex, determining who grants access to collections may be even more so. Permission to access foreign-held human remains should come from both the holding institution and the appropriate public body (and possibly other stakeholders) in the country of origin. In our experience, however, it is rare to require African governmental permission to sample in non-African institutions. Conversely, even if access is granted by the country of origin, it may be denied by the foreign institution based upon their own internal criteria. African stakeholders are themselves heterogeneous in that they include not only researchers, curators and government entities, but also communities who consider themselves descendants or guardians of human remains. These are by no means © Antiquity Publications Ltd, 2018

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Debate Mary E. Prendergast & Elizabeth Sawchuk

Where, how and by whom should aDNA results be presented and interpreted? The colonial legacy must be considered throughout interpretation and publication. Target journals for most aDNA papers are based in Europe or North America, and author lists are weighted heavily towards specialists from these regions. Future publications must be collaborative with African scholars and heritage managers, and made open access. Results should be made available not only through scientific journals, but also through multiple lines of dissemination to non-specialists. This might include materials designed specifically for students, educators, descendant or guardian communities, and the broader public in the countries where research takes place (written in appropriate languages). We must collectively consider how research results will be presented to, received within and mobilised by public audiences—including descendants for whom the line between archaeological and modern human remains may be indistinct. Unlike North America and Oceania, where legislation has generated decades of debate on ownership, repatriation and reburial, parallel public discussions have not happened in much of Africa, with the important exception of South Africa (Nienaber & Steyn 2011; Morris 2014). Potential outcomes of African aDNA research may include new efforts to define descendant groups, activism for repatriation and reburial, and political engagement with narratives—often based upon oral tradition—of migration and ethnic origins. These discussions will likely involve arguments concerning ties among genes, language and contemporary identities, concepts that have often been treated in reductionist ways in the history of African anthropology and archaeology (MacEachern 2000). A well-known example of this is the conflation and abuse of linguistic, archaeological and biological data to support the Hamitic Myth. This myth holds that descendants of the biblical figure Ham migrated into North-eastern Africa and were responsible for the continent’s cultural and technological development (Seligman 1930; critical discussion by Sanders 1969). These fallacies have serious implications, particularly where land disputes are tied to notions of identity. An especially devastating example was the invocation of the Hamitic myth to justify violence in the Rwandan genocide (Eller 1999). While archaeologists cannot offer specific ‘answers’ to complex arguments surrounding genetic, linguistic and cultural identities, we contribute to the tone of discussion, and we shape the quality of evidence on which debates rest.

Best practices for aDNA research in institutional collections Stakeholders involved in aDNA research include museum or other institutional curators, archaeologists, geneticists and heterogeneous public audiences. There may be yet other voices shaping the research process, including university employers, funding bodies, journals, professional associations and government agencies. Stakeholders are concerned not only about the destruction of cultural heritage in pursuit of new research, but also about how sampling will reflect upon themselves or their institution. Most also appreciate the potential for exploration made possible only through destructive methods. How do we balance the cost of destroying human remains with the benefit to scientific discovery? To return to our central question, when is it acceptable to destroy human remains? © Antiquity Publications Ltd, 2018

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Debate Mary E. Prendergast & Elizabeth Sawchuk

Table 1. Best practices for destructive sampling of archaeological human remains. Goal Best practices

Minimise • Wear gloves and change them frequently. contamination • Avoid touching hair, skin and surfaces. • Handle specimens as little as possible. • Use individual sterile foils to weigh/photograph each specimen. • Use sterile bags and avoid re-opening. • When drilling, use protective equipment (goggles, mask, gloves) and tool sterilisation protocols. • Store samples in a cool, dry, secure place. Document all steps • Leave clearly written tags on acid-free paper in bags and/or trays from of sampling which samples are taken. • Tags should minimally include: site, accession number, relevant catalogue and/or context codes, project-speciﬁc sample number, skeletal element, date removed and contact person for follow-up questions. • Tags should be updated upon sample return but left in tray. • Photograph each specimen from several perspectives. • If drilling, take before and after photographs. • Create a digital database of all samples. • Deposit a copy of database and photographs with the curating institution. This should be maintained, even after the specimens are returned. Minimise impacts For teeth: on future • Choose isolated teeth, not those still within jaws. bioarchaeological • Choose teeth with broken crowns and/or that have an unbroken antimere research (opposite-side pair). • Avoid teeth with signiﬁcant dental calculus residues. • Avoid teeth affected by dental disease. • Avoid teeth with rare morphologies, e.g. peg teeth. • Avoid teeth in the process of eruption. For temporal bones/petrous pyramids: • Choose isolated petrous pyramids instead of those attached (naturally or through reconstruction) to the skull. • When a cranium is intact, consult the museum on the possibility of cranial base drilling (Sirak et al. 2017). This should only be done if the specimen is well preserved and highly relevant to research questions. • Select petrous pyramids for which an antimere is present, whenever possible. • If a site has many individuals with isolated petrous pyramids, choose a subset (e.g. only left or only right), to prevent double-sampling individuals, and to leave unsampled individuals for future research. For other types of bone: • Choose small, morphologically uninformative bone (e.g. a limb shaft fragment) with no articular areas. • If morphologically informative, then choose bones with an antimere or other morphologically similar elements present (phalanges, for example). • Avoid pathologically altered bone, unless relevant to research. • Avoid elements informative about age, sex, or life history (e.g. bones in the process of fusing, erupting teeth, diagnostic pelvic features).

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Debate Mary E. Prendergast & Elizabeth Sawchuk

5. Researchers should strive to maintain long-term ties with collaborators and colleagues, and to build capacities by developing new research projects, mentoring and co-writing communications that build upon the initial results. Discussion: the future of the African aDNA ‘revolution’ Ethical aDNA research starts with adherence to a commonly agreed upon set of best practices that respect the sensitive history of African human remains, facilitate meaningful collaborations among laboratories, archaeologists and curators, and guide responsible sampling. It takes time to build relationships and to make deliberate, conservative sampling decisions. Time, in fact, is a key point of tension regarding current sampling practices, which seem to be driven largely by competition among laboratories. Only archaeologist- and curator-driven approaches—grounded in and limited by specific research questions— can change this situation and build a more sustainable and ethical future for African aDNA research. By calling for discipline-wide guidelines, we do not intend to create barriers to research or scare away those interested in archaeogenetic questions. Rather, we hope to stimulate a research-positive environment committed to open scholarship and scientific rigour, which also incorporates anthropological values and paves the way for long-term research and engagement. Many open questions remain. Which professional bodies and public institutions, in and outside of Africa, will design and enforce codes of ethics? Can existing bioethical codes be expanded to include archaeogenetic research, and how are the issues distinct (or not) from those of sampling modern DNA from living people? Which stakeholders must be consulted for permission to conduct destructive research on human remains? Straight et al. (2015) collaborated with Samburu community members in the excavation of burial cairns in Kenya and received permission based on informed consent for destructive scientific analyses (P. Lane pers. comm.). While this may be a good model for future excavations (notwithstanding the problems of defining descendant or guardian communities), granting or denying access to museum collections is arguably a more complex matter. How should public engagement be led by curating institutions, especially when the collections in question have been held for decades or centuries? Are there certain types of collections that should never be analysed— those younger than a certain age, for example? And if so, where is the line between ‘archaeological’ and ‘modern’? Given that in much of modern Africa, Muslim burials are left unexcavated out of respect for tradition, should analyses therefore proceed on museum collections with Islamic origins? Perhaps the most challenging questions will arise with public reception of aDNA results. Political manipulation of archaeological data has long been an issue throughout the field (e.g. Trigger 2006), but genetic data are perhaps particularly sensitive to such exploitation. Current debates in the Indian press, for example, contrast new archaeogenetic findings with old narratives about Aryan origins (Joseph 2017). The tone in some articles demonstrates how quickly research can be contested and abused for political aims. In a few clicks, one can easily find racist and pseudoscientific online discussions of legitimate genetic studies, including African ones. We must all strive for public debates to remain rooted in truth. Big-picture ethical questions must start with well-grounded foundations, and a common framework for destructive human remains sampling represents a good start. Finding a better © Antiquity Publications Ltd, 2018

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Reich, first David and joint and are MacEachern and Scott paper, Morris, this Alan to equally contributed Prendergast and Sawchuk (Giblin topic this on ethics issue special archaeological recent that a surprising in observed is debated—as it rarely history, so research. are post-colonial Africanist in and invested colonial those Africa’s among debate Given and dialogue more requires forward way ntdysciaeo atpcdrsac,sc eaei urgent. is Acknowledgements debate such research, fast-paced of climate today’s In https://doi.org/10.1073/pnas.1314445110 USA the 15758–63. of Sciences of Academy National fragment. DNA reconstructed ultrashort bear from cave Pleistocene Middle a of sequence genome mitochondrial Complete 2013. .Garcia N. .Weihmann A. archaeologist. field the for research—guidelines DNA acse 7My2018). May 17 (accessed https://www.antiquity.ac.uk/projgall/allentoft338/ at: Available protocol-en.pdf https://www.cbd.int/abs/doc/protocol/nagoya- at: Available Diversity. Biological Biological on Diversity Convention the from to arising utilization benefits their of the sharing and equitable resources and genetic fair to access on protocol Nagoya Series. Research Survey Archeological Arkansas Fayetteville: 44). Series skeletal human remains from collection data for Standards Heritage. analysis scientific human for archaeological remains of sampling destructive the for 2013. England). in Museum. British London: (ed.) 20–30. Hill J.D. Fletcher, & A. Antoine in D. Valley, Nile the from examples and potential research British Collection: the Museum from remains human of analysis , , J. , D. J.E. , , Akna rhooia uvyResearch Survey Archeological (Arkansas .Knapp M. M.E. ubc ertra fteCneto on Convention the of Secretariat Quebec: . & , & .Pääbo S. .Ambers J. ..Ubelaker D.H. Antiquity 03 eoeigsmlsfrancient for samples Recovering 2013. , .Nickel B. acse 7My2018). 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