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Chapter 2: Destructive sampling on archaeological remains

Archaeological samples, specifically human remains, are a source of information for many different disciplines including archaeology, bioarchaeology, anthropology, archaeogenetics, forensic science, and others, and can be analysed with a multitude of scientific methods. Some of these methods are destructive and involve invasive procedures that result in the permanent destruction or alteration of part or all of a specimen. Users of destructive methods must carefully balance potential gains with the effective loss of parts of the material for other scientific purposes, some of which might not be foreseeable now, but possibly available in the future.

In archaeological fieldwork the loss of evidence weighs especially heavy, as excavation is — by definition — a large-scale destructive method. It therefore serves as a cautionary tale for sample preservation. In an early phase of archaeological research the subject was characterised by extensive field work projects at extraordinary sites with — from the vantage point of the present — not completely unsystematic or unscientific, but still insufficient, coarse and irreproducible methods. The research interests were in extreme cases more akin to treasure hunting than sustainable science (Lucas 2002). Many famous prehistoric burial mounds and Palaeolithic cave sites in Central Europe as well as urban and sacred sites in the Mediterranean region and the Near East were targeted by these expeditions (e.g. Cave sites in the Swabian Jura (Bolus 2015), Olympia (Fellmann 1973), Herculaneum and Pompeii (Parslow 1998) or Babylon (Seymour 2016)). Realising the tremendous loss of information, later generations of archaeologists from the first half of the 20th century onwards emphasized the development of fieldwork methods and made them an object of scientific discussion (Bowman/Douglas 1996, Harris 2006), including detailed documentation of every step of work. With that arose the core principle of in situ preservation. The UNESCO Recommendation on International Principles Applicable to Archaeological Excavations from 1956 formulates this principle as follows:

II. 9. Each Member State should consider maintaining untouched, partially or totally, a certain number of archaeological sites of different periods in order that their excavation may benefit from improved techniques and more advanced archaeological knowledge. On each of the larger sites now being excavated, in so far as the nature of the land permits, well defined "witness" areas might be left unexcavated in several places in order to allow for eventual verification of the stratigraphy and archaeological composition of the site.

The general principle to leave untouched "witness" material for future analysis can not just be applied to the context of archaeological fieldwork, but also to destructive sampling in wet lab procedures. The latter may indeed consist both of removal of small fragments from a larger specimen or even the complete destruction of an entire specimen. In the wider context of archaeogenetics, analyses that typically require destructive methods include genetic, proteomic, and metabolomic analyses, microscopy, isotopic analysis, and absolute dating (e.g., dendrochronology, radiocarbon dating, and other forms of radiometric dating). To meet the challenges formulated above and to fulfil our responsibility towards future generations we recommend the following strategies:

  • Work closely with collaborators (scientists and other stakeholders) to develop a plan for sample acquisition, taking care to preserve the integrity of physical specimens and associated metadata during sample transfer and temporary storage at laboratory facilities. Store information about each step of the processing workflow for documentation purposes, such as photographic records before and after sampling. 
  • Coordinate with collaborators to facilitate return of skeletal material to responsible institutions after the analysis. Work with collaborators to develop strategies for long-term storage of samples and intermediate products as well as digital raw data. This includes efforts to ensure funding for permanent storage, the maintenance of sample location and metadata catalogues and the development of open data standards for easy and standardized access to past analyses (see section 6). 
  • Target sampling efforts to answer specific research questions. Archaeological material may be sampled for exploratory research, especially in cases where there is insufficient knowledge to formulate explicit hypotheses. Nevertheless, wherever possible, seek to design studies around clearly defined questions with the potential to advance scientific knowledge, thus limiting extraneous sampling and preserving skeletal material for future study. 
  • Refrain from fully exhausting samples where possible. Save sufficient raw material and intermediate processed products of laboratory work for future sampling and processing.
  • Use and develop minimal loss methods. In recent years, techniques to sample material with minimal loss have been and are continuing to be developed and improved (Korlević et al. 2018; Fagernäs et al. 2020; Harney et al. 2021). Researchers should be aware of newest developments in this area.
  • Carefully assess the selection of skeletal elements where possible. Different skeletal elements allow for unique research questions, and come in different numbers. For example, with 32 teeth per individual vs. two petrous bones, teeth are a less scarce resource and potentially less destructive than removing a petrous bone from a skull. At the same time, they allow for more simultaneous analysis, including human DNA, pathogen DNA, Isotope analysis of enamel and dentine, calculus DNA and proteomics, and radiocarbon dating, compared to petrous bones and other elements. On the other hand, petrous bones and potentially other elements (Parker et al. 2020) have typically better preservation and hence allow for the generation of deeper sequencing data.
  • Together with research partners, discuss suitable extended documentation measures, such as methods of image and (3D) model creation, to digitally preserve the structure of specimens. Petrous bones, for example, are particularly valuable for comparative analyses of the inner ear structure, whose features are correlated to population structure at a relatively fine level (Ponce de Leon et al. 2018). Strive for a balance between additional investment of time for such analyses and the wish to return remainders of samples within a reasonable timeframe.

In summary, archaeological remains are a finite and scientifically precious source of information that requires a high standard of treatment to extract the most possible insight from it. For this particular ethical challenge there fortunately exist a number of technical solutions that significantly lessen the detrimental impact archaeogenetic research might have. The major challenge therefore boils down to implementing these and to carefully balance the costs and possible gains of particular, invasive analyses. Minimal loss methods and better specimen documentation may also raise the costs both in money and time spent per sample. So this requires sensible decision-making for each individual specimen, which should always include consultation with archaeologists (or conservators) and other affected stakeholders and collaborators.


Bolus, Michael. 2015. “History of Research and the Aurignacian of the Sites in the Swabian Jura.” In Human Origin Sites and the World Heritage Convention in Eurasia, edited by Nuria Sanz Anjelica Young, 2:32–49.

Browman, David L., and Douglas R. Givens. 1996. “Stratigraphic Excavation: The First ‘New Archaeology.’” American Anthropologist 98 (1): 80–95. https://www.jstor.org/stable/682955

Fagernäs, Zandra, Maite I. García-Collado, Jessica Hendy, Courtney A. Hofman, Camilla Speller, Irina Velsko, and Christina Warinner. 2020. “A Unified Protocol for Simultaneous Extraction of DNA and Proteins from Archaeological Dental Calculus.” Journal of Archaeological Science 118 (June): 105135.

Fellmann, Berthold. 1973. “The History of Excavations at Olympia.” Olympic Review 64 (65): 109–18. https://doi.org/10.1016/j.jas.2020.105135

Harney, Éadaoin, Olivia Cheronet, Daniel M. Fernandes, Kendra Sirak, Matthew Mah, Rebecca Bernardos, Nicole Adamski, et al. 2021. “A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth.” Genome Research, February. https://doi.org/10.1101/gr.267534.120.

Harris, Edward C. 2006. “Archaeology and the Ethics of Scientific Destruction.” In Between Dirt and Discussion: Methods, Methodology, and Interpretation in Historical Archaeology, edited by Steven N. Archer and Kevin M. Bartoy, 141–50. Boston, MA: Springer US.

Korlević, Petra, Sahra Talamo, and Matthias Meyer. 2018. “A Combined Method for DNA Analysis and Radiocarbon Dating from a Single Sample.” Scientific Reports 8 (1): 4127. doi.org/10.1038/s41598-018-22472-w

Lucas, Gavin. 2002. Critical Approaches to Fieldwork: Contemporary and Historical Archaeological Practice. Routledge.

Parker, C., Rohrlach, A.B., Friederich, S. et al. A systematic investigation of human DNA preservation in medieval skeletons. Sci Rep 10, 18225 (2020). https://doi.org/10.1038/s41598-020-75163-w

Parslow, Christopher Charles. 1998. Rediscovering Antiquity: Karl Weber and the Excavation of Herculaneum, Pompeii and Stabiae. Cambridge University Press.

Seymour, Michael. 2016. Babylon: Legend, History and the Ancient City. Reprint edition. I.B. Tauris.