Tracing prehistoric human activity using biomolecules in soil


Often the excavation of prehistoric sites yields very little preserved artefacts, a problem common to dry land archaeology. As a result little is known about prehistoric communities where there has been little success in excavation. Recent developments in molecular analyses of sedimentary archives presents an opportunity to revolutionise our understanding of prehistoric settlements and society. Lipid biomarkers originating from the faeces of invertebrate mammals (faecal steroids) are preserved in situ within sedimentary archives and can be used to directly trace the presence of humans and animals, potentially differentiating between species (Prost et al., 2017). Faecal steroids have been applied to characterise animal husbandry (Harrault et al., 2019) and spatial differences in activities and the cleanliness of living conditions associated with individual archaeological structures (Mackay et al., 2020). Ancient environmental DNA can also be extracted from latrines and soil deposits and has been used to reconstruct elements of past human diets, including crops, domesticated animals, fish, and specific parasites of humans and livestock as evidence for activities at archaeological sites (Søe et al., 2018). Despite their fledgling success at specific sites, their wider applicability to a range of archaeological settings needs to be determined.

This project aims to examine the functional differentiation of prehistoric enclosed settlements and assess the applicability of molecular analysis, in particular the sensitivity of molecular compounds and their resilience to degradation by using (1) modern biomolecular analyses of material from controlled experimental settings, and (2) biomolecular analyses of excavated remains from key UK late-prehistoric sites from within a range of different soil conditions.

The project will address the following research questions:
• How do environmental factors (such as soil chemistry, hydrology and post-depositional disturbances) affect the preservation of faecal lipid biomarkers and ancient environmental DNA in soils and sediments?
• To what extent do faecal lipid biomarkers and ancient DNA extracted from sediments and soils record differences in animal population densities and compositions?
• To what extent do sampling procedures and resolution influence interpretations of anthropogenic activities?
• What can we learn about settlement spatial use and prehistoric societies from applying these geochemical and biomolecular techniques at key UK archaeological sites?

The findings from this project will not only provide new insight into late prehistoric societies in the UK, but also will provide a series of methodological developments and recommendations for the incorporation of biomolecular approaches within archaeological investigations. These recommendations will contribute to heritage resource management and planning research and strategies adopted by organisations such as Historic Environment Scotland (HES) and Historic England (HE) who are end-user partners within this project.


This lab- and field-based project applies a combination of novel biomolecular techniques to modern experimental settings and excavated remains from key UK archaeological settlements.

Geochemical methods
• Lipid biomarkers: faecal steroid lipid biomarkers (faecal sterols and bile acids) from humans and animals will be extracted from sediments and analysed using GC-MS (Prost et al., 2017). These results will identify the presence of animals and indicate general living conditions such as cleanliness/co-occupation of humans and animals.
• Ancient environmental DNA: DNA will be extracted from sediments and analysed using shotgun DNA sequencing (Søe et al., 2018). Results from plant DNA will characterise store houses and/or food processing and mammal DNA will characterise byres and/or processing of animal products.
• Other geochemical indicators: more traditional analyses of phosphorus (Holliday and Gartner, 2007) and other elements via X-Ray Fluorescence will be conducted to compare with findings with existing literature and settlement classifications.
• Dating of prehistoric samples will be carried out using radiocarbon dating and robust chronologies will be developed using Bayesian models.

Experimental analyses
The experimental side of this project aims to characterise the preservation of faecal lipid biomarkers and ancient environmental DNA in different soil environments. This is possible by working with well-characterised soils available via collaboration with Dr Andy Neal (Rothamsted Research). Material from experimental plots with standardised manure application going back 170 years have been shotgun sequenced in 2015. The molecular data and additional soil chemistry information (water content, nutrients, elemental composition) are available to this project to test sensitivity and preservation of biomolecules in different conditions.

Application of experimental findings to key field sites
This project will select study sites of prehistoric settlements located within different sedimentary environments and associated with different levels of preservation. Chosen sites will be refined based on the candidates interests and findings from the experimental research, however key sites may include:
• The Black Loch of Myrton, southwest Scotland: hailed as ‘Scotland’s Glastonbury Lake Village’ this lowland wetland site dates back 2500 years and superb levels of preservation. Working in collaboration with CASE partners AOC Archaeology, new analyses can be calibrated against past excavations to test hypotheses on the specific functions of discrete buildings including byres, workshops, stores and living areas.
• High Knowes, Northumberland, England: this upland site contains juxtaposed palisaded settlements dating back 2500 years. Partial excavations revealed differences in the size and number of houses between settlements, suggesting that they had different functions which can be tested here using the biomolecular approaches.

Fieldwork at the key sites will include site surveying, collection of sediment cores and excavation of test pits.

Placements and collaborations
The successful applicant will do a placement with AOC Archaeology working on a number of their ongoing projects and selected key sites and work closely will all project partners including Dr Mikkel Winther Pedersen (University of Copenhagen) and Dr Andy Neal (Rothamsted Research) and HES and HE through the end-user partnership.

Project Timeline

Year 1

Background reading and literature review
• Visit to Rothamsted Research to collect modern soils and reference samples and receive training in experimental design for the construction of laboratory experimental work
• Training in the extraction and analysis of lipid biomarkers, targeting faecal steroids (sterols and bile acids)
• Extraction and analysis of lipid biomarkers and sedimentary DNA from experimental farming soils and laboratory experimental samples collected after 0 and 6 months.
• Fieldwork at key site one to obtain sediment samples with training in field techniques from AOC Archaeology and support from HES.

Year 2

• Radiocarbon dating of key site one sediments and training in Bayesian modelling.
• Extraction and analysis of lipid biomarkers and ancient environmental DNA from laboratory experimental samples collected after 12 and 18 months and key site one.
• Fieldwork at key site two to obtain sediment samples in collaboration with HE.
• Radiocarbon dating of key site two sediments
• Data analysis and write up of experimental results

Year 3

• Data analysis and write up of results from key sites one and two
• Extraction and analysis of lipid biomarkers and ancient environmental DNA from key site two

Year 3.5

Integration of all results and thesis writing

& Skills

This project will develop transferable skills in problem solving, project management, experimental design, data analysis and visualisation and report writing.

High-levels skills will be developed in:
• Field techniques and archaeological excavations including training in site surveying, coring and the excavation of settlement sediments which will be provided on-site from AOC CASE partners.
• Geochemical and biomolecular laboratory analyses with training on sediment core logging, radiocarbon dating and the extraction, processing and analysis of lipid biomarkers provided at Durham University. Sedimentary DNA extraction training will take place at Newcastle University and training on shotgun DNA sequencing and bio-information will take place at the University of Copenhagen.
• Computational/statistical analyses with training on computer programming in R for data visualisation and statistical analyses provided at Durham and Newcastle Universities.

The candidate also benefits from broad skills training provided in-house at Durham (e.g. thesis, paper and grant writing, presentation skills), from CASE Partners AOC Archaeology and end-users HES and HE (science communication and heritage resource management research) and from the broad range of environmental science training provided within the IAPETUS Doctoral Training Partnership. Training requirements of the individual will be identified and met through the development of a personal training plan.

The presence of national and international collaborators ensures that the student has excellent opportunities to develop a strong multidisciplinary research network. Research skills and awareness of on-going research will be developed through regular participation in Durham’s Physical Geography weekly seminar series and other research group meetings, and participation in external national and international conferences will support development as an independent researcher.

References & further reading

Harrault L., Milek K., Jardé E., Jeanneau L., Derrien M., Anderson D.G. 2019. Faecal biomarkers can distinguish specific mammalian species in modern and past environments. PLOS ONE, 14: e0211119.

Holliday, V.T., Gartner, W.G. 2007. Methods of soil P analysis in archaeology. Journal of Archaeological Science 34(2):301-333

Mackay, H., Davies, K.L., Robertson, L., Roy, L., Bull, I.D., Whitehouse, N.J., Crone, A., Cavers, G., McCormick, F., Brown, A.G., Henderson, C.G. 2020. Characterising life in settlements and structures: Incorporating faecal lipid biomarkers within a multiproxy case study of a wetland village. Journal of Archaeological Science 121, 105202.

Prost, K., Birk, J. J., Lehndorff, E., Gerlach, R., and Amelung, W. 2017. Steroid Biomarkers Revisited – Improved Source Identification of Faecal Remains in Archaeological Soil Material. PLOS ONE 12, e0164882-e0164882.

Søe M.J., Nejsum P., Seersholm F.V., Fredensborg B.L., Habraken R., Haase K., Hald M.M., Simonsen R., Højlund F., Blanke L., Merkyte I., Willerslev E., Kapel C.M.O. 2018. Ancient DNA from latrines in Northern Europe and the Middle East (500 BC–1700 AD) reveals past parasites and diet. PLOS ONE, 13: e0195481.

Further Information

Please contact Dr Helen Mackay ( when applying to this project. Note that there is scope to tailor specific components of this project towards the individual interests of the student.

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