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The Ancient Ports of Europe: A Novel Genetic Window on Ancient Lives (PortGEN)

The ancient ports of Europe provide a unique window into the lives and economic activities of past civilisations, potentially world-wide. Ports are the life-blood of complex societies and can reveal how society adapted to changing environmental conditions from disease to floods. So far the ‘past of ports’ has been explored using archaeology, texts, plant/animal remains, and geochemistry – but the molecular/genetic potential is immense (Brown et al. 2024). Since the discovery that extra-cellular ancient DNA can be preserved in sediments 20 years ago (Willerslev et al. 2003) it has been used in lakes, estuaries, floodplains and soils (Capo et al. 2021; Brown et al. 2022; Hudson et al 2022; Subm.). This implies that the sedimentary traps of ancient ports are an untapped source of invaluable archaeological information as ports are the ultimate transport nodes recording imports, exports, industrial activities as well as the lives of the local inhabitants. Whereas long-established methods (geochemistry, pollen, plant remains) can reveal valuable information (Véron et al. 2018; Goiran et al. 2015; Salomon et al. 2016) we believe that this is the tip of the ice-berg with molecular methods able to provide far deeper and more comprehensive data on the full ‘port-ecosystem’ ranging from plant and animal products to raw materials and diseases. Through our collaborators we have material already promised from a number high-profile sites including Rome (Ostia Antica, Portus), Spina, Venice, Ephesus, Corinth and the Levant.

    The hypotheses to be tested in PortGEN ascend in ambition from the lowest (presence of sedaDNA) to much more ambitious hypotheses and objectives as below:

  • Bona-fide and authenticated sedaDNA can be obtained from dated harbour sediments
  • We can determine imports, exports and local resources from port sedaDNA
  • SedaDNA can reveal changing social and environmental conditions during port-life times
  • SedaDNA can record disease of plants, animals and humans

These hypotheses will be tackled through five objectives:

  • Extract sedaDNA for both metabarcoding and shotgun sequencing from harbour sediments
  • Match the sequences to the best available libraries for plants, animals and microbes (incl. diseases)
  • Relate the sedaDNA data to pollen, diatoms and plant and animal macroscopic remains
  • Identify provenance and separate imports from exports and from local sources (using Global databases).
  • Provide a molecular biography of the port during the period of the sedimentary archive

Significance

This is three-fold: a new depth of understanding which, based on our ongoing work on archaeological middens, will likely double the identified food resource-types and so broaden the dietary breadth of the hinterland’s inhabitants. This feeds into some big-debates in archaeology e.g. the health of the inhabitants of Classical Rome and its trade networks. The second potential area of significance is through port character – itemizing and even quantifying (in relative terms) the trade patterns of individual ports. Lastly, because port sediments also record floods and marine influence, we can reveal changing environmental conditions. This project will be the first to apply sedaDNA to buried port harbours in Europe (or anywhere). It builds on research experience on Roman ports at the University of Southampton (Roman Ports Project) and a German Research Council special project on harbours (SPP1630) neither of which included any molecular methods. PortGEN proposed project goes beyond any previous work through collaboration between the PI and co-applicants (Walsh, Salomon, Gioran) and collaborators (Morhange) to utilize a sophisticated approach to the study of port history through sediments. One result of agriculture and geomorphic change is a legacy of silted ancient ports from the Mediterranean to the Baltic which contain rich environmental archives (Marriner et al. 2010). These sites offer an unparalleled opportunity to investigate past trade, economy and even health over the last 3000 years in Classical and Post-Classical Europe. Using both standard geoarchaeological approaches to Classical and Medieval ports this project will trial the rapidly developing power of sedaDNA to determine imports, exports at the species level enabling accurate reconstructions of cargoes and locally consumed foods as well as other economically important materials. This approach provides a unique window on international trade-networks, the real economies of these ports and their hinterlands, past dietary patterns and potentially disease.

Taphonomy & Methods

The project combines sedaDNA methods (PI) with the current state-of-the art methodology for the analysis of ports – the ‘Palaeoenvironmental Age-Depth Model’ (Fig. 1) which was devised by co-applicant (Salomon) and which combines flood sediments analyses (Pears et al. 2023) with explicit modelling of the effect of dredging (Morhange et al. 2010). We believe this will work because we now know that sedaDNA is carried into lakes and basins attached to particles and particularly clay minerals (Capo et al. 2021). So it represents the catchment and particularly the land close to the river, which in most ports is the city and its outskirts. We will also get direct DNA input from the port and some from the marine environment. These sources can also be traced using diagnostic organisms such as diatoms and human parasites both in the sedaDNA and using traditional techniques. Because the project is relatively short (36 months), we will largely use sediments that have already been collected or will collected by 2025/6 from sites to which traditional methods have already been applied. These come from both the PI and co-applicants network of contacts in the Mediterranean who are very eager to be involved in this novel approach. We have suitable sediments (unopened cold-stored cores) promised from Ostia Antica and Portus (Rome, Gioran (CI), Southampton collaboration), Ephesus (Bruckner, Stock et al. 2014), Spina (Salomon), Venice (Bivolaru) and the Levant Ports (Nantet, SHIPs Project). Another advantage of using these sites is that dating and sediment geochemistry have been done allowing prompt publishing, with the lead researchers at each site. However, this approach biases the project to the large high-profile ports, and so to get a less biased picture of the World-wide potential we will also core and analyses two or three minor sites – such as Caerleon, Wales (part-excavated) and/or Portus Lemanis at Lympne, Kent and Fos-sur-Mer in the Camargue (Marius Canal). The methods will be extraction for metabarcoding (p6 loop for plants, 12S and 16S for animals) at the dedicated clean laboratory at Southampton run by the PI, then PCR and sequencing at the ArcEcoGEN Centre (Tromsø Museum, UiT) with which we have a long-standing research collaboration and which has bioinformatic expertise/pipelines for all the essential reference databases. We will apply stringent filtering (to remove any false positives) and use quality assessment tools (Mathieu et al. 2020). We will also apply shotgun sequencing with an adequate depth (20+ M reads) to authenticate critical samples using DNA damage patterns (MAPDAMAGE, Ginolhac et al. 2011) and we will trial multiplexing whereby many primers are used to extract the DNA of target taxa (Zhang et al. 2018) – for example parasites, diseases and for sub-species (e.g. the variety of key cereals) using a new MiniION sequencing system.

Outputs & Dissemination

The results will be published in four ways; firstly by individual papers with the team who has been working on the port who provided the sediments, as articles but also chapters in their final publications (often Monographs), and secondly as at least one large synthesis paper, probably focusing on Classical ports and thirdly as a popular industry magazine (e.g. Ports & Harbours Magazine) and a contribution to J of Maritime Archaeology. In addition, we want to broaden our output through publishing results on an interactive ports webpage (at Southampton) and will engage a company (Heritage 360) to accomplish this. Ports are nodes so they lend themselves to this type of approach. Although a novel project it has key antecedents, the most notable of which was the PI and CIs involvement with the Roman Ports Project (ERC) and led by the late Simon Keay at Southampton. PortGEN is also supported by both the Centre for Maritime Archaeology at Southampton and the University of Southampton’s Marine & Maritime Institute (SMMI) who are sponsoring this application and will be providing in-kind support for meetings, some administration and outreach with the ports industry and in particular evidence relating to heritage protection in ports.