Vincent Gaffney

Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago

Early wheat movement into Britain The transition into the New Stone Age, or Neolithic period, in Great Britain and Europe was characterized by a change from hunter-gatherers to farmers. However, the early stages of this transition are not well understood. Smith et al. studied archaeological remains at an 8000-year-old site that has been underwater ever since the Neolithic (see the Perspective by Larson). The finds include evidence of wheat (or a relative of wheat) 2000 years before the first documented farmers in Britain. It seems that trade may have preceded the adoption of farming. Science, this issue p. 998; see also p. 945 Wheat was being consumed in Britain 2000 years earlier than expected. [Also see Perspective by Larson] The Mesolithic-to-Neolithic transition marked the time when a hunter-gatherer economy gave way to agriculture, coinciding with rising sea levels. Bouldnor Cliff, is a submarine archaeological site off the Isle of Wight in the United Kingdom that has a well-preserved Mesolithic paleosol dated to 8000 years before the present. We analyzed a core obtained from sealed sediments, combining evidence from microgeomorphology and microfossils with sedimentary ancient DNA (sedaDNA) analyses to reconstruct floral and faunal changes during the occupation of this site, before it was submerged. In agreement with palynological analyses, the sedaDNA sequences suggest a mixed habitat of oak forest and herbaceous plants. However, they also provide evidence of wheat 2000 years earlier than mainland Britain and 400 years earlier than proximate European sites. These results suggest that sophisticated social networks linked the Neolithic front in southern Europe to the Mesolithic peoples of northern Europe.

Visual Heritage in the Digital Age

This book presents methods for capturing data, modeling and engaging with heritage through digital interfaces, plus case studies of sites in Europe, North and Central America and collections relating to ancient Middle Eastern and North African civilizations.

Medieval military logistics: a case for distributed agent-based simulation

Historical studies are frequently perceived to be characterised as clear narratives defined by a series of fixed events or actions. In reality, even where critical historic events may be identified, historic documentation frequently lacks corroborative detail that supports verifiable interpretation. Consequently, for many periods and areas of research, interpretation may rarely rise above the level of unproven assertion and is rarely tested against a range of evidence. Simulation provides an opportunity to break cycles of academic claim and counter-claim. This paper discusses the development and utilisation of large scale distributed Agent-based simulations designed to investigate the medieval military logistics in order to generate new evidence to supplement existing historical analysis. The work aims at modelling logistical arrangements relating to the battle of Manzikert (AD 1071), a key event in Byzantine history. The paper discusses the distributed simulation infrastructure and provides an overview of the agent models developed for this exercise.

Simulation and Visualisation of Agent Survival and Settlement Behaviours in the Hunter-Gatherer Colonisation of Mesolithic Landscapes

Agent-based modelling and simulation of survival and settlement behaviour via interactive visualisation could potentially become a useful technique for generating new knowledge in those areas that sparse information, acquired through traditional methods, does not allow researchers to make informed decisions about past behaviour. This is particularly important following the development of remote sensing technologies that, in marine environments, are permitting novel exploration of previously inaccessible historic landscapes. This article explores and develops an agent-based model for basic survival and settlement behaviour for Mesolithic communities based within a marine palaeolandscape. It discusses the issues regarding how agents can be created to react to resource and environmental needs and limitations. The methodological study examines individual agent behaviour and sets the foundation for future, more complex scenarios that span large spatio-temporal landscapes including the North Sea and European coastal shelves. The article also considers the key technical challenges that must be met if large complex scenarios emerge in which the modelling of interaction between vegetation, animals and human groups becomes a priority.

Stigmergy in comparative settlement choice and palaeoenvironment simulation

Decisions on settlement location in the face of climate change and coastal inundation may have resulted in success, survival or even catastrophic failure for early settlers in many parts of the world. In this study, we investigate various questions related to how individuals respond to a palaeoenvironmental simulation, on an interactive tabletop device where participants have the opportunity to build a settlement on a coastal landscape, balancing safety, and access to resources, including sea and terrestrial foodstuffs, while taking into consideration the threat of rising sea levels. The results of the study were analyzed to consider whether decisions on settlement were predicated to be near to locations where previous structures were located, stigmergically, and whether later settler choice would fare better, and score higher, as time progressed. The proximity of settlements was investigated and the reasons for clustering were considered. The interactive simulation was exhibited to thousands of visitors at the 2012 Royal Society Summer Science Exhibition at the “Europes Lost World” exhibit. 347 participants contributed to the simulation, providing a sufficiently large sample of data for analysis.

Thermal age, cytosine deamination and the veracity of 8,000 year old wheat DNA from sediments

Recently, the finding of 8,000 year old wheat DNA from submerged marine sediments (1) was challenged on the basis of a lack of signal of cytosine deamination relative to three other data sets generated from young samples of herbarium and museum specimens, and a 7,000 year old human skeleton preserved in a cave environment (2). The study used a new approach for low coverage data sets to which tools such as mapDamage cannot be applied to infer chemical damage patterns. Here we show from the analysis of 148 palaeogenomic data sets that the rate of cytosine deamination is a thermally correlated process, and that organellar generally shows higher rates of deamination than nuclear DNA in comparable environments. We categorize four clusters of deamination rates (α,β,γ,ε) that are associated with cold stable environments, cool but thermally fluctuating environments, and progressively warmer environments. These correlations show that the expected level of deamination in the sedaDNA would be extremely low. The low coverage approach to detect DNA damage by Weiss et al. (2) fails to identify damage samples from the cold class of deamination rates. Finally, different enzymes used in library preparation processes exhibit varying capability in reporting cytosine deamination damage in the 5’ region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5’ cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3’ end. The 8,000 year old sedaDNA matches both the thermal age prediction of fragmentation, and the expected level of cytosine deamination for the preservation environment. Given these facts and the use of rigorous controls these data meet the criteria of authentic ancient DNA to an extremely stringent level.

Response to Comment on “Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago”

Bennett questions the rigor of the dating of our sample from which sedimentary ancient DNA was obtained and the reliability of the taxonomic identification of wheat. We present a further radiocarbon date from S308 that confirms the lateral consistency of the palaeosol age. The suggestion of taxonomic false positives in our data illustrates a misinterpretation of the phylogenetic intersection analysis.

Seeing Things: Heritage Computing, Visualisation and the Arts and Humanities

Digital technology and visualisation play an increasingly large role within the strategic framework of the Arts and Humanities. This is not in itself unexpected given the nature of research in these disciplines but the need to obtain and process large amounts of data, to gather this from disparate locations and then to link and disseminate this information in a manner that challenges researchers and informs the wider public which is both a challenge and an opportunity. Digital technology in Heritage is at the forefront of such a development through its relationship with large scale or pervasive visualisation and emerging human–computer interfaces with efficient algorithms for the processing, analysis and access of linked large-scale datasets. The “Big Data” worlds created by Arts and Humanities and Heritage research are proxies through which we may access the past and also make sense of the world in which we live. In this context therefore, the state-of-the-art applications presented in this volume provide a snapshot of our current position in this exciting new research landscape. The collection of chapters presents digital technology as part of an iterative process of investigation within Arts and Humanities, encompassing data capture, processing, analysis, interpretation and dissemination via interactive visualisation. The content of this book is inspired by the themes—objects, monuments, landscapes and behaviours and each chapter presents original research associated with the exploration and application of digital visual technologies within these research domains within. As a whole, the chapters demonstrate the diversity and scale of research in the discipline, and the utilisation of a wide range of digital technology to facilitate research on the frontiers of digital heritage.

Sentinel-1 bathymetry for North Sea palaeolandscape analysis

ABSTRACT Submerged palaeolandscapes can contain pristine underwater heritage. Regular monitoring of these areas is essential to assess and mitigate threats from development including construction, mining, and commercial trawling. While bathymetry alone may be insufficient to detect submerged palaeolandscape features, it can nonetheless recognize previously mapped structures that have a topographic expression. The Sentinel-1 constellation will provide unprecedented access to freely available, high-resolution Synthetic Aperture Radar (SAR) data, acquired systematically and with long-term continuity, and may constitute a cost-effective solution for the monitoring of submerged palaeolandscapes. The article shows the application of a recently developed bathymetric algorithm to Sentinel-1 SAR data over a region of the southern North Sea. Results show general agreement with water depth data obtained from the European Marine Observation and Data Network portal for bathymetry (EMODnet). To assess the support that SAR bathymetry can provide to the analysis of submerged palaeolandscapes, the Sentinel-1-derived water depths were compared to a palaeolandscape map of the same area produced by the North Sea Palaeolandscapes Project (NSPP). Results show a clear correspondence between certain topographic structures identified in the Sentinel-1 water depth map and features interpreted by the NSPP as early Holocene lakes, rivers, and landscape topography.

Merging the real with the virtual: Crowd behaviour mining with virtual environments

The first recorded crowdsourcing activity was in 1714 [1], with intermittent public event occurrences up until the millennium when such activities become widespread, spanning multiple domains. Crowdsourcing, however, is relatively novel as a methodology within virtual environment studies, in archaeology, and within the heritage domains where this research is focused. The studies that are being conducted are few and far between in comparison to other areas. This paper aims to develop a recent concept in crowdsourcing work termed ‘crowd behaviour mining’ [2] using virtual environments, and to develop a unique concept in crowdsourcing activities that can be applied beyond the case studies presented here and to other domains that involve human behaviour as independent variables. The case studies described here use data from experiments involving separate heritage projects and conducted during two Royal Society Summer Science Exhibitions, in 2012 and 2015 respectively. ‘Crowd Behaviour Mining’ analysis demonstrated a capacity to inform research in respect of potential patterns and trends across space and time as well as preferences between demographic user groups and the influence of experimenters during the experiments.