Method development for screening archaeological samples for ancient pathogens

Recent advances in sequencing technology made it possible to retrieve DNA from archaeological samples that are hundreds or thousand years old Working with DNA retrieved from archaeological samples poses its own unique challenges. Firstly, DNA has a half-life and will decay after death, that means, only a very small part of a samples DNA content is endogenous DNA. Further the small amount of endogenous DNA that is left tends to be very short and fragmented. In this thesis, we address the main challenges faced by paleomicrobiology. With HOPS, we created a novel screening tool tailored to the characteristics of ancient DNA. HOPS produced reliable results both with in silico as well as real data for as few as 50 reads per species, which are an adequate representation of most screening Samples. While HOPS is designed to be still sensitive when working with low endogenous degraded DNA, it is dependent on the quality of the metagenomic reference database that is the foundation of the analysis. A novel tool DatabaseZen downloads and generates metagenomic databases from NCBI RefSeq, while using several filters to ensure database quality by removing contaminated sequences and avoid database bias by ensuring a balanced database composition. The low-endogenous DNA content in archaeological samples has negative consequences for paleomicrobiology, as most of the sequencing effort will go towards environmental contaminants instead of the remnants of the microbiome preserved in a sample. To that and we use a novel 16S/18S rRNA in-solution capture as an alternative to whole genome shotgun sequencing. The 16S capture was highly efficient in enriching for 16S/18S rRNA in all analyzed samples. The capture has the advantage of removing the length bias, which is present in 16S amplicon sequencing. Overall, we provided a screening tool for paleomicrobiology, an application to generate and clean reference databases and an alternative sequencing technology

Automated detection in remote sensing archaeology: a reading list

The applications of automated object detection in remote sensing archaeology have grown considerably in the last few years. This reading list has been compiled as a contribution to consolidating current perspectives at September 2016, and in support of the preceding paper on the broader issues of human and computer vision in archaeological prospection (Traviglia et al. 2016)

Remote Sensing and Geosciences for Archaeology

This book collects more than 20 papers, written by renowned experts and scientists from across the globe, that showcase the state-of-the-art and forefront research in archaeological remote sensing and the use of geoscientific techniques to investigate archaeological records and cultural heritage. Very high resolution satellite images from optical and radar space-borne sensors, airborne multi-spectral images, ground penetrating radar, terrestrial laser scanning, 3D modelling, Geographyc Information Systems (GIS) are among the techniques used in the archaeological studies published in this book. The reader can learn how to use these instruments and sensors, also in combination, to investigate cultural landscapes, discover new sites, reconstruct paleo-landscapes, augment the knowledge of monuments, and assess the condition of heritage at risk. Case studies scattered across Europe, Asia and America are presented: from the World UNESCO World Heritage Site of Lines and Geoglyphs of Nasca and Palpa to heritage under threat in the Middle East and North Africa, from coastal heritage in the intertidal flats of the German North Sea to Early and Neolithic settlements in Thessaly. Beginners will learn robust research methodologies and take inspiration; mature scholars will for sure derive inputs for new research and applications

Analysis of the efficacy of LiDAR data as a tool for archaeological prospection at the Highland Valley Copper Mine

As heritage resource management and Indigenous heritage stewardship moves into the forefront of project design and operational planning in British Columbia, researchers look for innovative ways to foster impact assessment efficiency without sacrificing quality. In this study I explore methods for employing LiDAR-derived digital elevation models as a tool for archaeological prospection within the Highland Valley Copper Mine. A review of contemporary and formative LiDAR-analysis archaeological prospection research was conducted to identify the most appropriate visualization techniques and data management workflow. Specific methods for the identification of microtopographic relief with the potential to contain archaeological resources were developed. The efficacy of LiDAR-based topographic analysis using manual feature extraction is validated through comparison with georeferenced survey and ground-truthing data provided by my research partners at the Nlaka’pamux Nation Tribal Council. The LiDAR analysis method identified a high percentage of recorded archaeological sites and meets provincial requirements for a moderately effective predictive model. Results of LiDAR analysis are presented along with recommendations for improved performance using best practices and an interpolation workflow. An analysis of the cost implications of incorporating LiDAR-survey into the heritage management workflow in the study area identified a significant benefit during survey. These savings would allow for redistribution of resources and potentially a greater focus on mitigative systematic data recovery. The use of remote sensing technologies and methods can have a positive impact on heritage resource management industry in BC by decreasing program costs while maintaining quality

Spatial patterns of Moroccan transhumance: Geoarchaeological field work & spatial analysis of herder sites in the High Atlas Mountains of Morocco

Seit geraumer Zeit, nicht zuletzt unter dem Einfluss des Klimawandels, nimmt das Interesse der Ethnologie an den Methoden einiger Nachbardisziplinen im Sinne der interdisziplinären Zusammenarbeit zu. Hierbei spielen die Geographie und in besonderem Maße fernerkundliche Methoden sowie räumliche Analysen eine herausragende Rolle. Ebenso wie, im Kontext diachroner Analysen, die Methoden der Geoarchäologie zur Erfassung der lokalen Historie. Um diese Forschungsansatze den Studierenden der Ethnologie nahezubringen habe ich Frau Mirijam Zickel gebeten mir ihre Masterarbeit, die von Herrn Prof. Dr. Georg Bareth und Frau Dr. Astrid Röpke betreut und mit dem zweiten Platz des Dr. Prill Preises 2020 der Gesellschaft für Erdkunde ausgezeichnet wurde, in leicht veränderter Form, für meine Reihe zur Verfügung zu stellen. Nach einer allgemeinen Darstellung der Methoden der Fernerkundung zeigt Frau Zickel am Beispiel transhumanter Ait Atta auf deren Sommerweiden im Hohen Atlas, wie durch die räumliche Analyse von Fernerkundungsdaten und unter Einbezug von geoarchäologischen Informationen, Erkenntnisse uber die Aufenthaltsplätze der Nomaden im Sommerlager gewonnen werden können. Hierbei zeigt sich, dass die Viehpferche der Nomaden eine zentrale Rolle für die räumliche und zeitliche Erfassung von Transhumanz im Untersuchungsgebiet spielen können. Weiterhin ist es ihr gelungen, mit unterschiedlichen, einander ergänzenden Methoden der Fernerkundung die ökologische Situation des Gebietes und insbesondere der Pferchstandorte zu beleuchten. Ihre Arbeit eröffnet eine neue Perspektive, um die Mensch-Umweltbeziehung im semiariden Bergland von Marokko zu erfassen

Employment, Utilization, and Development of Airborne Laser Scanning in Fenno-Scandinavian Archaeology-A Review

This paper gives a presentation of how airborne laser scanning (ALS) has been adopted in archaeology in the North over the period 2005-2019. Almost two decades have passed since ALS first emerged as a potential tool to add to the archaeologist's toolbox. Soon after, it attracted the attention of researchers within archaeological communities engaged with remote sensing in the Fenno-Scandinavian region. The first archaeological ALS projects gave immediate good results and led to further use, research, and development through new projects that followed various tracks. The bulk of the research and development focused on studying how well-suited ALS is for identifying, mapping, and documenting archaeological features in outfield land, mainly in forested areas. The poor situation in terms of lack of information on archaeological records in outfield areas has been challenging for research and especially for cultural heritage management for a long period of time. Consequently, an obvious direction was to study how ALS-based mapping of cultural features in forests could help to improve the survey situation. This led to various statistical analyses and studies covering research questions related to for instance effects on detection success of laser pulse density, and the size and shape of the targeted features. Substantial research has also been devoted to the development and assessment of semi-automatic detection of archaeological features based on the use of algorithms. This has been studied as an alternative approach to human desk-based visual analyses and interpretations of ALS data. This approach has considerable potential for detecting sites over large regions such as the vast roadless and unbuilt wilderness regions of northern Fennoscandia, and has proven highly successful. In addition, the current review presents how ALS has been employed for monitoring purposes and for landscape studies, including how it can influence landscape understanding. Finally, the most recent advance within ALS research and development has been discussed: testing of the use of drones for data acquisition. In conclusion, aspects related to the utilization of ALS in archaeological research and cultural heritage management are summarized and discussed, together with thoughts about future perspectives.Peer reviewe

Archaeological remote sensing: visualisation and analysis of grass-dominated environments using airborne laser scanning and digital spectral data

The use of airborne remote sensing data for archaeological prospection is not a novel concept, but it is one that has been brought to the forefront of current work in the discipline of landscape archaeology by the increasing availability and application of airborne laser scanning data (ALS). It is considered that ALS, coupled with imaging of the non-visible wavelengths using digital spectral sensors has the potential to revolutionise the field of archaeological remote sensing, overcoming some of the issues identified with the most common current technique of oblique aerial photography. However, as with many methods borrowed from geographic or environmental sciences, archaeologists have yet to understand or utilise the full potential of these sensors for deriving archaeological feature information. This thesis presents the work undertaken between 2008-11 at Bournemouth University that aimed to assess the full information content of airborne laser scanned and digital spectral data systematically with respect to identifying archaeological remains in non-alluvial environments. A range of techniques were evaluated for two study areas on Salisbury Plain, Wiltshire (Everleigh and Upavon) to establish how the information from these sensors can best be extracted and utilised. For the Everleigh Study Area archive airborne data were analysed with respect to the existing transcription from archive aerial photographs recorded by English Heritage's National Mapping Programme. At Upavon, spectral and airborne laser scanned data were collected by the NERC Airborne Research and Survey Facility to the specifications of the project in conjunction with a series of ground-based measures designed to shed light on the contemporary environmental factors influencing feature detectability. Through the study of visual and semi-automatic methods for detection of archaeological features, this research has provided a quantitative and comparative assessment of airborne remote sensing data for archaeological prospection, the first time that this has been achieved in the UK. In addition the study has provided a proof of concept for the use of the remote sensing techniques trialled in temperate grassland environments, a novel application in a field previously dominated by examples from alluvial and Mediterranean landscapes. In comparison to the baseline record of the Wiltshire HER, ALS was shown to be the most effective technique, detecting 76% of all previously know features and 72% of all the total number of features recorded in the study. Combining the spectral data from both January and May raised this total to 83% recovery of all previously known features, illustrating the value of multi-sensor survey. It has also been possible to clarify the strengths and weaknesses of a wide range of visualisation techniques through detailed comparative analysis and to show that some techniques in particular local relief modelling (ALS) and single band mapping (digital spectral data) are more suited to the aims of archaeological prospection than others, including common techniques such as shaded relief modelling (ALS) and True Colour Composites (digital spectral data). In total the use of “non-standard” or previously underused visualisation techniques was shown to improve feature detection by up to 18% for a single sensor type. Investigation of multiple archive spectral acquisitions highlighted seasonal differences in detectability of features that had not been previously observed in these data, with the January spectral data allowing the detection of 7% more features than the May acquisition. A clearer picture of spectral sensitivity of archaeological features was also gained for this environment with the best performing spectral band lying in the NIR for both datasets (706-717nm) and allowing detection c.68% of all the features visible across all the wavelengths. Finally, significant progress has been made in the testing of methods for combining data from different airborne sensors and analysing airborne data with respect to ground observations, showing that Brovey sharpening can be used to combine ALS and spectral data with up to 87% recovery of the features predicted by transcription from the contributing source data. This thesis concludes that the airborne remote sensing techniques studied have quantifiable benefit for detection of archaeological features at a landscape scale especially when used in conjunction with one another. The caveat to this is that appropriate use of the sensors from deployment, to processing, analysis and interpretation of features must be underpinned by a detailed understanding of how and why archaeological features might be represented in the data collected. This research goes some way towards achieving this, especially for grass-dominated environments but it is only with repeated, comparative analyses of these airborne data in conjunction with environmental observations that archaeologists will be able to advance knowledge in this field and thus put airborne remote sensing data to most effective use

Assessment of the CORONA series of satellite imagery for landscape archaeology: a case study from the Orontes valley, Syria

In 1995, a large database of satellite imagery with worldwide coverage taken from 1960 until 1972 was declassified. The main advantages of this imagery known as CORONA that made it attractive for archaeology were its moderate cost and its historical value. The main disadvantages were its unknown quality, format, geometry and the limited base of known applications. This thesis has sought to explore the properties and potential of CORONA imagery and thus enhance its value for applications in landscape archaeology. In order to ground these investigations in a real dataset, the properties and characteristics of CORONA imagery were explored through the case study of a landscape archaeology project working in the Orontes Valley, Syria. Present-day high-resolution IKONOS imagery was integrated within the study and assessed alongside CORONA imagery. The combination of these two image datasets was shown to provide a powerful set of tools for investigating past archaeological landscape in the Middle East. The imagery was assessed qualitatively through photointerpretation for its ability to detect archaeological remains, and quantitatively through the extraction of height information after the creation of stereomodels. The imagery was also assessed spectrally through fieldwork and spectroradiometric analysis, and for its Multiple View Angle (MVA) capability through visual and statistical analysis. Landscape archaeology requires a variety of data to be gathered from a large area, in an effective and inexpensive way. This study demonstrates an effective methodology for the deployment of CORONA and IKONOS imagery and raises a number of technical points of which the archaeological researcher community need to be aware of. Simultaneously, it identified certain limitations of the data and suggested solutions for the more effective exploitation of the strengths of CORONA imagery