The application of extensive 3D Seismic Reflection Data for the exploration of extensive inundated Palaeolandscapes

Ye

The West Coast Palaeolandscape Project

Ye

BradPhys to BradViz or from archaeological science to heritage science

YesArchaeology is a broad church and its role as a “two culture” discipline is frequently cited. This position at the interface of the arts and sciences remains central to archaeological activity but there have been significant changes in the structure of archaeology and its relationship to society overall. The growth of heritage science, in particular, is driving change and development within archaeology at a national and international level. This paper discusses these developments in relation to the author's own research trajectory and discusses the significance of such change

Unveiling the prehistoric landscape at Stonehenge through multi-receiver EMI

YesArchaeological research at Stonehenge (UK) is increasingly aimed at understanding the dynamic of the wider archaeological landscape. Through the application of state-of-the-art geophysical techniques, unprecedented insight is being gathered into the buried archaeological features of the area. However, applied survey techniques have rarely targeted natural soil variation, and the detailed knowledge of the palaeotopography is consequently less complete. In addition, metallic topsoil debris, scattered over different parts of the Stonehenge landscape, often impacts the interpretation of geophysical datasets. The research presented here demonstrates how a single multi-receiver electromagnetic induction (EMI) survey, conducted over a 22 ha area within the Stonehenge landscape, offers detailed insight into natural and anthropogenic soil variation at Stonehenge. The soil variations that were detected through recording the electrical and magnetic soil variability, shed light on the genesis of the landscape, and allow for a better definition of potential palaeoenvironmental and archaeological sampling locations. Based on the multi-layered dataset, a procedure was developed to remove the influence of topsoil metal from the survey data, which enabled a more straightforward identification of the detected archaeology. The results provide a robust basis for further geoarchaeological research, while potential to differentiate between modern soil disturbances and the underlying sub-surface variations can help in solving conservation and management issues. Through expanding this approach over the wider area, we aim at a fuller understanding of the human–landscape interactions that have shaped the Stonehenge landscape

Cityscapes without figures: geophysics, computing and the future of urban studies

Ye

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

YesRecently, 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 (alpha,beta,gamma,epsilon) 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 prime region of fragments. The PCR enzyme used in the sedaDNA study would not have had the capability to report 5 prime cytosine deamination, as they do not read over uracil residues, and signatures of damage would have better been sought at the 3 prime 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

PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea

YesAssigning metagenomic reads to taxa presents significant challenges. Existing approaches address some issues, but are mostly limited to metabarcoding or optimized for microbial data. We present PIA (Phylogenetic Intersection Analysis): a taxonomic binner that works from standard BLAST output while mitigating key effects of incomplete databases. Benchmarking against MEGAN using sedaDNA suggests that, while PIA is less sensitive, it can be more accurate. We use known sequences to estimate the accuracy of PIA at up to 96% when the real organism is not represented in the database. For ancient DNA, where taxa of interest are frequently over-represented domesticates or absent, poorly-known organisms, more accurate assignment is critical, even at the expense of sensitivity. PIA offers an approach to objectively filter out false positive hits without the need to manually remove taxa and so make presuppositions about past environments and their palaeoecologies.European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (ERC funded project no. 670518 LOST FRONTIE

Gene expression time delays & Turing pattern formation systems

The incorporation of time delays can greatly affect the behaviour of partial differential equations and dynamical systems. In addition, there is evidence that time delays in gene expression due to transcription and translation play an important role in the dynamics of cellular systems. In this paper, we investigate the effects of incorporating gene expression time delays into a one-dimensional putative reaction diffusion pattern formation mechanism on both stationary domains and domains with spatially uniform exponential growth. While oscillatory behaviour is rare, we find that the time taken to initiate and stabilise patterns increases dramatically as the time delay is increased. In addition, we observe that on rapidly growing domains the time delay can induce a failure of the Turing instability which cannot be predicted by a naive linear analysis of the underlying equations about the homogeneous steady state. The dramatic lag in the induction of patterning, or even its complete absence on occasions, highlights the importance of considering explicit gene expression time delays in models for cellular reaction diffusion patterning

A massive, Late Neolithic pit structure associated with Durrington Walls Henge

YesA series of massive geophysical anomalies, located south of the Durrington Walls henge monument, were identified during fluxgate gradiometer survey undertaken by the Stonehenge Hidden Landscapes Project (SHLP). Initially interpreted as dewponds, these data have been re-evaluated, along with information on similar features revealed by archaeological contractors undertaking survey and excavation to the north of the Durrington Walls henge. Analysis of the available data identified a total of 20 comparable features, which align within a series of arcs adjacent to Durrington Walls. Further geophysical survey, supported by mechanical coring, was undertaken on several geophysical anomalies to assess their nature, and to provide dating and environmental evidence. The results of fieldwork demonstrate that some of these features, at least, were massive, circular pits with a surface diameter of 20m or more and a depth of at least 5m. Struck flint and bone were recovered from primary silts and radiocarbon dating indicates a Late Neolithic date for the lower silts of one pit. The degree of similarity across the 20 features identified suggests that they could have formed part of a circuit of large pits around Durrington Walls, and this may also have incorporated the recently discovered Larkhill causewayed enclosure. The diameter of the circuit of pits exceeds 2km and there is some evidence that an intermittent, inner post alignment may have existed within the circuit of pits. One pit may provide evidence for a recut; suggesting that some of these features could have been maintained through to the Middle Bronze Age. Together, these features represent a unique group of features related to the henge at Durrington Walls, executed at a scale not previously recorded.The University of Bradford Research Development Fund and the University of St Andrews funded this open access publication.Supplementary data can be found at https://intarch.ac.uk/journal/issue55/4/supp-text.htm

Multi-Proxy Characterisation of the Storegga Tsunami and Its Impact on the Early Holocene Landscapes of the Southern North Sea

This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (ERC funded project No. 670518 LOST FRONTIERS, https://europa.eu/european-union/index_en, https://lostfrontiers.teamapp.com/). The project gratefully acknowledges the support of the Estonian Research Council (https://www.etag.ee/en/estonian-research-council/, Grant number: PUTJD829). PGS (https://www.pgs.com/) is acknowledged through provision of data used in this paper under license CA-BRAD-001-2017.Doggerland was a landmass occupying an area currently covered by the North Sea until marine inundation took place during the mid-Holocene, ultimately separating the British landmass from the rest of Europe. The Storegga Event, which triggered a tsunami reflected in sediment deposits in the northern North Sea, northeast coastlines of the British Isles and across the North Atlantic, was a major event during this transgressive phase. The spatial extent of the Storegga tsunami however remains unconfirmed as, to date, no direct evidence for the event has been recovered from the southern North Sea. We present evidence of a tsunami deposit in the southern North Sea at the head of a palaeo-river system that has been identified using seismic survey. The evidence, based on lithostratigraphy, geochemical signatures, macro and microfossils and sedimentary ancient DNA (sedaDNA), supported by optical stimulated luminescence (OSL) and radiocarbon dating, suggests that these deposits were a result of the tsunami. Seismic identification of this stratum and analysis of adjacent cores showed diminished traces of the tsunami which was largely removed by subsequent erosional processes. Our results confirm previous modelling of the impact of the tsunami within this area of the southern North Sea, and also indicate that these effects were temporary, localized, and mitigated by the dense woodland and topography of the area. We conclude that clear physical remnants of the wave in these areas are likely to be restricted to now buried, palaeo-inland basins and incised river valley systems.Publisher PDFPeer reviewe