Investigating the preservation of ancient sedimentary DNA (sedaDNA) from three case study wetland environments : towards better understanding of sedaDNA as a tool for palaeoecological reconstruction

This PhD is a contribution to the rapidly expanding application of sedimentary ancient DNA (sedaDNA) as a tool for palaeoecological reconstruction. Using the current understanding of preservation of sedaDNA within lacustrine sediments, this PhD applies the technique to three case studies from fluvial (Brown Bank) and intertidal (Tan-y-Bwlch and Orkney) depositional environments often considered problematic for conventional proxy analysis as a methodological approach for testing the framework of sedaDNA preservation. This PhD examines both the taxonomic output and the approaches for understanding preservation of sedaDNA. As a comparative, conventional proxy datasets such as pollen and diatoms are analysed to examine the overall preservation potential across the sedimentary sequences and as means to compare taxonomic outputs and provide overall assessment of the complementary role of sedaDNA for palaeoecological reconstruction. As part of this PhD, the MetaDamage tool is presented as a new tool to undertake DNA damage analysis on a metagenomic scale as meant to provide additional confidence in the assessment of the sedaDNA outputs. The results of this PhD demonstrated low level preservation and low taxonomic diversity of sedaDNA associated with vegetation across the Brown Bank, Tan-y-Bwlch and Orkney sedaDNA analysis. The assemblage that is presented demonstrates ancient DNA relating to the plant growth within the sequences described above, supporting the current understanding of a localised mechanism for deposition and preservation. Although limited by inconsistent comparative conventional proxy datasets, this PhD also demonstrates a patterning of preservation within highly organic matrices, leading to the formation of testable working hypotheses for future work. This PhD is a demonstration of the challenges of applying theoretical models for proxy archive formation and the reality of an output of working within depositional environments that are often considered problematic for palaeoenvironmental reconstruction. It is clear from this sedaDNA analysis that there is potential for preservation within fluvial and intertidal deposits, and that there is future work to be undertaken to better understand the mechanisms for sedaDNA preservation within these depositional environments

MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale

The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better understanding of key questions of preservation for paleoecological reconstruction

Running out of time? Peatland rehabilitation, archaeology and cultural ecosystem services

The United Nations Decade on Ecosystem Restoration places ecosystem rehabilitation at the forefront of global efforts to restore biodiversity and tackle climate change. From a cultural and historical perspective, peatland environments are essential for the preservation of important archaeological sites, artefacts and palaeoecological records that do not survive on drier landscapes. Peatland degradation and destruction has in the past resulted in the damage and loss of significant numbers of sites and those that remain are vulnerable to human activities and processes associated with climate change. Although peatland restoration offers significant positive benefits for the in situ preservation of surviving peatland archaeology, explicit consideration of the nature and vulnerability of the archaeological resource tends to be omitted from academic discussions and practical peatland restoration schemes. This short communication highlights the key issues associated with the maintenance and protection of the cultural heritage of peatlands and concludes that improved communication between heritage and peatland restoration programmes and agendas is now urgently needed to ensure the preservation in situ of archaeological sites and deposits

An In-vivo 1H-MRS short-echo time technique at 7T: Quantification of metabolites in chronic multiple sclerosis and neuromyelitis optica brain lesions and normal appearing brain tissue

Highlights NAAG likely contributes to the total NAA differences between multiple sclerosis lesion and normal appearing brain tissue. myo-Inositol was not shown to be different between chronic AQP4Ab-NMOSD brain lesions and normal appearing brain tissue. An optimised MRS methodology is described, using 7T field strength and correcting for tissue T2 water relaxion differences. 7-tesla MRS profiles of chronic brain lesions and normal appearing white matter are presented for MS and AQP4Ab-NMOSD. Abstract Magnetic Resonance Spectroscopy (MRS) allows for the non-invasive quantification of neurochemicals and has the potential to differentiate between the pathologically distinct diseases, multiple sclerosis (MS) and AQP4Ab-positive neuromyelitis optica spectrum disorder (AQP4Ab-NMOSD). In this study we characterised the metabolite profiles of brain lesions in 11 MS and 4 AQP4Ab-NMOSD patients using an optimised MRS methodology at ultra-high field strength (7T) incorporating correction for T2 water relaxation differences between lesioned and normal tissue. MS metabolite results were in keeping with the existing literature: total N-acetylaspartate (NAA) was lower in lesions compared to normal appearing brain white matter (NAWM) with reciprocal findings for myo-Inositol. An unexpected subtlety revealed by our technique was that total NAA differences were likely driven by NAA-glutamate (NAAG), a ubiquitous CNS molecule with functions quite distinct from NAA though commonly quantified together with NAA in MRS studies as total NAA. Surprisingly, AQP4Ab-NMOSD showed no significant differences for total NAA, NAA, NAAG or myo-Inositol between lesion and NAWM sites, nor were there any differences between MS and AQP4Ab-NMOSD for a priori hypotheses. Post-hoc testing revealed a significant correlation between NAWM Ins:NAA and disability (as measured by EDSS) for disease groups combined, driven by the AP4Ab-NMOSD group. Utilising an optimised MRS methodology, our study highlights some under-explored subtleties in MRS profiles, such as the absence of myo-Inositol concentration differences in AQP4Ab-NMOSD brain lesions versus NAWM and the potential influence of NAAG differences between lesions and normal appearing white matter in MS

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

Reimagining the language of engagement in a post-stakeholder world

Language matters in shaping perceptions and guiding behaviour. The term stakeholder is widely used, yet little attention is paid to the possibility that its use may inadvertently perpetuate colonial narratives and reinforce systemic inequities. In this article, we critically examine the limitations of the stakeholder concept and its ambiguity, normativity, and exclusionary implications. We emphasise the importance of using language that gives a voice to marginalised groups, promotes inclusion and equity, and fosters meaningful and reflexive participation in decision-making processes. In critiquing the use of the term and calling for alternative practices, we aim to contribute to the decolonisation of research norms and the creation of more inclusive and equitable societies. Therefore, rather than advocating a single alternative term, we suggest a focus on the people, places, and species affected by decisions, interventions, projects, and issues