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.