Dung, Dirt & DNA: unearthing past and present biodiversity using environmental DNA metabarcoding

Abstract

The rapid loss of biodiversity highlights the urgency of large-scale biodiversity monitoring for conservation, as well as the importance of understanding biodiversity in all its dimensions, especially in light of environmental change. In order to understand the causes of these changes in biodiversity, we need to track them over time, either through continued biomonitoring, or through reconstructions of past changes. Trace DNA in environmental samples such as sediments and faeces, allows for the detection of species and biodiversity monitoring without the need to sight or sample the actual organisms. This is not only useful for conservation purposes, but also for the detection of species in palaeo records, such as those presented by lakes, caves, and permafrost. Particularly eDNA metabarcoding, a tool for the simultaneous identification of many organisms in an environmental sample, is a useful tool that can provide a window to the biological past. With initial technological issues involved in these methods largely worked out, and many guides are being published on how to apply them (including chapter 1), the field of eDNA metabarcoding can now move towards enhancing the interpretation of the resulting data. This is especially complex in interdisciplinary contexts and testing of its application to a range of topics and contexts is therefore needed. By applying these methods to faecal and sediment samples, this thesis provides insight into its applications through the biomonitoring of herbivores in a wildlife reserve in India (chapter 2), reconstructing the diets and habitats of extinct and extant megafauna (chapter 3), the untangling of human-environment interactions (chapter 4) and the assessment of DNA metabarcoding for reconstructing prehistoric human plant use (chapter 5). In interdisciplinary collaborations such as many of these chapters, good communication is very important. Environmental DNA metabarcoding, combined with statistical approaches as well as clear visualisation of the obtained results, such as those employed here, provide a way forward, untangling the complexity of biodiversity in all its dimensions. Application of these methods to modern (chapter 2) and palaeo (chapters 3-5) records can provide unprecedented insight into past and present biodiversity, including biological interactions, effects of climate change and human activities.