Environmental DNA metabarcoding and the study of marine biodiversity and biological invasions

Abstract

Human activities negatively impact the biodiversity of oceanic and coastal ecosystems. Studies show that marine biodiversity is linked to ecosystem function and in turn to the ecosystem services upon which humans depend. A key driver of biodiversity loss is the introduction of non-native species which have a dramatic negative effect on biodiversity and carry a vast global economic cost. It is therefore critical to understand the causes of anthropogenic biodiversity loss, monitor the effect of management actions and, ultimately, document ecosystem recovery. The use of DNA isolated from environmental samples such as water or sediment(environmental DNA or eDNA) to infer the presence or absence of an organism is revolutionising our ability to monitor aquatic ecosystems. Yet, we have a limited understanding how eDNA can be deployed to answer fundamental and applied questions in marine biodiversity and invasion biology. This thesis begins by showing eDNA metabarcoding to be an accurate and sensitive tool for detection of marine non-native species and demonstrates how methodological choices affect the biodiversity that is detected. The utility of eDNA metabarcoding in broad-scale biogeographic analyses is then shown by identifyingt hat marine animals, protists and bacteria can have remarkably similar biogeographic patterns. The thesis then reveals the limitations of eDNA metabarcoding data in comparison to manual biodiversity surveys and mitochondrial DNA sequences isolated from tissue samples for several non-native species. Finally, it develops a method for non-invasively genotyping organisms using eDNA, showing that eDNA contains both mitochondrial and nuclear genetic biodiversity.
Overall, this thesis leverages the sensitivity, accuracy and taxonomic breadth of eDNA-based tools to answer key questions in invasion biology and marine biodiversity

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ORCID for Luke, Earl Holman: orcid.org/0000-0002-8139-3760

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