Molecular insights into ecosystem health: Comparative characterisation of dietary ecology and spatial biodiversity patterns through DNA metabarcoding of threatened predator species in Aotearoa New Zealand

Abstract

Predator species play critical ecological roles, influencing food web dynamics, regulating prey populations, and reflecting the health of their surrounding ecosystems. In Aotearoa New Zealand, many threatened predators inhabit environments under pressure from habitat modification, invasive species, and climate change. Understanding their dietary ecology and the biodiversity of their habitats is essential for effective conservation management. Environmental DNA (eDNA) metabarcoding, which uses genetic material shed into the environment to identify taxa, offers a non-invasive and highly sensitive approach to investigating both diet and broader biodiversity patterns. My thesis aimed to compare the dietary ecology and incidental biodiversity detection of two threatened predators inhabiting contrasting ecosystems, and to evaluate how ecological context shapes the information recovered through molecular analyses.

The first analysis (Chapter 2) examined the diet of the long-tailed bat (Chalinolobus tuberculatus) across multiple roosting locations within a single plantation forest over the summer season. This was the first study of its kind at this scale for the species, generating an unprecedented molecular dataset. Metabarcoding revealed a diet dominated by arthropods from multiple insect orders, encompassing both native and introduced taxa. Differences linked to reproductive status suggested shifts in prey choice driven by energetic demands, while variation between pre- and post-harvest periods indicated sensitivity to forestry management cycles. These results highlight both the potential role of this species in regulating introduced insects and its value as a bioindicator in managed forest systems.

The second analysis (Chapter 3) investigated little blue penguins (Eudyptula minor) from an island breeding colony within a sheltered harbour, focusing on both dietary and non-diet biodiversity signals. While direct dietary resolution was limited, eDNA recovered a rich record of terrestrial and nearshore taxa, reflecting seasonal and spatial variation in colony-adjacent biodiversity. These patterns were potentially influenced by seasonal ocean productivity, prey migration, microhabitat heterogeneity, and anthropogenic disturbance, demonstrating the capacity of faecal eDNA to capture wider ecosystem information.

Together, these studies demonstrate that predator faecal metabarcoding can provide complementary insights into species ecology and environmental condition, even when direct dietary resolution is constrained. By integrating trophic and incidental biodiversity data, this research contributes molecular baselines for long-term monitoring, enables the characterisation of hard-to-study or cryptic species that are otherwise difficult to observe directly, underscores the influence of ecological context on eDNA recovery, and supports the use of non-invasive molecular tools to inform evidence-based management and the conservation of threatened species and their habitats in Aotearoa New Zealand.