Estimating diet of the European hedgehog (Erinaceus europaeus) using molecular analysis of faeces and colon content : A thesis submitted in partial fulfilment of the requirements for the Degree of Master of Science at Lincoln University

New Zealand has a unique ecosystem that evolved without the presence of mammalian predators. Since human colonisation, several species of mammalian predators have been introduced, including the European hedgehog (Erinaceus europaeus). The hedgehog, in its native range, mainly feeds on invertebrates, with minor dietary components of bird eggs and lizards. I used molecular methods to analyse the diet of hedgehog in New Zealand. Molecular methods have an important advantage over the traditional visual analysis of faeces and stomach contents as they allow for better identification of soft-bodied remnants of prey items. I successfully used species-specific primers to detect a known species (mealworms, Tenebrio molitor) in hedgehog faeces after a controlled feeding trial. Next, I trialled a simple visualisation method to compare the quality of DNA extracted from hedgehog stomach and colon contents. Unfortunately, the visualisation method trialled did not determine any differences in the DNA quality of the two sample sources and further trials are required. I created a local reference database of invertebrates collected from pitfall trapping at Kaitorete Spit. Barcode sequences developed for the local reference library were uploaded to BOLD systems to contribute to the growing global database of sequences. This local reference database successfully enhanced the taxonomic rank assignment of amplicon sequence variations produced during metabarcoding. I used high throughput sequencing on faecal and colon samples. Several taxa from the phyla Arthropoda, Annelida, Mollusca, Nematoda, and Rotifera were identified and reported at the genus and family (for Arthropoda) taxonomic level. There was a considerable level of taxon heterogeneity in the prey items not between samples. High abundances of Arthropoda were identified in colon samples, while faecal samples had higher abundances of all other phyla. The results from this study are consistent with earlier morphological studies of hedgehog diets in New Zealand and Europe but add greater detail. The dietary results from this study are important and applicable in both New Zealand and worldwide. For New Zealand, this study contributes to understanding the ecological impacts that hedgehogs have in New Zealand while providing justification for ongoing monitoring plans that control hedgehogs to prevent detrimental impacts. Worldwide, these methods can be used, especially in the hedgehog’s natural habitat, to understand their natural diet to assist with conservation where this species is endangered. Future studies should expand the area studied to explore dietary variation across a spatial scale and where other endangered species are at risk from hedgehog predation.