Sequencing data for seabird eDNA in long-nosed fur seal diets from southeastern Australia

Wildlife conflicts require robust quantitative data on incidence and
impacts, particularly among species of conservation and cultural concern.
We apply a multi-assay framework to quantify predation in a southeastern
Australian scenario where complex management implications and calls for
predator culling have grown despite a paucity of data on seabird predation
by recovering populations of long-nosed fur seals (Arctocephalus
forsteri). We apply two ecological surveillance techniques to analyse this
predator’s diet – traditional morphometric (prey hard-part) and
environmental DNA metabarcoding (genetic) analyses using an avian specific
primer for the 12S ribosomal RNA (rRNA) gene – to provide managers with
estimated predation incidence, number of seabird species impacted and
inter-prey species relative importance to the predator. DNA metabarcoding
identified additional seabird taxa and provided relative quantitative
information where multiple prey species occur within a sample; while
parallel use of both genetic and hard-part analyses revealed a greater
diversity of taxa than either method alone. Using data from both assays,
the estimated frequency of occurrence of predation on seabirds by
long-nosed fur seals ranged from 9.1–29.3% of samples and included up to 6
detected prey species. The most common seabird prey was the culturally
valued little penguin (Eudyptula minor) that occurred in 6.1–25.3% of
samples, higher than previously reported from traditional morphological
assays alone. We then explored DNA haplotype diversity for little penguin
genetic data, as a species of conservation concern, to provide a
preliminary estimate of the number of individuals consumed. Polymorphism
analysis of consumed little penguin DNA identified five distinct
mitochondrial haplotypes – representing a minimum of 16 individual
penguins consumed across 10 fur seal scat samples from 99 sampled across
southeastern Australia. We recommend rapid uptake and development of
cost-effective genetic techniques and broader spatiotemporal sampling of
fur seal diets to further quantify predation and hotspots of concern for
wildlife conflict management.