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Citation: Quantifying wildlife conflicts with metabarcoding and traditional dietary analyses: applied to seabird predation by long-nosed fur seals Provisionally Accepted DOI: 10.3389/fmars.2024.1288769/abstract

Raw data publication: Sequencing data for seabird eDNA in long-nosed fur seal diets from southeastern Australia DOI: 10.5061/dryad.stqjq2cb3

Natasha A. Hardy1,2,3* Tina E. Berry4,5, Michael Bunce6, Nathan Bott7, Will F. Figueira2, Rebecca R. McIntosh1*

1 Department of Conservation, Phillip Island Nature Parks, Australia

2 School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Australia

3 SMRU Consulting (Canada), Canada

4 Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Australia

5 eDNA Frontiers, Department of Environment and Agriculture, Curtin University, Australia

6 Environmental Protection Authority, New Zealand

7 School of Science, RMIT University, Australia

Abstract: 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. 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.

Keywords: Ecological surveillance, Conservation management and monitoring, predator-prey interaction, Predation impact, eDNA, Fur Seal (Arctocephalus forsteri), Little Penguin (Eudyptula minor), Diet analysis techniques

Received: 04 Sep 2023; Accepted: 25 Apr 2024. Copyright: © 2024 Hardy, Berry, Bunce, Bott, Figueira and McIntosh. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

• Correspondence: Dr. Natasha A. Hardy, Department of Conservation, Phillip Island Nature Parks, Cowes, 3922, Victoria, Australia Dr. Rebecca R. McIntosh, Department of Conservation, Phillip Island Nature Parks, Cowes, 3922, Victoria, Australia