Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals

Ghazali, Muhammad; Harper, Lynsey R.; Lawson Handley, Lori; Carpenter, Angus I.; Murray-Dickson, Gillian; Di Muri, Cristina; Macgregor, Callum J.; Logan, Thomas W.; Law, Alan; Breithaupt, Thomas; Read, Daniel S.; McDevitt, Allan D.; Hänfling, Bernd

Abstract

© 2019 Elsevier Ltd Environmental DNA (eDNA) metabarcoding can identify terrestrial taxa utilising aquatic habitats alongside aquatic communities, but terrestrial species' eDNA dynamics are understudied. We evaluated eDNA metabarcoding for monitoring semi-aquatic and terrestrial mammals, specifically nine species of conservation or management concern, and examined spatiotemporal variation in mammal eDNA signals. We hypothesised eDNA signals would be stronger for semi-aquatic than terrestrial mammals, and at sites where individuals exhibited behaviours. In captivity, we sampled waterbodies at points where behaviours were observed (‘directed’ sampling) and at equidistant intervals along the shoreline (‘stratified’ sampling). We surveyed natural ponds (N = 6) where focal species were present using stratified water sampling, camera traps, and field signs. eDNA samples were metabarcoded using vertebrate-specific primers. All focal species were detected in captivity. eDNA signal strength did not differ between directed and stratified samples across or within species, between semi-aquatic or terrestrial species, or according to behaviours. eDNA was evenly distributed in artificial waterbodies, but unevenly distributed in natural ponds. Survey methods deployed at natural ponds shared three species detections. Metabarcoding missed badger and red fox recorded by cameras and field signs, but detected small mammals these tools overlooked, e.g. water vole. Terrestrial mammal eDNA signals were weaker and detected less frequently than semi-aquatic mammal eDNA signals. eDNA metabarcoding could enhance mammal monitoring through large-scale, multi-species distribution assessment for priority and difficult to survey species, and provide early indication of range expansions or contractions. However, eDNA surveys need high spatiotemporal resolution and metabarcoding biases require further investigation before routine implementation.

Citation

Ghazali, M., Harper, L. R., Lawson Handley, L., Carpenter, A. I., Murray-Dickson, G., Di Muri, C., Macgregor, C. J., Logan, T. W., Law, A., Breithaupt, T., Read, D. S., McDevitt, A. D., & Hänfling, B. (2019). Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals. Biological Conservation, 238(October 2019), Article 108225. https://doi.org/10.1016/j.biocon.2019.108225

• Journal Article Type: Article
• Acceptance Date: Aug 26, 2019
• Online Publication Date: Sep 4, 2019
• Publication Date: Oct 1, 2019
• Deposit Date: Sep 12, 2019
• Publicly Available Date: Sep 5, 2020
• Journal: Biological Conservation
• Print ISSN: 0006-3207
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 238
• Issue: October 2019
• Article Number: 108225
• DOI: https://doi.org/10.1016/j.biocon.2019.108225
• Keywords: Camera traps; Field signs; Lentic; Monitoring; Semi-aquatic mammals; Terrestrial mammals
• Public URL: https://hull-repository.worktribe.com/output/1299662
• Related Public URLs: Preprint available at: https://www.biorxiv.org/content/10.1101/546218v6
• Contract Date: Sep 16, 2019