Skip to main content

Research Repository

Advanced Search

Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian

Harper, Lynsey R.; Lawson Handley, Lori; Hahn, Christoph; Boonham, Neil; Rees, Helen C.; Lewis, Erin; Adams, Ian P.; Brotherton, Peter; Phillips, Susanna; Hänfling, Bernd


Lynsey R. Harper

Christoph Hahn

Neil Boonham

Helen C. Rees

Erin Lewis

Ian P. Adams

Peter Brotherton

Susanna Phillips

Bernd Hänfling


Background: Environmental DNA (eDNA) metabarcoding is revolutionizing biodiversity monitoring, but has unrealized potential for ecological hypothesis generation and testing. Aims: Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. Materials & Methods: We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T.cristatus detection at the pondscape. Furthermore, we test the status of T.cristatus as an umbrella species for pond conservation by assessing whether vertebrate species richness is greater in ponds with T.cristatus and higher T.cristatus Habitat Suitability Index (HSI) scores. Results: Triturus cristatus detection was positively correlated with amphibian and waterfowl species richness. Specifically, T.cristatus was positively associated with smooth newt (Lissotriton vulgaris), common coot (Fulica atra), and common moorhen (Gallinula chloropus), but negatively associated with common toad (Bufo bufo). Triturus cristatus detection did not significantly decrease as fish species richness increased, but negative associations with common carp (Cyprinus carpio), three-spined stickleback (Gasterosteus aculeatus), and ninespine stickleback (Pungitius pungitius) were identified. Triturus cristatus detection was negatively correlated with mammal species richness, and T.cristatus was negatively associated with gray squirrel (Sciurus carolinensis). Triturus cristatus detection was negatively correlated with larger pond area, presence of inflow, and higher percentage of shading, but positively correlated with HSI score, supporting its application to T.cristatus survey. Vertebrate species richness was significantly higher in T.cristatus ponds and broadly increased as T.cristatus HSI scores increased. Discussion: We reaffirm reported associations (e.g., T.cristatus preference for smaller ponds) but also provide novel insights, including a negative effect of pond inflow on T.cristatus. Conclusion: Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis generation and testing at landscape scale, and dramatic enhancement of freshwater conservation, management, monitoring, and research.


Harper, L. R., Lawson Handley, L., Hahn, C., Boonham, N., Rees, H. C., Lewis, E., …Hänfling, B. (2020). Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian. Environmental DNA, 2(2), 184-199.

Journal Article Type Article
Acceptance Date Nov 5, 2019
Online Publication Date Nov 28, 2019
Publication Date 2020-04
Deposit Date Jul 1, 2020
Publicly Available Date Oct 27, 2022
Journal Environmental DNA
Print ISSN 2637-4943
Electronic ISSN 2637-4943
Publisher Wiley Open Access
Peer Reviewed Peer Reviewed
Volume 2
Issue 2
Pages 184-199
Keywords Biodiversity assessment; Environmental DNA (eDNA); Hypothesis testing; Metabarcoding; Ponds; Species associations; Triturus cristatus
Public URL
Publisher URL


Published article (2.1 Mb)

Publisher Licence URL

Copyright Statement
© 2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd<br /> <br /> This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial‐NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

You might also like

Downloadable Citations