RT Journal Article
SR Electronic
T1 Testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: a case study on a threatened amphibian
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 278309
DO 10.1101/278309
A1 Lynsey R. Harper
A1 Lori Lawson Handley
A1 Christoph Hahn
A1 Neil Boonham
A1 Helen C. Rees
A1 Erin Lewis
A1 Ian P. Adams
A1 Peter Brotherton
A1 Susanna Phillips
A1 Bernd Hänfling
YR 2019
UL http://biorxiv.org/content/early/2019/04/11/278309.abstract
AB Environmental DNA (eDNA) metabarcoding is revolutionising biodiversity monitoring, but has unrealised potential for ecological hypothesis testing. Here, we validate this potential in a large-scale analysis of vertebrate community data generated by eDNA metabarcoding of 532 UK ponds. We test biotic associations between the threatened great crested newt (Triturus cristatus) and other vertebrates as well as abiotic factors influencing T. cristatus occupancy 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. T. cristatus occupancy 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). T. cristatus occupancy 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. T. cristatus occupancy was negatively correlated with mammal species richness, and T. cristatus was negatively associated with grey squirrel (Sciurus carolinensis). T. cristatus occupancy was negatively influenced by 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. 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. Our findings demonstrate the prospects of eDNA metabarcoding for ecological hypothesis testing at landscape scale and dramatic enhancement of freshwater conservation, management, monitoring and research.