TY - JOUR
T1 - Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding
T2 - A case study on a threatened amphibian
AU - Harper, Lynsey R.
AU - Lawson Handley, Lori
AU - Hahn, Christoph
AU - Boonham, Neil
AU - Rees, Helen C.
AU - Lewis, Erin
AU - Adams, Ian P.
AU - Brotherton, Peter
AU - Phillips, Susanna
AU - Hänfling, Bernd
N1 - Funding Information:
This work was funded by the University of Hull. We would like to thank Jennifer Hodgetts (Fera Science Ltd) for assisting with sample collection and Jianlong Li (University of Hull) for sequencing primer design and advice on laboratory protocols. Tissue samples for primer validation and Sanger sequencing were provided by Andrew Buxton and Richard Griffiths (DICE, University of Kent) under license from Natural England, and Barbara Mabel and Elizabeth Kilbride (University of Glasgow).
Funding Information:
This work was funded by the University of Hull. We would like to thank Jennifer Hodgetts (Fera Science Ltd) for assisting with sample collection and Jianlong Li (University of Hull) for sequencing primer design and advice on laboratory protocols. Tissue samples for primer validation and Sanger sequencing were provided by Andrew Buxton and Richard Griffiths (DICE, University of Kent) under license from Natural England, and Barbara Mabel and Elizabeth Kilbride (University of Glasgow).
Publisher Copyright:
© 2019 The Authors. Environmental DNA published by John Wiley & Sons Ltd
PY - 2019/11/28
Y1 - 2019/11/28
N2 - 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.
AB - 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.
KW - biodiversity assessment
KW - environmental DNA (eDNA)
KW - hypothesis testing
KW - metabarcoding
KW - ponds
KW - species associations
KW - Triturus cristatus
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UR - http://www.scopus.com/inward/citedby.url?scp=85093514377&partnerID=8YFLogxK
U2 - 10.1002/edn3.57
DO - 10.1002/edn3.57
M3 - Article
AN - SCOPUS:85093514377
SN - 2637-4943
VL - 2
SP - 184
EP - 199
JO - Environmental DNA
JF - Environmental DNA
IS - 2
ER -