2019
DOI: 10.1002/edn3.57
|View full text |Cite
|
Sign up to set email alerts
|

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

Abstract: 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 th… Show more

Help me understand this report
View preprint versions

Search citation statements

Order By: Relevance

Paper Sections

Select...
3
1
1

Citation Types

2
20
1

Year Published

2019
2019
2023
2023

Publication Types

Select...
7
1

Relationship

2
6

Authors

Journals

citations
Cited by 17 publications
(23 citation statements)
references
References 69 publications
2
20
1
Order By: Relevance
“…For example, using a post hoc probabilistic co-occurrence analysis to show which taxa are simultaneously present in the same faecal samples. This can be done using r package cooccur (Griffith et al, 2016) as per other studies using metabarcoding data (Brandl et al, 2020;Harper et al, 2020;Holmes et al, 2019); the analysis statistically measures whether species co-occur in diet samples nonrandomly. Conducting a co-occurrence analysis can, in some circumstances, highlight whether an insect herbivore and its host plant significantly co-occur in faecal samples of the study species.…”
Section: Con Cluding Remark Smentioning
confidence: 99%
“…For example, using a post hoc probabilistic co-occurrence analysis to show which taxa are simultaneously present in the same faecal samples. This can be done using r package cooccur (Griffith et al, 2016) as per other studies using metabarcoding data (Brandl et al, 2020;Harper et al, 2020;Holmes et al, 2019); the analysis statistically measures whether species co-occur in diet samples nonrandomly. Conducting a co-occurrence analysis can, in some circumstances, highlight whether an insect herbivore and its host plant significantly co-occur in faecal samples of the study species.…”
Section: Con Cluding Remark Smentioning
confidence: 99%
“…indexes, heterogeneity spacers, sequencing primers and pre-adapters) to amplify a region of the 12S ribosomal RNA (rRNA) mitochondrial gene (Riaz et al 2011). These primers have been validated in silico, in vitro and in situ for UK vertebrates (Hänfling et al 2016;Harper et al 2019aHarper et al , 2019b. Exotic cichlid (Maylandia zebra) DNA (0.05 ng/µl) was the PCR positive control and sterile molecular grade water (Fisher Scientific UK Ltd, Loughborough, UK) was the PCR negative control.…”
Section: Dna Metabarcodingmentioning
confidence: 99%
“…Raw sequence reads were demultiplexed with a custom Python script. Sequences underwent quality trimming, merging, chimera removal, clustering and taxonomic assignment against our custom reference database for UK vertebrates (Harper et al 2019b) using metaBEAT v0.97.11…”
Section: Dna Metabarcodingmentioning
confidence: 99%
“…In contrast, eDNA metabarcoding can be used to characterize entire species assemblages (Cilleros et al, ; Deiner et al, ; DiBattista et al, ; Yamamoto et al, ). Environmental DNA metabarcoding can be used to simultaneously determine species distributions, ecologically important patterns of species diversity, and detect novel species (Blackman et al, ; Elbrecht, Vamos, Meissner, Aroviita, & Leese, ; Harper et al, ). Metabarcoding surveys are able to provide comprehensive presence/absence data, although sampling, laboratory, and analytical protocols can influence biodiversity estimates (Alberdi et al, ; Deiner, Walser, Mächler, & Altermatt, ).…”
Section: Introductionmentioning
confidence: 99%