The application of <scp>eDNA</scp> for monitoring of the Great Crested Newt in the UK

Rees, Helen C.; Bishop, Keith; Middleditch, David J.; Patmore, James R. M.; Maddison, Ben C.; Gough, Kevin C.

doi:10.1002/ece3.1272

Cited by 99 publications

(86 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For example, eDNA assays have been used to detect the eastern hellbender (Cryptobranchus a. alleganiensis), an amphibian of high conservation concern, in Indiana and Missouri, USA (Olson et al 2012). In the UK, eDNA assays have been validated for detection of the threatened great crested newt Triturus cristatus (Rees et al 2014a). Sigsgaard et al (2015) reported that eDNA surveys for endangered fish in Denmark outperformed traditional methods.…”

Section: Introductionmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

View full text Add to dashboard Cite

Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

show abstract

Section: Introductionmentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

View full text Add to dashboard Cite

show abstract

“…Multimethod species distribution modelling or site occupancy modelling is one example for how this can be achieved and has been demonstrated in cases comparing qPCR for a single species and conventional methods (Hunter et al, 2015;Rees, Bishop, Middleditch, et al 2014;Schmelzle & Kinziger, 2016;Schmidt, Kery, Ursenbacher, Hyman, & Collins, 2013), but rarely for eDNA metabarcoding . Thus, we expect the robustness of eDNA metabarcoding to reveal species richness estimates for animals and plants will be improved by coupling distribution or occupancy modelling with studies to determine the scale of inference in space and time for an eDNA sample (Figure 1).…”

Section: Molecular Operational Taxonomic Unit (Motu)mentioning

confidence: 99%

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

et al. 2017

View full text Add to dashboard Cite

The genomic revolution has fundamentally changed how we survey biodiversity on earth. High-throughput sequencing ("HTS") platforms now enable the rapid sequencing of DNA from diverse kinds of environmental samples (termed "environmental DNA" or "eDNA"). Coupling HTS with our ability to associate sequences from eDNA with a taxonomic name is called "eDNA metabarcoding" and offers a powerful molecular tool capable of noninvasively surveying species richness from many ecosystems. Here, we review the use of eDNA metabarcoding for surveying animal and plant richness, and the challenges in using eDNA approaches to estimate relative abundance. We highlight eDNA applications in freshwater, marine and terrestrial environments, and in this broad context, we distill what is known about the ability of different eDNA sample types to approximate richness in space and across time. We provide guiding questions for study design and discuss the eDNA metabarcoding workflow with a focus on primers and library preparation methods.We additionally discuss important criteria for consideration of bioinformatic filtering of data sets, with recommendations for increasing transparency. Finally, looking to the future, we discuss emerging applications of eDNA metabarcoding in ecology, conservation, invasion biology, biomonitoring, and how eDNA metabarcoding can empower citizen science and biodiversity education.--

show abstract

“…Most of these studies investigated the presence of fish, including Chinook salmon (Oncorhynchus tshawytscha; Laramie et al 2015), brook and bull trout (Salvelinus fontinalis and S. confluentus; Wilcox et al 2013), and slackwater darter (Etheostoma boschungi; Janosik & Johnston 2015), as well as amphibians such as the great crested newt (Triturus cristatus; Rees et al 2014;Biggs et al 2015), Idaho salamander (Dicamptodon aterrimus), Rocky Mountain tailed frog (Ascaphus montanus; Goldberg et al 2011;Pilliod et al 2013) and eastern hellbender (Cryptobranchus alleganiensis alleganiensis; Olson et al 2012;Spear et al 2015). With the exception of the bull trout and slackwater darter, which are respectively classified as vulnerable and endangered (IUCN Red List version 2.3), these organisms may be locally rare, but are otherwise classified as low risk in terms of their conservation status.…”

Section: Studies Conducted On Rare Organismsmentioning

confidence: 99%

“…Jerde et al 2013;Takahara & Minimoto 2013), amphibians (e.g. Goldberg et al 2011;Olson et al 2012;Rees et al 2014), and invertebrates (e.g. Goldberg et al 2013;Machler et al 2014).…”

Section: Study Environmentsmentioning

confidence: 99%

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Lear¹,

Dickie²,

Banks³

et al. 2018

107

112

View full text Add to dashboard Cite

Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use. Our recommendations describe important steps for sample pre-processing and include the use of (a) Qiagen DNeasy PowerSoil ® and PowerMax ® kits for extraction of DNA from soil, sediment, faeces and leaf litter; (b) DNeasy PowerSoil ® for extraction of DNA from plant tissue; (c) DNeasy Blood and Tissue kits for extraction of DNA from animal tissue; (d) DNeasy Blood and Tissue kits for extraction of DNA from macroorganisms in water and ice; and (e) DNeasy PowerWater ® kits for extraction of DNA from microorganisms in water and ice. Based on key parameters, including the specificity and inclusivity of the primers for the target sequence, we recommend the use of the following primer pairs to amplify DNA for analysis by Illumina MiSeq DNA sequencing: (a) 515f and 806RB to target bacterial 16S rRNA genes (including regions V3 and V4); (b) #3 and #5RC to target eukaryote 18S rRNA genes (including regions V7 and V8); (c) #3 and #5RC are also recommended for the routine analysis of protist community DNA; (d) ITS6F and ITS7R to target the chromistan ITS1 internal transcribed spacer region; (e) S2F and S3R to target the ITS2 internal transcribed spacer in terrestrial plants; (f) fITS7 or gITS7, and ITS4 to target the fungal ITS2 region; (g) NS31 and AML2 to target glomeromycota 18S rRNA genes; and (h) mICOIintF and jgHCO2198 to target cytochrome c oxidase subunit I (COI) genes in animals. More research is currently required to confirm primers suitable for the selective amplification of DNA from specific vertebrate taxa such as fish. Combined, these recommendations represent a framework for efficient, comprehensive and robust DNA-based investigations of biodiversity, applicable to most taxa and ecosystems. The adoption of standardised protocols for biodiversity assessment and monitoring using DNA extracted from environmental samples will enable more informative comparisons among datasets, generating significant benefits for ecological science and biosecurity applications.

show abstract

The application of eDNA for monitoring of the Great Crested Newt in the UK

Cited by 99 publications

References 41 publications

The ecology of environmental DNA and implications for conservation genetics

The ecology of environmental DNA and implications for conservation genetics

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples

Contact Info

Product

Resources

About