The detection of great crested newts year round via environmental DNA analysis

Rees, Helen C.; Baker, Claire A.; Gardner, David; Maddison, Ben C.; Gough, Kevin C.

doi:10.1186/s13104-017-2657-y

Cited by 29 publications

(29 citation statements)

References 7 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Metabarcoding is an increasingly popular tool in ecological and palaeoecological research, mainly due to its simplicity and low cost. eDNA can be used, for example, to characterize biodiversity of a particular taxonomic group (Ushio et al., ) or to estimate the ranges of rare, extinct or cryptic species (Haile et al., ; Jerde, Mahon, Chadderton, & Lodge, ; Pedersen et al., ; Rees, Baker, Gardner, Maddison, & Gough, ). Additionally, metabarcoding has been used to calculate differences in haplotype or allele frequency between populations of the same species (Sigsgaard et al., ) and to link changes in community composition over time to climatic shifts (Haile et al., ; Willerslev et al., , , ).…”

Section: Introductionmentioning

confidence: 99%

“…Biological differences include organism size, seasonal presence and senescence, preservation and dispersal strategy, among others. Larger taxa, taxa that are present year‐round or taxa whose DNA is readily transported across long distances by wind or water, may be more likely to be observed in environmental samples than smaller, seasonal and sedentary taxa (Andersen et al., ; Barnes & Turner, ; Buxton, Groombridge, Zakaria, & Griffiths, ; Dunn, Priestley, Herraiz, Arnold, & Savolainen, ; Hemery, Politano, & Henkel, ; Rees et al., ). Even when the same number of cells is present in an environmental sample, the starting copy number of target loci may vary between taxa and tissue type.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Minimizing polymerase biases in metabarcoding

Nichols

Vollmers

Newsom

et al. 2018

Molecular Ecology Resources

187

175

View full text Add to dashboard Cite

DNA metabarcoding is an increasingly popular method to characterize and quantify biodiversity in environmental samples. Metabarcoding approaches simultaneously amplify a short, variable genomic region, or "barcode," from a broad taxonomic group via the polymerase chain reaction (PCR), using universal primers that anneal to flanking conserved regions. Results of these experiments are reported as occurrence data, which provide a list of taxa amplified from the sample, or relative abundance data, which measure the relative contribution of each taxon to the overall composition of amplified product. The accuracy of both occurrence and relative abundance estimates can be affected by a variety of biological and technical biases. For example, taxa with larger biomass may be better represented in environmental samples than those with smaller biomass. Here, we explore how polymerase choice, a potential source of technical bias, might influence results in metabarcoding experiments. We compared potential biases of six commercially available polymerases using a combination of mixtures of amplifiable synthetic sequences and real sedimentary DNA extracts. We find that polymerase choice can affect both occurrence and relative abundance estimates and that the main source of this bias appears to be polymerase preference for sequences with specific GC contents. We further recommend an experimental approach for metabarcoding based on results of our synthetic experiments.

show abstract

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Minimizing polymerase biases in metabarcoding

Nichols

Vollmers

Newsom

et al. 2018

Molecular Ecology Resources

187

175

View full text Add to dashboard Cite

show abstract

“…All aquatic organisms shed DNA traces in their environment 17 , and it is now possible to detect a specific species (barcoding) or assess an entire community (metabarcoding) by sampling an aquatic system and amplifying the existing DNA traces using PCR (Polymerase Chain Reaction) based techniques 17 . Since the implementation of eDNA techniques in environmental studies last decade, it has been proven to be successful for the monitoring of invasive 18–22 , endangered 23,24 and/or economically important species from a wide range of taxa 25–27 . However, few studies have used eDNA for monitoring rare or indicator macroinvertebrate species 28–30 .…”

Section: Introductionmentioning

confidence: 99%

Improving detection capabilities of a critically endangered freshwater invertebrate with environmental DNA using digital droplet PCR

Mauvisseau

Davy‐Bowker

Bulling

et al. 2019

Preprint

View full text Add to dashboard Cite

21Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, the 22 species was recently rediscovered in one location of the river Dee in Wales after 22 years of absence. As 23 many species belonging to the Perlodidae, this species can be a bio-indicator, utilised for assessing 24 water quality and health status of a given freshwater system. However, conventional monitoring of 25 invertebrates via kick-sampling for example, is an invasive and expensive (time consuming). Further, 26 such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-27 sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we 28 sampled eDNA from twelve locations on the river Dee. I. nubecula was detected using kick-sampling in 29 five of these locations, three locations using both eDNA detection and kick-sampling and one location 30 using eDNA detection alone -resulting in a total of six known and distinct populations of this critically 31 endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and 32 results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In 33 contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that 34 inhibition most likely explains the big discrepancy between the obtained qPCR and ddPCR results. It is 35 therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR 36 may well be the best option for the detection of aquatic organisms which are either rare or likely to shed 37 low levels of eDNA into their environment. 38

show abstract

“…Another exponentially growing use for eDNA in aquatic systems is the detection of endangered and secretive taxa [20,[54][55][56][57][58][59][60]. Many endangered species presences have been identified in this way, including in areas where presence had not been confirmed using traditional methods [11,[61][62][63][64].…”

Section: Introductionmentioning

confidence: 99%

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (<em>Chrysemys picta</em>) eDNA under Field Conditions

Adams¹,

Hoekstra²,

Muell³

et al. 2019

Preprint

View full text Add to dashboard Cite

Environmental DNA (eDNA) is an increasingly used non-invasive molecular tool for detecting species presence and monitoring populations. In this article, we review the current state of non-avian reptile eDNA work in aquatic systems, as well as present a field experiment on detecting the presence of painted turtle (Chrysemys picta) eDNA. Thus far, turtle and snake eDNA studies have been successful mostly in detecting the presence of these animals in field conditions. However, some instances of low detection rates and non-detection occur for these non-avian reptiles, especially for squamates. We explored this matter by sampling lentic ponds with different densities (0 kg/ha, 6 kg/ha, 9 kg/ha, and 13 kg/ha) of painted turtles over three months, attempting to detect differences in eDNA accumulation using a qPCR assay. Only one sample of the highest density pond readily amplified eDNA. Yet, estimates of eDNA concentration from pond eDNA were rank-order correlated with turtle density. We present a “shedding hypothesis”–the possibility that animals with hard, keratinized integument do not shed as much DNA as mucus-covered organisms–as a potential challenge for turtle eDNA studies. Despite challenges with eDNA inhibition and availability in water samples, we remain hopeful that eDNA can be used to detect freshwater turtles in the field. We provide key recommendations for biologists wishing to use eDNA methods for detecting non-avian reptiles.

show abstract

The detection of great crested newts year round via environmental DNA analysis

Cited by 29 publications

References 7 publications

Minimizing polymerase biases in metabarcoding

Minimizing polymerase biases in metabarcoding

Improving detection capabilities of a critically endangered freshwater invertebrate with environmental DNA using digital droplet PCR

A Brief Review of Non-Avian Reptile Environmental DNA (eDNA), with a Case Study of Painted Turtle (<em>Chrysemys picta</em>) eDNA under Field Conditions

Contact Info

Product

Resources

About