scholarly journals Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

2017 ◽  
Author(s):  
Lynsey R. Harper ◽  
Lori Lawson Handley ◽  
Christoph Hahn ◽  
Neil Boonham ◽  
Helen C. Rees ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Detection Threshold ◽  
Environmental Dna ◽  
Cost Effective ◽  
Triturus Cristatus ◽  
Species Detection ◽  
Survey Tool ◽  
Crested Newt ◽  
Species Specific ◽  
Freshwater Monitoring

SummaryEnvironmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and ‘metabarcoding’ have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real-time quantitative PCR (qPCR) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using High-Throughput Sequencing technology. With qPCR and a detection threshold of 1/12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4/12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species-specific surveys.

scholarly journals Development of an eDNA metabarcoding tool for surveying the world’s largest amphibian

2021 ◽  
Author(s):  
Jie Wang ◽  
Ping Liu ◽  
Jiang Chang ◽  
Cheng Li ◽  
Feng Xie ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Survey Methods ◽  
Environmental Dna ◽  
Cost Effective ◽  
Isolated Populations ◽  
Specificity And Sensitivity ◽  
Chinese Giant Salamander ◽  
Elusive Species ◽  
Primer Sets ◽  
Species Specific

Abstract Due to the overexploitation of farming, as well as habitat loss or degradation, the wild population of Chinese giant salamander Andrias davidianus (CGS), a species with seven genetically distinct lineages, has decreased by over 80% in the past 70 years. Traditional survey methods have proven to be unsuitable for finding this rare and elusive species. We evaluated the efficacy of environmental DNA (eDNA) sampling to detect CGS indirectly from its aquatic environment. We developed several species-specific primer sets; validated their specificity and sensitivity; and assessed their utility in silico, in the laboratory, and in two field sites having released farm-bred CGSs. We detected the presence of CGS DNA by using polymerase chain reaction (PCR) and Sanger sequencing. We also sequenced an amplicon mixture of seven haplotype-represented samples using high-throughput sequencing. Our eDNA methods could detect the presence of CGS at moderate densities reported across its range, proving them as a cost-effective way to establish broad-scale patterns of occupancy for CGS. In addition, our primers enabled the detection of a mitochondrial lineage mixture or introduced individuals from geographically isolated populations of CGS.

Environmental DNA (eDNA): A Promising Biological Survey Tool for Aquatic Species Detection

2018 ◽  
Vol 72 (3) ◽  
pp. 211-228 ◽  
Author(s):  
Debabrata Senapati ◽  
Manojit Bhattacharya ◽  
Avijit Kar ◽  
Deep Sankar Chini ◽  
Basanta Kumar Das ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Aquatic Species ◽  
Species Detection ◽  
Survey Tool ◽  
Biological Survey

scholarly journals Improving herpetological surveys in eastern North America using the environmental DNA method

Genome ◽  
2016 ◽  
Vol 59 (11) ◽  
pp. 991-1007 ◽  
Author(s):  
Anaïs Lacoursière-Roussel ◽  
Yohann Dubois ◽  
Eric Normandeau ◽  
Louis Bernatchez
Keyword(s):  
Large Scale ◽  
Habitat Type ◽  
Environmental Dna ◽  
Conservation Strategies ◽  
Natural Environments ◽  
Detection Rates ◽  
Survey Tool ◽  
Declining Species ◽  
Species Specific ◽  
Wood Turtle

Among vertebrates, herpetofauna has the highest proportion of declining species. Detection of environmental DNA (eDNA) is a promising method towards significantly increasing large-scale herpetological conservation efforts. However, the integration of eDNA results within a management framework requires an evaluation of the efficiency of the method in large natural environments and the calibration of eDNA surveys with the quantitative monitoring tools currently used by conservation biologists. Towards this end, we first developed species-specific primers to detect the wood turtle (Glyptemys insculpta) a species at risk in Canada, by quantitative PCR (qPCR). The rate of eDNA detection obtained by qPCR was also compared to the relative abundance of this species in nine rivers obtained by standardized visual surveys in the Province of Québec (Canada). Second, we developed multi-species primers to detect North American amphibian and reptile species using eDNA metabarcoding analysis. An occurrence index based on the distribution range and habitat type was compared with the eDNA metabarcoding dataset from samples collected in seven lakes and five rivers. Our results empirically support the effectiveness of eDNA metabarcoding to characterize herpetological species distributions. Moreover, detection rates provided similar results to standardized visual surveys currently used to develop conservation strategies for the wood turtle. We conclude that eDNA detection rates may provide an effective semiquantitative survey tool, provided that assay calibration and standardization is performed.

Cost-effectiveness of two monitoring strategies for the great crested newt (Triturus cristatus)

2010 ◽  
Vol 31 (3) ◽  
pp. 403-410 ◽  
Author(s):  
Jérôme Pellet ◽  
Madeleine Kröpfli ◽  
Patrick Heer
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Amphibian Conservation ◽  
Submerged Vegetation ◽  
Vegetation Density ◽  
Triturus Cristatus ◽  
Monitoring Strategies ◽  
Cost Effective Method ◽  
Crested Newt ◽  
Monitoring Protocols

AbstractDesigning cost-effective monitoring protocols is a fundamental prerequisite for amphibian conservation. Here, we report a comparison of flashlight survey and trapping (with and without light sticks as trap baits) in order to determine flashlight detectability and trap detectability of great crested newts (Triturus cristatus). Twelve ponds were surveyed in Switzerland where T. cristatus had been known to occur. We measured covariates affecting both flashlight detectability and trap detectability. Newt flashlight detectability using 20 min long flashlight surveys was on average ± SE = 39% ± 10%). Flashlight detectability was mostly influenced by surface and submerged vegetation density, as well as by water temperature. Newt trap detectability during one night using six funnel traps per pond was on average±SE = 41%±10%. Trap detectability was mainly affected by trap position in the pond, with traps lying on the pond floor being more likely to attract newts. The use of light sticks did not enhance the trap detectability. Estimates of flashlight detectability and trap detectability were used to define how many times the sites have to be visited to be 95% certain of not missing T. cristatus in ponds where they are present. In both cases multiple visits (7 flashlight surveys or 6 trapping sessions) have to be performed. Flashlight surveys are the most easily applied and most cost-effective method to use in large scale programs.

An eDNA approach to detect eastern hellbenders (Cryptobranchus a. alleganiensis) using samples of water

2012 ◽  
Vol 39 (7) ◽  
pp. 629 ◽  
Author(s):  
Zachary H. Olson ◽  
Jeffrey T. Briggler ◽  
Rod N. Williams
Keyword(s):  
Water Samples ◽  
Effective Means ◽  
Environmental Dna ◽  
Cost Effective ◽  
Negative Control ◽  
Specificity And Sensitivity ◽  
Genetic Sampling ◽  
Conservation Concern ◽  
Species Specific ◽  
Eastern Hellbender

Context Environmental DNA, or eDNA, methods are a novel application of non-invasive genetic sampling in which DNA from organisms is detected via sampling of water or soil, typically for the purposes of determining the presence or absence of an organism. eDNA methods have the potential to revolutionise the study of rare or endangered taxa. Aims We evaluated the efficacy of eDNA sampling to detect populations of an amphibian of conservation concern, the eastern hellbender (Cryptobranchus a. alleganiensis), indirectly from their aquatic environments. Methods We developed species-specific primers, validated their specificity and sensitivity, and assessed the utility of our methods in silico and in laboratory trials. In the field, we collected water samples from three sites with known densities of hellbenders, and from one site where hellbenders do not occur. We filtered water samples, extracted DNA from filters, and assayed the extraction products for hellbender DNA by using polymerase chain reaction (PCR) and gel electrophoresis. Key results Our methods detected hellbenders at densities approaching the lowest of reported natural densities. The low-density site (0.16 hellbenders per 100 m2) yielded two positive amplifications, the medium-density site (0.38 hellbenders per 100 m2) yielded eight positive amplifications, and the high-density site (0.88 hellbenders per 100 m2) yielded 10 positive amplifications. The apparent relationship between density and detection was obfuscated when river discharge was considered. There was no amplification in any negative control. Conclusion eDNA methods may represent a cost-effective means by which to establish broad-scale patterns of occupancy for hellbenders. Implications eDNA can be considered a valuable tool for detecting many species that are otherwise difficult to study.

scholarly journals Scanning ferry routes: looking for eDNA traces of marine mammals and their preys

2021 ◽  
Vol 4 ◽  
Author(s):  
Elena Valsecchi
Keyword(s):  
Marine Mammals ◽  
High Throughput Sequencing ◽  
Simultaneous Detection ◽  
Environmental Dna ◽  
Trophic Levels ◽  
Systematic Sampling ◽  
Marine Biodiversity ◽  
Tyrrhenian Sea ◽  
Night Time ◽  
Species Specific

Marine environmental DNA (eDNA) surveys are becoming a promising approach to monitor biodiversity status and its variation over time. However, monitoring offshore areas could be extremely costly when using dedicated vessels, beside the impossibility to sample simultaneously geographically distant (even if adjacent) areas. The unexplored possibility of availing on operating ferries as an opportunistic platform for eDNA sampling offers several advantages besides opening limitless opportunities for systematic surveys on marine biodiversity.We present the results of both metabarcoding and barcoding approaches obtained from the analysis of water samples collected on board of a ferry boat along a pilot Mediterranean route crossing the Pelagos Sanctuary for Mediterranean Marine Mammals. The recently described MarVer primer sets (12SrDNA and 16SrDNA regions), specifically designed for the simultaneous detection of marine mammals and other marine vertebrates, were employed. The High Throughput Sequencing (HTS) outcome showed that the markers successfully detected most trophic levels of vertebrate marine communities, and classes, including bony fish, rays, cetaceans and birds. Ferry-based sampling allow to collect sample at any time of the day, and we indeed found diel differences in both quantitative and qualitative distribution of read counts. For instances, we observed an increased abundance of lantern fish amplicons in night-time collect samples (50%), reflecting nocturnal migration through the water column. In general, the number of read counts was significantly higher in nocturnal samples. Such diel differences within our sample indirectly provides evidence of the efficiency of the eDNA approach to detect contemporary signals in the sampled environment. Similarly, cetaceans were detected in correspondence of visual sightings (when these occurred, supplementary samples were collected). Rare species, such as the monk seal, are difficult to be detected in metabarcoding surveys, thus we opted to side the screening of the ferry-samples with a panel of species-specific qPCR assays, which were able to detect DNA traces of the endangered pinniped in the Tuscany archipelago (Tyrrhenian Sea) long before visual observations witnessed its presence in the same area. The study demonstrates the feasibility of using commercial shipping as a platform for eDNA marine sampling without dedicated survey cruises. Commercial shipping routes have potential to act as regular systematic sampling transects which can contribute to evaluating and monitoring marine biodiversity.

scholarly journals Species‐specific habitat preferences do not shape the structure of a crested newt hybrid zone ( Triturus cristatus  x  T. carnifex )

2019 ◽  
Vol 9 (22) ◽  
pp. 12446-12458 ◽  
Author(s):  
Zdeněk Mačát ◽  
Martin Rulík ◽  
Daniel Jablonski ◽  
Antonín Reiter ◽  
Lenka Jeřábková ◽  
...  
Keyword(s):  
Hybrid Zone ◽  
Habitat Preferences ◽  
Triturus Cristatus ◽  
Crested Newt ◽  
Species Specific

Cost effective drift fences for toads and newts

1995 ◽  
Vol 16 (2) ◽  
pp. 137-145 ◽  
Author(s):  
D.M. Latham ◽  
J.W. Arntzen ◽  
R.S. Oldham
Keyword(s):  
Cost Effective ◽  
Breeding Population ◽  
Bufo Bufo ◽  
Triturus Cristatus ◽  
Breeding Sites ◽  
Crested Newt ◽  
And Performance ◽  
Study Sites ◽  
Toad Bufo ◽  
Toad Bufo Bufo

AbstractThe construction, cost and performance of toad and newt drift fences and associated traps used at three study sites is described. Fence efficiency, in terms of the capture of animals immigrating to breeding sites, was calculated to lie between 39 and 63% of the estimated breeding population for the common toad (Bufo bufo), and between 45 and 61% for the crested newt (Triturus cristatus). Fences were consistently less efficient at intercepting emigrating animals; less than 10% of toads and between 34 and 40% of newts were captured. Cost and performance of the systems are compared with data from the literature.

scholarly journals Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia

2020 ◽  
Author(s):  
Katrina West ◽  
Matthew Heydenrych ◽  
Rose Lines ◽  
Tony Tucker ◽  
Sabrina Fossette ◽  
...  
Keyword(s):  
Simultaneous Detection ◽  
Environmental Dna ◽  
Cost Effective ◽  
Distribution Data ◽  
Freshwater Turtles ◽  
Northern Australia ◽  
Non Invasive ◽  
Sea Snakes ◽  
Reptile Species ◽  
Species Specific

AbstractA severe lack of distribution data for aquatic reptiles in northern Australia leaves many taxa vulnerable to extirpation and extinction. Environmental DNA (eDNA) technologies offer sensitive and non-invasive genetic alternatives to trapping and visual surveys and are increasingly employed for the detection of aquatic and semi-aquatic reptiles. However, at present, these studies have largely applied species-specific primers which do not provide a cost-effective avenue for the simultaneous detection of multiple reptilian taxa. Here, we present a 16S rRNA metabarcoding assay for the broad detection of aquatic and semi-aquatic reptile species. This assay is tested on water samples collected at multiple sampling sites at two tropical locations: 12 marine/estuarine sites in Roebuck Bay, Western Australia, and 4 estuarine sites in Cooktown, Queensland, Australia. A total of nine reptile taxa were detected from 10 of the 16 sampled sites, including marine and freshwater turtles, aquatic and semi-aquatic/terrestrial snakes, and terrestrial skinks. However, inconsistencies in the detection of previously observed aquatic reptiles at our sampled sites, such as saltwater crocodile and sea snakes, indicates that further research is required to assess the reliability, strengths and limitations of eDNA methods for aquatic reptile detection before it can be integrated as a broad-scale bioassessment tool.

scholarly journals How reliable is the habitat suitability index as a predictor of great crested newt presence or absence?

2021 ◽  
pp. 111-117
Author(s):  
Andrew S. Buxton
Keyword(s):  
Habitat Suitability ◽  
Sampling Error ◽  
Large Data ◽  
Environmental Dna ◽  
Habitat Suitability Index ◽  
Triturus Cristatus ◽  
High Importance ◽  
Conventional View ◽  
Suitability Index ◽  
Crested Newt

The application of a habitat suitability index (HSI) assessment to predict the use of ponds by great crested newts (Triturus cristatus) is commonly used in association with distribution and monitoring projects. Such projects are often used to inform development and planning decision making. However, this type of assessment is frequently misused, and misinterpreted. We used a large, commercially collected environmental DNA (eDNA) survey for great crested newt pond occupancy (489 ponds) to; (1) assess whether it is appropriate to use low HSI scores to rule out occupancy, (2) discuss the use of high HSI scores to identify ponds of high importance for the species and, (3) explore the eDNA detection method. We conclude that there is no evidence to support ruling out pond occupancy based on low HSI scores. However, the conventional view that ponds with HSI scores above 0.7 are of high importance to great crested newts is somewhat supported by the data. Both eDNA and direct observational survey methodologies suffer from sampling error and these need to be acknowledged in the analysis of large data sets.

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