scholarly journals Environmental DNA as a non‐invasive sampling tool to detect the spawning distribution of European anadromous shads ( Alosa  spp.)

2019 ◽  
Vol 29 (1) ◽  
pp. 148-152 ◽  
Author(s):  
Caterina Maria Antognazza ◽  
J. Robert Britton ◽  
Caitlin Potter ◽  
Elizabeth Franklin ◽  
Emilie A. Hardouin ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Non Invasive

scholarly journals Monitoring spawning migrations of potamodromous fish species via eDNA

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bettina Thalinger ◽  
Elisabeth Wolf ◽  
Michael Traugott ◽  
Josef Wanzenböck
Keyword(s):  
Fish Species ◽  
Anthropogenic Impacts ◽  
Environmental Dna ◽  
Signal Strength ◽  
Digital Pcr ◽  
Freshwater Ecosystems ◽  
Non Invasive ◽  
River Stretch ◽  
Daily Discharge ◽  
Invasive Techniques

Abstract Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.

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

2019 ◽  
Author(s):  
Clare I. M. Adams ◽  
Luke A. Hoekstra ◽  
Morgan R. Muell ◽  
Fredric J. Janzen
Keyword(s):  
Rank Order ◽  
Environmental Dna ◽  
Chrysemys Picta ◽  
Field Conditions ◽  
Painted Turtle ◽  
Freshwater Turtles ◽  
Detection Rates ◽  
Non Invasive ◽  
Painted Turtles ◽  
Current State

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.

scholarly journals Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modelling

2018 ◽  
Author(s):  
Keiichi Fukaya ◽  
Hiroaki Murakami ◽  
Seokjin Yoon ◽  
Kenji Minami ◽  
Yutaka Osada ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Cost Effective ◽  
Population Monitoring ◽  
Fish Population ◽  
Abundance Estimation ◽  
Population Abundance ◽  
Jack Mackerel ◽  
Non Invasive ◽  
Quantitative Measurements ◽  
Japanese Jack Mackerel

AbstractWe propose a general framework of abundance estimation based on spatially replicated quantitative measurements of environmental DNA in which production, transport, and degradation of DNA are explicitly accounted for. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. These findings indicate the ability of environmental DNA to reliably reflect population abundance of aquatic macroorganisms and may offer a new avenue for population monitoring based on the fast, cost-effective, and non-invasive sampling of genetic information.

scholarly journals Environmental DNA for conservation

2021 ◽  
pp. 157-176
Author(s):  
Antoinette J. Piaggio
Keyword(s):  
Wildlife Conservation ◽  
Empirical Studies ◽  
Sampling Site ◽  
Environmental Dna ◽  
Successful Implementation ◽  
Pilot Studies ◽  
Sampling Schemes ◽  
Non Invasive ◽  
Elusive Species ◽  
Negative Impacts

Detection and monitoring of wildlife species of concern is a costly and time-consuming challenge that is critical to the management of such species. Tools such as lures and traps can cause unnecessary stress or other health impacts to sensitive species. Development and refinement of tools that provide means to detect rare and elusive species without requiring contact with them reduce such impacts. Further, the potential of detection after the target species has moved on from a sampling site could allow for higher potential for detection of rare species. The ability to amplify DNA from environmental samples (e.g. water, soil, air, and other substrates) has provided a non-invasive method for detection of rare or elusive species while reducing negative impacts to wildlife. Like other non-invasive methods, such as cameras, there are methodological pitfalls associated with environmental DNA (eDNA) sampling to consider. Each study system will provide unique challenges to adequate eDNA sampling. Thus, pilot studies are critical for successful implementation of a larger-scale detection and monitoring study. This chapter will describe the benefits and challenges of using eDNA, detail types of eDNA sampling, and provide guidance on designing appropriate study design and sampling schemes. Empirical studies using eDNA applied to wildlife conservation efforts will be highlighted and discussed.

scholarly journals Non-invasive surveys of mammalian viruses using environmental DNA

2020 ◽  
Author(s):  
Niccolò Alfano ◽  
Anisha Dayaram ◽  
Jan Axtner ◽  
Kyriakos Tsangaras ◽  
Marie-Louise Kampmann ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Environmental Dna ◽  
List Type ◽  
Dna Viruses ◽  
Remote Areas ◽  
Hybridization Capture ◽  
Non Invasive ◽  
Zoonotic Viruses ◽  
Wildlife Pathogens ◽  
Rna And Dna

ABSTRACTEnvironmental DNA (eDNA) and invertebrate-derived DNA (iDNA) have been used to survey biodiversity non-invasively to mitigate difficulties of obtaining wildlife samples, particularly in remote areas or for rare species. Recently, eDNA/iDNA have been applied to monitor known wildlife pathogens, however, most wildlife pathogens are unknown and often evolutionarily divergent.To detect and identify known and novel mammalian viruses from eDNA/iDNA sources, we used a curated set of RNA oligonucleotides as viral baits in a hybridization capture system coupled with high throughput sequencing.We detected multiple known and novel mammalian RNA and DNA viruses from multiple viral families from both waterhole eDNA and leech derived iDNA. Congruence was found between detected hosts and viruses identified in leeches and waterholes.Our results demonstrate that eDNA/iDNA samples represent an effective non-invasive resource for studying wildlife viral diversity and for detecting novel potentially zoonotic viruses prior to their emergence.

scholarly journals An assay validation framework to compare and evaluate targeted environmental DNA assays for routine species monitoring

2021 ◽  
Vol 4 ◽  
Author(s):  
Bettina Thalinger ◽  
Kristy Deiner ◽  
Lynsey Harper ◽  
Helen Rees ◽  
Rosetta Blackman ◽  
...  
Keyword(s):  
Meta Analysis ◽  
Environmental Dna ◽  
Single Species ◽  
End Users ◽  
Specific System ◽  
Initial Development ◽  
Assay Validation ◽  
Non Invasive ◽  
Detection Probabilities ◽  
User Friendly

Environmental DNA (eDNA) analysis utilises trace DNA released by organisms into their environment for species detection and is revolutionising non ‐ invasive species and biodiversity monitoring. However, this technology requires rigorous validation along the whole workflow – from field sampling to statistical analysis – to ensure appropriate and meaningful interpretation of results. Targeted eDNA assays are often validated within a specific system and with particular aims, but without fulfilling predefined criteria. Consequently, their applicability beyond initial development often remains undetermined. Additionally, there tends to be poor understanding of the uncertainties and limitations associated with already published assays and thus potentially inappropriate interpretation of the results they produce. The lack of a “gold standard” limits the incorporation of targeted eDNA assays into species monitoring and policy making by end-users and is therefore key for the future implementation of eDNA-based surveys. Here, we present a framework (https://edna-validation.com/) and user-friendly criteria for the classification of assays, which is based on previous validation efforts. A 5 ‐ level assay validation scale (“incomplete” to “operational”) was defined by reviewing the current eDNA literature and conducting a meta-analysis on sampling, laboratory practices, detection limits, and detection probabilities. The so far published single species eDNA assays were reviewed for their performance in this new framework and we identified steps within the validation process that often remain untouched. Finally, we provide guidance for end ‐ users as to which criteria are most important for validation and suggest how results obtained from assays at different levels of the validation scale should be interpreted.

scholarly journals A eDNA-qPCR assay to non-invasively detect the presence of the parasiteSchistocephalus solidusinside its threespine stickleback host

2017 ◽  
Author(s):  
Chloé Suzanne Berger ◽  
Nadia Aubin-Horth
Keyword(s):  
Detection Method ◽  
Abdominal Cavity ◽  
Environmental Dna ◽  
Threespine Stickleback ◽  
Complex Life Cycle ◽  
Non Invasive ◽  
Schistocephalus Solidus ◽  
Host Parasite Interactions ◽  
Ventilation Rates ◽  
Host Parasite

ABSTRACTDetecting the presence of a parasite within its host is crucial to the study of host-parasite interactions. TheSchistocephalus solidus- threespine stickleback pair has been studied extensively to investigate host phenotypic alterations associated with a parasite with a complex life cycle. This cestode is localized inside the stickleback’s abdominal cavity and can be visually detected only once it passes a mass threshold. We present a non-invasive quantitative PCR approach based on detection of environmental DNA from the worm(eDNA),sampled in the fish abdominal cavity. Using this approach on two fish populations (n=151), 98% of fish were correctly assigned to theirS. solidusinfection status. There was a significant correlation between eDNA concentration and total parasitic mass. We also assessed ventilation rates as a complimentary mean to detect infection. Our eDNA detection method gives a reliable presence/absence response and its future use for quantitative assessment is promising.

Monitoring post-release survival of the northern corroboree frog, Pseudophryne pengilleyi, using environmental DNA

2018 ◽  
Vol 45 (7) ◽  
pp. 620 ◽  
Author(s):  
Jack Rojahn ◽  
Dianne Gleeson ◽  
Elise M. Furlan
Keyword(s):  
Water Samples ◽  
Survey Methods ◽  
Quantitative Polymerase Chain Reaction ◽  
Environmental Dna ◽  
Life Stages ◽  
Breeding Programs ◽  
Non Invasive ◽  
Naturally Occurring ◽  
Cause Of Failure

Context Translocations are becoming an increasingly important conservation tool to combat rising levels of species extinction. Unfortunately, many translocation efforts fail; yet, the timing and cause of failure often remain unknown. Monitoring individuals in the days and weeks following release can provide valuable information on their capacity to survive this initial hurdle. In Australia, breeding programs have been established for the endangered northern corroboree frog, Pseudophryne pengilleyi, to enable reintroduction to the wild via captive-reared individuals, typically, early life stages such as eggs or juvenile frogs that cannot be monitored via traditional survey methods that target adult frogs (e.g. shout–response). Environmental DNA (eDNA) detects trace amounts of DNA that organisms release into their environment and could provide a means to infer population persistence for wildlife releases and translocations. Aims In the present study, we aim to develop an eDNA assay capable of detecting both sexes of P. pengilleyi across multiple life stages, and use it to monitor their survival. Methods An eDNA assay was developed to target the two corroboree frog species (P. pengilleyi and P. corroboree, the southern corroboree frog) and was tested for its sensitivity and specificity in silico and in vitro. Pseudophryne pengilleyi eggs were released into three naturally occurring ponds and water samples were, subsequently, collected from each pond on several occasions over a period of 78 days. Quantitative polymerase chain reaction was used to detect P. pengilleyi eDNA from water samples. Key Results The developed assay was shown to be sensitive and specific to corroboree frogs. eDNA monitoring of reintroduced P. pengilleyi detected the species’ DNA at three of three release ponds and DNA remained detectable until at least 78 days post-release at two of three ponds. Conclusions We show how the development of a corroboree frog-specific assay allowed us to monitor the post-release survival of P. pengilleyi in naturally occurring pools. Implications eDNA surveys may provide a useful tool to monitor post-release survival of translocated populations in a non-invasive manner, with the potential to identify the timing and causes of failure. Such knowledge can be used to inform the management of translocated populations and future release strategies.

scholarly journals Towards an eDNA assay for decapodiform cephalopods

2021 ◽  
Vol 4 ◽  
Author(s):  
Gustavo Sanchez ◽  
Fernando Fernández-Álvarez
Keyword(s):  
Dna Barcoding ◽  
Environmental Dna ◽  
Mitochondrial Genomes ◽  
Specific Primer ◽  
Non Invasive ◽  
Traditional Approaches ◽  
Complete Mitochondrial Genomes

Assessing the distribution and diversity of cephalopods using traditional approaches (standard fishing, market collection, and DNA barcoding) is time-consuming. Environmental DNA (eDNA) assays are non-invasive, fast, and can capture the diversity of the species of interest using a specific primer-set. For Cephalopods, standardization of such primers has been challenging because of a poor database of several markers, and the absence of complete mitochondrial genomes for its design. In this fast-talk, I will briefly talk about our new 87 complete mitochondrial genomes from specimens correctly identify and with museum vouchers, and how these mitogenomes promise to resolve the database limitation for eDNA assays in decapodiform cephalopods.

scholarly journals The amount of environmental DNA increases with freshwater crayfish density and over time

2021 ◽  
Vol 4 ◽  
Author(s):  
Corinna Wallinger ◽  
Daniela Sint ◽  
Bernhard Kolp ◽  
Leopold Füreder ◽  
Michael Traugott
Keyword(s):  
Invasive Species ◽  
Native Species ◽  
Laboratory Experiments ◽  
High Sensitivity ◽  
Environmental Dna ◽  
Freshwater Crayfish ◽  
Population Densities ◽  
Non Invasive ◽  
Crayfish Population ◽  
The Relationship

eDNA analysis is ideally suited to monitor the occurrence of endangered or invasive species because of its non-invasive nature and high sensitivity. European freshwater crayfish are threatened across the whole continent. Classical crayfish monitoring is challenging and time consuming due to their nocturnal activity and hidden lifestyle. Therefore, eDNA-based monitoring of native as well as invasive species seems to be of great benefit for the conservation of the native species and it has indeed been increasingly applied in recent years. Nevertheless, comparably little is known on the relationship between eDNA concentration and crayfish population densities, a prerequisite for estimating population size based on eDNA measurements. Here, we performed laboratory experiments to investigate the relationship between the concentration of crayfish eDNA and population densities - measured as crayfish size and biomass. There was a strong correlation between the two measurements. Moreover, the amount of eDNA increased at least during the first three days after crayfish stocking in the aquarium. The experiments also indicate, that crayfish activity might have a strong influence on the eDNA signal strength. Our findings will significantly contribute to an optimization of the monitoring of freshwater crayfish via the analysis of eDNA and therefore be important for the conservation of these threatened species.

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