scholarly journals There's always a better way: The application of eDNA to effectively assess biodiversity

2021 ◽  
Vol 4 ◽  
Author(s):  
Prabir Roy ◽  
Mary Thiess
Keyword(s):  
Species Abundance ◽  
Environmental Dna ◽  
Detection Methods ◽  
Mitigation Measures ◽  
Ecological Change ◽  
Ecosystem Monitoring ◽  
Site Specific ◽  
Species Detection ◽  
Conservation Practice ◽  
Parks Canada

Our ecosystem monitoring methodologies focus on data collection for reporting purposes that may not serve to identify the systematic causes of ecological change. Managers need precise and timely information at appropriate scales to build ecosystem resilience. Traditional species detection methodologies offer little information when species abundance are low, especially in large water ecosystems such as the Great Lakes. Species not found during monitoring doesn’t necessarily mean that species are absent. Moreover, even if a change in the ecosystem is detected, it is often not possible to determine its cause at a spatiotemporal scale or a trophic cascade level. As a result, we often find ourselves being reactive in our mitigation measures. Before irreversible change occurs, we must be guided by a better understanding of the actual ecological landscape which Environmental DNA (eDNA) may help provide. eDNA is a potential tool to effectively overcome traditional species survey limitations currently in use at many Parks Canada sites (Supplemental file 1). As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings. Such samples can be analyzed by high-throughput DNA sequencing methods for rapid measurement and monitoring of biodiversity. Access to this genetic information makes a critical contribution to the understanding of population size, species distribution, and population dynamics for species not well documented. Despite the increasing use of eDNA in conservation practice, it requires further methodological improvement for greater influence on management decisions. The tool requires standardized protocols based on site-specific covariates and objectives. We’re working to tackle the challenge with 2 objectives: (1) to combine traditional biomonitoring knowledge and metagenomics to further develop eDNA as a reliable sampling tool for Parks Canada and (2) to support site-specific monitoring objectives for species-at-risk, invasive species, aquatic species inventories, and/or culturally significant species. The overall goal is to increase our capacity to make more informed, timely, regionally-coordinated conservation decisions through the rapid and sensitive species detection methods offered by eDNA.

scholarly journals Estimation accuracy of species abundance based on environmental DNA with relation to its production source, state, and assay methodology suggested by meta-analyses

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Hiroki Yamanaka
Keyword(s):  
Meta Analysis ◽  
Empirical Studies ◽  
Species Abundance ◽  
Environmental Dna ◽  
Efficient Estimation ◽  
Estimation Accuracy ◽  
Accurate Estimation ◽  
Abundance Estimation ◽  
Natural Environments ◽  
Promising Tool

Environmental DNA (eDNA) analysis is a promising tool for non-disruptive and cost-efficient estimation of species abundance. However, its practical applicability in natural environments is limited because it is unclear whether eDNA concentrations actually represent species abundance in the field. Although the importance of accounting for eDNA dynamics, such as transport and degradation, has been discussed, the influences of eDNA characteristics, including production source and state, and methodology, including collection and quantification strategy and abundance metrics, on the accuracy of eDNA-based abundance estimation were entirely overlooked. We conducted a meta-analysis using 56 previous eDNA literature and investigated the relationships between the accuracy (R2) of eDNA-based abundance estimation and eDNA characteristics and methodology. Our meta-regression analysis found that R2 values were significantly lower for crustaceans than fish, suggesting that less frequent eDNA production owing to their external morphology and physiology may impede accurate estimation of their abundance via eDNA. Moreover, R2 values were positively associated with filter pore size, indicating that selective collection of larger-sized eDNA, which is typically fresher, could improve the estimation accuracy of species abundance. Furthermore, R2 values were significantly lower for natural than laboratory conditions, while there was no difference in the estimation accuracy among natural environments. Our findings shed a new light on the importance of what characteristics of eDNA should be targeted for more accurate estimation of species abundance. Further empirical studies are required to validate our findings and fully elucidate the relationship between eDNA characteristics and eDNA-based abundance estimation.

scholarly journals Review ArticleDigital change detection methods in ecosystem monitoring: a review

2004 ◽  
Vol 25 (9) ◽  
pp. 1565-1596 ◽  
Author(s):  
P. Coppin ◽  
I. Jonckheere ◽  
K. Nackaerts ◽  
B. Muys ◽  
E. Lambin
Keyword(s):  
Change Detection ◽  
Detection Methods ◽  
Ecosystem Monitoring

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 A non-lethal method for detection of Bonamia ostreae in flat oyster (Ostrea edulis) using environmental DNA

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Louise von Gersdorff Jørgensen ◽  
Johan Wedel Nielsen ◽  
Mikkel Kehler Villadsen ◽  
Bent Vismann ◽  
Sussie Dalvin ◽  
...  
Keyword(s):  
Water Samples ◽  
Sea Water ◽  
Diagnostic Technique ◽  
Environmental Dna ◽  
Detection Methods ◽  
Ostrea Edulis ◽  
Breeding Programs ◽  
Bonamia Ostreae ◽  
Flat Oyster ◽  
Selection Of

Abstract Surveillance and diagnosis of parasitic Bonamia ostreae infections in flat oysters (Ostrea edulis) are prerequisites for protection and management of wild populations. In addition, reliable and non-lethal detection methods are required for selection of healthy brood oysters in aquaculture productions. Here we present a non-lethal diagnostic technique based on environmental DNA (eDNA) from water samples and demonstrate applications in laboratory trials. Forty oysters originating from Limfjorden, Denmark were kept in 30 ppt sea water in individual tanks. Water was sampled 6 days later, after which all oysters were euthanized and examined for infection, applying PCR. Four oysters (10%) were found to be infected with B. ostreae in gill and mantle tissue. eDNA purified from the water surrounding these oysters contained parasite DNA. A subsequent sampling from the field encompassed 20 oysters and 15 water samples from 5 different locations. Only one oyster turned out positive and all water samples proved negative for B. ostreae eDNA. With this new method B. ostreae may be detected by only sampling water from the environment of isolated oysters or isolated oyster populations. This non-lethal diagnostic eDNA method could have potential for future surveys and oyster breeding programs aiming at producing disease-free oysters.

scholarly journals Inferring macro-ecological patterns from local species' occurrences

2018 ◽  
Author(s):  
Anna Tovo ◽  
Marco Formentin ◽  
Samir Suweis ◽  
Samuele Stivanello ◽  
Sandro Azaele ◽  
...  
Keyword(s):  
Species Richness ◽  
Negative Binomial ◽  
Spatial Scales ◽  
Species Abundance ◽  
Analytical Framework ◽  
Invariance Property ◽  
Practical Reasons ◽  
Conservation Practice ◽  
Unique Framework ◽  
Using Data

Biodiversity provides support for life, vital provisions, regulating services and has positive cultural impacts. It is therefore important to have accurate methods to measure biodiversity, in order to safeguard it when we discover it to be threatened. For practical reasons, biodiversity is usually measured at fine scales whereas diversity issues (e.g. conservation) interest regional or global scales. Moreover, biodiversity may change across spatial scales. It is therefore a key challenge to be able to translate local information on biodiversity into global patterns. Many databases give no information about the abundances of a species within an area, but only its occurrence in each of the surveyed plots. In this paper, we introduce an analytical framework to infer species richness and abundances at large spatial scales in biodiversity-rich ecosystems when species presence/absence information is available on various scattered samples (i.e. upscaling). This framework is based on the scale-invariance property of the negative binomial. Our approach allows to infer and link within a unique framework important and well-known biodiversity patterns of ecological theory, such as the Species Accumulation Curve (SAC) and the Relative Species Abundance (RSA) as well as a new emergent pattern, which is the Relative Species Occupancy (RSO). Our estimates are robust and accurate, as confirmed by tests performed on both in silico-generated and real forests. We demonstrate the accuracy of our predictions using data from two well-studied forest stands. Moreover, we compared our results with other popular methods proposed in the literature to infer species richness from presence-absence data and we showed that our framework gives better estimates. It has thus important applications to biodiversity research and conservation practice.

scholarly journals Estimation accuracy of species abundance based on environmental DNA with relation to its production source and state suggested by meta-analyses

2021 ◽  
Author(s):  
Toshiaki Jo ◽  
Hiroki Yamanaka
Keyword(s):  
Empirical Studies ◽  
Species Abundance ◽  
Environmental Dna ◽  
Molecular State ◽  
Efficient Estimation ◽  
Estimation Accuracy ◽  
Accurate Estimation ◽  
Abundance Estimation ◽  
Natural Environments ◽  
Meta Analyses

Environmental DNA (eDNA) analysis is a promising tool for non-disruptive and cost-efficient estimation of species abundance. However, its practical applicability in natural environments is limited owing to a potential gap between eDNA concentration and species abundance in the field. Although the importance of accounting for eDNA dynamics, such as transport and degradation, has been discussed, the influence of eDNA characteristics, including production source and cellular/molecular state, on the accuracy of eDNA-based abundance estimation was entirely overlooked. We conducted meta-analyses using 44 of previous eDNA studies and investigated the relationships between the accuracy (R) of eDNA-based abundance estimation and eDNA characteristics. First, we found that estimated R values were significantly lower for crustaceans and mussels than fish. This finding suggests that less frequent eDNA production of these taxa owing to their external morphology and physiology may impede accurate estimation of their abundance via eDNA. Moreover, linear mixed modeling showed that, despite high variances, R values were positively correlated with filter pore size, indicating that selective collection of larger-sized eDNA, which is typically fresher, could improve the estimation accuracy of species abundance. Although our collected dataset was somewhat biased to the studies targeting specific taxa, our findings shed a new light on the importance of what characteristics of eDNA should be targeted for more accurate estimation of species abundance. Further empirical studies are required to validate our findings and fully elucidate the relationship between eDNA characteristics and eDNA-based abundance estimation.

scholarly journals Species detection using environmental DNA from water samples

2008 ◽  
Vol 4 (4) ◽  
pp. 423-425 ◽  
Author(s):  
Gentile Francesco Ficetola ◽  
Claude Miaud ◽  
François Pompanon ◽  
Pierre Taberlet
Keyword(s):  
Dna Sequences ◽  
Developmental Stages ◽  
Rana Catesbeiana ◽  
Environmental Dna ◽  
Species Detection ◽  
Novel Approach ◽  
Molecular Imprint ◽  
Massive Sequencing ◽  
Natural Wetlands ◽  
Controlled Environments

The assessment of species distribution is a first critical phase of biodiversity studies and is necessary to many disciplines such as biogeography, conservation biology and ecology. However, several species are difficult to detect, especially during particular time periods or developmental stages, potentially biasing study outcomes. Here we present a novel approach, based on the limited persistence of DNA in the environment, to detect the presence of a species in fresh water. We used specific primers that amplify short mitochondrial DNA sequences to track the presence of a frog ( Rana catesbeiana ) in controlled environments and natural wetlands. A multi-sampling approach allowed for species detection in all environments where it was present, even at low densities. The reliability of the results was demonstrated by the identification of amplified DNA fragments, using traditional sequencing and parallel pyrosequencing techniques. As the environment can retain the molecular imprint of inhabiting species, our approach allows the reliable detection of secretive organisms in wetlands without direct observation. Combined with massive sequencing and the development of DNA barcodes that enable species identification, this approach opens new perspectives for the assessment of current biodiversity from environmental samples.

Life in a drop: Sampling environmental DNA for marine fishery management and ecosystem monitoring

Marine Policy ◽  
2021 ◽  
Vol 124 ◽  
pp. 104331
Author(s):  
John Gilbey ◽  
Gary Carvalho ◽  
Rita Castilho ◽  
Ilaria Coscia ◽  
Mark W. Coulson ◽  
...  
Keyword(s):  
Fishery Management ◽  
Environmental Dna ◽  
Ecosystem Monitoring ◽  
Marine Fishery

scholarly journals At the forefront: evidence of the applicability of using environmental DNA to quantify the abundance of fish populations in natural lentic waters with additional sampling considerations

2017 ◽  
Vol 74 (12) ◽  
pp. 2030-2034 ◽  
Author(s):  
Stephen L. Klobucar ◽  
Torrey W. Rodgers ◽  
Phaedra Budy
Keyword(s):  
Aquatic Ecosystems ◽  
Salvelinus Alpinus ◽  
Species Abundance ◽  
Environmental Dna ◽  
Future Studies ◽  
Natural Lakes ◽  
Quantitative Estimates ◽  
Promising Application ◽  
The Relationship ◽  
Lentic Waters

Environmental DNA (eDNA) sampling has proven to be a valuable tool for detecting species in aquatic ecosystems. Within this rapidly evolving field, a promising application is the ability to obtain quantitative estimates of relative species abundance based on eDNA concentration rather than traditionally labor-intensive methods. We investigated the relationship between eDNA concentration and Arctic char (Salvelinus alpinus) abundance in five well-studied natural lakes; additionally, we examined the effects of different temporal (e.g., season) and spatial (e.g., depth) scales on eDNA concentration. Concentrations of eDNA were linearly correlated with char population estimates ([Formula: see text] = 0.78) and exponentially correlated with char densities ([Formula: see text] = 0.96 by area; 0.82 by volume). Across lakes, eDNA concentrations were greater and more homogeneous in the water column during mixis; however, when stratified, eDNA concentrations were greater in the hypolimnion. Overall, our findings demonstrate that eDNA techniques can produce effective estimates of relative fish abundance in natural lakes. These findings can guide future studies to improve and expand eDNA methods while informing research and management using rapid and minimally invasive sampling.

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