Detecting marine pests using environmental DNA and biophysical models

Ellis, Morgan R.; Clark, Zach; Treml, Eric A.; Brown, Morgan S.; Matthews, Ty G.; Pocklington, Jacqueline B.; Stafford-Bell, Richard; Bott, Nathan J.; Nai, Yi Heng; Miller, Adam D.; Sherman, Craig D. H.

doi:10.1016/j.scitotenv.2021.151666

Cited by 22 publications

(18 citation statements)

References 54 publications

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“…More generally, Andruszkiewicz et al (2019) promoted the use of process-oriented models to understand the spatio-temporal distribution of eDNA, attempting to reconstruct, from observations, the origin in space and time of eDNA shed by anchovies. Also, Ellis et al (2021) have developed a similar model and compared simulations with observations to quantify the spatial range for the detection of eDNA shed by two sources: a kelp and a sea star species. They found very similar results regarding the order of magnitude of both the horizontal extent, and the duration to reach a detection limit from a shedding time.…”

Section: Discussionmentioning

confidence: 99%

A new simulation framework to evaluate the suitability of eDNA for marine and aquatic Environmental Impact Assessments

Coston‐Guarini¹,

Hinz²,

Mirimin

et al. 2022

Preprint

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This study evaluates how eDNA information could be used within Environmental Impact Assessment (EIA). We developed an original model to simulate the conditions for which an eDNA signal detects, or does not detect, an impact on a targeted (receptor) species in a given project area. The simulation has four consecutive steps. First, a deterministic model simulated the dynamics of the receptor population and their eDNA fragment concentrations in the environment. Second, random distributions of receptor organisms and eDNA fragment quantities at steady-state were simulated within the project area. Then Simple Random Samplings were performed for both the receptor and eDNA. Third, post-sampling processes (eDNA extraction, amplification, analysis) were simulated to estimate the detection probability of the species from sample plan characteristics (size of sampling unit, number of samples collected). Fourth, we simulated an impact by modifying the growth, mortality and mobility (null, passive and active) parameters of the receptor species, then determined if an impact was detected. Detection probability curves were estimated for a range of sample volumes fitted with a Weibull cumulative distribution function. An F-like statistic compared detection curves before and after impact. Twelve scenarios were simulated. A statistically significant impact was detected with eDNA when receptor species growth rate was halved, but only in cases of null or passive mobility. When the receptor experienced both reduced growth and increased mortality rates, an impact was detected in all three mobility cases (null, passive and active). Our results suggest that an impact could be detected using eDNA if both the population dynamics of the receptor and the dynamics of DNA shed into the environment are known. These results indicate that caution should be exercised with eDNA data for EIA, but the proposed framework provides a valuable starting point to improve interpretation of indirect observation methods such as eDNA.

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Section: Discussionmentioning

confidence: 99%

A new simulation framework to evaluate the suitability of eDNA for marine and aquatic Environmental Impact Assessments

Coston‐Guarini¹,

Hinz²,

Mirimin

et al. 2022

Preprint

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“…Uncertainties surrounding the interpretation and implementation of eNAs‐base surveillance are primarily explained by limited knowledge on the eNAs dynamics (dispersion and degradation) in the environment (Hinz et al, 2022). Recent efforts have been made to characterize the “ecology” of eNAs, which includes their origin, state, transport, and fate within an environment and to understand how to harness this information to go beyond the absence or presence of target species (Barnes et al, 2014; Eble et al, 2020; Ellis et al, 2022; Fukaya et al, 2021). For example, in an effort to help develop predictive probability maps of eDNA within a marine environment, researchers have begun to combine high‐resolution data on biological characteristics of eDNA (decay, shedding, state, etc.)…”

Section: Introductionmentioning

confidence: 99%

“…For example, in an effort to help develop predictive probability maps of eDNA within a marine environment, researchers have begun to combine high‐resolution data on biological characteristics of eDNA (decay, shedding, state, etc.) and oceanographic data (upwelling, along‐shore currents, wind‐driven surface currents and tidal forcing) to build biophysical models (Andruszkiewicz et al, 2019; Ellis et al, 2022; Fukaya et al, 2021). Other studies have explored in‐situ eDNA spatial–temporal distribution patterns (Ely et al, 2021; Minamoto et al, 2017; Murakami et al, 2019; Sevellec et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

Harnessing decay rates for coastal marine biosecurity applications: A review of environmental DNA and RNA fate

et al. 2023

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Marine nonindigenous species (NIS) are spreading at an alarming rate internationally through anthropogenic activities such as shipping and aquaculture, affecting local biodiversity and negatively impacting the ecosystem and human well‐being. Countries and international organizations have recognized this global threat and have begun implementing biosecurity management programs to ensure early detection, effective surveillance, and mitigation of marine NIS spread. Molecular techniques based on environmental DNA and RNA (eDNA/eRNA), collectively referred to as environmental nucleic acids (eNAs), have become a popular noninvasive tool for detecting NIS and monitoring biodiversity locally and globally. However, uncertainties about eNAs detection probabilities and the location of the source population impede the broad uptake of this tool in marine biosecurity programs. It's been hypothesized that most of these uncertainties can be explained by studying the molecules' dynamics within a marine environment and implementing eNAs distribution models. To contribute to further knowledge development in this area, our study reviews data from 20 recent reports on the degradation mechanisms and fate of eNAs in the marine environment. We classified the critical factors influencing eNAs' persistence that should be considered by biosecurity practitioners, outlining the complex interaction between the molecules' degradation processes and particular environmental conditions. To help guide the parameterization of eNAs distribution models, this review also summarizes and standardizes the marine decay rates of eDNA/eRNA from the literature. Finally, this manuscript outlines guidelines to help calculate accurate decay rates to build appropriate “fit‐for‐purpose” marine biosecurity tools for improved target detectability and greater resolution in assessing biodiversity.

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“…eDNA technologies are centred around species identification via the detection of genetic material shed or excreted by an organism into its local environment (Taberlet et al, 2012). Previous studies implementing these applications have focused on targeted, single‐species detection and monitoring in aquatic environments, with an emphasis on threatened species and pest incursions (Thomsen et al, 2012; Smart et al, 2015; Tingley et al, 2019; Ellis et al, 2022). More recently, eDNA metabarcoding approaches have permitted multispecies detections, thereby transforming the ability to characterize patterns of biodiversity at the community or assemblage scale in marine, freshwater and terrestrial ecosystems (Taberlet et al, 2012; Valentini et al, 2016; Sasso et al, 2017; Bylemans et al, 2018; Ushio et al, 2018; Stat et al, 2019; Zou et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

Contrasting patterns of biodiversity across wetland habitats using single‐time‐point environmental DNA surveys

Coleman,

Matthews,

Sherman

et al. 2023

Aquatic Conservation

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Wildlife surveys are central to the conservation and restoration management of wetland habitats; however, the often laborious and costly nature of traditional survey methods can constrain the spatial and temporal extent and replication of survey efforts. Environmental DNA (eDNA) technologies now provide the opportunity to reduce some of these limitations, but applications in temporary and permanent freshwater marshes and meadows (herein referred to as ‘wetland habitats’) remain limited. This study investigates the performance of single‐time‐point eDNA surveys for characterizing fish, amphibian and bird assemblages of wetland habitats in south‐eastern Australia. Comparisons were made between coastal and inland wetlands, between wetlands of varying condition and between eDNA and traditional surveys. Findings show that eDNA surveys can provide comprehensive descriptions of faunal assemblages associated with wetland habitats, with resolution similar to that provided by traditional survey approaches. Analyses also revealed significant differences in patterns of biodiversity between wetland types (coastal vs. inland) but not between wetland habitats varying in condition. Overall, this study confirms that eDNA surveys provide a reliable option for undertaking wetland biodiversity assessments aimed at improving biodiversity data coverage for otherwise data deficient wetlands.

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Detecting marine pests using environmental DNA and biophysical models

Cited by 22 publications

References 54 publications

A new simulation framework to evaluate the suitability of eDNA for marine and aquatic Environmental Impact Assessments

A new simulation framework to evaluate the suitability of eDNA for marine and aquatic Environmental Impact Assessments

Harnessing decay rates for coastal marine biosecurity applications: A review of environmental DNA and RNA fate

Contrasting patterns of biodiversity across wetland habitats using single‐time‐point environmental DNA surveys

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