Methodology of fish eDNA and its applications in ecology and environment

Wang, Shuping; Yan, Zhenguang; Hänfling, Bernd; Zheng, Xin; Wang, Pengyuan; Fan, Jun; Li, Jianlong

doi:10.1016/j.scitotenv.2020.142622

Cited by 142 publications

(107 citation statements)

References 151 publications

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“…Advanced in situ validation may investigate the influence of biotic (e.g., abundance, biomass, life stages, microbial activity) and abiotic (e.g., temperature, pH, ultraviolet light, salinity) factors influencing eDNA origin, state, fate, and transport (Barnes & Turner, 2016; Lacoursière‐Roussel & Deiner, 2021; Wang et al., 2021). Assays that account for spatial (e.g., shoreline vs. offshore) and temporal (e.g., summer vs. winter) variation in eDNA distribution and abundance due to the ecology of a species can be implemented with greater confidence (Lawson Handley et al., 2019; de Souza et al., 2016).…”

Section: Criteria and Principles Of Validationmentioning

confidence: 99%

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

et al. 2021

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The use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation-from field sampling to the analysis of PCR-based results-for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Hence, the general applicability of assays, as well as associated uncertainties and limitations, often remain undetermined. The absence of clear guidelines for assay validation prevents targeted eDNA assays from being incorporated into species monitoring and policy; thus, their establishment is essential for realizing the potential of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks (e.g., "in silico analysis"), and arranged on a 5-level validation scale from "incomplete" to "operational" with defined minimum validation criteria for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. Of the 122 variables, 20% to 76% were reported; the majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterized by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling the appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.

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Section: Criteria and Principles Of Validationmentioning

confidence: 99%

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

et al. 2021

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“…The detection of eDNA in seawater is partly due to its persistence in the environment, which depends on biotic and abiotic factors driving eDNA production, degradation, and transport [60][61][62]. Much is still unknown about the spatial and temporal resolution of eDNA in the marine coastal environment.…”

Section: (B) Potential and Limitations Of Edna Metabarcodingmentioning

confidence: 99%

Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

et al. 2021

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Although we are currently experiencing worldwide biodiversity loss, local species richness does not always decline under anthropogenic pressure. This conservation paradox may also apply in protected areas but has not yet received conclusive evidence in marine ecosystems. Here, we survey fish assemblages in six Mediterranean no-take reserves and their adjacent fishing grounds using environmental DNA (eDNA) while controlling for environmental conditions. We detect less fish species in marine reserves than in nearby fished areas. The paradoxical gradient in species richness is accompanied by a marked change in fish species composition under different managements. This dissimilarity is mainly driven by species that are often overlooked by classical visual surveys but detected with eDNA: cryptobenthic, pelagic, and rare fishes. These results do not negate the importance of reserves in protecting biodiversity but shed new light on how under-represented species groups can positively react to fishing pressure and how conservation efforts can shape regional biodiversity patterns.

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“…abundance, biomass, life stages, microbial activity) and abiotic (e.g. temperature, pH, ultraviolet light, salinity) factors influencing eDNA origin, state, fate, and transport (Barnes & Turner, 2016; Lacoursière-Roussel & Deiner, 2019; Wang et al, 2021). Assays that account for spatial (e.g.…”

Section: Criteria and Principles Of Validationmentioning

confidence: 99%

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

Thalinger

Deiner

Harper

et al. 2020

Preprint

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32 33 1. Environmental DNA (eDNA) analysis utilises trace DNA released by organisms into their 34 environment for species detection and is revolutionising non-invasive species monitoring. The 35 use of this technology requires rigorous validation -from field sampling to interpretation of PCR-36 based results -for meaningful application and interpretation. Assays targeting eDNA released by 37 individual species are typically validated with no predefined criteria to answer specific research 38 questions in one ecosystem. Their general applicability, uncertainties and limitations often 39 remain undetermined. The absence of clear guidelines prevents targeted eDNA assays from 40 being incorporated into species monitoring and policy, thus their establishment will be key for the 41 future implementation of eDNA-based surveys. 42 2. We describe the measures and tests necessary for successful validation of targeted eDNA 43 assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was 44 compiled and consolidated into a scale to assess the validation status of individual assays. 45These variables were evaluated for 546 published single-species assays. The resulting dataset 46 was used to provide an overview of current validation practices and test the applicability of the 47 (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve 52 this first level. These assays were characterised by minimal in silico and in vitro testing, but their 53 share in annually published eDNA assays has declined since 2014. The total number of reported 54 variables ranged from 20% to 76% and deviated both between and within levels. 55 4. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing 56 targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future 57 4 research and routine monitoring, while also enabling appropriate interpretation of results. Finally, 58 it provides guidance on validation and reporting standards for newly developed assays. 59 60

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Methodology of fish eDNA and its applications in ecology and environment

Cited by 142 publications

References 151 publications

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

Environmental DNA metabarcoding reveals and unpacks a biodiversity conservation paradox in Mediterranean marine reserves

A validation scale to determine the readiness of environmental DNA assays for routine species monitoring

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