Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea

Knudsen, Steen Wilhelm; Ebert, Rasmus Bach; Hesselsøe, Martin; Kuntke, Franziska; Hassingboe, Jakob; Mortensen, Peter; Thomsen, Philip Francis; Sigsgaard, Eva Egelyng; Hansen, Brian Klitgaard; Nielsen, Einar Eg; Møller, Peter Rask

doi:10.1016/j.jembe.2018.09.004

Cited by 91 publications

(92 citation statements)

References 64 publications

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“…Granted, assessing marine species richness and approximate abundance is a relatively new foray for eDNA (e.g. Günther et al 2018;Knudsen et al 2019) and has proven successful for accurate detection, read abundance has failed to find correlations with DNA proportions (Günther et al 2018) or traditional visual biomass measures such as trawling (Knudsen et al 2019). Undoubtedly marine and freshwater systems are likely to experience difference abiotic parameters affecting eDNA dynamics, but whether production rates in marine systems vary in vastly dissimilar ways compared to freshwater habitats, is a yet unknown facet of this methodology.…”

Section: Temperature and Salinitymentioning

confidence: 99%

Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA

2019

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Analysis of environmental DNA (eDNA) offers an unprecedented ability to accurately survey biodiversity from aquatic ecosystems. Although eDNA methods have been applied to myriad taxa, scientists are now moving away from proof-of-concept work, ultimately evaluating the limits and opportunities of this technology to detect and quantify abundance across organisms and environments. Important considerations enabling such methodology to be used for aquatic conservation contexts includes understanding both the effects of (1) the amount of eDNA released from focal taxa-sources, and (2) the removal of eDNA in the environment-sinks. I review publications on aquatic macroorganism eDNA that have evaluated or considered the effect of sources on signal detection (or quantification) and find few studies acknowledge, and fewer still evaluate, the impact of eDNA production on genomic signal recovery. In this review, I encourage readers to carefully consider source dynamics, and using previously published literature, dissect what roles biotic (e.g. lifehistory traits, species interactions including stressors) and abiotic (e.g. temperature, salinity) factors likely play in eDNA deposition and recovery, and how this impacts detection, abundance, biomass estimation, and ultimately informed signal interpretation. I further explore the physical sources of eDNA and propose other methods (spatial and temporal) and markers to assist in identifying eDNA origins in aquatic systems. Understanding how these parameters influence variation in eDNA sources will allow for a more comprehensive survey tool, and potentially give insights into environment-population responses.

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Section: Temperature and Salinitymentioning

confidence: 99%

Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA

2019

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“…The methodology was tested on an artificial (mock) community with 30 bony fish species, two cartilaginous fish species, and eight marine invertebrate species. Quantitative PCR, in many studies used for eDNA quantification of single species (e.g., Doi et al, 2015;Fernandez et al, 2018;Harper et al, 2018;Knudsen et al, 2019;Nevers et al, 2018;Weltz et al, 2017), was here used to determine the in situ eDNA concentration (copies/L seawater) of the entire vertebrate community (Ushio et al, 2018). Species-specific eDNA concentrations of 39 fishes were inferred from the total eDNA concentration and the relative read abundance.…”

Section: Introductionmentioning

confidence: 99%

Analysis of a coastal North Sea fish community: Comparison of aquatic environmental DNA concentrations to fish catches

et al. 2020

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“…Recent eDNA studies have detected A. anguilla through eDNA markers through both single species methods and metabarcoding (Cardeñosa, Gollock, & Chapman, 2019;Knudsen et al, 2019;Seymour et al, 2018;Thomsen, Kielgast, Iversen, Wiuf, et al, 2012).…”

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confidence: 99%

A comparison of European eel Anguilla anguilla eDNA concentrations to fyke net catches in five Irish lakes

et al. 2020

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Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea

Cited by 91 publications

References 64 publications

Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA

Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA

Analysis of a coastal North Sea fish community: Comparison of aquatic environmental DNA concentrations to fish catches

A comparison of European eel Anguilla anguilla eDNA concentrations to fyke net catches in five Irish lakes

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