Integration of eDNA‐Based Biological Monitoring within the U.S. Geological Survey’s National Streamgage Network

Pilliod, David S.; Laramie, Matthew B.; MacCoy, Dorene E.; Maclean, Scott H.

doi:10.1111/1752-1688.12800

Cited by 16 publications

(15 citation statements)

References 63 publications

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“…Regarding the detection of fish species, eDNA-based monitoring outperforms traditional methods such as electrofishing: for example, for the detection of the endangered European weather loach, Misgurnus fossilis (Sigsgaard et al, 2015), the assessment of fish communities in Australian streams (McColl-Gausden et al, 2020), and the distribution of brook trout, Salvelinus fontinalis in a US watershed (Evans et al, 2017). The manifold successes of eDNA-based species detection lead to a call for more standardization and better reporting practices (Goldberg et al, 2016;Minamoto et al, 2020;Thalinger et al, 2021a) and to an international effort for implementing the technology into routine species monitoring (Leese et al, 2016;Pilliod et al, 2019). Although reporting the presence/absence of particular species is the starting point of these endeavors, a more quantitative interpretation of field-derived eDNA data is key for the general application of this technology.…”

Section: Introductionmentioning

confidence: 99%

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

et al. 2021

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The quantitative measurement of environmental DNA (eDNA) from field-collected water samples is gaining importance for the monitoring of fish communities and populations. The interpretation of these signal strengths depends, among other factors, on the amount of target eDNA shed into the water. However, shedding rates are presumably associated with species-specific traits such as physiology and behavior. Although such differences between juvenile and adult fish have been previously detected, the general impact of movement and energy use in a resting state on eDNA release into the surrounding water remains hardly addressed. In an aquarium experiment, we compared eDNA shedding between seven fish species occurring in European freshwaters. The investigated salmonids, cyprinids, and sculpin exhibit distinct adaptions to microhabitats, diets, and either solitary or schooling behavior. The fish were housed in aquaria with constant water flow and their activity was measured by snapshots taken every 30 s. Water samples for eDNA analysis were taken every 3 h and energy use was determined in an intermittent flow respirometer. After controlling for the effect of fish mass, our results demonstrate a positive correlation between target eDNA quantities as measured with digital PCR, fish activity, and energy use, as well as species-specific differences. For cyprinids, the model based on data from individual fish was only partly transferable to groups, which showed lower activity and higher energy use. Our findings highlight the importance of fish physiology and behavior for the comparative interpretation of taxon-specific eDNA quantities. Species traits should therefore be incorporated into eDNA-based monitoring and conservation efforts.

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Section: Introductionmentioning

confidence: 99%

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Regarding the detection of fish species, eDNA-based monitoring outperforms traditional methods such as electrofishing: for example, for the detection of the endangered European weather loach, Misgurnus fossilis (Sigsgaard et al, 2015), the assessment of fish communities in Australian streams (McColl‐Gausden et al, 2020), and the distribution of brook trout, Salvelinus fontinalis in a US watershed (Evans et al, 2017). The manifold successes of eDNA-based species detection lead to a call for more standardization and better reporting practices (Goldberg et al, 2016; Minamoto et al, 2020; Thalinger et al, 2020a) and to an international effort for implementing the technology into routine species monitoring (Leese et al, 2016; Pilliod et al, 2019). Although reporting the presence/absence of particular species is the starting point of these endeavors, a more quantitative interpretation of field-derived eDNA data is key for the broader applicability of this technology.…”

Section: Introductionmentioning

confidence: 99%

The effect of activity, energy use, and species identity on environmental DNA shedding of freshwater fish

Thalinger

Rieder

Teuffenbach

et al. 2020

Preprint

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The quantitative measurement of eDNA form field-collected water samples is gaining importance for the monitoring of fish communities and populations. The interpretation of these signal strengths depends, among other factors, on the amount of target eDNA shed into the water. However, shedding rates are presumably associated with species-specific traits such as physiology and behavior. Although such differences between juvenile and adult fish have been previously detected, the general impact of movement and energy use in a resting state on eDNA release into the surrounding water remains hardly addressed. In an aquarium experiment, we compared eDNA shedding between seven fish species occurring in European freshwaters. The investigated salmonids, cyprinids and sculpin exhibit distinct adaptions to microhabitats, diets, and either solitary or schooling behavior. The fish were housed in aquaria with constant water flow and their activity was measured by snapshots taken every 30 s. Water samples for eDNA analysis were taken every 3 h and energy use was determined in an intermittent flow respirometer. After controlling for the effect of fish mass, our results demonstrate a positive correlation between target eDNA quantities as measured with digital PCR, fish activity and energy use, as well as species-specific differences. For cyprinids, the model based on data from individual fish was only partly transferable to groups, which exhibited lower activity and higher energy use. Our findings highlight the importance of fish physiology and behavior for the comparative interpretation of taxon-specific eDNA quantities. Species traits should therefore be incorporated into eDNA-based monitoring and conservation efforts.

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“…In the future, we hope to add a coherent dynamic modelling framework that accommodates longitudinal eDNA surveys. Continued research into dynamic multi‐scale occupancy models is essential as longitudinal eDNA monitoring programs gain popularity (Bálint et al., 2018; Hutchins, Sepulveda, Hopper, & Staigmiller, 2019; Pilliod, Laramie, MacCoy, & Maclean, 2019; Uchii, Doi, Yamanaka, & Minamoto, 2017). Once these methods have been developed, we intend to add them to msocc.…”

Section: Discussionmentioning

confidence: 99%

msocc: Fit and analyse computationally efficient multi‐scale occupancy models in r

2020

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Environmental DNA (eDNA) sampling is a promising tool for the detection of rare and cryptic taxa, such as aquatic pathogens, parasites and invasive species. Environmental DNA sampling workflows commonly rely on multi‐stage hierarchical sampling designs that induce complicated dependencies within the data. This complex dependence structure can be intuitively modelled with Bayesian multi‐scale occupancy models. However, current software for such models are computationally demanding, impeding their use. We present an r package, msocc, that implements a data augmentation strategy to fit fully Bayesian, computationally efficient multi‐scale occupancy models. The msocc package allows users to fit multi‐scale occupancy models, to estimate and visualize posterior summaries of site, sample and replicate‐level occupancy, and to compare different models using Bayesian information criterion. Additionally, we provide a supplemental web application that allows users to investigate study design for multi‐scale occupancy models and acts as a graphical user interface to the msocc package. The utility of the msocc package is illustrated on a published dataset and the functions in msocc are compared to the primary Bayesian toolkit for multi‐scale occupancy modelling, eDNAoccupancy, using various computational benchmarks. These benchmarks indicate that msocc is capable of fitting models 50 times faster than eDNAoccupancy. We hope that access to software that efficiently fits, analyses and conducts study design investigations for multi‐scale occupancy models facilitates their implementation by the research and wildlife management communities.

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Integration of eDNA‐Based Biological Monitoring within the U.S. Geological Survey’s National Streamgage Network

Cited by 16 publications

References 63 publications

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

The Effect of Activity, Energy Use, and Species Identity on Environmental DNA Shedding of Freshwater Fish

The effect of activity, energy use, and species identity on environmental DNA shedding of freshwater fish

msocc: Fit and analyse computationally efficient multi‐scale occupancy models in r

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