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The potential to provide inferences about fish abundance from environmental (e)DNA samples has generated great interest. However, the accuracy of these abundance estimates is often low and variable across species and space. A plausible refinement is the use of common aquatic habitat monitoring data to account for attributes that influence eDNA dynamics. We therefore evaluated the relationships between eDNA concentration and abundance of bull trout (Salvelinus confluentus), westslope cutthroat trout (Oncorhynchus clarkii lewisi) and rainbow trout (Oncorhynchus mykiss) at 42 stream sites in the Intermountain West (USA and Canada) and tested whether accounting for site- specific habitat attributes improved the accuracy of fish abundance estimates. eDNA concentrations were positively associated with fish abundance, but these relationships varied by species and site, and there was still considerable variation unaccounted for. Random site-level differences explained much of this variation, but specific habitat attributes of those sites explained relatively small amounts of this variation. Our results underscore that either eDNA sampling or environmental characterization will require further refinement before eDNA can be used reliably to estimate fish abundance in streams. La possibility de faire des inferences concernant l'abondance de poissons a partir d'echantillons d'ADN environnemental (ADNe) suscite beaucoup d'interet. L'exactitude de telles estimations de l'abondance est toutefois souvent faible et variable pour differentes especes et dans l'espace. Une amelioration plausible consiste a utiliser des donnees courantes de surveillance des habitats aquatiques pour y incorporer des attributs qui influencent la dynamique de l'ADNe. Nous avons ainsi evalue les relations entre les concentrations d'ADNe et l'abondance d'ombles a tete plate (Salvelinus confluentus), de truites fardees versant de l'Ouest (Oncorhynchus clarkii lewisi) et de truites arc-en-ciel (Oncorhynchus mykiss) dans 42 sites de cours d'eau dans la region des montagnes de l'Ouest (Etats-Unis et Canada) et verifie si l'integration d'attributs de l'habitat propres au site ameliore l'exactitude des estimations d'abondance des poissons. Les concentrations d'ADNe presentent une association positive avec l'abondance de poissons, mais ces relations varient selon l'espece et le site, et une variation considerable demeure. Des differences aleatoires a l'echelle du site expliquent une bonne partie de cette variation, mais certains attributs de l'habitat dans ces sites expliquent des proportions relativement faibles de cette variation. Nos resultats soulignent le fait que l'utilisation de l'ADNe pour estimer de maniere fiable l'abondance de poissons dans les cours d'eau necessitera d'autres ameliorations a l'echantillonnage d'ADNe ou a la caracterisation des conditions ambiantes. [Traduit par la Redaction], Introduction Declines in abundances and distributions of freshwater salmonids across the Northern Hemisphere have resulted in the listing or petition for listing of many species and subspecies as threatened or [...]

Early detection and rapid response (EDRR) can minimize the impacts of invasive species, which cost billions of dollars globally. To bolster EDRR across the United States, the U.S. Department of the Interior is working with the U.S. Geological Survey and other partners to advance a National EDRR Framework that strengthens tools, actions, and processes to find and eradicate invasive species before they establish and cause negative impacts. An important component of this framework is to strengthen molecular tools for detecting new invasions. The Rapid Environmental (e)DNA Assessment and Deployment Initiative & Network (READI-Net) project is developing automated eDNA sampling tools and processes to ensure that eDNA results are reliable for management decision-making, and information structures to deliver eDNA results to end-users. To improve the potential uptake of this molecular EDRR toolbox, READINet investigators met with a group of end-users, partners, developers, and subjectmatter experts from federal agencies, tribes, universities, and an NGO representing state agencies from February 28 to March 1, 2023, in Moss Landing, CA. Here, we summarize the READI-Net project and the corresponding participant feedback. [ABSTRACT FROM AUTHOR]

Early detection of dreissenid mussels (Dreissena polymorpha and D. rostriformis bugensis) is crucial to mitigating the economic and environmental impacts of an infestation. Plankton tow sampling is a common method used for early detection of dreissenid mussels, but little is known about the sampling intensity required for a high probability of early detection using the method. We used implicit dynamic occupancy models to estimate plankton tow detection probabilities of dreissenid mussels from a long-term data set containing plankton tow samples collected across central and western United States. We fit models using a) the entire data set, including water bodies with unknown occupancy status in addition to heavily infested water bodies, b) a data subset that included water bodies with paired water temperature data, and c) a data subset that included water bodies with lower dreissenid densities. For the entire data set, we found that estimated detection probabilities varied by water body size and ranged from approximately 0.10 to 0.86. For the water temperature subset, we observed the same pattern between detection probability and water body size as we did for the full data but additionally found that the estimated detection probabilities were much higher when water temperatures were above 12 °C. For the lower dreissenid density subset, we found that the estimated probability of detecting dreissenid mussels with a single aggregated plankton tow sample was near zero. Given these estimates, we conclude that the number of aggregated plankton tow samples taken per water body in the data is far fewer than the number needed to ensure a high probability of detecting dreissenid mussels, especially if they are at low densities. We summarize the analyses with a discussion of plankton tow sampling protocol changes needed to improve estimates of dreissenid detection probabilities. [ABSTRACT FROM AUTHOR]

Interior cutthroat trout occupy small fractions of their historic ranges and existing populations often are relegated to headwater habitats. Conservation requires balancing protection for isolated genetically pure populations with restoration of migratory life histories by reconnecting corridors between headwater and mainstem habitats. Identification of alternative life history strategies within a population is critical to these efforts. We tested the application of nitrogen stable isotopes to discern fluvial from resident Bonneville cutthroat trout (BCT; Oncorhynchus clarkii utah) in a headwater stream. Fluvial BCT migrate from headwater streams with good water quality to mainstem habitats with impaired water quality. Resident BCT remain in headwater streams. We tested two predictions: (i) fluvial BCT have a higher δ[sup.15]N than residents, and (ii) fluvial BCT δ[sup.15]N reflects diet and δ[sup.15]N enrichment characteristics of mainstem habitats. We found that fluvial δ[sup.15]N was greater than resident δ[sup.15]N and that δ[sup.15]N was a better predictor of life history than fish size. Our data also showed that fluvial and resident BCT had high diet overlap in headwater sites and that δ[sup.15]N of lower trophic levels was greater in mainstem sites than in headwater sites. We conclude that the high δ[sup.15]N values of fluvial BCT were acquired in mainstem sites. Les truites fardees de l'interieur du continent n'occupent plus que de petites portions de leur aire de repartition du passe et les populations actuelles sont souvent confinees aux habitats d'amont. Leur conservation necessite un equilibre entre la protection des populations isolees genetiquement pures et le retablissement du cycle biologique migrateur en restituant les corridors qui relient les habitats d'amont et ceux du cours principal. Il essentiel dans ces efforts d'identifier les strategies de rechange des cycles biologiques au sein des populations. Nous avons teste l'utilisation des isotopes stables d'azote pour reconnaitre les formes fluviales et residentes de la truite fardee de Bonneville (BCT; Oncorhynchus clarkii utah) dans un cours d'eau d'amont. Les BCT fluviales migrent des cours d'eau d'amont a qualite d'eau superieure vers les habitats du cours principal qui ont une qualite d'eau degradee. Les BCT residentes demeurent dans les cours d'eau d'amont. Nous avons verifie deux predictions: (i) les BCT fluviales ont une valeur de δ[sup.15]N plus elevee que celle des residentes et (ii) les valeurs de δ[sup.15]N des BCT fluviales refletent leur alimentation et l'enrichissement en δ[sup.15]N caracteristique des habitats du cours principal. Nous observons que le δ[sup.15]N des truites fluviales est plus eleve que le δ[sup.15]N des residentes et que δ[sup.15]N est une meilleure variable explicative du cycle biologique que ne l'est la taille du poisson. Nos donnees montrent aussi que les BCT fluviales et residentes ont un fort chevauchement de regime alimentaire dans les sites d'amont et que les valeurs de δ[sup.15]N des niveaux trophiques inferieurs sont plus elevees dans les sites du cours principal que dans les sites d'amont. Nous en concluons que les valeurs elevees de δ[sup.15]N des BCT fluviales ont ete acquises dans les sites du cours principal. [Traduit par la Redaction], Introduction Long-distance movements (LDMs) of individuals influence fundamental ecological and evolutionary processes, including population persistence and gene flow (e.g., Gross 1987; Lowe et al. 2006). However, the frequency and scale [...]

Environmental (e)DNA tools are sensitive and cost-effective for early detection of invasive species. However, the uncertainty associated with the interpretation of positive eDNA detections makes it challenging to determine appropriate natural resource management responses. Multiple sources of error can give rise to positive detections of eDNA in a sample when individuals of that species are not present at the site or a widespread infestation is not imminent. Acting on an erroneous eDNA inference could result in needless costs or reductions in desirable resources. Alternatively, failure to rapidly act on eDNA results that truly indicate invader presence could compound negative impacts and lead to high, long-term costs to manage infestations. We used a structured decision making (SDM) process, which incorporates tradeoffs and uncertainties, to evaluate appropriate response actions following hypothetical eDNA detections of invasive dreissenid mussel (Dreissena spp.) eDNA in Jordanelle Reservoir, Utah (USA). We worked with decision-makers and stakeholders to identify objectives and discrete management action alternatives to assess consequences and tradeoffs. Alternatives ranged from no action to intensive and expensive control efforts. The best performing alternative was delayed containment described by immediate attempts to confirm the eDNA detections using nonmolecular sampling techniques followed by mandatory watercraft exit inspections to prevent dreissenid mussel spread to regional water bodies. Non-molecular sampling increased public support for management by demonstrating a commitment to monitor the invasion state before action, whereas containment decreased likelihood of regional spread to other waters. Delayed containment had the lowest downside risk, and the highest upside gains relative to other alternative actions. Sensitivity analyses showed our results to be robust to parameter and outcome uncertainty. [ABSTRACT FROM AUTHOR]

Environmental (e)DNA methods have enabled rapid, sensitive and specific inferences of taxa presence throughout diverse fields of ecological study. However, use of eDNA results for decision‐making has been impeded by uncertainties associated with false positive tests putatively caused by sporadic or systemic contamination. Sporadic contamination is a process that is inconsistent across samples and systemic contamination occurs consistently over a group of samples. Here, we used empirical data and laboratory experiments to (i) estimate the sporadic contamination rate for each stage of a common, targeted eDNA workflow employing best practice quality control measures under simulated conditions of rare and common target DNA presence, (ii) determine the rate at which negative controls (i.e., "blanks") detect varying concentrations of systemic contamination, and (iii) estimate the effort that would be required to consistently detect sporadic and systemic contamination. Sporadic contamination rates were very low across all eDNA workflow steps, and, therefore, an intractably high number of negative controls (>100) would be required to determine occurrence of sporadic contamination with any certainty. Contrarily, detection of intentionally introduced systemic contamination was more consistent; therefore, very few negative controls (<5) would be needed to consistently alert to systemic contamination. These results have considerable implications to eDNA study design when resources for sample analyses are constrained. [ABSTRACT FROM AUTHOR]