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File Troff document Fall and Early Winter Movement and Habitat Use of Wild Brook Trout
Brook Trout Salvelinus fontinalis populations face a myriad of threats throughout the species’ native range in the eastern United States. Understanding wild Brook Trout movement patterns and habitat requirements is essential for conserving existing populations and for restoring habitats that no longer support self-sustaining populations. To address uncertainties related to wild Brook Trout movements and habitat use, we radio-tracked 36 fish in a headwater stream system in central Pennsylvania during the fall and early winter of 2010–2011.We used generalized additive mixed models and discrete choice models with random effects to evaluate seasonal movement and habitat use, respectively. There was variability among fish in movement patterns; however, most of the movement was associated with the onset of the spawning season and was positively correlated with fish size and stream flow. There was heterogeneity among fish in selection of intermediate (0.26–0.44 m deep) and deep (0.44–1.06 m deep) residual pools, while all Brook Trout showed similar selection for shallow (0.10–0.26 m) residual pools. There was selection for shallow residual pools during the spawning season, followed by selection for deep residual pools as winter approached. Brook Trout demonstrated a threshold effect for habitat selection with respect to pool length, and selection for pools increased as average pool length increased up to approximately 30 m, and then use declined rapidly for pool habitats greater than 30 m in length. The heterogeneity and nonlinear dynamics of movement and habitat use of wild Brook Trout observed in this study underscores two important points: (1) linear models may not always provide an accurate description of movement and habitat use, which can have implications for management, and (2) maintaining stream connectivity and habitat heterogeneity is important when managing self-sustaining Brook Trout populations.
Located in Science and Data / Brook Trout Related Publications
File The temperature–productivity squeeze: constraints on brook trout growth along an Appalachian river continuum
We tested the hypothesis that brook trout growth rates are controlled by a complex interaction of food availability, water temperature, and competitor density. We quantified trout diet, growth, and consumption in small headwater tributaries characterized as cold with low food and high trout density, larger tributaries characterized as cold with moderate food and moderate trout density, and large main stems characterized as warm with high food and low trout density. Brook trout consumption was highest in the main stem where diets shifted from insects in headwaters to fishes and crayfish in larger streams. Despite highwater temperatures, trout growth rates also were consistently highest in the main stem, likely due to competitively dominant trout monopolizing thermal refugia. Temporal changes in trout density had a direct negative effect on brook trout growth rates. Our results suggest that competition for food constrains brook trout growth in small streams, but access to thermal refugia in productive main stem habitats enables dominant trout to supplement growth at a watershed scale. Brook trout conservation in this region should seek to relieve the ‘‘temperature–productivity squeeze,’’ whereby brook trout productivity is constrained by access to habitats that provide both suitable water temperature and sufficient prey.
Located in Science and Data / Brook Trout Related Publications
File A regional neural network ensemble for predicting mean daily river water temperature
Water temperature is a fundamental property of river habitat and often a key aspect of river resource management, but measurements to characterize thermal regimes are not available for most streams and rivers. As such, we developed an artificial neural network (ANN) ensemble model to predict mean daily water temperature in 197,402 individual stream reaches during the warm season (May–October) throughout the native range of brook trout Salvelinus fontinalis in the eastern U.S. We compared four models with different groups of predictors to determine how well water temperature could be predicted by climatic, landform, and land cover attributes, and used the median prediction from an ensemble of 100 ANNs as our final prediction for each model. The final model included air temperature, landform attributes and forested land cover and predicted mean daily water temperatures with moderate accuracy as determined by root mean squared error (RMSE) at 886 training sites with data from 1980 to 2009 (RMSE = 1.91 C). Based on validation at 96 sites (RMSE = 1.82) and separately for data from 2010 (RMSE = 1.93), a year with relatively warmer conditions, the model was able to generalize to new stream reaches and years. The most important predictors were mean daily air temperature, prior 7 day mean air temperature, and network catchment area according to sensitivity analyses. Forest land cover at both riparian and catchment extents had relatively weak but clear negative effects. Predicted daily water temperature averaged for the month of July matched expected spatial trends with cooler temperatures in headwaters and at higher elevations and latitudes. Our ANN ensemble is unique in predicting daily temperatures throughout a large region, while other regional efforts have predicted at relatively coarse time steps. The model may prove a useful tool for predicting water temperatures in sampled and unsampled rivers under current conditions and future projections of climate and land use changes, thereby providing information that is valuable to management of river ecosystems and biota such as brook trout.
Located in Science and Data / Brook Trout Related Publications
File chemical/x-pdb Quantifying the effect of semi-natural riparian cover on stream temperatures: implications for salmonid habitat management
Previous studies examining the effects of riparian cover on stream temperatures have led to highly variable findings. In an attempt to reduce these uncertainties, this study examines the relationship between stream temperature variability and local climatic conditions over discrete 300-m sections of a watercourse. Seventeen stream sections were chosen within the Slaney catchment on the basis of riparian cover and size. Continuous monitoring over a 2-year period from May 2010 found that riparian cover had a measurable cooling effect on water temperatures at small spatial scales. The magnitude of this effect was dependent on stream size and local climactic conditions.
Located in Science and Data / Brook Trout Related Publications
File Efficacy of Environmental DNA to Detect and Quantify Brook Trout Populations in Headwater Streams of the Adirondack Mountains, New York
Environmental DNA (eDNA) analysis is rapidly evolving as a tool for monitoring the distributions of aquatic species. Detection of species’ populations in streams may be challenging because the persistence time for intact DNA fragments is unknown and because eDNA is diluted and dispersed by dynamic hydrological processes. During 2015, the DNA of Brook Trout Salvelinus fontinalis was analyzed from water samples collected at 40 streams across the Adirondack region of upstate New York, where Brook Trout populations were recently quantified. Study objectives were to evaluate different sampling methods and the ability of eDNA to accurately predict the presence and abundance of resident Brook Trout populations. Results from three-pass electrofishing surveys indicated that Brook Trout were absent from 10 sites and were present in low (<100 fish/0.1 ha), moderate (100–300 fish/0.1 ha), and high (>300 fish/0.1 ha) densities at 9, 11, and 10 sites, respectively. The eDNA results correctly predicted the presence and confirmed the absence of Brook Trout at 85.0–92.5% of the study sites; eDNA also explained 44% of the variability in Brook Trout population density and 24% of the variability in biomass. These findings indicate that eDNA surveys will enable researchers to effectively characterize the presence and abundance of Brook Trout and other species’ populations in headwater streams across the Adirondack region and elsewhere.
Located in Science and Data / Brook Trout Related Publications
File Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis
Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout (Salvelinus fontinalis) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection N0.99 at densities of ≥3 fish per 100 m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.
Located in Science and Data / Brook Trout Related Publications
File application/x-troff-ms A Protocol for Collecting Environmental DNA Samples From Streams
Environmental DNA (eDNA) is DNA that has been released by an organism into its environment, such that the DNA can be found in air, water, or soil. In aquatic systems, eDNA has been shown to provide a sampling approach that is more sensitive for detecting target organisms faster, and less expensively than previous approaches. However, eDNA needs to be sampled in a manner that has been tested and found effective and, because single copies of target DNA are detected reliably, rigorous procedures must be designed to avoid sample contamination. Here we provide the details of a sampling protocol designed for detecting fish. This protocol, or very similar prototypes, has been used to collect data reported in multiple peer reviewed journal articles and from more than 5,000 additional samples at the time of publication. This process has been shown to be exceedingly sensitive and no case of field contamination has been detected. Over time, we have refined the process to make it more convenient. Our policy at the National Genomics Center for Wildlife and Fish Conservation is to provide collaborators with kits that contain all of the materials necessary to properly collect and store eDNA samples. Although the instructions in this protocol assume that the collaborator will have this same equipment, we also describe how users can create their own kit, and where we think there is flexibility in the equipment used.
Located in Science and Data / Brook Trout Related Publications
File D source code Environmental DNA Sampling Informs Fish Eradication Efforts: Case Studies and Lessons Learned
Worldwide, freshwater ecosystems are threatened by invasive species, resulting in adverse effects on infrastructure, economy, recreation, and native aquatic communities. In stream settings, chemical piscicides can be an effective tool for eradicating invasive fishes. However, chemical treatments are expensive and time consuming, and they do not discriminate between invasive and native species in a system. Therefore, managers would ideally limit treatment to only the area occupied by the invasive species. Because traditional survey methods may not accurately detect individuals in low abundance (e.g., at the edge of their distribution, or following an eradication effort), chemical treatments may be applied more broadly and more often than is necessary to ensure complete coverage. Furthermore, inadequate post-treatment sampling can fail to detect survivors of a treatment. As a result, managers may erroneously conclude that eradication was successful, leaving the ecosystem vulnerable to reestablishment by the invader. More sensitive sampling tools should allow for more precise definition of the treatment area and more accurate evaluation of project success. This would reduce project costs and overall effects on native species. Here, we illustrate how environmental DNA (eDNA) sampling addressed these challenges through three case studies, each of which used eDNA sampling to inform the removal of Brook Trout Salvelinus fontinalis in small streams. We found that eDNA methods can be informative throughout all stages of eradication projects in stream settings. It can assist with delimiting the population prior to treatment, provide detailed location data on surviving target individuals, and serve as an efficient and relatively inexpensive monitoring tool to assess long-term treatment efficacy. When combined with traditional survey tools, such as electrofishing, eDNA sampling may help reduce the size and number of treatments that are necessary to reach project goals. This translates directly to increased efficacy of treatments, reduced labor and cost, and reduced adverse effects on the native community.
Located in Science and Data / Brook Trout Related Publications
File An Economic Analysis of Improved Road‐Stream Crossings
Road‐stream crossings, which include culverts and bridges, are an essential element of our transportation networks, allowing roads to pass over rivers and streams. Our communities and our economies depend on functioning road networks and safe crossings. We also depend on healthy rivers and streams for clean water, recreation, and a host of other benefits, and we are learning more about the relationships between road‐stream crossing designs and their effect on natural areas. Undersized or poorly designed crossings fragment streams and disrupt the natural movement of water, sediment and aquatic organisms, causing erosion and degraded habitat. The most problematic of these crossings prevent aquatic organisms, such as brook trout, from accessing the upstream habitat they need to survive and reproduce. Yet crossings can be designed to avoid these problems. Improved road‐stream crossings deliver social, economic and ecological benefits and are a key element of adapting our infrastructure to a changing climate. Unfortunately, their initial cost can be a significant obstacle for highway departments with limited budgets.
Located in Science and Data / Brook Trout Related Publications
File Technical Guide for Field Practitioners: Understanding and Monitoring Aquatic Organism Passage at Road-Stream Crossings
Stream connectivity has become increasingly important for river restoration and fish-habitat improvement projects (Fullerton et al. 2010) amidst increasing evidence that it plays a vital role in supporting aquatic organism populations (Roni et al. 2002; Gibson et al. 2005) and species diversity (Nislow et al. 2011). Recent emphasis on identifying and removing barriers in order to restore aquatic organism passage (AOP) is based on well-documented negative effects of road-stream crossings on fish (Rieman et al. 1997; Hudy et al. 2005) and the potential for cost-effective restoration of aquatic habitat. However, challenges remain in identifying barriers and prioritizing road-stream crossings for remediation. The U.S. Department of Agriculture Forest Service (USFS) has been working to stream-line the process of identifying and remediating road-stream crossings that are inadequate for AOP.
Located in Science and Data / Brook Trout Related Publications
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