Perry, Stephen

SEACAP: Southeast Aquatic Connectivity Assessment Project: Assessing the ecological impact of dams on Southeastern rivers: The Southeast Aquatic Connectivity Assessment Project (SEACAP) grew out of and builds on the conceptual framework of the Chesapeake Fish Passage Prioritization Project and the Northeast Aquatic Connectivity Project.
Located in Science and Data / Brook Trout Related Publications
Northeast Aquatic Connectivity - An Assessment of Dams on Northeastern Rivers: Throughout the Northeast, hundreds of dams have been removed and hundreds of culverts have been replaced or retrofitted over the last two decades in projects where ecological restoration was a goal. To many working in the field of aquatic resource management it is apparent that given likely future constraints on availability of funds and staffing, it will be critical to be more strategic about investments in connectivity restoration projects. One approach to strategic investment is to assess the likely ecological “return on investment” associated with connectivity restoration. In order to complete an assessment at the regional scale, the Northeast Association of Fish and Wildlife Agencies (NEAFWA) awarded the Nature Conservancy (TNC) a 2007 Regional Conservation Needs (RCN) Grant. This RCN grant was designed to have TNC support state resource agencies in the Northeast U.S. (fish and wildlife, marine fisheries, dam safety, etc.) in efforts to strategically reconnect fragmented river, stream, coastal, reservoir, lake and estuarine habitat by removing or bypassing key barriers to fish passage. The primary ecological goal of mitigating fish passage barriers is to enhance populations of fish including anadromous fish, coldwater species, and other species of greatest conservation need (SGCN).
Located in Science and Data / Brook Trout Related Publications
Modified Culvert Inventory and Assessment Protocol: This culvert inventory and assessment method is a modified version of the National Inventory and Assessment Procedure (NIAP; Clarkin et al 2003) developed to collect data needed to run coarse filter evaluations of fish passage (Coffman 2005).
Located in Science and Data / Brook Trout Related Publications
Fisheries - Responding to Drought and Water Challenges: A presentation of coldwater fisheries and climate adaptation case studies in the Eastern and Western United States.
Located in The Story of Wild Brook Trout / Brook Trout Video and Webinar Gallery
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
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
Sensitivity and Vulnerability of Brook Trout Populations to Climate Change: Predicting future brook trout Salvelinus fontinalis distributions at the population scale under various climate scenarios is of interest to the Eastern Brook Trout Joint Venture. Previous larger scale models have been useful in highlighting the potential threat; however, the predicted air and water temperature errors associated with these models makes predictions of the persistence of individual brook trout populations problematic. We directly measured paired air and water temperatures in watersheds (N = 77) containing reproducing populations of brook trout in Virginia. We found that paired air and water temperature relationships are highly variable among patches but are a useful dataset to classify sensitivity and vulnerability of existing brook trout patches. We developed a classification system using sensitivity and vulnerability metrics that classified sampled brook trout habitats into four categories (High Sensitivity- High Vulnerability (51.9% ); High Sensitivity-Low Vulnerability (10.4 % ); Low Sensitivity-High Vulnerability (7.8 % ); Low Sensitivity-Low Vulnerability (29.9 % ). Our direct measurement approach identified potential refugia for brook trout at lower elevations and with higher air temperatures than previous larger scale modeling efforts. Our sensitivity and vulnerability groupings should be useful for managers making investment decisions in protecting and restoring brook trout.
Located in Science and Data / Brook Trout Related Publications
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
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
Sampling strategies for estimating brook trout effective population size: The influence of sampling strategy on estimates of effective population size (Ne) from single-sample genetic methods has not been rigorously examined, though these methods are increasingly used. For headwater salmonids, spatially close kin association among age-0 individuals suggests that sampling strategy (number of individuals and location from which they are collected) will influence estimates of Ne through family representation effects. We collected age-0 brook trout by completely sampling three headwater habitat patches, and used microsatellite data and empirically parameterized simulations to test the effects of different combinations of sample size (S = 25, 50, 75, 100, 150, or 200) and number of equally-spaced sample starting locations (SL = 1, 2, 3, 4, or random) on estimates of mean family size and effective number of breeders (Nb). Both S and SL had a strong influence on estimates of mean family size and ^ Nb; however the strength of the effects varied among habitat patches that varied in family spatial distributions. The sampling strategy that resulted in an optimal balance between precise estimates of Nb and sampling effort regardless of family structure occurred with S = 75 and SL = 3. This strategy limited bias by ensuring samples contained individuals from a high proportion of available families while providing a large enough sample size for precise estimates. Because this sampling effort performed well for populations that vary in family structure, it should provide a generally applicable approach for genetic monitoring of iteroparous headwater stream fishes that have overlapping generations.
Located in Science and Data / Brook Trout Related Publications / Stream Assessment and Monitoring

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