Perry, Stephen

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
Enhancing and Connecting Wild Brook Trout Populations in VT’s West Mountain Wildlife Management Area: This project will replace one stream crossing and remove another that currently prevents the movement of fish and other aquatic organisms in the West Mountain Pond watershed. The new structures will open 2.5 stream miles and permit fish and other aquatic organisms to move in search of cold water refugia, food, and spawning habitat. In addition, woody habitat will be restored to 1.25 stream. Total project cost is $143,000.
Located in Projects / 2006 - 2018 Projects / 2017 Projects
Enhancing and connecting wild brook trout populations in VT’s West Mountain Wildlife Management Area: Project application
Located in Projects / … / 2017 Projects / Enhancing and Connecting Wild Brook Trout Populations in VT’s West Mountain Wildlife Management Area
Enhancing Connectivity in the Androscoggin River Watershed, ME_FY08 Project: This project improved fish passage and assessed fish passage barriers within the watershed.
Located in Projects / Project Completion Reports
Enhancing Connectivity in the West Branch Narraguagus River, ME_FY11 Project: This project replaced degraded road-stream crossings (culverts) with bankfull channel width spanning open bottom structures.
Located in Projects / Project Completion Reports
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
Estimating size-specific brook trout abundance in continuously sampled headwater streams using Bayesian mixed models with zero inflation and overdispersion: We examined habitat factors related to reach-scale brook trout Salvelinus fontinalis counts of four size classes in two headwater stream networks within two contrasting summers in Connecticut, USA. Two study stream networks (7.7 and 4.4 km) were surveyed in a spatially continuous manner in their entirety, and a set of Bayesian generalised linear mixed models was compared. Trout abundance was best described by a zero-inflated overdispersed Poisson model. The effect of habitat covariates was not always consistent among size classes and years. There were nonlinear relationships between trout counts and stream temperature in both years. Colder reaches harboured higher trout counts in the warmer summer of 2008, but this pattern was not observed in the cooler and very wet summer of 2009. Amount of pool habitat was nearly consistently important across size classes and years, and counts of the largest size class were correlated positively with maximum depth and negatively with stream gradient. Spatial mapping of trout distributions showed that reaches with high trout counts may differ among size classes, particularly between the smallest and largest size classes, suggesting that movement may allow the largest trout to exploit spatially patchy habitats in these small headwaters.
Located in Science and Data / Brook Trout Related Publications
Evaluating the Barrier Assessment Technique Derived from FishXing Software and the Upstream Movement of Brook Trout through Road Culverts: Anthropogenic barriers to fish passage, such as culverts and dams, are major factors impeding the persistence and recovery of aquatic species. Considerable work has focused on mitigating these impacts; however, activities associated with measuring and restoring connectivity of aquatic ecosystems often face challenges in determining the passability of barriers by aquatic species. Hydrological modeling software that incorporates biological aspects of a focal species is often used as a relatively inexpensive method for assessing barrier passability for restoration decisions. However, the biological relevance of these approaches remains to be rigorously tested. We assessed passage rates of PIT-tagged Brook Trout Salvelinus fontinalis through four road culverts and adjacent reference sites (unaltered areas of the streams) on the island of Newfoundland to determine whether upstream passage through road culverts was more restrictive than unaltered reference areas of the stream. Next, we examined the usefulness of barrier passability predictions derived from FishXing software by comparing them with in situ movement data for this species. Brook Trout passage for three of the four reference sites had a significantly higher range of passable stream flows compared with that for culverts, indicating the presence of velocity barriers in culverts. However, FishXing predictions of suitable fish passage discharges were conservative, and tagged fish successfully navigated partial barriers that were at least 2–3 times the upper limits of stream flow predicted to allow successful passage. The results of our study show a clear need for an improved understanding of fish movement through these structures so that barrier assessment techniques can be refined. The implications of not doing so may lead to restoration actions that result in limited biological benefit.
Located in Science and Data / Brook Trout Related Publications
Evaluating the Trade-Offs between Invasion and Isolation for Native Brook Trout and Nonnative Brown Trout in Pennsylvania Streams: A popular conservation strategy for native trout species in western North America is to prevent invasions by nonnative trout by installing barriers that isolate native trout populations into headwater streams. In eastern North America, native Brook Trout Salvelinus fontinalis are frequently replaced in coolwater habitats by nonnative Brown Trout Salmo trutta and relegated to small headwater streams. In this study, we compared the effects of isolation and invasion by nonnative Brown Trout on the distribution and demographic structure of Brook Trout populations from 78 trout streams in northwestern Pennsylvania. The Brook Trout and Brown Trout distributions varied in predictable ways along the stream size gradient, with Brown Trout becoming dominant in larger streams. However, there was a prominent barrier effect, with streams 12 times more likely to have Brook Trout than Brown Trout when a downstream barrier was present between the sample site and the nearest Brown Trout stocking location. In comparison, 91% of the streams with Brown Trout had no downstream barrier, suggesting that barriers are important in creating refugia for Brook Trout. Brown Trout also appeared to have a negative impact on Brook Trout population demographics, as Brook Trout populations in sympatry with Brown Trout had fewer age-classes and lower population densities than allopatric Brook Trout populations. Isolating Brook Trout to small headwater streams with downstream barriers that prevent Brown Trout invasion could be a viable conservation strategy in regions where barriers would serve to reduce the negative impacts from Brown Trout. Since barriers could further fragment local Brook Trout populations, however, they would need to be strategically placed to allow for seasonal movements to maintain metapopulation structure and ensure population persistence.
Located in Science and Data / Brook Trout Related Publications
Evaluation of Catch-and-Release Regulations on Brook Trout in Pennsylvania Streams: In 2004, the Pennsylvania Fish and Boat Commission implemented catch-and-release (CR) regulations on headwater stream systems to determine if eliminating angler harvest would result in an increase in the number of adult (≥100 mm) or large (≥175 mm) Brook Trout Salvelinus fontinalis. Under the CR regulations, angling was permitted on a year-round basis, no Brook Trout could be harvested at any time, and there were no tackle restrictions. A before-after–control-impact design was used to evaluate the experimental regulations. Brook Trout populations were monitored in 16 treatment (CR regulations) and 7 control streams (statewide regulations) using backpack electrofishing gear periodically for up to 15 years (from 1990 to 2003 or 2004) before the implementation of the CR regulations and over a 7–8-year period (from 2004 or 2005 to 2011) after implementation. We used Poisson mixed models to evaluate whether electrofishing catch per effort (CPE; catch/100 m2) of adult (≥100 mm) or large (≥175 mm) Brook Trout increased in treatment streams as a result of implementing CR regulations. Brook Trout CPE varied among sites and among years, and there was no significant effect (increase or decrease) of CR regulations on the CPE of adult or large Brook Trout. Results of our evaluation suggest that CR regulations were not effective at improving the CPE of adult or large Brook Trout in Pennsylvania streams. Low angler use, high voluntary catch and release, and slow growth rates in infertile headwater streams are likely the primary reasons for the lack of response.
Located in Science and Data / Brook Trout Related Publications

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