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Brook Trout Related Publications

Distribution, Status, and Land Use Characteristics of Subwatersheds within the Native Range of Brook Trout in the Eastern United States

We examined and summarized existing knowledge regarding the distribution and status of self- sustaining populations of brook trout Salvelinus fontinalis at the subwatershed scale cross their native range in the eastern USA. This region represents approximately 25% of the species’ entire native range and 70% of the U.S. portion of the native range. This assessment resulted in an updated and detailed range map of historical and current brook trout distribution in the study area.

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Assessment and predictive model for brook trout (Salvelinus fontinalis) population status in the eastern United States

Over the last 200 years, brook trout (Salvelinus fontinalis) have been subjected to numerous anthropogenic physical, chemical, and biological perturbations that threaten the long term viability of brook trout throughout their historic native range. The historic and current decline in brook trout populations and the threat of further habitat degradation have led to a desire to develop a large scale conservation strategy to protect and rehabilitate brook trout populations and habitat. Understanding both the current distribution of brook trout and the relationships between the brook trout population status and perturbations is essential to developing meaningful conservation strategies and tactics.

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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.

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Predicting Brook Trout Occurrence in Stream Reaches throughout their Native Range in the Eastern United States

The Brook Trout Salvelinus fontinalis is an important species of conservation concern in the eastern USA. We developed a model to predict Brook Trout population status within individual stream reaches throughout the species’ native range in the eastern USA. We utilized hierarchical logistic regression with Bayesian estimation to predict Brook Trout occurrence probability, and we allowed slopes and intercepts to vary among ecological drainage units (EDUs). Model performance was similar for 7,327 training samples and 1,832 validation samples based on the area under the receiver operating curve (»0.78) and Cohen’s kappa statistic (0.44). Predicted water temperature had a strong negative effect on Brook Trout occurrence probability at the stream reach scale and was also negatively associated with the EDU average probability of Brook Trout occurrence (i.e., EDU-specific intercepts). The effect of soil permeability was positive but decreased as EDU mean soil permeability increased. Brook Trout were less likely to occur in stream reaches surrounded by agricultural or developed land cover, and an interaction suggested that agricultural land cover also resulted in an increased sensitivity to water temperature. Our model provides a further understanding of how Brook Trout are shaped by habitat characteristics in the region and yields maps of stream-reach-scale predictions, which together can be used to support ongoing conservation and management efforts. These decision support tools can be used to identify the extent of potentially suitable habitat, estimate historic habitat losses, and prioritize conservation efforts by selecting suitable stream reaches for a given action. Future work could extend the model to account for additional landscape or habitat characteristics, include biotic interactions, or estimate potential Brook Trout responses to climate and land use changes.

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The Importance of Scale: Assessing and Predicting Brook Trout Status in its Southern Native Range

Occupancy models are of increasing interest to managers and natural resource decision makers. Assessment of status and trends, as well as the specific drivers influencing occupancy, both may change as a function of scale, and analyses conducted at multiple scales can help identify important mechanisms leading to changes in distributions. We analyzed extensive fine-scale occupancy data across the southern historic range of the brook trout, Salvelinus fontinalis to determine which landscape metrics and thresholds were useful in predicting brook trout presence across three relevant spatial scales and how brook trout occupancy varied by scale. Percentage occupancy declined markedly with increased spatial resolution, as 52% of watersheds (HUC10) but only 32% of subwatersheds (HUC12) and 14% of catchments (HUC14) were occupied. Across all three scales, habitats which were exclusively occupied by native brook trout (without non-native trout) were rare (<10%). CART models using GIS-derived landscape predictor variables were developed for three classification cases: Case 1:(brook trout; no brook trout), Case 2 (brook trout; non-native trout only; no trout), and Case 3 (brook trout only; brook and non-native trout; non-native trout only and no trout). Model results were sensitive to both scale and the number of classification categories with respect to classification accuracy, variable selection and variable threshold values. Classification accuracy tended to be lowest at the finest (catchment) scale potentially reflecting stochastic population processes and barriers to movement. Classification rates for the overall models were: Case 1: Watershed (80.19%); Subwatershed (85.06%); Catchment (71.13%); Case 2: Watershed (69.31%); Subwatershed (68.72%); Catchment (57.38%); Case 3: Watershed (58.91%); Subwatershed (59.83%); Catchment (47.59%). Our multiscale approach revealed soil permeability (positive) and atmospheric pollution (negative) to be important predictors. The predicted occupancy and observed status of brook trout appear to be influenced by the scale the data are collected and reported.

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Dynamics and regulation of the southern brook trout (Salvelinus fontinalis) population in an Appalachian stream

1. We used information theoretic statistics [Akaike’s Information Criterion (AIC)] and regression analysis in a multiple hypothesis testing approach to assess the processes capable of explaining long-term demographic variation in a lightly exploited brook trout population in Ball Creek, NC. We sampled a 100-m-long second-order site during both spring and autumn 1991–2004, using three-pass electrofishing. 2. Principle component analysis indicated that the site had lower average velocity, greater amounts of depositional substrata and lower amount of erosional substrata during the 1999–2002 drought than in non-drought years. In addition, drought years had lower flows, and lower variation in flows, than non-drought years. 3. Both young-of-the-year (YOY) and adult densities varied by an order of magnitude during the study. AIC analysis conducted on regressions of per capita rate of increase versus various population and habitat parameters for the population, adults and YOY, for both spring and autumn data sets, indicated that simple density dependence almost always was the only interpretable model with Akaike weights (wi) ranging from 0.262 to 0.836. 4. Growth analyses yielded more variable results, with simple density dependence being the only interpretable model for both adult spring data (wi = 0.999) and YOY autumn data (wi = 0.905), and positive density dependence (wi = 0.636) and simple density independence (wi = 0.241) representing interpretable models for spring YOY data. 5. We detected a significant stock–recruitment relationship between both spring and autumn densities of adults in year t and autumn YOY density in year t + 1. Finally, spring YOY density was positively correlated with both autumn YOY density and spring mean YOY standard length (SL), suggesting that processes affecting recruitment show residual effects at least in the first year of life. This population appears to be regulated primarily by density dependent processes, although high flows also negatively affected mean SLs of YOY.

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Population Response to Habitat Fragmentation in a Stream-Dwelling Brook Trout Population

Fragmentation can strongly influence population persistence and expression of life-history strategies in spatially-structured populations. In this study, we directly estimated size-specific dispersal, growth, and survival of stream-dwelling brook trout in a stream network with connected and naturally-isolated tributaries. We used multiple-generation, individual-based data to develop and parameterize a size-class and location-based population projection model, allowing us to test effects of fragmentation on population dynamics at local (i.e., subpopulation) and system-wide (i.e., metapopulation) scales, and to identify demographic rates which influence the persistence of isolated and fragmented populations. In the naturally-isolated tributary, persistence was associated with higher early juvenile survival (,45% greater), shorter generation time (one-half) and strong selection against large body size compared to the open system, resulting in a stage-distribution skewed towards younger, smaller fish. Simulating barriers to upstream migration into two currently-connected tributary populations caused rapid (2–6 generations) local extinction. These local extinctions in turn increased the likelihood of system-wide extinction, as tributaries could no longer function as population sources. Extinction could be prevented in the open system if sufficient immigrants from downstream areas were available, but the influx of individuals necessary to counteract fragmentation effects was high (7–46% of the total population annually). In the absence of sufficient immigration, a demographic change (higher early survival characteristic of the isolated tributary) was also sufficient to rescue the population from fragmentation, suggesting that the observed differences in size distributions between the naturally-isolated and open system may reflect an evolutionary response to isolation. Combined with strong genetic divergence between the isolated tributary and open system, these results suggest that local adaptation can ‘rescue’ isolated populations, particularly in one-dimensional stream networks where both natural and anthropogenically-mediated isolation is common. However, whether rescue will occur before extinction depends critically on the race between adaptation and reduced survival in response to fragmentation.

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Population regulation of brook trout (Salvelinus fontinalis) in Hunt Creek, Michigan: a 50-year study

1. Fisheries models generally are based on the concept that strong density dependence exists in fish populations. Nonetheless, there are few examples of long-term density dependence in fish populations. 2. Using an information theoretical approach (AIC) with regression analyses, we examined the explanatory power of density dependence, flow and water temperature on the per capita rate of change and growth (annual mean total length) for the whole population, adults, 1+ and young-of-the-year (YOY) brook trout (Salvelinus fontinalis) in Hunt Creek, Michigan, USA, between 1951 and 2001. This time series represents one of the longest quantitative population data sets for fishes. 3. Our analysis included four data sets: (i) Pooled (1951–2001), (ii) Fished (1951–65), (iii) Unfished (1966–2001) and (iv) Temperature (1982–2001). 4. Principle component analyses of winter flow data identified a gradient between years with high mean daily winter flows, high daily maximum and minimum flows and frequent high flow events, and years with an opposite set of flow characteristics. Flows were lower during the Fished Period than during the Unfished Period. Winter temperature analyses elucidated a gradient between warm mean, warm minimum and maximum daily stream temperatures and a high number of minimum daily temperatures >6.1 C, and years with the opposite characteristics. Summer temperature analyses contrasted years with warm summer stream temperatures vs years with cool summer stream temperatures. 5. Both YOY and adult densities varied several-fold during the study. Regression analysis did not detect a significant linear or nonlinear stock–recruitment relationship. AIC analysis indicated that density dependence was present in 15 of 16 cases (four population segments · four data sets) for both per capita rate of increase (wi values 0.46–1.00) and growth data (wi values 0.28–0.99). The almost ubiquitous presence of density dependence in both population and growth data is concordant with results from other trout populations and other studies in Michigan.

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What predicts the use by brook trout (Salvelinus fontinalis) of terrestrial invertebrate subsidies in headwater streams?

1. Spatial subsidies are important resources for organisms in receiving habitats, particularly when production in those habitats is low. Terrestrial invertebrates provide a critical subsidy for trout, including eastern brook trout (Salvelinus fontinalis), but we have limited understanding of what causes input and use of these subsidies to vary among streams. 2. We predicted that forest successional stage would be an especially important driver of variation in terrestrial invertebrate subsidies to brook trout in headwater streams due to differences in terrestrial invertebrate biomass in early and late successional habitats. Specifically, we expected biomass of aerial invertebrates, those capable of dispersal to the stream, to be greater in early successional habitat than late successional habitat due to the nutrient-rich, herbaceous vegetation typical of early successional habitat. 3. We measured aerial terrestrial invertebrate biomass in early and late successional habitats, input to streams and use by resident brook trout in 12 first- and second-order catchments in northern New Hampshire, U.S.A. The study catchments represented a range of early successional habitat coverage (0–51.5%). We also measured a suite of reach-scale variables that might influence terrestrial invertebrate input and use by brook trout, including riparian forest conditions and benthic invertebrate biomass. 4. Within study catchments, aerial terrestrial invertebrate biomass and abundance were significantly higher in early successional habitats than late successional habitats. However, terrestrial invertebrate input to streams and use by brook trout were unrelated to per cent early successional habitat in the catchment, and to other catchment and riparian forest characteristics. These results indicate that the management for upland early successional habitat has little effect on terrestrial invertebrate subsidies to headwater streams and fish. 5. Surprisingly, benthic invertebrate biomass was the one significant predictor of per cent terrestrial invertebrates in brook trout diets. Use of terrestrial invertebrate subsidies declined with increasing benthic invertebrate biomass, suggesting that productivity in the aquatic environment influences the degree to which brook trout use terrestrial subsidies. Although subsidy inputs are controlled by the donor system, this study shows that use of these subsidies by consumers can be determined by conditions in the recipient habitat.

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Geomorphic, Flood, and Groundwater-Flow Characteristics of Bayfield Peninsula Streams, Wisconsin, and Implications for Brook-Trout Habitat

In 2002–03, the U.S. Geological Survey conducted a study of the geomorphic, flood, and groundwater-flow characteristics of five Bayfield Peninsula streams, Wisconsin (Cranberry River, Bark River, Raspberry River, Sioux River, and Whittlesey Creek) to determine the physical limitations for brook-trout habitat. The goals of the study were threefold: (1) to describe geomorphic characteristics and processes, (2) to determine how land-cover characteristics affect flood peaks, and (3) to determine how regional groundwater flow patterns affect base flow. The geomorphic characterization consisted of analyses of historical aerial photographs and General Land Office Survey notes, observations from helicopter video footage, surveys of valley cross sections, and coring. Sources of sediment were identified from the helicopter video and field surveys, and past erosion-control techniques were evaluated. Geomorphic processes, such as runoff sediment erosion, transport, and deposition, are driven by channel location within the drainage network, texture of glacial deposits, and proximity to postglacial lake shorelines; these processes have historically increased because of decreases in upland forest cover and channel roughness. Sources of sediment for all studied streams mainly came from bank, terrace, or bluff erosion along main stem reaches and along feeder tributaries that bisect main-stem entrenched valley sides. Bluff, terrace, and bank erosion were the major sources of sediment to Whittlesey Creek and the Sioux River. No active bluff erosion was observed on the Cranberry River or the Bark River but anecdotal information suggests that landslides occasionally happen on the Cranberry River. For the Bark River, sources of sediment were somewhat evenly divided among road crossings (bridges, culverts, and unimproved forest lanes), terrace erosion, bank erosion, and incision along upper main stems and feeder channels along valley sides. Evaluation of past erosion-control techniques indicated that bluffs were stabilized by a combination of artificial hardening and bioengineering of the bluff base and reducing mass wasting of the tops of the bluffs. Flood hydrographs for the Cranberry River were simulated for four land-cover scenarios—late 20th century (1992–93), presettlement (before 1870), peak agriculture (1928), and developed (25 percent urban). Results were compared to previous simulations of flood peaks for Whittlesey Creek and for North Fish Creek (southern adjacent basin to Whittlesey Creek). Even though most uplands are presently forested, flood peaks simulated for 1992–93 were 1.5 to 2 times larger than presettlement flood peaks. The increased flood peaks caused (1) increased incision along upper main stems and tributaries that bisect entrenched valley sides, (2) bluff and terrace erosion along reaches with entrenched valleys, (3) overbank deposition and bar formation in middle and lower main stems, and (4) aggradation in mouth areas. A base-flow survey was conducted and a groundwater-flow model was developed for the Bayfield Peninsula to delineate groundwater contributing areas. A deep aquifer system, which includes thick deposits of sand and the upper part of the bedrock, is recharged through the permeable sands in the center of the peninsula. Base flow is unevenly distributed among the Bayfield streams and depends on the amount of channel incision and the proximity of the channels to the recharge area and coarse outwash deposits. Groundwater contributing areas for the five streams do not coincide with surface-water-contributing areas. About 89 percent of total recharge to the deep aquifer system discharges to Bayfield streams; the remaining 11 percent directly discharges to Lake Superior. Historical land-cover changes have had negligible effects on groundwater-flow from the deep aquifer system. Available brook-trout habitat is dependent on the locations of groundwater upwellings, the sizes of flood peaks, and sediment loads. Management practices that focus on reducing or slowing runoff from upland areas and increasing channel roughness have potential to reduce flood peaks, erosion, and sedimentation and improve brook-trout habitat in all Bayfield Peninsula streams.

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Acid Mine Drainage and Effects on Fish Health and Ecology: A Review

Acid rock drainage (ARD) is produced by the oxidation of sulfide minerals, chiefly iron pyrite or iron disulfide (FeS2). This is a natural chemical reaction which can proceed when minerals are exposed to air and water. Acidic drainage is found around the world both as a result of naturally occurring processes and activities associated with land disturbances, such as highway construction and mining where acid-forming minerals are exposed at the surface of the earth. These acidic conditions can cause metals in geologic materials to dissolve, which can lead to impairment of water quality when acidic and used by terrestrial or aquatic organisms. metal laden discharges enter waters.

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Response of fish assemblages to declining acidic deposition in Adirondack Mountain lakes, 1984-2012

Adverse effects of acidic deposition on the chemistry and fish communities were evident in Adirondack Mountain lakes during the 1980s and 1990s. Fish assemblages and water chemistry in 43 Adirondack Long-Term Monitoring (ALTM) lakes were sampled by the Adirondack Lakes Survey Corporation and the New York State Department of Environmental Conservation during three periods (1984-87, 1994-2005, and 2008-12) to document regional impacts and potential biological recovery associated with the 1990 amendments to the 1963 Clean Air Act (CAA). We assessed standardized data from 43 lakes sampled during the three periods to quantify the response of fish-community richness, total fish abundance, and brook trout (Salvelinus fontinalis) abundance to declining acidity that resulted from changes in U.S. airquality management between 1984 and 2012. During the 28-year period, mean acid neutralizing capacity (ANC) increased significantly from 3 to 30 meq/L and mean inorganic monomeric Al concentrations decreased significantly from 2.22 to 0.66 mmol/L, yet mean species richness, all species or total catch per net night (CPNN), and brook trout CPNN did not change significantly in the 43 lakes. Regression analyses indicate that fishery metrics were not directly related to the degree of chemical recovery and that brook trout CPNN may actually have declined with increasing ANC. While the richness of fish communities increased with increasing ANC as anticipated in several Adirondack lakes, observed improvements in water quality associated with the CAA have generally failed to produce detectable shifts in fish assemblages within a large number of ALTM lakes. Additional time may simply be needed for biological recovery to progress, or else more proactive efforts may be necessary to restore natural fish assemblages in Adirondack lakes in which water chemistry is steadily recovering from acidification.

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Broad-Scale Patterns of Brook Trout Responses to Introduced Brown Trout in New York

Brook Trout Salvelinus fontinalis and Brown Trout Salmo trutta are valuable sport fish that coexist in many parts of the world due to stocking introductions. Causes for the decline of Brook Trout within their native range are not clear but include competition with Brown Trout, habitat alteration, and repetitive stocking practices. New York State contains a large portion of the Brook Trout’s native range, where both species are maintained by stocking and other management actions.We used artificial neural network models, regression, principal components analysis, and simulation to evaluate the effects of Brown Trout, environmental conditions, and stocking on the distribution of Brook Trout in the center of their native range. We found evidence for the decline of Brook Trout in the presence of Brown Trout across many watersheds; 22% of sampled reaches where both species were expected to occur contained only Brown Trout. However, a model of the direct relationship between Brook Trout and Brown Trout abundance explained less than 1% of data variation. Ordination showed extensive overlap of Brook Trout and Brown Trout habitat conditions, with only small components of the hypervolume (multidimensional space) being distinctive. Subsequent analysis indicated higher abundances of Brook Trout in highly forested areas, while Brown Trout were more abundant in areas with relatively high proportions of agriculture. Simulation results indicated that direct interactions and habitat conditions were relatively minor factors compared with the effects of repeated stocking of Brown Trout into Brook Trout habitat. Intensive annual stocking of Brown Trout could eliminate resident Brook Trout in less than a decade. Ecological differences, harvest behavior, and other habitat changes can exacerbate Brook Trout losses. Custom stocking scenarios with Brown Trout introductions at relatively low proportions of resident Brook Trout populations may be able to sustain healthy populations of both species within their present range.

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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.

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Impacts of Exotic Rainbow Trout on Habitat Use by Native Juvenile Salmonid Species at an Early Invasive Stage

The detrimental impact of introduced Rainbow Trout Oncorhynchus mykiss on native communities has been well documented around the world. Previous studies have focused on streams where the invasion has been successful and the species is fully established. In eastern Quebec, the invasion of Rainbow Trout is an ongoing process and, for now, there are few established populations. The presence of two native salmonids in these rivers, Atlantic Salmon Salmo salar and Brook Trout Salvelinus fontinalis, implies a risk of competition for habitat, despite the relatively low density of the Rainbow Trout populations, as all three species are known to use similar resources. In order to evaluate the strength of the interaction between the invading fish and the native species, we sampled nine rivers (five with Rainbow Trout and four free of Rainbow Trout) and characterized the habitat used by the three salmonids at the juvenile stage. River-scale analysis revealed that in invaded rivers, Rainbow Trout were associated with habitats characterized by closer proximity to the shoreline and by increasing shoreline cover. Estimates of habitat niche overlap integrating depth, water velocity, and substrate size revealed that niche overlap between Brook Trout and Atlantic Salmon significantly increased in the presence of Rainbow Trout. Furthermore, the two indigenous species preferred full cover in the absence of Rainbow Trout but in the presence of Rainbow Trout, which also preferred full cover, the indigenous species moved to more open habitats. Rainbow Trout showed a high growth rate, despite a size disadvantage at the beginning of the growing season, as compared with Atlantic Salmon and Brook Trout. It thus appears that even at an early stage of invasion, when its density is still low, Rainbow Trout significantly impact native salmonids.

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Conservation Genetics of Remnant Coastal Brook Trout Populations at the Southern Limit of Their Distribution: Population Structure and Effects of Stocking

We examined genetic variation within and among a group of remnant coastal brook trout Salvelinus fontinalis populations along the coast of the northeastern United States. These populations occur at the southern limits of anadromy for this species and could form the foundation of a restored anadromous metapopulation. We also tested for genetic introgression between these populations and the hatchery source that has been used to stock these sites. The overall FST for the natural populations at 12 microsatellite loci was 0.145 (95% confidence interval, 0.108–0.183), and D was 0.225 (0.208–0.243). On average, 94.6% of individuals were correctly assigned to the population where they were collected. Our results suggest that there is little gene flow even between geographically proximate populations. We found little evidence that repeated historic stocking from a known hatchery source has led to genetic introgression into these wild coastal brook trout populations. One hybrid individual appeared to be a backcross between an F1 and a hatchery individual. Another hybrid individual could not be classified. Our results suggest that nonintrogressed and potentially locally adapted populations of brook trout persist in several small coastal New England streams. These populations should be the focus of future efforts to restore anadromous brook trout in this region.

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The influence of land cover composition and groundwater on thermal habitat availability for brook trout populations

Brook charr (Salvelinus fontinalis) is a sentinel fish species that requires clean, cold water habitats generally resulting from landscapes that allow for surface water flows devoid of sediment and contaminants and high groundwater discharge of cold water. As such, brook charr are impacted by land cover changes that alter stream temperature regimes. We evaluated brook charr populations across their eastern and midwestern range in the United States with reference to thermal habitat availability in relationship to land cover and percent baseflow. We found that while forest cover does protect brook charr thermal habitat, high levels of groundwater discharge can allow for increased levels of agriculture within a watershed by keeping the water cold in spite of warm ambient summer temperatures. Our study concludes that with enhanced communication among land, water and fisheries managers, society can provide for sustainable stream salmonid populations despite increased threats on cold water resources.

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Individual behaviour and resource use of thermally stressed brook trout Salvelinus fontinalis portend the conservation potential of thermal refugia

Individual aggression and thermal refuge use were monitored in brook trout Salvelinus fontinalis in a controlled laboratory to determine how fish size and personality influence time spent in forage and thermal habitat patches during periods of thermal stress. On average, larger and more exploratory fish initiated more aggressive interactions and across all fish there was decreased aggression at warmer temperatures. Individual personality did not explain changes in aggression or habitat use with increased temperature; however, larger individuals initiated comparatively fewer aggressive interactions at warmer temperatures. Occupancy of forage patches generally declined as ambient stream temperatures approached critical maximum and fish increased thermal refuge use, with a steeper decline in forage patch occupancy observed in larger fish. These findings suggest that larger individuals may be more vulnerable to stream temperature rise. Importantly, even at thermally stressful temperatures, all fish periodically left the thermal refuge to forage. This indicates that the success of refugia at increasing population survival during periods of stream temperature rise may depend on the location of thermal refugia relative to forage locations within the larger habitat mosaic. These results provide insights into the potential for thermal refugia to improve population survival and can be used to inform predictions of population vulnerability to climate change.

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Linking movement and reproductive history of brook trout to assess habitat connectivity in a heterogeneous stream network

1. Defining functional connectivity between habitats in spatially heterogeneous landscapes is a particular challenge for small-bodied aquatic species. Traditional approaches (e.g. mark–recapture studies) preclude an assessment of animal movement over the life cycle (birth to reproduction), and movement of individuals may not represent the degree of gene movement for fecund species. 2. We investigated the degree of habitat connectivity (defined as the exchange of individuals and genes between mainstem and tributary habitats) in a stream brook trout (Salvelinus fontinalis) population using mark–recapture [passive integrated transponder (PIT) tags], stationary PIT-tag antennae and genetic pedigree data collected over 4 years (3425 marked individuals). We hypothesised that: (i) a combination of these data would reveal higher estimates of animal movement over the life cycle (within a generation), relative to more temporally confined approaches, and (ii) movement estimates of individuals within a generation would differ from between-generation movement of genes because of spatial variation in reproductive success associated with high fecundity of this species. 3. Over half of PIT-tagged fish (juveniles and adults) were recaptured within 20 m during periodic sampling, indicating restricted movement. However, continuous monitoring with stationary PIT-tag antennae revealed distinct peaks in trout movements in June and October–November, and sibship data inferred post-emergence movements of young-of-year trout that were too small to be tagged physically. A combination of these methods showed that a moderate portion of individuals (28–33%) moved between mainstem and tributary habitats over their life cycle. 4. Patterns of reproductive success varied spatially and temporally. The importance of tributaries as spawning habitat was discovered by accounting for reproductive history. When individuals born in the mainstem reproduced successfully, over 50% of their surviving offspring were inferred to have been born in tributaries. This high rate of gene movement to tributaries was cryptic, and it would have been missed by estimates based only on movement of individuals. 5. This study highlighted the importance of characterising animal movement over the life cycle for inferring habitat connectivity accurately. Such movements of individuals can contribute to substantial gene movements in a fecund species characterised by high variation in reproductive success.

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Brook Trout Movement in Response to Temperature, Flow, and Thermal Refugia within a Complex Appalachian Riverscape

We quantified movements of brook trout Salvelinus fontinalis and brown trout Salmo trutta in a complex riverscape characterized by a large, open-canopy main stem and a small, closed-canopy tributary in easternWest Virginia, USA. Our objectives were to quantify the overall rate of trout movement and relate movement behaviors to variation in streamflow, water temperature, and access to coldwater refugia. The study area experienced extremely high seasonal, yearly, and among-stream variability in water temperature and flow. The relative mobility of brook trout within the upper Shavers Fork watershed varied significantly depending on whether individuals resided within the larger main stem or the smaller tributary. The movement rate of trout inhabiting the main stem during summer months (50 m/d) was an order of magnitude higher than that of tributary fish (2 m/d). Movement rates of main-stem-resident brook trout during summer were correlated with the maximum water temperature experienced by the fish and with the fish’s initial distance from a known coldwater source. For main-stem trout, use of microhabitats closer to cover was higher during extremely warm periods than during cooler periods; use of microhabitats closer to cover during warm periods was also greater for main-stem trout than for tributary inhabitants. Main-stem-resident trout were never observed in water exceeding 19.5◦C. Our study provides some of the first data on brook trout movements in a large Appalachian river system and underscores the importance of managing trout fisheries in a riverscape context. Brook trout conservation in this region will depend on restoration and protection of coldwater refugia in larger river main stems as well as removal of barriers to trout movement near tributary and main-stem confluences.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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).

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Chesapeake Fish Passage Prioritization: An Assessment of Dams in the Chesapeake Bay Watershed

The Chesapeake Fish Passage Prioritization (CFPP or “the project”) project grew out of and builds on the conceptual framework of the Northeast Aquatic Connectivity.

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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.

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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.

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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).

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Is motivation important to brook trout passage through culverts?

Culverts can restrict movement of stream-dwelling fish. Motivation to enter and ascend these structures is an essential precursor for successful passage. However, motivation is challenging to quantify. Here, we use attempt rate to assess motivation of 447 brook trout (Salvelinus fontinalis) entering three culverts under a range of hydraulic, environmental, and biological conditions. A passive integrated transponder system allowed for the identification of passage attempts and success of individual fish. Attempt rate was quantified using time-to-event analysis allowing for time-varying covariates and recurrent events. Attempt rate was greatest during the spawning period, at elevated discharge, at dusk, and for longer fish. It decreased during the day and with increasing number of conspecifics downstream of the culvert. Results also show a positive correlation between elevated motivation and successful passage. This study enhances understanding of factors influencing brook trout motivation to ascend culverts and shows that attempt rate is a dynamic phenomenon, variable over time and among individuals. It also presents methods that could be used to investigate other species’ motivation to pass natural or anthropogenic barriers.

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Evaluation of Wild Brook Trout Populations in Vermont Streams

Wild brook trout populations in Vermont streams appeared to be relatively stable over a period of five decades as evidenced in this evaluation of 150 sites. Present-day brook trout populations sampled in 138 streams within 17 watersheds were characterized by abundant natural reproduction and multiple age-classes, including the contribution of older, larger fish. While most population measures were consistent between the two time periods, significantly higher densities of young-of-year brook trout were observed in current populations which may reflect improved environmental protections initiated since the 1950s. A decline in sympatric brown trout and rainbow trout sites also suggest that non-native trout populations have not appreciably expanded over the past 50 years.

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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.

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Movement Patterns of Brook Trout in a Restored Coastal Stream System in Southern Massachusetts

Populations of anadromous brook trout can be found from northern Canada into New England. It is believed that the extent of anadromy exhibited by coastal brook trout populations decreases with latitude, but the ecology and movements of the more southern populations are less studied. A 33-month acoustic telemetry study of anadromous brook trout (Salvelinus fontinalis) was conducted in a restored coastal stream and adjacent marine system in southeastern Massachusetts. Movement and migration patterns of 54 brook trout were investigated for individual differences and common features. Individuals exhibited a range of movement patterns. Some were more resident and only moved short distances, while others moved great distances covering the entire stretch of the stream (7.25 km) and moving into the marine environment. General Additive Mixed Models revealed that date was the major influence on brook trout movement between habitats and predicted peaks in movement in the spring and fall. Downstream movement peaked in the spring and in the fall, suggesting post-spawning feeding migration. Fish transitioned between habitats more often at new and full moons and when stream temperature was between 8 and 12 °C. Upstream transitions peaked as temperatures declined in winter 2011. Fifty percent of tagged brook trout were detected in the estuary during the study, suggesting that it is an important habitat for the population. In summer 2012, 14 tagged brook trout (20% of active tags) resided near one receiver at the head of the tide, which contained a thermal refugium in the form of a cold-water spring seep. Of the 84 tagged brook trout, 9.5% moved to the marine environment. Warm temperatures in saline Buttermilk Bay in the summer and cold temperatures in winter probably discourage some individuals from entering the marine environment. Compared to more northern coastal populations of brook trout, the Red Brook population appears to be less anadromous.

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Metabolic rates of embryos and alevin from a cold-adapted salmonid differ with temperature, population and family of origin: implications for coping with climate change

Early developmental stages of cold-adapted ectotherms such as brook trout (Salvelinus fontinalis) are at higher risk of mortality with increasing water temperatures. To determine the amount of variation present in early life, which may allow for potential adaptation to increasing temperature, we examined the routine metabolic rates (RMR) of wild-origin brook trout embryos and alevins reared at normal (5°C) and elevated (9°C) temperatures. The experiment was structured to examine variation in RMR within and among several levels of biological organization (family, population and ancestral type (native vs. mixed ancestry)). As expected, family and temperature variables were most important for predicting RMR and body mass, although population-level differences also existed when family was excluded for more detailed analysis. Additionally, body mass strongly influenced RMR at all life stages except for eyed embryos. When family identity was removed from the analysis, population became the most significant variable. Variation in RMR and mass within and among populations may indicate existing adaptive potential within and among brook trout populations to respond to predicted warming under climate change scenarios.

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Probabilistic measures of climate change vulnerability, adaptation action benefits, and related uncertainty from maximum temperature metric selection

Predictions of the projected changes in species distribution models and potential adaptation action benefits can help guide conservation actions. There is substantial uncertainty in projecting species distributions into an unknown future, however, which can undermine confidence in predictions or misdirect conservation actions if not properly considered. Recent studies have shown that the selection of alternative climate metrics describing very different climatic aspects (e.g., mean air temperature vs. mean precipitation) can be a substantial source of projection uncertainty. It is unclear, however, how much projection uncertainty might stem from selecting among highly correlated, ecologically similar climate metrics (e.g., maximum temperature in July, maximum 30-day temperature) describing the same climatic aspect (e.g., maximum temperatures) that is known to limit a species’ distribution. It is also unclear how projection uncertainty might propagate into predictions of the potential benefits of adaptation actions that might lessen climate change effects. We provide probabilistic measures of climate change vulnerability, adaptation action benefits, and related uncertainty stemming from the selection of four maximum temperature metrics for brook trout (Salvelinus fontinalis), a cold-water salmonid of conservation concern in the eastern U.S. Projected losses in suitable stream length varied by as much as 20% among alternative maximum temperature metrics for mid-century climate projections, which was similar to variation among three climate models. Similarly, the regional average predicted increase in brook trout occurrence probability under an adaptation action scenario of full riparian forest restoration varied by as much as 0.2 among metrics. Our use of Bayesian inference provides probabilistic measures of vulnerability and adaptation action benefits for individual stream reaches that properly address statistical uncertainty and can help guide conservation actions. Our study demonstrates that even relatively small differences in the definitions of climate metrics can result in very different projections and reveal high uncertainty in predicted climate change effects.

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Stream Assessment and Monitoring

Research publications related to assessing and monitoring streams.

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Brook Trout Related Climate Change Vulnerability Research

Research publications on Brook Trout vulnerability to climate change.

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Brook Trout Genetics Research

Research studies related to Brook Trout genetics.

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Chesapeake Bay Brook Trout Management Strategy-References

This folder contains the publications cited in the Chesapeake Bay Brook Trout Management Strategy (2015-2025).

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A new species of Myxobolus (Myxozoa: Bivalvulida) infecting the medulla oblongata and nerve cord of brook trout Salvelinus fontinalis in southern Appalachia (New River, NC, USA)

Myxobolus neurofontinalis n. sp. infects the brain and medulla oblongata of brook trout (Salvelinus fontinalis [Mitchill, 1814]) in the New River, western NC. It is the first species of Myxobolus described from the brook trout and resembles another congener (Myxobolus arcticus Pugachev and Khokhlov, 1979) that infects nerve tissue of chars (Salvelinus spp.). The new species differs from M. arcticus and all congeners bymyxospore dimensions and by having a mucous envelope and distinctive suturalmarkings. A phylogenetic analysis of the small subunit rDNA (18S) suggests that the new species shares a recent common ancestor with some isolates identified as M. arcticus and that the new species and its close relatives (except Myxobolus insidiosus Wyatt and Pratt, 1973) comprise a clade of salmonid nerve-infecting myxobolids. The phylogenetic analysis indicates that several isolates of “M. arcticus” (sensu lato) in GenBank are misidentified and distantly related to other isolates taken from the type host (Oncorhynchus nerka [Walbaum, 1792]) and from nearby the type locality (Kamchatka Peninsula, Russia). Serial histological sections of infected brook trout confirmed that myxospores of the new species are intercellular and infect nerve cord and medulla oblongata only. A single infected brook trout showed an inflammatory response characterized by focal lymphocytic infiltrates and eosinophilic granulocytes; however, the remaining 4 brook trout lacked evidence of a histopathological change or demonstrable host response. These results do not support the notion that this infection is pathogenic among brook trout.

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An updated geographic distribution of Myxobolus cerebralis (Hofer, 1903) (Bivalvulida: Myxobolidae) and the first diagnosed case of whirling disease in wild-caught trout in the south-eastern United States

Myxobolus cerebralis (Bivalvulida: Myxobolidae), the aetiological agent of salmonid whirling disease, was detected in 2 river basins of North Carolina during 2015, which initiated the largest spatial–temporal monitoring project for the disease ever conducted within the south-eastern United States (focused mainly in eastern Tennessee and western North Carolina). A total of 2072 rainbow trout Oncorhynchus mykiss, 1,004 brown trout Salmo trutta and 468 brook trout Salvelinus fontinalis were screened from 113 localities within 7 river basins during June 2017 through October 2019. Infections were detected by pepsin–trypsin digest, microscopy and the species-specific nested polymerase chain reaction (PCR) in 19 localities across 6 river basins. Myxospore morphology was indistinguishable from the published literature. In 2019, five rainbow trout that symptomatic for whirling disease (sloping neurocranium and lordosis) were captured and processed for histopathology. Myxospores were detected in the calvarial cartilage of two deformed trout with associated erosion of the cartilage consistent with reported whirling disease lesions. This is the first report of M. cerebralis in Tennessee and the first histologically confirmed cases of whirling disease in southern Appalachian (south-eastern United States) rivers and streams and expands the distribution of M. cerebralis throughout western North Carolina and eastern Tennessee.

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Wood placement in river restoration: fact, fiction, and future direction

Despite decades of research on wood in rivers, the addition of wood as a river restoration technique remains controversial. We reviewed the literature on natural and placed wood to shed light on areas of continued debate. Research on river ecology demonstrates that large woody debris has always been a natural part of most rivers systems. Although a few studies have reported high structural failure rates (>50%) of placed instream wood structures, most studies have shown relatively low failure rates (<20%) and that placed wood remains stable for several years, though long-term evaluations of placed wood are rare. The vast majority of studies on wood placement have reported improvements in physical habitat (e.g., increased pool frequency, cover, habitat diversity). Studies that have not reported improvements in physical habitat often found that watershed processes (e.g., sediment, hydrology, water quality) had not been addressed. Finally, most evaluations of fish response to wood placement have shown positive responses for salmonids, though few studies have looked at long-term watershed-scale responses or studied a wide range of species.

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Development of Genetic Baseline Information to Support the Conservation and Management of Wild Brook Trout in North Carolina

After centuries of declines, there is growing interest in conserving extant wild populations of Brook Trout Salvelinus fontinalis and reintroducing Brook Trout populations of native ancestry. A population genetic baseline can enhance conservation outcomes and promote restoration success. Consequently, it is important to document existing patterns of genetic variation across the landscape and translate these data into an approachable format for fisheries managers. We genotyped 9,507 Brook Trout representing 467 wild collections at 12 microsatellite loci to establish a genetic baseline for North Carolina, USA. Rarefied allelic richness (mean = 3.12) and observed heterozygosity (mean = 0.42), which reflect within-population diversity, were low to moderate relative to levels typically observed at higher latitudes. Effective population sizes (Ne) varied widely but were often very low (151 collections had an estimated Ne < 10). Despite decades of intensive stocking across the state, we found little to no evidence of hatchery introgression in most populations. Although genetic variation was significant at a variety of spatial scales (mean pairwise = urn:x-wiley:02755947:media:nafm10569:nafm10569-math-0001 0.73), substantial genetic variation occurred between patches within individual watersheds. Analysis of molecular variance indicated that a substantial portion (28.5%) of the observed genetic variation was attributable to differences among populations, with additional genetic variation among hydrologic unit codes (HUCs; 16.0, 16.6, 12.1, and 9.4% of the overall variation among 12-, 10-, 8-, and 6-digit HUCs, respectively). We discuss a suite of potential applications for this type of genetic data to enhance management outcomes, such as conservation prioritization and selection of source stocks for reintroductions or genetic rescue.

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Population genetics of Brook Trout (Salvelinus fontinalis) in the southern Appalachian Mountains

Broad-scale patterns of genetic diversity for Brook Trout remain poorly understood across their endemic range in the eastern United States. We characterized variation at 12 microsatellite loci in 22,020 Brook Trout among 836 populations from Georgia, USA, to Quebec, Canada, to the western Great Lakes region. Within-population diversity was typically lower in the southern Appalachians relative to the mid-Atlantic and northeastern regions. Effective population sizes in the southern Appalachians were often very small, with many estimates less than 30 individuals. The population genetics of Brook Trout in the southern Appalachians are far more complex than a conventionally held simple “northern” versus “southern” dichotomy would suggest.

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