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Brook Trout ( Salvelinus fontinalis ) populations have experienced marked declines throughout their native range and are presently threatened due to isolation in small habitat fragments, land use changes, and climate change. The existence of numerous, spatially distinct populations poses substantial challenges for monitoring population status (e.g., abundance, recruitment, or occupancy). Genetic monitoring with estimates of effective number of breeders ( N b ) provides a potentially powerful metric to complement existing population monitoring, assessment, and prioritization. We estimated N b for 71 Brook Trout habitat units in mid-Atlantic region of the United States and obtained a mean N b of 73.2 (range 6.90-493). Our modeling approach tested whether N b estimates were sensitive to differences in habitat size, presence of non-native salmonids, base flow index, temperature, acidic precipitation, and indices of anthropogenic disturbance. We found significant support for three of our hypotheses including the positive influences of available habitat and base flow index and negative effect of temperature. Our results are consistent with presently observed and predicted future impacts of climate change on populations of this cold-water fish. Importantly, these findings support the use of N b in population assessments as an index of relative population status., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Author(s). Evolutionary Applications published by John Wiley & Sons Ltd.)

Small surface-release dams are prevalent across North American watersheds and can alter stream flow, thermal regimes, nutrient dynamics, and sediment transport. These dams are often implicated as a cause of negative water quality impacts-including reduced dissolved oxygen (DO)-and dam removal is increasingly employed to restore natural stream processes and improve DO. Published impacts of small dams on DO vary widely across sites, and even less is known about the extent and timescale of DO recovery following removal. Therefore, we sought to quantify the effects of small dams and dam removal on DO and determine the dam, stream, and watershed characteristics driving inter-site variation in responses. We deployed continuous data loggers for 3 weeks during summer months in upstream (reference), impoundment, and downstream reaches at each of 15 dammed sites and collected equivalent data at 10 of those sites following dam removal. Prior to dam removal, most sites (60%) experienced a decrease in DO (an average of 1.15 mg/L lower) within the impoundment relative to upstream, but no consistent impacts on diel ranges or on downstream reaches. Before dam removal, 5 impacted stream reaches experienced minimum DO levels below acceptable water quality standards (<5 mg/L); after dam removal, 4 of 5 of these reaches met DO standards. Sites with wider impoundments relative to upstream widths and sites located in watersheds with more cultivated land experienced the greatest decreases in impoundment DO relative to upstream. Within one year following dam removal, impoundment DO recovered to upstream reference conditions at 80% of sites, with the magnitude of recovery strongly related to the magnitude of pre-removal impacts. These data suggest that broadly, small dams negatively affect stream DO, and the extent of effects are modulated by impoundment geometry and watershed characteristics. These results may help practitioners to prioritize restoration efforts at those sites where small dams are having outsized impacts, and therefore where the greatest water quality benefits may occur., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Organisms can modify their surrounding environment, but whether these changes are large enough to feed back and alter their evolutionary trajectories is not well understood, particularly in wild populations. Here we show that nutrient pulses from decomposing Atlantic salmon (Salmo salar) parents alter selection pressures on their offspring with important consequences for their phenotypic and genetic diversity. We found a strong survival advantage to larger eggs and faster juvenile metabolic rates in streams lacking carcasses but not in streams containing this parental nutrient input. Differences in selection intensities led to significant phenotypic divergence in these two traits among stream types. Stronger selection in streams with low parental nutrient input also decreased the number of surviving families compared to streams with high parental nutrient levels. Observed effects of parent-derived nutrients on selection pressures provide experimental evidence for key components of eco-evolutionary feedbacks in wild populations., (© 2017 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.)

For organisms with overlapping generations that occur in metapopulations, uncertainty remains regarding the spatiotemporal scale of inference of estimates of the effective number of breeders (N^b) and whether these estimates can be used to predict generational N e . We conducted a series of tests of the spatiotemporal scale of inference of estimates of N b in nine consecutive cohorts within a long-term study of brook trout ( Salvelinus fontinalis ). We also tested a recently developed approach to estimate generational N e from N^b and compared this to an alternative approach for estimating N^e that also accounts for age structure. Multiple lines of evidence were consistent with N^b corresponding to the local (subpopulation) spatial scale and the cohort-specific temporal scale. We found that at least four consecutive cohort-specific estimates of N^b were necessary to obtain reliable estimates of harmonic mean N^b for a subpopulation. Generational N^e derived from cohort-specific N^b was within 7%-50% of an alternative approach to obtain N^e, suggesting some population specificity for concordance between approaches. Our results regarding the spatiotemporal scale of inference for N b should apply broadly to many taxa that exhibit overlapping generations and metapopulation structure and point to promising avenues for using cohort-specific N^b for local-scale genetic monitoring.

Water temperature is a primary driver of stream ecosystems and commonly forms the basis of stream classifications. Robust models of stream temperature are critical as the climate changes, but estimating daily stream temperature poses several important challenges. We developed a statistical model that accounts for many challenges that can make stream temperature estimation difficult. Our model identifies the yearly period when air and water temperature are synchronized, accommodates hysteresis, incorporates time lags, deals with missing data and autocorrelation and can include external drivers. In a small stream network, the model performed well (RMSE = 0.59°C), identified a clear warming trend (0.63 °C decade(-1)) and a widening of the synchronized period (29 d decade(-1)). We also carefully evaluated how missing data influenced predictions. Missing data within a year had a small effect on performance (∼0.05% average drop in RMSE with 10% fewer days with data). Missing all data for a year decreased performance (∼0.6 °C jump in RMSE), but this decrease was moderated when data were available from other streams in the network.

Climate change is predicted to change the distribution and abundance of species, yet underlying physiological mechanisms are complex and methods for detecting populations at risk from rising temperature are poorly developed. There is increasing interest in using physiological mediators of the stress response as indicators of individual and population-level response to environmental stressors. Here, we use laboratory experiments to show that the temperature thresholds in brook trout (Salvelinus fontinalis) for increased gill heat shock protein-70 (20.7°C) and plasma glucose (21.2°C) are similar to their proposed thermal ecological limit of 21.0°C. Field assays demonstrated increased plasma glucose, cortisol and heat shock protein-70 concentrations at field sites where mean daily temperature exceeded 21.0°C. Furthermore, population densities of brook trout were lowest at field sites where temperatures were warm enough to induce a stress response, and a co-occurring species with a higher thermal tolerance showed no evidence of physiological stress at a warm site. The congruence of stress responses and proposed thermal limits supports the use of these thresholds in models of changes in trout distribution under climate change scenarios and suggests that the induction of the stress response by elevated temperature may play a key role in driving the distribution of species.

Low productivity in aquatic ecosystems is associated with reduced individual growth of fish and increased concentrations of methylmercury (MeHg) in fish and their prey. However, many stream-dwelling fish species can use terrestrially-derived food resources, potentially subsidizing growth at low-productivity sites, and, because terrestrial resources have lower MeHg concentrations than aquatic resources, preventing an increase in diet-borne MeHg accumulation. We used a large-scale field study to evaluate relationships among terrestrial subsidy use, growth, and MeHg concentrations in two stream-dwelling fish species across an in-stream productivity gradient. We sampled young-of-the-year brook trout (Salvelinus fontinalis) and Atlantic salmon (Salmo salar), potential competitors with similar foraging habits, from 20 study sites in streams in New Hampshire and Massachusetts that encompassed a wide range of aquatic prey biomass. Stable isotope analysis showed that brook trout used more terrestrial resources than Atlantic salmon. Over their first growing season, Atlantic salmon tended to grow larger than brook trout at sites with high aquatic prey biomass, but brook grew two-fold larger than Atlantic salmon at sites with low aquatic prey biomass. The MeHg concentrations of brook trout and Atlantic salmon were similar at sites with high aquatic prey biomass and the MeHg concentrations of both species increased at sites with low prey biomass and high MeHg in aquatic prey. However, brook trout had three-fold lower MeHg concentrations than Atlantic salmon at low-productivity, high-MeHg sites. These results suggest that differential use of terrestrial resource subsidies reversed the growth asymmetry between potential competitors across a productivity gradient and, for one species, moderated the effect of low in-stream productivity on MeHg accumulation.

Competitive effects of younger cohorts on older ones are frequently assumed to be negligible in species where older, larger individuals dominate in pairwise behavioural interactions. Here, we provide field estimates of such competition by recruits on an older age class in Atlantic salmon (Salmo salar), a species where observational studies have documented strong body size advantages which should favour older individuals in direct interactions. By creating realistic levels of spatial variation in the density of underyearling (YOY) recruits over a 1-km stretch of a stream, and obtaining accurate measurements of individual growth rates of overyearlings (parr) from capture-mark-recapture data on a fine spatial scale, we demonstrate that high YOY density can substantially decrease parr growth. Models integrating multiple spatial scales indicated that parr were influenced by YOY density within 16 m. The preferred model suggested parr daily mass increase to be reduced by 39% when increasing YOY density from 0.0 to 1.0 m(-2), which is well within the range of naturally occurring densities. Reduced juvenile growth rates will in general be expected to reduce juvenile survival (via increased length of exposure to freshwater mortality) and increase generation times (via increased age at seaward migrations). Thus, increased recruitment can significantly affect the performance of older cohorts, with important implications for population dynamics. Our results highlight that, even for the wide range of organisms that rely on defendable resources, the direction of competition among age classes cannot be assumed a priori or be inferred from behavioural observations alone.

Phenotypic variation in body size can result from within-cohort variation in birth dates, among-individual growth variation and size-selective processes. We explore the relative effects of these processes on the maintenance of wide observed body size variation in stream-dwelling brook trout (Salvelinus fontinalis). Based on the analyses of multiple recaptures of individual fish, it appears that size distributions are largely determined by the maintenance of early size variation. We found no evidence for size-dependent compensatory growth (which would reduce size variation) and found no indication that size-dependent survival substantially influenced body size distributions. Depensatory growth (faster growth by larger individuals) reinforced early size variation, but was relatively strong only during the first sampling interval (age-0, fall). Maternal decisions on the timing and location of spawning could have a major influence on early, and as our results suggest, later (>age-0) size distributions. If this is the case, our estimates of heritability of body size (body length = 0.25) will be dominated by processes that generate and maintain early size differences. As a result, evolutionary responses to environmental change that are mediated by body size may be largely expressed via changes in the timing and location of reproduction.

By dispersing from localized aggregations of recruits, individuals may obtain energetic benefits due to reduced experienced density. However, this will depend on the spatial scale over which individuals compete. Here, we quantify this scale for juvenile Atlantic salmon (Salmo salar) following emergence and dispersal from nests. A single nest was placed in each of ten replicate streams during winter, and information on the individual positions (±1 m) and the body sizes of the resulting young-of-the-year (YOY) juveniles was obtained by sampling during the summer. In six of the ten streams, model comparisons suggested that individual body size was most closely related to the density within a mean distance of 11 m (range 2-26 m). A link between body size and density on such a restricted spatial scale suggests that dispersal from nests confers energetic benefits that can counterbalance any survival costs. For the four remaining streams, which had a high abundance of trout and older salmon cohorts, no single spatial scale could best describe the relation between YOY density and body size. Energetic benefits of dispersal associated with reduced local density therefore appear to depend on the abundance of competing cohorts or species, which have spatial distributions that are less predictable in terms of distance from nests. Thus, given a trade-off between costs and benefits associated with dispersal, and variation in benefits among environments, we predict an evolving and/or phenotypically plastic growth rate threshold which determines when an individual decides to disperse from areas of high local density.

1. Estimating the relative importance of factors affecting key vital rates is an essential challenge for population ecology. In spite of a large literature on individual growth rates of north temperate-zone fishes, relative effect sizes for the wide range of abiotic and biotic factors affecting fish growth are not well characterized, strongly limiting our ability to predict the effects of environmental change on fish populations. 2. We applied generalized linear mixed models to data from a long-term (nine cohorts over 10 years) individual-based (7685 records from 4203 individuals) study of stream-dwelling juvenile Atlantic salmon (Salmo salar) to estimate the relative importance and interactive effects of stream discharge, water temperature and population density on season-specific growth rates. The model explained a large proportion (r(2) = 0.95) of observed variation in growth. 3. Elasticity analysis was used to estimate the relative importance of model variables on growth in length for Atlantic salmon between age 0+ autumn and the end of age 1+ winter. Effects of population density were substantially weaker than effects of discharge and temperature across all seasons. Opposing among-season temperature effects reduced the overall importance of temperature on growth in contrast to discharge, where effects were generally positive among seasons. Consistent among-season effects and a greater range of observed variation combined to increase the effect of discharge on growth compared to temperature. 4. These results suggest that robust predictions of body growth in north temperate stream fishes will need to include season-specific estimates of variation in both abiotic (temperature and discharge) and biotic (density) factors, but that variation in discharge will dominate growth responses.

Realistic population models and effective conservation strategies require a thorough understanding of mechanisms driving stage-specific mortality. Mortality bottlenecks for many species occur in the juvenile stage and are thought to result from limitation on food or foraging habitat during a "critical period" for growth and survival. Without a way to account for maternal effects or to measure integrated consumption rates in the field, it has been virtually impossible to test these relationships directly. Hence uncertainties about mechanisms underlying such bottlenecks remain. In this study we randomize maternal effects across sites and apply a new method for measuring consumption integrated over weeks to months to test the hypothesis that food limitation drives early-season juvenile mortality bottlenecks in Atlantic salmon (Salmo salar). Using natural signatures of geologically derived cesium (133Cs), we estimated consumption rates of >400 fry stocked into six streams. Two to four weeks after stocking, consumption was extremely low across sites (0.005 g x g(-1) x d(-1)) and was predicted to be below maintenance rations (i.e., yielding negative energy balances) for the majority of individuals from five of six sites. However, consumption during this time was positively correlated with growth rates and survival (measured at the end of the growing season). In contrast, consumption rates increased in mid- (0.030 g x g(-1) x d(-1)) and late (0.035 g x g(-1) x d(-1)) seasons, but juvenile survival and consumption were not correlated, and correlations between growth and consumption were weak. These findings are consistent with predictions of a habitat-based bioenergetic model constructed using the actual stream positions of the individual fish in the present study, which indicates that habitat-based models capture important environmental determinants of juvenile growth and survival. Hence, by combining approaches, reducing maternal effects and controlling initial conditions, we offer a general framework for linking foraging with juvenile survival and present the first direct consumption-based evidence for the early season bottleneck hypothesis.

The effect of predators on prey populations depends on how predator-caused mortality changes with prey population density. Predators can enforce density-dependent prey mortality and contribute to population stability, but only if they have a positive numerical or behavioral response to increased prey density. Otherwise, predator saturation can result in inversely density-dependent mortality, destabilizing prey populations and increasing extinction risk. Juvenile salmon and trout provide some of the clearest empirical examples of density-dependent mortality in animal populations. However, although juvenile salmon are very vulnerable to predators, the demographic effects of predators on juvenile salmon are unknown. We tested the interactive effects of predators and population density on the mortality of juvenile Atlantic salmon (Salmo salar) using controlled releases of salmon in natural streams. We introduced newly hatched juvenile salmon at three population density treatments in six study streams, half of which contained slimy sculpin (Cottus cognatus), a common generalist predator (18 release sites in total, repeated over two summers). Sculpin reversed the direction of density dependence for juvenile salmon mortality. Salmon mortality was density dependent in streams with no sculpin, but inversely density dependent in streams where sculpin were abundant. Such predator-mediated inverse density dependence is especially problematic for prey populations suppressed by other factors, thereby presenting a fundamental challenge to persistence of rare populations and restoration of extirpated populations.

1. Spatial heterogeneity in population density is predicted to have important effects on population characteristics, such as competition intensity and carrying capacity. Patchy breeding distributions will tend to increase spatial heterogeneity in population density, whereas dispersal from breeding patches will tend to decrease it. The potential for dispersal to homogenize densities is likely to differ both among organisms (e.g. plants vs. mobile animals) and throughout ontogeny (e.g. larvae vs. adults). However, for mobile organisms, experimental studies of the importance of breeding distributions from the wild are largely lacking. 2. In the present study, experimental manipulations replicated over eight natural streams and 2 years enabled us to test for effects of the distribution of Atlantic salmon eggs over spatial scales which are relevant to local interactions among individuals. Artificial nests were placed along 250 m study reaches at one of two levels of nest dispersion - patchy (two nests per stream) and dispersed (10 nests per stream) - while holding total egg density (eggs m(-2) stream area) constant. 3. Nest dispersion had significant effects on the spatial distribution of the resulting juveniles in their first summer. Patchy nest distributions resulted in a highly right-skewed frequency distribution of local under-yearling densities (among 25 m sampling sections), as sample sections adjacent to the nest sites had relatively high densities. In contrast, dispersed nest distributions yielded approximately normal density distributions. Sections with high relative densities in the patchy nest distribution treatments also had relatively small juvenile body sizes, and patchy egg distribution appeared to produce a higher redistribution of individuals from the first to the second juvenile growth season than the dispersed distribution. 4. Because patchy breeding distribution combined with limited early dispersal can create spatial variation in density over scales directly relevant for individual interactions, this will be one important component in determining mean levels of early juvenile competition and its spatial variation within populations. Assuming random or ideal-free distribution of individuals may therefore underestimate the mean level of density experienced by juveniles over surprisingly small spatial scales (orders of magnitude smaller than total spatial extent of populations), even for mobile organisms.

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 ( approximately 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.

1. Empirical studies show that average growth of stream-dwelling salmon and trout often declines with increasing density in a characteristic concave relationship. However, the mechanisms that generate negative density-growth relationships in populations in natural streams are not certain. 2. In a recent study, Imre, Grant & Cunjak (2005; Journal of Animal Ecology, 74, 508-516) argue that density-dependent growth due to exploitative competition for prey causes the negative density-growth relationships for stream salmonids. They argue that the concave shape of empirical density-growth relationships is consistent with a simple model of exploitative competition and not consistent with interference competition for space. 3. We use a simple model to show that competition for space can yield concave density-growth relationships consistent with the empirical pattern when individuals compete for foraging sites that vary spatially in quality and lower-quality sites predominate. Thus, the predictions of the exploitative competition and spatial competition models overlap. 4. The shape of the density-growth relationship does not differentiate between candidate mechanisms underlying density-dependent growth for stream salmonids. Our results highlight the general problem with determining the mechanism driving an ecological process from patterns in observational data within the context of linking population demographics to habitat structure and animal behaviour.

For organisms with restricted mobility, density dependence may occur on spatial scales much smaller than that of the whole population. Averaging densities over whole populations in such organisms gives a more or less inaccurate description of the real variation in competitive intensity over time and space. The potential for local density dependence in more mobile organisms is less well understood, particularly for organisms living in continuous habitats. To test for local density-dependent processes in such an organism, we manipulated egg density (the number of eggs nest(-1)) among ten artificial nests of Atlantic salmon along an 1,848-m long river during two consecutive years. Eggs in different nests were given unique thermal otolith-banding patterns to allow identification of juvenile nest origin. At capture, 1-2 months after emergence, the spatial distribution of juveniles reflected nest locations, with the median absolute dispersal distance being 92 and 41 m in the 2 years. Estimated nest-specific survival rates were strongly negatively related to hatched-egg density in both years (r(2)=0.72 and 0.62), despite dramatic differences in overall mean survival (0.22 and 0.02). Thus, density-dependent survival following emergence in Atlantic salmon juveniles occurs on spatial scales much smaller than that of whole populations. The consistency across years suggests that the phenomenon is likely to occur over most environmental conditions. Our observation of local-scale density dependence is consistent with strong juvenile territoriality, which forces individuals emerging in high-initial density areas to disperse farther, and a high cost (metabolic or predation) of dispersal. We conclude that for mobile organisms with patchy distributions of propagules and constrained juvenile dispersal, increased emphasis on local-scale dynamics should enable a more mechanistic understanding of population regulation even in continuous habitats, and hence increase the predictive power of population models.