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Declining body size in fishes and other aquatic ectotherms associated with anthropogenic climate warming has significant implications for future fisheries yields, stock assessments and aquatic ecosystem stability. One proposed mechanism seeking to explain such body-size reductions, known as the gill oxygen limitation (GOL) hypothesis, has recently been used to model future impacts of climate warming on fisheries but has not been robustly empirically tested. We used brook trout (Salvelinus fontinalis), a fast-growing, cold-water salmonid species of broad economic, conservation and ecological value, to examine the GOL hypothesis in a long-term experiment quantifying effects of temperature on growth, resting metabolic rate (RMR), maximum metabolic rate (MMR) and gill surface area (GSA). Despite significantly reduced growth and body size at an elevated temperature, allometric slopes of GSA were not significantly different than 1.0 and were above those for RMR and MMR at both temperature treatments (15°C and 20°C), contrary to GOL expectations. We also found that the effect of temperature on RMR was time-dependent, contradicting the prediction that heightened temperatures increase metabolic rates and reinforcing the importance of longer-term exposures (e.g. >6 months) to fully understand the influence of acclimation on temperature-metabolic rate relationships. Our results indicate that although oxygen limitation may be important in some aspects of temperature-body size relationships and constraints on metabolic supply may contribute to reduced growth in some cases, it is unlikely that GOL is a universal mechanism explaining temperature-body size relationships in aquatic ectotherms. We suggest future research focus on alternative mechanisms underlying temperature-body size relationships, and that projections of climate change impacts on fisheries yields using models based on GOL assumptions be interpreted with caution., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

Climate change affects populations over broad geographic ranges due to spatially autocorrelated abiotic conditions known as the Moran effect. However, populations do not always respond to broad-scale environmental changes synchronously across a landscape. We combined multiple datasets for a retrospective analysis of time-series count data (5-28 annual samples per segment) at 144 stream segments dispersed over nearly 1,000 linear kilometers of range to characterize the population structure and scale of spatial synchrony across the southern native range of a coldwater stream fish (brook trout, Salvelinus fontinalis), which is sensitive to stream temperature and flow variations. Spatial synchrony differed by life stage and geographic region: it was stronger in the juvenile life stage than in the adult life stage and in the northern sub-region than in the southern sub-region. Spatial synchrony of trout populations extended to 100-200 km but was much weaker than that of climate variables such as temperature, precipitation, and stream flow. Early life stage abundance changed over time due to annual variation in summer temperature and winter and spring stream flow conditions. Climate effects on abundance differed between sub-regions and among local populations within sub-regions, indicating multiple cross-scale interactions where climate interacted with local habitat to generate only a modest pattern of population synchrony over space. Overall, our analysis showed higher degrees of response heterogeneity of local populations to climate variation and consequently population asynchrony than previously shown based on analysis of individual, geographically restricted datasets. This response heterogeneity indicates that certain local segments characterized by population asynchrony and resistance to climate variation could represent unique populations of this iconic native coldwater fish that warrant targeted conservation. Advancing the conservation of this species can include actions that identify such priority populations and incorporate them into landscape-level conservation planning. Our approach is applicable to other widespread aquatic species sensitive to climate change., (© 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)

Human activities and climate change threaten coldwater organisms in freshwater ecosystems by causing rivers and streams to warm, increasing the intensity and frequency of warm temperature events, and reducing thermal heterogeneity. Cold-water refuges are discrete patches of relatively cool water that are used by coldwater organisms for thermal relief and short-term survival. Globally, cohesive management approaches are needed that consider interlinked physical, biological, and social factors of cold-water refuges. We review current understanding of cold-water refuges, identify gaps between science and management, and evaluate policies aimed at protecting thermally sensitive species. Existing policies include designating cold-water habitats, restricting fishing during warm periods, and implementing threshold temperature standards or guidelines. However, these policies are rare and uncoordinated across spatial scales and often do not consider input from Indigenous peoples. We propose that cold-water refuges be managed as distinct operational landscape units, which provide a social and ecological context that is relevant at the watershed scale. These operational landscape units provide the foundation for an integrated framework that links science and management by (1) mapping and characterizing cold-water refuges to prioritize management and conservation actions, (2) leveraging existing and new policies, (3) improving coordination across jurisdictions, and (4) implementing adaptive management practices across scales. Our findings show that while there are many opportunities for scientific advancement, the current state of the sciences is sufficient to inform policy and management. Our proposed framework provides a path forward for managing and protecting cold-water refuges using existing and new policies to protect coldwater organisms in the face of global change., (© 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Understanding how genetic diversity is distributed across spatiotemporal scales in species of conservation or management concern is critical for identifying large-scale mechanisms affecting local conservation status and implementing large-scale biodiversity monitoring programmes. However, cross-scale surveys of genetic diversity are often impractical within single studies, and combining datasets to increase spatiotemporal coverage is frequently impeded by using different sets of molecular markers. Recently developed molecular tools make surveys based on standardized single-nucleotide polymorphism (SNP) panels more feasible than ever, but require existing genomic information. Here, we conduct the first survey of genome-wide SNPs across the native range of brook trout (Salvelinus fontinalis), a cold-adapted species that has been the focus of considerable conservation and management effort across eastern North America. Our dataset can be leveraged to easily design SNP panels that allow datasets to be combined for large-scale analyses. We performed restriction site-associated DNA sequencing for wild brook trout from 82 locations spanning much of the native range and domestic brook trout from 24 hatchery strains used in stocking efforts. We identified over 24,000 SNPs distributed throughout the brook trout genome. We explored the ability of these SNPs to resolve relationships across spatial scales, including population structure and hatchery admixture. Our dataset captures a wide spectrum of genetic diversity in native brook trout, offering a valuable resource for developing SNP panels. We highlight potential applications of this resource with the goal of increasing the integration of genomic information into decision-making for brook trout and other species of conservation or management concern., (© 2023 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd.)

As air temperature increases, it has been suggested that smaller individual body size may be a general response to climate warming. However, for ectotherms inhabiting cold, highly seasonal environments, warming temperatures may increase the scope for growth and result in larger body size. In a long-term study of individual brook trout Salvelinus fontinalis and brown trout Salmo trutta inhabiting a small stream network, individual lengths increased over the course of 15 years. As size-selective gains and losses to the population acted to reduce body sizes and mean body size at first tagging in the autumn (<60 mm) were not observed to change substantially over time, the increase in body size was best explained by higher individual growth rates. For brook trout, increasing water temperatures during the spring (when both trout species accomplish most of their total annual growth) was the primary driver of growth rate for juvenile fish and the environmental factor which best explained increases in individual body size over time. For brown trout, by contrast, reduction in and subsequent elimination of juvenile Atlantic salmon Salmo salar midway through the study period explained most of the increases in juvenile growth and body size. In addition to these major trends, a considerable amount of interannual variation in trout growth and body size was explained by other abiotic (stream flow) and biotic (population density) factors with the direction and magnitude of these effects differing by season, age-class and species. For example, stream flow was the dominant growth rate driver for adult fish with strong positive effects in the summer and autumn, but flow variation could not explain increases in body size as we observed no trend in flow. Overall, our work supports the general contention that for high-latitude ectotherms, increasing spring temperatures associated with a warming climate can result in increased growth and individual body size (up to a point), but context-dependent change in other factors can substantially contribute to both interannual variation and longer-term effects., (© 2022 The Authors. Journal of Animal Ecology © 2022 British Ecological Society. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Climate-change adaptation focuses on conducting and translating research to minimize the dire impacts of anthropogenic climate change, including threats to biodiversity and human welfare. One adaptation strategy is to focus conservation on climate-change refugia (that is, areas relatively buffered from contemporary climate change over time that enable persistence of valued physical, ecological, and sociocultural resources). In this Special Issue, recent methodological and conceptual advances in refugia science will be highlighted. Advances in this emerging subdiscipline are improving scientific understanding and conservation in the face of climate change by considering scale and ecosystem dynamics, and looking beyond climate exposure to sensitivity and adaptive capacity. We propose considering refugia in the context of a multifaceted, long-term, network-based approach, as temporal and spatial gradients of ecological persistence that can act as "slow lanes" rather than areas of stasis. After years of discussion confined primarily to the scientific literature, researchers and resource managers are now working together to put refugia conservation into practice.

Within the context of climate adaptation, the concept of climate refugia has emerged as a framework for addressing future threats to freshwater fish populations. We evaluated recent climate-refugia management associated with water use and landscape modification by comparing efforts in the US states of Oregon and Massachusetts, for which there are contrasting resource use patterns. Using these examples, we discuss tools and principles that can be applied more broadly. Although many early efforts to identify climate refugia have focused on water temperature, substantial gains in evaluating other factors and processes regulating climate refugia (eg stream flow, groundwater availability) are facilitating refined mapping of refugia and assessment of their ecological value. Major challenges remain for incorporating climate refugia into water-quality standards, evaluating trade-offs among policy options, addressing multiple species' needs, and planning for uncertainty. However, with a procedurally transparent and conceptually sound framework to build upon, recent efforts have revealed a promising path forward.

As stream temperatures increase due to factors such as heated runoff from impervious surfaces, deforestation, and climate change, fish species adapted to cold water streams are forced to move to more suitable habitat, acclimate or adapt to increased thermal regimes, or die. To estimate the potential for adaptation, a (within individual) repeatable metric of thermal tolerance is imperative. Critical thermal maximum (CT max ) is a dynamic test that is widely used to measure thermal tolerance across many taxa and has been used in fishes for decades, but its repeatability in most species is unknown. CT max tests increase water temperature steadily over time until loss of equilibrium (LOE) is achieved. To determine if CT max is a consistent metric within individual fish, we measured CT max on the same lab-held individually-marked adult brook trout Salvelinus fontinalis at three different times (August & September 2016, September 2017). We found that CT max is a repeatable trait (Repeatability ± S.E.: 0.48 ± 0.14). CT max of individuals males was consistent over time, but the CT max of females increased slightly over time. This result indicates that CT max is a robust, repeatable estimate of thermal tolerance in a cold-water adapted fish., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Population dynamics are often correlated in space and time due to correlations in environmental drivers as well as synchrony induced by individual dispersal. Many statistical analyses of populations ignore potential autocorrelations and assume that survey methods (distance and time between samples) eliminate these correlations, allowing samples to be treated independently. If these assumptions are incorrect, results and therefore inference may be biased and uncertainty underestimated. We developed a novel statistical method to account for spatiotemporal correlations within dendritic stream networks, while accounting for imperfect detection in the surveys. Through simulations, we found this model decreased predictive error relative to standard statistical methods when data were spatially correlated based on stream distance and performed similarly when data were not correlated. We found that increasing the number of years surveyed substantially improved the model accuracy when estimating spatial and temporal correlation coefficients, especially from 10 to 15 yr. Increasing the number of survey sites within the network improved the performance of the nonspatial model but only marginally improved the density estimates in the spatiotemporal model. We applied this model to brook trout data from the West Susquehanna Watershed in Pennsylvania collected over 34 yr from 1981 to 2014. We found the model including temporal and spatiotemporal autocorrelation best described young of the year (YOY) and adult density patterns. YOY densities were positively related to forest cover and negatively related to spring temperatures with low temporal autocorrelation and moderately high spatiotemporal correlation. Adult densities were less strongly affected by climatic conditions and less temporally variable than YOY but with similar spatiotemporal correlation and higher temporal autocorrelation., (Published 2018. This article is a U.S. Government work and is in the public domain in the USA.)

Genetic rescue is an increasingly considered conservation measure to address genetic erosion associated with habitat loss and fragmentation. The resulting gene flow from facilitating migration may improve fitness and adaptive potential, but is not without risks (e.g., outbreeding depression). Here, we conducted a test of genetic rescue by translocating ten (five of each sex) brook trout (Salvelinus fontinalis) from a single source to four nearby and isolated stream populations. To control for the demographic contribution of translocated individuals, ten resident individuals (five of each sex) were removed from each recipient population. Prior to the introduction of translocated individuals, the two smallest above-barrier populations had substantially lower genetic diversity, and all populations had reduced effective number of breeders relative to adjacent below-barrier populations. In the first reproductive bout following translocation, 31 of 40 (78%) translocated individuals reproduced successfully. Translocated individuals contributed to more families than expected under random mating and generally produced larger full-sibling families. We observed relatively high (>20%) introgression in three of the four recipient populations. The translocations increased genetic diversity of recipient populations by 45% in allelic richness and 25% in expected heterozygosity. Additionally, strong evidence of hybrid vigour was observed through significantly larger body sizes of hybrid offspring relative to resident offspring in all recipient populations. Continued monitoring of these populations will test for negative fitness effects beyond the first generation. However, these results provide much-needed experimental data to inform the potential effectiveness of genetic rescue-motivated translocations., (© 2017 John Wiley & Sons Ltd.)

Estimating thermal performance of organisms is critical for understanding population distributions and dynamics and predicting responses to climate change. Typically, performance curves are estimated using laboratory studies to isolate temperature effects, but other abiotic and biotic factors influence temperature-performance relationships in nature reducing these models' predictive ability. We present a model for estimating thermal performance curves from repeated field observations that includes environmental and individual variation. We fit the model in a Bayesian framework using MCMC sampling, which allowed for estimation of unobserved latent growth while propagating uncertainty. Fitting the model to simulated data varying in sampling design and parameter values demonstrated that the parameter estimates were accurate, precise, and unbiased. Fitting the model to individual growth data from wild trout revealed high out-of-sample predictive ability relative to laboratory-derived models, which produced more biased predictions for field performance. The field-based estimates of thermal maxima were lower than those based on laboratory studies. Under warming temperature scenarios, field-derived performance models predicted stronger declines in body size than laboratory-derived models, suggesting that laboratory-based models may underestimate climate change effects. The presented model estimates true, realized field performance, avoiding assumptions required for applying laboratory-based models to field performance, which should improve estimates of performance under climate change and advance thermal ecology., (© 2017 by the Ecological Society of America.)

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.

Understanding how multiple extrinsic (density-independent) factors and intrinsic (density-dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size and whether there is a strong role for density-dependence. The primary goal of this study was to identify the roles of seasonal variation in climate driven environmental direct effects (mean stream flow and temperature) vs. density-dependence on population size and mean body size in eastern brook trout (Salvelinus fontinalis). We use data from a 10-year capture-mark-recapture study of eastern brook trout in four streams in Western Massachusetts, USA to parameterize a discrete-time population projection model. The model integrates matrix modeling techniques used to characterize discrete population structures (age, habitat type, and season) with integral projection models (IPMs) that characterize demographic rates as continuous functions of organismal traits (in this case body size). Using both stochastic and deterministic analyses we show that decreases in population size are due to changes in stream flow and temperature and that these changes are larger than what can be compensated for through density-dependent responses. We also show that the declines are due mostly to increasing mean stream temperatures decreasing the survival of the youngest age class. In contrast, increases in mean body size over the same period are the result of indirect changes in density with a lesser direct role of climate-driven environmental change., (Published 2015. This article is a U.S. Government work and is in the public domain in the USA.)

The effective number of breeders that give rise to a cohort (N(b)) is a promising metric for genetic monitoring of species with overlapping generations; however, more work is needed to understand factors that contribute to variation in this measure in natural populations. We tested hypotheses related to interannual variation in N(b) in two long-term studies of brook trout populations. We found no supporting evidence for our initial hypothesis that N^(b) reflects N^(c) (defined as the number of adults in a population at the time of reproduction). N^(b) was stable relative to N^(C) and did not follow trends in abundance (one stream negative, the other positive). We used stream flow estimates to test the alternative hypothesis that environmental factors constrain N(b). We observed an intermediate optimum autumn stream flow for both N^(b) (R(2) = 0.73, P = 0.02) and full-sibling family evenness (R(2) = 0.77, P = 0.01) in one population and a negative correlation between autumn stream flow and full-sib family evenness in the other population (r = -0.95, P = 0.02). Evidence for greater reproductive skew at the lowest and highest autumn flow was consistent with suboptimal conditions at flow extremes. A series of additional tests provided no supporting evidence for a related hypothesis that density-dependent reproductive success was responsible for the lack of relationship between N(b) and N(C) (so-called genetic compensation). This work provides evidence that N(b) is a useful metric of population-specific individual reproductive contribution for genetic monitoring across populations and the link we provide between stream flow and N(b) could be used to help predict population resilience to environmental change., (© 2015 John Wiley & Sons Ltd.)

Climate change affects seasonal weather patterns, but little is known about the relative importance of seasonal weather patterns on animal population vital rates. Even when such information exists, data are typically only available from intensive fieldwork (e.g., mark-recapture studies) at a limited spatial extent. Here, we investigated effects of seasonal air temperature and precipitation (fall, winter, and spring) on survival and recruitment of brook trout (Salvelinus fontinalis) at a broad spatial scale using a novel stage-structured population model. The data were a 15-year record of brook trout abundance from 72 sites distributed across a 170-km-long mountain range in Shenandoah National Park, Virginia, USA. Population vital rates responded differently to weather and site-specific conditions. Specifically, young-of-year survival was most strongly affected by spring temperature, adult survival by elevation and per-capita recruitment by winter precipitation. Low fall precipitation and high winter precipitation, the latter of which is predicted to increase under climate change for the study region, had the strongest negative effects on trout populations. Simulations show that trout abundance could be greatly reduced under constant high winter precipitation, consistent with the expected effects of gravel-scouring flows on eggs and newly hatched individuals. However, high-elevation sites would be less vulnerable to local extinction because they supported higher adult survival. Furthermore, the majority of brook trout populations are projected to persist if high winter precipitation occurs only intermittently (≤3 of 5 years) due to density-dependent recruitment. Variable drivers of vital rates should be commonly found in animal populations characterized by ontogenetic changes in habitat, and such stage-structured effects may increase population persistence to changing climate by not affecting all life stages simultaneously. Yet, our results also demonstrate that weather patterns during seemingly less consequential seasons (e.g., winter precipitation) can have major impacts on animal population dynamics., (© 2014 John Wiley & Sons Ltd.)

Modelling the effects of environmental change on populations is a key challenge for ecologists, particularly as the pace of change increases. Currently, modelling efforts are limited by difficulties in establishing robust relationships between environmental drivers and population responses. We developed an integrated capture-recapture state-space model to estimate the effects of two key environmental drivers (stream flow and temperature) on demographic rates (body growth, movement and survival) using a long-term (11 years), high-resolution (individually tagged, sampled seasonally) data set of brook trout (Salvelinus fontinalis) from four sites in a stream network. Our integrated model provides an effective context within which to estimate environmental driver effects because it takes full advantage of data by estimating (latent) state values for missing observations, because it propagates uncertainty among model components and because it accounts for the major demographic rates and interactions that contribute to annual survival. We found that stream flow and temperature had strong effects on brook trout demography. Some effects, such as reduction in survival associated with low stream flow and high temperature during the summer season, were consistent across sites and age classes, suggesting that they may serve as robust indicators of vulnerability to environmental change. Other survival effects varied across ages, sites and seasons, indicating that flow and temperature may not be the primary drivers of survival in those cases. Flow and temperature also affected body growth rates; these responses were consistent across sites but differed dramatically between age classes and seasons. Finally, we found that tributary and mainstem sites responded differently to variation in flow and temperature. Annual survival (combination of survival and body growth across seasons) was insensitive to body growth and was most sensitive to flow (positive) and temperature (negative) in the summer and fall. These observations, combined with our ability to estimate the occurrence, magnitude and direction of fish movement between these habitat types, indicated that heterogeneity in response may provide a mechanism providing potential resilience to environmental change. Given that the challenges we faced in our study are likely to be common to many intensive data sets, the integrated modelling approach could be generally applicable and useful., (Published 2014. This article is a U.S. Government work and is in the public domain in the USA.)

Environmental DNA (eDNA) detection has emerged as a powerful tool for monitoring aquatic organisms, but much remains unknown about the dynamics of aquatic eDNA over a range of environmental conditions. DNA concentrations in streams and rivers will depend not only on the equilibrium between DNA entering the water and DNA leaving the system through degradation, but also on downstream transport. To improve understanding of the dynamics of eDNA concentration in lotic systems, we introduced caged trout into two fishless headwater streams and took eDNA samples at evenly spaced downstream intervals. This was repeated 18 times from mid-summer through autumn, over flows ranging from approximately 1-96 L/s. We used quantitative PCR to relate DNA copy number to distance from source. We found that regardless of flow, there were detectable levels of DNA at 239.5 m. The main effect of flow on eDNA counts was in opposite directions in the two streams. At the lowest flows, eDNA counts were highest close to the source and quickly trailed off over distance. At the highest flows, DNA counts were relatively low both near and far from the source. Biomass was positively related to eDNA copy number in both streams. A combination of cell settling, turbulence and dilution effects is probably responsible for our observations. Additionally, during high leaf deposition periods, the presence of inhibitors resulted in no amplification for high copy number samples in the absence of an inhibition-releasing strategy, demonstrating the necessity to carefully consider inhibition in eDNA analysis., (© 2014 John Wiley & Sons Ltd.)

Migrations between different habitats are key events in the lives of many organisms. Such movements involve annually recurring travel over long distances usually triggered by seasonal changes in the environment. Often, the migration is associated with travel to or from reproduction areas to regions of growth. Young anadromous Atlantic salmon (Salmo salar) emigrate from freshwater nursery areas during spring and early summer to feed and grow in the North Atlantic Ocean. The transition from the freshwater ('parr') stage to the migratory stage where they descend streams and enter salt water ('smolt') is characterized by morphological, physiological and behavioural changes where the timing of this parr-smolt transition is cued by photoperiod and water temperature. Environmental conditions in the freshwater habitat control the downstream migration and contribute to within- and among-river variation in migratory timing. Moreover, the timing of the freshwater emigration has likely evolved to meet environmental conditions in the ocean as these affect growth and survival of the post-smolts. Using generalized additive mixed-effects modelling, we analysed spatio-temporal variations in the dates of downstream smolt migration in 67 rivers throughout the North Atlantic during the last five decades and found that migrations were earlier in populations in the east than the west. After accounting for this spatial effect, the initiation of the downstream migration among rivers was positively associated with freshwater temperatures, up to about 10 °C and levelling off at higher values, and with sea-surface temperatures. Earlier migration occurred when river discharge levels were low but increasing. On average, the initiation of the smolt seaward migration has occurred 2.5 days earlier per decade throughout the basin of the North Atlantic. This shift in phenology matches changes in air, river, and ocean temperatures, suggesting that Atlantic salmon emigration is responding to the current global climate changes., (© 2013 John Wiley & Sons Ltd.)

The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark-recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark-recapture) and extensive (e.g., counts) data sources.

GONe is a user-friendly, Windows-based program for estimating effective size (N(e) ) in populations with overlapping generations. It uses the Jorde-Ryman modification to the temporal method to account for age structure in populations. This method requires estimates of age-specific survival and birth rate and allele frequencies measured in two or more consecutive cohorts. Allele frequencies are acquired by reading in genotypic data from files formatted for either GENEPOP or TEMPOFS. For each interval between consecutive cohorts, N(e) is estimated at each locus and over all loci. Furthermore, N(e) estimates are output for three different genetic drift estimators (F(s) , F(c) and F(k) ). Confidence intervals are derived from a chi-square distribution with degrees of freedom equal to the number of independent alleles. GONe has been validated over a wide range of N(e) values, and for scenarios where survival and birth rates differ between sexes, sex ratios are unequal and reproductive variances differ. GONe is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/., (© 2011 Blackwell Publishing Ltd.)

Linear and heterogeneous habitat makes headwater stream networks an ideal ecosystem in which to test the influence of environmental factors on spatial genetic patterns of obligatory aquatic species. We investigated fine-scale population structure and influence of stream habitat on individual-level genetic differentiation in brook trout (Salvelinus fontinalis) by genotyping eight microsatellite loci in 740 individuals in two headwater channel networks (7.7 and 4.4 km) in Connecticut, USA. A weak but statistically significant isolation-by-distance pattern was common in both sites. In the field, many tagged individuals were recaptured in the same 50-m reaches within a single field season (summer to fall). One study site was characterized with a hierarchical population structure, where seasonal barriers (natural falls of 1.5-2.5 m in height during summer base-flow condition) greatly reduced gene flow and perceptible spatial patterns emerged because of the presence of tributaries, each with a group of genetically distinguishable individuals. Genetic differentiation increased when pairs of individuals were separated by high stream gradient (steep channel slope) or warm stream temperature in this site, although the evidence of their influence was equivocal. In a second site, evidence for genetic clusters was weak at best, but genetic differentiation between individuals was positively correlated with number of tributary confluences. We concluded that the population-level movement of brook trout was limited in the study headwater stream networks, resulting in the fine-scale population structure (genetic clusters and clines) even at distances of a few kilometres, and gene flow was mitigated by 'riverscape' variables, particularly by physical barriers, waterway distance (i.e. isolation-by-distance) and the presence of tributaries., (© 2011 Blackwell Publishing Ltd.)

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.

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.

A 5 year individual-based data set was used to estimate size-specific survival rates in a wild brook trout Salvelinus fontinalis population in a stream network encompassing a mainstem and three tributaries (1.5-6 m wetted width), western Massachusetts, U.S.A. The relationships between survival in summer and temperature and flow metrics derived from continuous monitoring data were then tested. Increased summer temperatures significantly reduced summer survival rates for S. fontinalis in almost all size classes in all four sites throughout the network. In contrast, extreme low summer flows reduced survival of large fish, but only in small tributaries, and had no significant effects on fish in smaller size classes in any location. These results provide direct evidence of a link between season-specific survival and environmental factors likely to be affected by climate change and have important consequences for the management of both habitats and populations.

pedagog is a Windows program that can be used to determine power for, and validate inferences drawn from, eco-evolutionary studies. It models dynamics of multiple populations and their interactions through individual-based simulations while simultaneously recording genotype, pedigree and trait information at the individual level. pedagog also allows for specification of heritable traits, natural and sexual selection acting upon those traits, population sampling schemes and incorporation of genetic and demographic errors into the output. Overall, parameters can be specified for genetic diversity, demographics, mating design, genetic and demographic errors, individual growth models, trait heritability and selection, and output formatting. Demographic parameters can be either age or function based, and all parameters can be drawn from 12 statistical distributions where appropriate. Simulation results can be automatically formatted for 57 existing software programs to facilitate postsimulation analyses. pedagog is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/., (© 2009 Blackwell Publishing Ltd.)

To study smolt behaviour and survival of a northern Atlantic salmon Salmo salar population during river descent, sea entry and fjord migration, 120 wild S. salar were tagged with acoustic tags and registered at four automatic listening station arrays in the mouth of the north Norwegian River Alta and throughout the Alta Fjord. An estimated 75% of the post-smolts survived from the river mouth, through the estuary and the first 17 km of the fjord. Survival rates in the fjord varied with fork length (LF), and ranged from 97.0 to 99.5% km(-1). On average, the post-smolts spent 1.5 days (36 h, range 11-365 h) travelling from the river mouth to the last fjord array, 31 km from the river mouth. The migratory speed was slower (1.8 LF s(-1)) in the first 4 km after sea entry compared with the next 27 km (3.0 LF s(-1)). Post-smolts entered the fjord more often during the high or ebbing tide (70%). There was no clear diurnal migration pattern within the river and fjord, but most of the post-smolts entered the fjord at night (66%, 2000-0800 hours), despite the 24 h daylight at this latitude. The tidal cycle, wind-induced currents and the smolts' own movements seemed to influence migratory speeds and routes in different parts of the fjord. A large variation in migration patterns, both in the river and fjord, might indicate that individuals in stochastic estuarine and marine environments are exposed to highly variable selection regimes, resulting in different responses to environmental factors on both temporal and spatial scales. Post-smolts in the northern Alta Fjord had similar early marine survival rates to those observed previously in southern fjords; however, fjord residency in the north was shorter.

How genomic expression differs as a function of life history variation is largely unknown. Atlantic salmon exhibits extreme alternative life histories. We defined the gene-expression signatures of wild-caught salmon at two different life stages by comparing the brain expression profiles of mature sneaker males and immature males, and early migrants and late migrants. In addition to life-stage-specific signatures, we discovered a surprisingly large gene set that was differentially regulated-at similar magnitudes, yet in opposite direction-in both life history transitions. We suggest that this co-variation is not a consequence of many independent cellular and molecular switches in the same direction but rather represents the molecular equivalent of a physiological shift orchestrated by one or very few master regulators.

create is a Windows program for the creation of new and conversion of existing data input files for 52 genetic data analysis software programs. Programs are grouped into areas of sibship reconstruction, parentage assignment, genetic data analysis, and specialized applications. create is able to read in data from text, Microsoft Excel and Access sources and allows the user to specify columns containing individual and population identifiers, birth and death data, sex data, relationship information, and spatial location data. create's only constraints on source data are that one individual is contained in one row, and the genotypic data is contiguous. create is available for download at http://www.lsc.usgs.gov/CAFL/Ecology/Software.html., (© 2007 The Authors.)

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.

Here we critically review the scale and extent of adaptive genetic variation in Atlantic salmon (Salmo salar L.), an important model system in evolutionary and conservation biology that provides fundamental insights into population persistence, adaptive response and the effects of anthropogenic change. We consider the process of adaptation as the end product of natural selection, one that can best be viewed as the degree of matching between phenotype and environment. We recognise three potential sources of adaptive variation: heritable variation in phenotypic traits related to fitness, variation at the molecular level in genes influenced by selection, and variation in the way genes interact with the environment to produce phenotypes of varying plasticity. Of all phenotypic traits examined, variation in body size (or in correlated characters such as growth rates, age of seaward migration or age at sexual maturity) generally shows the highest heritability, as well as a strong effect on fitness. Thus, body size in Atlantic salmon tends to be positively correlated with freshwater and marine survival, as well as with fecundity, egg size, reproductive success, and offspring survival. By contrast, the fitness implications of variation in behavioural traits such as aggression, sheltering behaviour, or timing of migration are largely unknown. The adaptive significance of molecular variation in salmonids is also scant and largely circumstantial, despite extensive molecular screening on these species. Adaptive variation can result in local adaptations (LA) when, among other necessary conditions, populations live in patchy environments, exchange few or no migrants, and are subjected to differential selective pressures. Evidence for LA in Atlantic salmon is indirect and comes mostly from ecological correlates in fitness-related traits, the failure of many translocations, the poor performance of domesticated stocks, results of a few common-garden experiments (where different populations were raised in a common environment in an attempt to dissociate heritable from environmentally induced phenotypic variation), and the pattern of inherited resistance to some parasites and diseases. Genotype x environment interactions occurr for many fitness traits, suggesting that LA might be important. However, the scale and extent of adaptive variation remains poorly understood and probably varies, depending on habitat heterogeneity, environmental stability and the relative roles of selection and drift. As maladaptation often results from phenotype-environment mismatch, we argue that acting as if populations are not locally adapted carries a much greater risk of mismanagement than acting under the assumption for local adaptations when there are none. As such, an evolutionary approach to salmon conservation is required, aimed at maintaining the conditions necessary for natural selection to operate most efficiently and unhindered. This may require minimising alterations to native genotypes and habitats to which populations have likely become adapted, but also allowing for population size to reach or extend beyond carrying capacity to encourage competition and other sources of natural mortality.

Atlantic salmon (Salmo salar) undergo spectacular marine migrations before homing to spawn in natal rivers. However, males that grow fastest early in life can adopt an alternative 'sneaker' tactic by maturing earlier at greatly reduced size without leaving freshwater. While the ultimate evolutionary causes have been well studied, virtually nothing is known about the molecular bases of this developmental plasticity. We investigate the nature and extent of coordinated molecular changes that accompany such a fundamental transformation by comparing the brain transcription profiles of wild mature sneaker males to age-matched immature males (future large anadromous males) and immature females. Of the ca. 3000 genes surveyed, 15% are differentially expressed in the brains of the two male types. These genes are involved in a wide range of processes, including growth, reproduction and neural plasticity. Interestingly, despite the potential for wide variation in gene expression profiles among individuals sampled in nature, consistent patterns of gene expression were found for individuals of the same reproductive tactic. Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the 'default' life cycle, may actually result from an active inhibition of development into a sneaker.

Organisms that share the same genotype can develop into divergent phenotypes, depending on environmental conditions. In Atlantic salmon, young males of the same age can be found either as sneakers or immature males that are future anadromous fish. Just as the organism-level phenotype varies between divergent male developmental trajectories, brain gene expression is expected to vary as well. We hypothesized that rearing environment can also have an important effect on gene expression in the brain and possibly interact with the reproductive tactic adopted. We tested this hypothesis by comparing brain gene expression profiles of the two male tactics in fish from the same population that were reared in either a natural stream or under laboratory conditions. We found that expression of certain genes was affected by rearing environment only, while others varied between male reproductive tactics independent of rearing environment. Finally, more than half of all genes that showed variable expression varied between the two male tactics only in one environment. Thus, in these fish, very different molecular pathways can give rise to similar macro-phenotypes depending on rearing environment. This result gives important insights into the molecular underpinnings of developmental plasticity in relationship to the environment.

The time course of morphometric variation among life histories for stream-dwelling Atlantic salmon ( Salmo salar L.) parr (age-0+ to age-2+) was analyzed. Possible life histories were combinations of parr maturity status in the autumn (mature or immature) and age at outmigration (smolt at age-2+ or later age). Actual life histories expressed with enough fish for analysis in the 1997 cohort were immature/age-2+ smolt, mature/age-2+smolt, and mature/age-2+ non-smolt. Tagged fish were assigned to one of the three life histories and digital pictures from the field were analyzed using landmark-based geometric morphometrics. Results indicated that successful grouping of fish according to life history varied with fish age, but that fish could be grouped before the actual expression of the life histories. By March (age-1+), fish were successfully grouped using a descriptive discriminant function and successful assignment ranged from 84 to 97% for the remainder of stream residence. A jackknife of the discriminant function revealed an average life history prediction success of 67% from age-1+ summer to smolting. Low sample numbers for one of the life histories may have limited prediction success. A MANOVA on the shape descriptors (relative warps) also indicated significant differences in shape among life histories from age-1+ summer through to smolting. Across all samples, shape varied significantly with size. Within samples, shape did not vary significantly with size for samples from December (age-0+) to May (age-1+). During the age-1+ summer however, shape varied significantly with size, but the relationship between shape and size was not different among life histories. In the autumn (age-1+) and winter (age-2+), life history differences explained a significant portion of the change in shape with size. Life history dependent morphometric variation may be useful to indicate the timing of early expressions of life history variation and as a tool to explore temporal and spatial variation in life history expression.