Spatial asynchrony and cross-scale climate interactions in populations of a coldwater stream fish.

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.

Smaller body size under warming is not due to gill-oxygen limitation in a cold-water salmonid.

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.

Closing the gap between science and management of cold-water refuges in rivers and streams.

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.

Identifying mechanisms underlying individual body size increases in a changing, highly seasonal environment: The growing trout of West brook.

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.

Managing climate refugia for freshwater fishes under an expanding human footprint.

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.

Climate-change refugia: biodiversity in the slow lane.

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.

A geostatistical state-space model of animal densities for stream networks.

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.

Experimental test of genetic rescue in isolated populations of brook trout.

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.

Estimating thermal performance curves from repeated field observations.

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.

Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout.

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.

Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid.

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.

Seasonal weather patterns drive population vital rates and persistence in a stream fish.

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.

Robust estimates of environmental effects on population vital rates: an integrated capture-recapture model of seasonal brook trout growth, survival and movement in a stream network.

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.

Modeling structured population dynamics using data from unmarked individuals.

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.

Basin-scale phenology and effects of climate variability on global timing of initial seaward migration of Atlantic salmon (Salmo salar).

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.

A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis).

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.

Fine-scale population structure and riverscape genetics of brook trout (Salvelinus fontinalis) distributed continuously along headwater channel networks.

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.

Drivers of growth variation in juvenile Atlantic salmon (Salmo salar): an elasticity analysis approach.

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.

Gene-expression signatures of Atlantic salmon's plastic life cycle.

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.

Keeping things local: Subpopulation Nb and Ne in a stream network with partial barriers to fish migration.

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 Ne. We conducted a series of tests of the spatiotemporal scale of inference of estimates of Nb in nine consecutive cohorts within a long-term study of brook trout (Salvelinus fontinalis). We also tested a recently developed approach to estimate generational Ne 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 Nb 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.