Climate and ecosystem linkages explain widespread declines in North American Atlantic salmon populations

Effects of polluted groundwater on chum salmon (Oncorhynchus keta) survival and body size

This study reports the effect of spatial variation in hyporheic water, partially influenced by urban-polluted groundwater, on the early life stage of chum salmon (Oncorhynchus keta) in the Toyohira River, Northern Japan. We hypothesized that increased groundwater influence would reduce the survival rate and body size of O. keta due to the combined effects (i.e., growth retardation effects) of chemical toxicants, low dissolved oxygen (DO), and high winter temperatures. Experimental tests were conducted in field and laboratory conditions to address the difficulties associated with field observations of fry emergence during snowmelt floods in spring and to examine the independent effects of water pollution in groundwater in relation to temperature and DO. Artificially fertilized eyed eggs, alevins, and fry of O. keta were monitored for several months with varying exposure to groundwater from winter to early spring. We noted that groundwater affected the fish by reducing their size and weight by >10% and by increasing their mortality in both tests. Moreover, independent effects of water pollution were identified in the swim-up fry stage in laboratory experiments, along with growth-retarding effects from warmer groundwater temperatures. Not all factorial combinations of potentially confounding factors were tested rigorously, and the specific toxicants are unidentified, leaving questions about how groundwater pollution affects Salmonidae fish. Immediate concerns regarding the current water quality (including DO) of hyporheic water associated with groundwater influence are low because no detrimental effects on survival were detected in the field. Nevertheless, spawning grounds formed in areas with high exposures to polluted groundwater require continuous management attention due to potential risks associated with low DO levels. Additionally, pollution-induced growth patterns could pose a risk of size- or weight-dependent mortality at the swim-up fry stage and in early juveniles.

Synchronicity of the Gulf Stream path downstream of Cape Hatteras and the region of maximum wind stress curl

The Gulf Stream, a major ocean current in the North Atlantic ocean is a key component in the global redistribution of heat and is important for marine ecosystems. Based on 27 years (1993-2019) of wind reanalysis and satellite altimetry measurements, we present observational evidence that the path of this freely meandering jet after its separation from the continental slope at Cape Hatteras, aligns with the region of maximum cyclonic vorticity of the wind stress field known as the positive vorticity pool. This synchronicity between the wind stress curl maximum region and the Gulf Stream path is observed at multiple time-scales ranging from months to decades, spanning a distance of 1500 km between 70 and 55W. The wind stress curl in the positive vorticity pool is estimated to drive persistent upward vertical velocities ranging from 5 to 17 cm day-1 over its ~ 400,000 km2 area; this upwelling may supply a steady source of deep nutrients to the Slope Sea region, and can explain as much as a quarter of estimated primary productivity there.

Body length changes for Atlantic salmon (Salmo salar) over five decades exhibit weak spatial synchrony over a broad latitudinal gradient

Understanding the factors that drive spatial synchrony among populations or species is important for management and recovery of populations. The range-wide declines in Atlantic salmon (Salmo salar) populations may be the result of broad-scale changes in the marine environment. Salmon undergo rapid growth in the ocean; therefore changing marine conditions may affect body size and fecundity estimates used to evaluate whether stock reference points are met. Using a dataset that spanned five decades, 172,268 individuals, and 19 rivers throughout Eastern Canada, we investigated the occurrence of spatial synchrony in changes in the body size of returning wild adult Atlantic salmon. Body size was then related to conditions in the marine environment (i.e., climate indices, thermal habitat availability, food availability, density-dependence, and fisheries exploitation rates) that may act on all populations during the ocean feeding phase of their life cycle. Body size increased during the 1980s and 1990s for salmon that returned to rivers after one (1SW) or two winters at sea (2SW); however, significant changes were only observed for 1SW and/or 2SW in some mid-latitude and northern rivers (10/13 rivers with 10 of more years of data during these decades) and not in southern rivers (0/2), suggesting weak spatial synchrony across Eastern Canada. For 1SW salmon in nine rivers, body size was longer when fisheries exploitation rates were lower. For 2SW salmon, body size was longer when suitable thermal habitat was more abundant (significant for 3/8 rivers) and the Atlantic Multidecadal Oscillation was higher (i.e., warmer sea surface temperatures; significant for 4/8 rivers). Overall, the weak spatial synchrony and variable effects of covariates on body size across rivers suggest that changes in Atlantic salmon body size may not be solely driven by shared conditions in the marine environment. Regardless, body size changes may have consequences for population management and recovery through the relationship between size and fecundity.

Swimming behaviour of Atlantic salmon kelts migrating past a hydropower plant dam: Effects of hydraulics and dam operations

Hydropower plants commonly impede the downstream migration of Atlantic salmon (Salmo salar) kelts. Thus, understanding the effects of hydraulic conditions on kelt behaviour and passage performance at dams is crucial for developing effective mitigation measures. In this study, we investigated the influence of hydraulic conditions on kelt passage performance and swimming behaviour at a Norwegian hydropower plant. We combined biological data from 48 kelts collected via acoustic telemetry with hydraulic data modelled using computational fluid dynamics. We assessed kelt passage performance using metrics such as time-to-pass, total number of detections, and total number of detections per day. Additionally, we analysed swimming depths and speeds in relation to the hydraulic conditions created by different dam operating conditions. We found that the dam operation schedule impacted the kelts' ability to find a route past the dam. Though kelts could have passed the dam throughout the study period via a submerged pipe at the dam (which had seemingly sufficient discharge for the kelts to find), 98 % of the kelts instead waited for a spill gate to open partway through the study period. The swimming depth analysis indicated diel variation, with kelts swimming nearer to the water surface during the night. We found that swimming speed increased with increasing kelt body length, particularly under high turbulence kinetic energy and during the day. Furthermore, kelts swam faster as water velocity increased, but slowed down again as turbulence intensity increased. Our findings reveal the effects of hydraulic conditions and dam operations on the migration behaviour of Atlantic salmon kelts. This provides valuable insights for developing strategies to optimise dam operations and improve fish passage performance, including the need to spill enough water to increase passage success and will contribute to sustainable management of Atlantic salmon populations in regulated rivers.

Estimating multiple years, tributary-specific, and overall Atlantic salmon smolt abundance in a large Canadian catchment using capture-mark-recapture experiments

Population monitoring of Atlantic salmon (Salmo salar L.) abundance is an essential element to understand annual stock variability and inform fisheries management processes. Smolts are the life stage marking the transition from the freshwater to the marine phase of anadromous Atlantic salmon. Estimating smolt abundance allows for subsequent inferences on freshwater and marine survival rates. Annual abundances of out-migrating Atlantic salmon smolts were estimated using Bayesian models and an 18-year capture-mark-recapture time series from two to five trapping locations within the Restigouche River (Canada) catchment. Some of the trapping locations were at the outlet of large upstream tributaries, and these sampled a portion of the total out-migrating population of smolts for the watershed, whereas others were located just above the head of tide of the Restigouche River and sampled the entire run of salmon smolts. Due to logistic and environmental conditions, not all trapping locations were operational each year. Additionally, recapture rates were relatively low (<5%), and the absolute number of recaptures was relatively few (most often a few dozen), leading to incoherent and highly uncertain estimates of tributary-specific and whole catchment abundance estimates when the data were modeled independently among trapping locations and years. Several models of increasing complexity were tested using simulated data, and the best-performing model in terms of bias and precision incorporated a hierarchical structure among years on the catchability parameters and included an explicit spatial structure to account for the annual variations in the number of sampled locations within the watershed. When the best model was applied to the Restigouche River catchment dataset, the annual smolt abundance estimates varied from 250,000 to 1 million smolts, and the subbasin estimates of abundance were consistent with the spatial structure of the monitoring programme. Ultimately, increasing the probabilities of capture and the absolute number of recaptures at the different traps will be required to improve the precision and reduce the bias of the estimates of smolt abundance for the entire basin and within subbasins of the watershed. The model and approach provide a significant improvement in the models used to date based on independent estimates of abundance by trapping location and year. Total abundance and relative production in discrete spawning, nesting, or rearing areas provide critical information to appropriately understand and manage the threats to species that can occur at subpopulation spatial scales.

The impacts of diel thermal variability on growth, development and performance of wild Atlantic salmon (Salmo salar) from two thermally distinct rivers

Temperature in many natural aquatic environments follows a diel cycle, but to date, we know little on how diel thermal cycles affect fish biology. The current study investigates the growth, development and physiological performance of wild Atlantic salmon collected from the Miramichi and Restigouche rivers (NB, Canada). Fish were collected as parr and acclimated to either 16-21 or 19-24°C diel thermal cycles throughout the parr and smolt life stages. Both Miramichi and Restigouche Atlantic salmon parr grew at similar rates during 16-21 or 19-24°C acclimations. However, as smolts, the growth rates of the Miramichi (-8% body mass day-1) and Restigouche (-38% body mass day-1) fish were significantly slower at 19-24°C, and were in fact negative, indicating loss of mass in this group. Acclimation to 19-24°C also increased Atlantic salmon CTmax. Our findings suggest that both life stage and river origin impact Atlantic salmon growth and performance in the thermal range used herein. These findings provide evidence for local adaptation of Atlantic salmon, increased vulnerability to warming temperatures, and highlight the differential impacts of these ecologically relevant diel thermal cycles on the juvenile life stages in this species.

A multi-population approach supports common patterns in marine growth and maturation decision in Atlantic salmon (Salmo salar L.) from southern Europe

This study provides a regional picture of long-term changes in Atlantic salmon growth at the southern edge of their distribution, using a multi-population approach spanning 49 years and five populations. We provide empirical evidence of salmon life history being influenced by a combination of common signals in the marine environment and population-specific signals. We identified an abrupt decline in growth from 1976 and a more recent decline after 2005. As these declines have also been recorded in northern European populations, our study significantly expands a pattern of declining marine growth to include southern European populations, thereby revealing a large-scale synchrony in marine growth patterns for almost five decades. Growth increments during their sea sojourn were characterized by distinct temporal dynamics. At a coarse temporal resolution, growth during the first winter at sea seemed to gradually improve over the study period. However, the analysis of finer seasonal growth patterns revealed ecological bottlenecks of salmon life histories at sea in time and space. Our study reinforces existing evidence of an impact of early marine growth on maturation decision, with small-sized individuals at the end of the first summer at sea being more likely to delay maturation. However, each population was characterized by a specific probabilistic maturation reaction norm, and a local component of growth at sea in which some populations have better growth in some years might further amplify differences in maturation rate. Differences between populations were smaller than those between sexes, suggesting that the sex-specific growth threshold for maturation is a well-conserved evolutionary phenomenon in salmon. Finally, our results illustrate that although most of the gain in length occurs during the first summer at sea, the temporal variability in body length at return is buffered against the decrease in post-smolt growth conditions. The intricate combination of growth over successive seasons, and its interplay with the maturation decision, could be regulating body length by maintaining diversity in early growth trajectories, life histories, and the composition of salmon populations.

The upper temperature and hypoxia limits of Atlantic salmon (Salmo salar) depend greatly on the method utilized

In this study, Atlantic salmon were: (i) implanted with heart rate (fH) data storage tags (DSTs), pharmacologically stimulated to maximum fH, and warmed at 10°C h-1 (i.e. tested using a 'rapid screening protocol'); (ii) fitted with Doppler® flow probes, recovered in respirometers and given a critical thermal maximum (CTmax) test at 2°C h-1; and (iii) implanted with fH DSTs, recovered in a tank with conspecifics for 4 weeks, and had their CTmax determined at 2°C h-1. Fish in respirometers and those free-swimming were also exposed to a stepwise decrease in water oxygen level (100% to 30% air saturation) to determine the oxygen level at which bradycardia occurred. Resting fH was much lower in free-swimming fish than in those in respirometers (∼49 versus 69 beats min-1) and this was reflected in their scope for fH (∼104 versus 71 beats min-1) and CTmax (27.7 versus 25.9°C). Further, the Arrhenius breakpoint temperature and temperature at peak fH for free-swimming fish were considerably greater than for those tested in the respirometers and given a rapid screening protocol (18.4, 18.1 and 14.6°C; and 26.5, 23.2 and 20.2°C, respectively). Finally, the oxygen level at which bradycardia occurred was significantly higher in free-swimming salmon than in those in respirometers (∼62% versus 53% air saturation). These results: highlight the limitations of some lab-based methods of determining fH parameters and thermal tolerance in fishes; and suggest that scope for fH may be a more reliable and predictive measure of a fish's upper thermal tolerance than their peak fH.

Predicting how environmental conditions and smolt body length when entering the marine environment impact individual Atlantic salmon Salmo salar adult return rates

Populations of Atlantic salmon Salmo salar have experienced precipitous declines in abundance since the 1970s. This decline has been associated with reduced numbers of adult salmon returning to fresh water from their marine migration, i.e., their marine return rates (MRR). Thus, understanding the factors that affect MRR is of crucial conservation importance. The authors used a state-space model with a 13-year time series of individually tagged salmon mark-recapture histories on the River Frome, southern England, to test the effect of smolt body length on their MRR. In addition to smolt length, the model tested for the influence of environmental covariates that were representative of the conditions experienced by the smolts in the early stages of their seaward migration, i.e., from the lower river to the estuary exit. The model indicated that, even when accounting for environmental covariates, smolt body length was an important predictor of MRR. Although larger smolts have a higher probability of returning to their natal river as adults than smaller smolts, and one-sea-winter salmon have a survival rate twice as high as multi-sea-winter salmon, the actual biological mechanisms underpinning this phenomenon remain uncertain. These results have important applications for salmon conservation, as efforts to bolster salmon populations in the freshwater environment should consider methods to improve smolt quality (i.e., body size) as well as smolt quantity.

An opinion piece: the evolutionary and ecological consequences of changing selection pressures on marine migration in Atlantic salmon

There are strong signals that the selection forces favouring the expression of long-distance sea migration by Atlantic salmon (Salmo salar) are changing. Unlike many other behavioural traits, the costs of migration are incurred before any fitness benefits become apparent to the migrant. The expression of this behaviour has thus been shaped by selection forces over multiple generations and cannot respond to short interval (within a single generation) environmental change as many other behavioural traits can. Here we provide a framework to examine the evolutionary and ecological consequences of a sustained increase in migration cost. We argue that Atlantic salmon may have entered an evolutionary trap, where long-distance sea migration has become maladaptive because of shifting environmental conditions. We predict that if higher migration costs (affecting survivorship and ultimately fitness) persist, then shifting selection pressures will result in continuing declines in population size. We suggest, however, that in some populations there is demonstrable capacity for evolutionary rescue responses within the species which is to be found in the variation in the expression of migration. Under a scenario of low to moderate change in the selection forces that previously promoted migration, we argue that disruptive, sex-based selection would result in partial migration, where females retain sea migration but with anadromy loss predominantly in males. With more acute selection forces, anadromy may be strongly selected against, under these conditions both sexes may become freshwater resident. We suggest that as the migration costs appear to be higher in catchments with standing waters, then this outcome is more likely in such systems. We also speculate that as a result of the genetic structuring in this species, not all populations may have the capacity to respond adequately to change. The consequences of this for the species and its management are discussed.

Acute critical thermal maximum does not predict chronic incremental thermal maximum in Atlantic salmon (Salmo salar)

Atlantic salmon is an important aquaculture species farmed in ocean net-pens and therefore subjected to changing environmental conditions, including rising temperatures. This creates a need for research on the thermal tolerance of this species for the future of sustainable aquaculture. We investigated the thermal tolerance of individually tagged Atlantic salmon post-smolts subjected sequentially to two common high-temperature challenges: critical thermal maximum (CTmax) followed by incremental thermal maximum (ITmax). Our goals were (1) to determine whether CTmax can predict ITmax for individual fish, and (2) to examine connections between various body size (mass, length, condition factor), cardiac (absolute and relative ventricle mass) and blood (hematocrit) metrics and thermal tolerance. We found no relationship between CTmax and ITmax. This is of concern because CTmax, which is a quick and easy test, is often used to predict upper lethal limits in fish despite not using real-world rates of temperature increase and not using death as the experimental endpoint (unlike ITmax). Also, some metrics which correlated in one direction with CTmax had the opposite correlation with ITmax. For instance, smaller fish or fish with smaller ventricles had a higher CTmax but a lower ITmax than larger fish or fish with larger ventricles. Taken together, these results highlight the need to take care when using acute thermal tolerance tests to predict real-world responses to rising temperatures.

The Trend and Interannual Variability of Marine Heatwaves over the Bay of Bengal

Marine heatwaves (MHWs) are long-lasting extreme oceanic warming events that can cause devastating effects on warm-water corals and associated ecosystems. The linear trend and interannual variability of MHWs over the Bay of Bengal (BOB) during 1982–2020 are investigated by a high-resolution daily sea surface temperature (SST) dataset. In regions where warm-water coral reefs are concentrated, annual MHW days and frequency significantly increase during 1982–2020, at rates exceeding that of the global mean. The coldest boreal winter season witnesses significant and steady increase trends in MHW days and frequency. In contrast, the trend is insignificant in the climatological warmest season (March to June) south of 15° N in the BOB, mainly due to large interannual variability. El Niño and Southern Oscillation (ENSO) dominates the interannual variability of BOB MHWs, which are highly consistent with the evolution of the mean SST. The negative phase of North Atlantic Oscillation (NAO) also modulates the occurrences of MHWs, especially over the northeastern BOB. The two climate modes synergistically explain about 50~70% of the interannual variances in the BOB’s MHWs. Correlation analysis reveals that south of 15° N in the BOB, the effect of El Niño on MHWs is evident from the boreal autumn of its developing phase to the boreal summer of its decaying phase, along with limited influence from NAO. However, in the northeast of the BOB, the effect of El Niño merely emerges from April to August of its decaying stage. In comparison, boreal winter-to-spring NAO exerts a strong control over March-to-June MHWs in the northeastern BOB. The results suggest that various climate modes may jointly or separately influence MHWs at certain seasons and locations, which is important for the seasonal prediction of MHWs. Indeed, when combining the Niño3.4 mature winter index and boreal winter-to-spring NAO index to build a regression model, it is more effective in reproducing the BOB’s MHW frequency compared to the Niño3.4 index alone.

Incursions of sea lamprey, Petromyzon marinus, and striped bass, Morone saxatilis, in Labrador waters: Episodic events or evidence of a northward range expansion?

We describe observations of sea lamprey (Petromyzon marinus) and striped bass (Morone saxatilis) incursions into Labrador, Canada. While P. marinus have been periodically observed in similar latitudes, their numbers have conspicuously increased in estuarine environments in 2020. In contrast, M. saxatilis were not observed from Labrador until 2017 but appear to be declining after the initial surge in abundance that peaked in 2018. It remains unclear whether spawning populations of either species exist. Given the potential to negatively affect species of commercial and cultural importance through predation, follow-up surveys are warranted.

Redefining the oceanic distribution of Atlantic salmon

Determining the mechanisms driving range-wide reductions in Atlantic salmon marine survival is hindered by an insufficient understanding of their oceanic ecology and distribution. We attached 204 pop-up satellite archival tags to post-spawned salmon when they migrated to the ocean from seven European areas and maiden North American salmon captured at sea at West Greenland. Individuals migrated further north and east than previously reported and displayed increased diving activity near oceanographic fronts, emphasizing the importance of these regions as feeding areas. The oceanic distribution differed among individuals and populations, but overlapped more between geographically proximate than distant populations. Dissimilarities in distribution likely contribute to variation in growth and survival within and among populations due to spatio-temporal differences in environmental conditions. Climate-induced changes in oceanographic conditions will alter the location of frontal areas and may have stock-specific effects on Atlantic salmon population dynamics, likely having the largest impacts on southern populations.

Climate change threatens Chinook salmon throughout their life cycle

Widespread declines in Atlantic and Pacific salmon (Salmo salar and Oncorhynchus spp.) have tracked recent climate changes, but managers still lack quantitative projections of the viability of any individual population in response to future climate change. To address this gap, we assembled a vast database of survival and other data for eight wild populations of threatened Chinook salmon (O. tshawytscha). For each population, we evaluated climate impacts at all life stages and modeled future trajectories forced by global climate model projections. Populations rapidly declined in response to increasing sea surface temperatures and other factors across diverse model assumptions and climate scenarios. Strong density dependence limited the number of salmon that survived early life stages, suggesting a potentially efficacious target for conservation effort. Other solutions require a better understanding of the factors that limit survival at sea. We conclude that dramatic increases in smolt survival are needed to overcome the negative impacts of climate change for this threatened species.

Snake River sockeye and Chinook salmon in a changing climate: Implications for upstream migration survival during recent extreme and future climates

In 2015, the Pacific marine heat wave, low river flows, and record high water temperatures in the Columbia River Basin contributed to a near-complete failure of the adult migration of endangered Snake River sockeye salmon (Oncorhynchus nerka, NOAA Fisheries 2016). These extreme weather events may become the new normal due to anthropogenic climate change, with catastrophic consequences for endangered species. Existing anthropogenic pressures may amplify vulnerability to climate change, but these potential synergies have rarely been quantified. We examined factors affecting survival of endangered sockeye (Oncorhynchus nerka) and threatened Chinook salmon (O. tshawytscha) as they migrated upstream through eight dams and reservoirs to spawning areas in the Snake River Basin. Our extensive database included histories of 17,279 individual fish that migrated since 2004. A comparison between conditions in 2015 and daily temperatures and flows in a regulated basin forced by output from global climate models showed that 2015 did have many characteristics of projected future mean conditions. To evaluate potential salmon responses, we modeled migration timing and apparent survival under historical and future climate scenarios (2040s). For Chinook salmon, adult survival from the first dam encountered to spawning grounds dropped by 4-15%, depending on the climate scenario. For sockeye, survival dropped by ~80% from their already low levels. Through sensitivity analyses, we observed that the adult sockeye migration would need to shift more than 2 weeks earlier than predicted to maintain survival rates typical of those seen during 2008-2017. Overall, the greater impacts of climate change on adult sockeye compared with adult Chinook salmon reflected differences in life history and environmental sensitivities, which were compounded for sockeye by larger effect sizes from other anthropogenic factors. Compared with Chinook, sockeye was more negatively affected by a history of juvenile transportation and by similar temperatures and flows. The largest changes in temperature and flow were projected to be upstream from the hydrosystem, where direct mitigation through hydrosystem management is not an option. Unfortunately, Snake River sockeye have likely lost much of their adaptive capacity with the loss of the wild population. Further work exploring habitat restoration or additional mitigation actions is urgently needed.

FiCli, the Fish and Climate Change Database, informs climate adaptation and management for freshwater fishes

Inland fishes provide important ecosystem services to communities worldwide and are especially vulnerable to the impacts of climate change. Fish respond to climate change in diverse and nuanced ways, which creates challenges for practitioners of fish conservation, climate change adaptation, and management. Although climate change is known to affect fish globally, a comprehensive online, public database of how climate change has impacted inland fishes worldwide and adaptation or management practices that may address these impacts does not exist. We conducted an extensive, systematic primary literature review to identify peer-reviewed journal publications describing projected and documented examples of climate change impacts on inland fishes. From this standardized Fish and Climate Change database, FiCli (pronounced fick-lee), researchers and managers can query fish families, species, response types, or geographic locations to obtain summary information on inland fish responses to climate change and recommended management actions. The FiCli database is updatable and provides access to comprehensive published information to inform inland fish conservation and adaptation planning in a changing climate.

Spatial synchrony in the response of a long range migratory species (Salmo salar) to climate change in the North Atlantic Ocean

A major challenge in understanding the response of populations to climate change is to separate the effects of local drivers acting independently on specific populations, from the effects of global drivers that impact multiple populations simultaneously and thereby synchronize their dynamics. We investigated the environmental drivers and the demographic mechanisms of the widespread decline in marine survival rates of Atlantic salmon (Salmo salar) over the last four decades. We developed a hierarchical Bayesian life cycle model to quantify the spatial synchrony in the marine survival of 13 large groups of populations (called stock units, SU) from two continental stock groups (CSG) in North America (NA) and Southern Europe (SE) over the period 1971-2014. We found strong coherence in the temporal variation in postsmolt marine survival among the 13 SU of NA and SE. A common North Atlantic trend explains 37% of the temporal variability of the survivals for the 13 SU and declines by a factor of 1.8 over the 1971-2014 time series. Synchrony in survival trends is stronger between SU within each CSG. The common trends at the scale of NA and SE capture 60% and 42% of the total variance of temporal variations, respectively. Temporal variations of the postsmolt survival are best explained by the temporal variations of sea surface temperature (SST, negative correlation) and net primary production indices (PP, positive correlation) encountered by salmon in common domains during their marine migration. Specifically, in the Labrador Sea/Grand Banks for populations from NA, 26% and 24% of variance is captured by SST and PP, respectively and in the Norwegian Sea for populations from SE, 21% and 12% of variance is captured by SST and PP, respectively. The findings support the hypothesis of a response of salmon populations to large climate-induced changes in the North Atlantic simultaneously impacting populations from distant continental habitats.

Thermal habitat of adult Atlantic salmon Salmo salar in a warming ocean

The year-round thermal habitat at sea for adult Atlantic salmon Salmo salar (n = 49) from northern Norway was investigated using archival tags over a 10 year study period. During their ocean feeding migration, the fish spent 90% of the time in waters with temperatures from 1.6-8.4°C. Daily mean temperatures ranged from -0.5 to 12.9°C, with daily temperature variation up to 9.6°C. Fish experienced the coldest water during winter (November-March) and the greatest thermal range during the first summer at sea (July-August). Trends in sea-surface temperatures influenced the thermal habitat of salmon during late summer and autumn (August-October), with fish experiencing warmer temperatures in warmer years. This pattern was absent during winter (November-March), when daily mean temperatures ranged from 3.4-5.0°C, in both colder and warmer years. The observations of a constant thermal habitat during winter in both warmer and colder years, may suggest that the ocean distribution of salmon is flexible and that individual migration routes could shift as a response to spatiotemporal alterations of favourable prey fields and ocean temperatures.

Evaluating the effect of dorsal muscle biopsies on adult Atlantic salmon growth and marine return rates

Increasing conservation and animal-welfare concerns have driven the development of non-lethal sampling of fish populations, with the use of muscle tissue biopsies now being routinely applied as a sampling method in the wild. Crucial to the success of non-lethal sampling, however, is an evaluation of the short- and long-term consequences of the treatment and ultimately the determination of how these may affect organism mortality and other fitness-related traits. The current study evaluated the use of a dorsal muscle biopsies on post-spawned Atlantic salmon emigrating to sea and undertaking a 2-month long-feeding migration before returning to spawn. Using mark-recapture, return rates and growth were compared between fish that were biopsied and externally tagged, and a control group tagged only with external tags. The biopsy treatment showed no lasting effects on fish as estimated from the two key fitness-related parameters. Results, therefore, suggest the technique can be more widely applied to gather information on marine migrating Atlantic salmon and other anadromous fishes that can be intercepted as they descend and ascend rivers during seasonal migrations. Coupled with modern tagging technologies, the use of biopsies may facilitate an improved understanding of movement and its consequences in terms of feeding patterns and growth.

The North Atlantic Ecosystem, from Plankton to Whales

Compared with terrestrial ecosystems, marine ecosystems have a higher proportion of heterotrophic biomass. Building from this observation, we define the North Atlantic biome as the region where the large, lipid-rich copepod Calanus finmarchicus is the dominant mesozooplankton species. This species is superbly adapted to take advantage of the intense pulse of productivity associated with the North Atlantic spring bloom. Most of the characteristic North Atlantic species, including cod, herring, and right whales, rely on C. finmarchicus either directly or indirectly. The notion of a biome rests inherently on an assumption of stability, yet conditions in the North Atlantic are anything but stable. Humans have reduced the abundance of many fish and whales (though some recovery is underway). Humans are also introducing physical and chemical trends associated with global climate change. Thus, the future of the North Atlantic depends on the biome's newest species, Homo sapiens.

Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids

Early marine survival of juvenile salmon is intimately associated with their physiological condition during smoltification and ocean entry. Smoltification (parr-smolt transformation) is a developmental process that allows salmon to acquire seawater tolerance in preparation for marine living. Traditionally, this developmental process has been monitored using gill Na⁺/K⁺-ATPase (NKA) activity or plasma hormones, but gill gene expression offers the possibility of another method. Here, we describe the discovery of candidate genes from gill tissue for staging smoltification using comparisons of microarray studies with particular focus on the commonalities between anadromous Rainbow trout and Sockeye salmon datasets, as well as a literature comparison encompassing more species. A subset of 37 candidate genes mainly from the microarray analyses was used for TaqMan quantitative PCR assay design and their expression patterns were validated using gill samples from four groups, representing three species and two ecotypes: Coho salmon, Sockeye salmon, stream-type Chinook salmon and ocean-type Chinook salmon. The best smoltification biomarkers, as measured by consistent changes across these four groups, were genes involved in ion regulation, oxygen transport and immunity. Smoltification gene expression patterns (using the top 10 biomarkers) were confirmed by significant correlations with NKA activity and were associated with changes in body brightness, caudal fin darkness and caudal peduncle length. We incorporate gene expression patterns of pre-smolt, smolt and de-smolt trials from acute seawater transfers from a companion study to develop a preliminary seawater tolerance classification model for ocean-type Chinook salmon. This work demonstrates the potential of gene expression biomarkers to stage smoltification and classify juveniles as pre-smolt, smolt or de-smolt.

Experimental investigation of the effects of temperature and feeding regime on scale growth in Atlantic salmon Salmo salar post-smolts

Salmo salar post-smolts were reared in seawater under controlled laboratory conditions for 12 weeks. The fish were exposed to three constant temperature treatments (15, 10.5 and 6°C) and four feeding treatments (constant feeding, food withheld for 7 days, food withheld for 14 days and food withheld intermittently for four periods of 7 days). Scale growth was proportional to fish growth across all treatments, justifying the use of scale measurements as a proxy for growth during the early marine phase. The rate of circuli deposition was dependant on temperature and feeding regime and was generally proportional to fish growth but with some decoupling of the relationship at 15°C. Deposition rates varied from 4.8 days per circulus at 15°C (constant feeding) to 15.1 days per circulus at 6°C (interrupted feeding). Cumulative degree day (^° D) was a better predictor of circuli number than age, although the rate of circuli deposition ^° D^-1 was significantly lower at 6°C compared with 15 and 10.5°C. Inter-circuli distances were highly variable and did not reflect growth rate; tightly packed circuli occurred during periods without food when growth was depressed, but also during periods of rapid growth at 15°C. The results further current understanding of scale growth properties and can inform investigations of declining marine growth in S. salar based on interpretations of scale growth patterns.

Co-inheritance of sea age at maturity and iteroparity in the Atlantic salmon vgll3 genomic region

Co-inheritance in life-history traits may result in unpredictable evolutionary trajectories if not accounted for in life-history models. Iteroparity (the reproductive strategy of reproducing more than once) in Atlantic salmon (Salmo salar) is a fitness trait with substantial variation within and among populations. In the Teno River in northern Europe, iteroparous individuals constitute an important component of many populations and have experienced a sharp increase in abundance in the last 20 years, partly overlapping with a general decrease in age structure. The physiological basis of iteroparity bears similarities to that of age at first maturity, another life-history trait with substantial fitness effects in salmon. Sea age at maturity in Atlantic salmon is controlled by a major locus around the vgll3 gene, and we used this opportunity demonstrate that these two traits are co-inherited around this genome region. The odds ratio of survival until second reproduction was up to 2.4 (1.8-3.5 90% CI) times higher for fish with the early-maturing vgll3 genotype (EE) compared to fish with the late-maturing genotype (LL). The L allele was dominant in individuals remaining only one year at sea before maturation, but the dominance was reversed, with the E allele being dominant in individuals maturing after two or more years at sea. Post hoc analysis indicated that iteroparous fish with the EE genotype had accelerated growth prior to first reproduction compared to first-time spawners, across all age groups, whereas this effect was not detected in fish with the LL genotype. These results broaden the functional link around the vgll3 genome region and help us understand constraints in the evolution of life-history variation in salmon. Our results further highlight the need to account for genetic correlations between fitness traits when predicting demographic changes in changing environments.

Evidence for long-term change in length, mass and migration phenology of anadromous spawners in French Atlantic salmon Salmo salar

This study provides new data on Atlantic salmon Salmo salar life-history traits across France. Using a long-term recreational angling database (1987-2013) covering 34 rivers in three regions (genetic units), a decline in individual length, mass and a delayed adult return to French rivers was reported. Temporal similarities in trait variations between regions may be attributed to common change in environmental conditions at sea. The relative rate of change in phenotypic traits was more pronounced in early maturing fish [1 sea-winter (1SW) fish] than in late maturing fish (2SW fish). Such contrasted response within populations highlights the need to account for the diversity in life histories when exploring mechanisms of phenotypic change in S. salar. Such detailed life-history data on returning S. salar have not previously been reported from France. This study on French populations also contributes to reducing the gap in knowledge by providing further empirical evidence of a global pattern in S. salar across its distribution range. Results are consistent with the hypothesis that the observed changes in life-history traits are primarily associated with environmental changes in the North Atlantic Ocean. They also emphasize the presence of less important, but still significant contrasts between region and life history.

Making sense of the relationships between Ne, Nb and Nc towards defining conservation thresholds in Atlantic salmon (Salmo salar)

Effective population size over a generation (Ne) or over a reproductive cycle (Nb) and the adult census size (Nc) are important parameters in both conservation and evolutionary biology. Ne provides information regarding the rate of loss of genetic diversity and can be tracked back in time to infer demographic history of populations, whereas Nb may often be more easily quantified than Nc for short-term abundance monitoring. In this study, we propose (1) an empirical context to Waples et al. (2014) who introduced a correction to bias due to overlapping generations, and (2) a mathematical relationship between Ne and Nb for direct application in Atlantic salmon populations in Québec, Canada. To achieve this, we investigate the relationships between Ne, Nb and Nc in 10 Atlantic salmon populations, Canada, for which we genotyped 100 randomly sampled young-of-the year individuals for 5 consecutive years. The results show a positive correlation between Ne, Nb and Nc, suggesting that Nb is an indicative parameter for tracking effective population size and abundance of Atlantic salmon. However, our model allows predicting Nc from Nb values at 27% that can be partly explained by high variance in Nb/Nc both among populations (37%) and among years (19%). This result illustrates the need for thorough calibration of Nb/Nc before using Nb in monitoring programs, as well as a full understanding of the limits of such an approach. Finally, we discuss the importance of these results for the management of wild populations.

Physiological preparedness and performance of Atlantic salmon Salmo salar smolts in relation to behavioural salinity preferences and thresholds

This study investigated the relationships between behavioural responses of Atlantic salmon Salmo salar smolts to saltwater (SW) exposure and physiological characteristics of smolts in laboratory experiments. It concurrently described the behaviour of acoustically tagged smolts with respect to SW and tidal cycles during estuary migration. Salmo salar smolts increased their use of SW relative to fresh water (FW) from April to June in laboratory experiments. Mean preference for SW never exceeded 50% of time in any group. Preference for SW increased throughout the course of smolt development. Maximum continuous time spent in SW was positively related to gill Na(+), K(+)-ATPase (NKA) activity and osmoregulatory performance in full-strength SW (measured as change in gill NKA activity and plasma osmolality). Smolts decreased depth upon reaching areas of the Penobscot Estuary where SW was present, and all fish became more surface oriented during passage from head of tide to the ocean. Acoustically tagged, migrating smolts with low gill NKA activity moved faster in FW reaches of the estuary than those with higher gill NKA activity. There was no difference in movement rate through SW reaches of the estuary based on gill NKA activity. Migrating fish moved with tidal flow during the passage of the lower estuary based on the observed patterns in both vertical and horizontal movements. The results indicate that smolts select low-salinity water during estuary migration and use tidal currents to minimize energetic investment in seaward migration. Seasonal changes in osmoregulatory ability highlight the importance of the timing of stocking and estuary arrival.

Condition-dependent migratory behaviour of endangered Atlantic salmon smolts moving through an inland sea

The Bras d'Or Lake watershed of Cape Breton Island, Nova Scotia, Canada is a unique inland sea ecosystem, UNESCO Biosphere Reserve and home to a group of regionally distinct Atlantic salmon (Salmo salar) populations. Recent population decreases in this region have raised concern about their long-term persistence. We used acoustic telemetry to track the migrations of juvenile salmon (smolts) from the Middle River into the Bras d'Or Lake and, subsequently, into the Atlantic Ocean. Roughly half of the tagged smolts transited the Bras d'Or Lakes to the Atlantic Ocean, using a migration route that took them through the Gulf of St Lawrence's northern exit at the Strait of Belle Isle (∼650 km from the home river) towards feeding areas in the Labrador Sea and Greenland. However, a significant fraction spent >70 days in the Lakes, suggesting that this population has an alternative resident form, in which smolts limit their migrations within the Bras d'Or. Smolts in good relative condition (as determined from length-to-mass relationships) tended to be residents, whereas fish in poorer condition were ocean migrants. We also found a covarying effect of river temperature that helped to predict residence vs. ocean migration. We discuss these results relative to their bioenergetic implications and provide suggestions for future studies aimed at the conservation of declining salmon populations in Canada.

Warming Ocean Conditions Relate to Increased Trophic Requirements of Threatened and Endangered Salmon

The trophic habits, size and condition of yearling Chinook salmon (Oncorhynchus tshawytscha) caught early in their marine residence were examined during 19 survey years (1981–1985; 1998–2011). Juvenile salmon consumed distinct highly piscivorous diets in cold and warm ocean regimes with major differences between ocean regimes driven by changes in consumption of juvenile rockfishes, followed by several other fish prey, adult euphausiids and decapod larvae. Notable, Chinook salmon consumed 30% more food in the warm versus cold ocean regime in both May and June. Additionally, there were about 30% fewer empty stomachs in the warm ocean regime in May, and 10% fewer in warm June periods. The total prey energy density consumed during the warmer ocean regime was also significantly higher than in cold. Chinook salmon had lower condition factor and were smaller in fork length during the warm ocean regime, and were longer and heavier for their size during the cold ocean regime. The significant increase in foraging during the warm ocean regime occurred concurrently with lower available prey biomass. Adult return rates of juvenile Chinook salmon that entered the ocean during a warm ocean regime were lower. Notably, our long term data set contradicts the long held assertion that juvenile salmon eat less in a warm ocean regime when low growth and survival is observed, and when available prey are reduced. Comparing diet changes between decades under variable ocean conditions may assist us in understanding the effects of projected warming ocean regimes on juvenile Chinook salmon and their survival in the ocean environment. Bioenergetically, the salmon appear to require more food resources during warm ocean regimes.

Quantifying patterns of change in marine ecosystem response to multiple pressures

The ability to understand and ultimately predict ecosystem response to multiple pressures is paramount to successfully implement ecosystem-based management. Thresholds shifts and nonlinear patterns in ecosystem responses can be used to determine reference points that identify levels of a pressure that may drastically alter ecosystem status, which can inform management action. However, quantifying ecosystem reference points has proven elusive due in large part to the multi-dimensional nature of both ecosystem pressures and ecosystem responses. We used ecological indicators, synthetic measures of ecosystem status and functioning, to enumerate important ecosystem attributes and to reduce the complexity of the Northeast Shelf Large Marine Ecosystem (NES LME). Random forests were used to quantify the importance of four environmental and four anthropogenic pressure variables to the value of ecological indicators, and to quantify shifts in aggregate ecological indicator response along pressure gradients. Anthropogenic pressure variables were critical defining features and were able to predict an average of 8-13% (up to 25-66% for individual ecological indicators) of the variation in ecological indicator values, whereas environmental pressures were able to predict an average of 1-5 % (up to 9-26% for individual ecological indicators) of ecological indicator variation. Each pressure variable predicted a different suite of ecological indicator’s variation and the shapes of ecological indicator responses along pressure gradients were generally nonlinear. Threshold shifts in ecosystem response to exploitation, the most important pressure variable, occurred when commercial landings were 20 and 60% of total surveyed biomass. Although present, threshold shifts in ecosystem response to environmental pressures were much less important, which suggests that anthropogenic pressures have significantly altered the ecosystem structure and functioning of the NES LME. Gradient response curves provide ecologically informed transformations of pressure variables to explain patterns of ecosystem structure and functioning. By concurrently identifying thresholds for a suite of ecological indicator responses to multiple pressures, we demonstrate that ecosystem reference points can be evaluated and used to support ecosystem-based management.