Summer temperature variation and implications for juvenile Atlantic salmon

Temperature is important to fish in determining their geographic distribution. For cool- and cold-water fish, thermal regimes are especially critical at the southern end of a species’ range. Although temperature is an easy variable to measure, biological interpretation is difficult. Thus, how to determine what temperatures are meaningful to fish in the field is a challenge. Herein, we used the Connecticut River as a model system and Atlantic salmon (Salmo salar) as a model species with which to assess the effects of summer temperatures on the density of age 0 parr. Specifically, we asked: (1) What are the spatial and temporal temperature patterns in the Connecticut River during summer? (2) What metrics might detect effects of high temperatures? and (3) How is temperature variability related to density of Atlantic salmon during their first summer? Although the most southern site was the warmest, some northern sites were also warm, and some southern sites were moderately cool. This suggests localized, within basin variation in temperature. Daily and hourly means showed extreme values not apparent in the seasonal means. We observed significant relationships between age 0 parr density and days at potentially stressful, warm temperatures (≥23°C). Based on these results, we propose that useful field reference points need to incorporate the synergistic effect of other stressors that fish encounter in the field as well as the complexity associated with cycling temperatures and thermal refuges. Understanding the effects of temperature may aid conservation efforts for Atlantic salmon in the Connecticut River and other North Atlantic systems.     

Assessing the transferability of hydraulic habitat models for juvenile Atlantic salmon

Hydraulic habitat models are logistically and technically challenging and expensive to produce. They are therefore frequently transferred between rivers, often with different environmental conditions, without validation. Although studies have recognised problems with model transfer, few have assessed the consequences for model predictions. This study investigated the local (within sub-catchment) transfer of hydraulic habitat models developed for Atlantic salmon (Salmo salar) fry. Two adjacent reaches were chosen for the study, each containing pool, riffle, glide and run habitats. Detailed topographic surveys were used to develop hydraulic models for the study reaches. Substrate and cover were characterised using transects. Seasonal fish habitat use was characterised by electrofishing. Uniform saturation stocking was employed to ensure standard starting densities across all habitats. Generalised additive models were fitted to fry abundance data. Depth, velocity, dominant substrate and cover were used as predictor variables. The distribution of depth, velocity, dominant substrate and cover differed between the two reaches, but was consistent within reaches across seasons. Substrate exhibited the greatest inter-reach difference. Velocity and depth were the most important individual predictors of fry abundance, with the highest densities observed at moderate velocities (∼0.4 m s⁻¹) and low depths (∼0.1 m) across all seasons. When models were transferred locally between reaches, those that were adjusted for inter-reach differences in mean fry abundance (i.e. those predicting changes in relative abundance) performed better than those transferred without adjustment. Complex models that included substrate and cover typically explained some of the variation in abundance in the transferred reach but performed less well than models containing hydraulic parameters alone. This potentially reflected inter-reach differences in the distribution of substrate and cover. This study suggests that (1) uniform stocking is useful for examining habitat-abundance relationships free from the influence of patchy egg deposition; (2) habitat models should be developed at sites offering maximum environmental complexity at a local level; (3) scientists and managers should avoid transferring models between locations with different environmental characteristics, especially in the absence of model validation; (4) complex models should be avoided, and those containing hydraulic variables alone should be considered, if predictions of habitat quality are to be made at new sites.     

Spatial variation in population dynamics of juvenile Atlantic salmon: implications for conservation and management

Application of habitat models for predicting expected local densities of Atlantic Salmon Salmo salar in healthy populations has been hampered by a lack of generality in their fit to data from different systems. It is believed that this problem results at least in part from difficulties of effectively integrating factors that act across a range of spatial and temporal scales. Here, as an aid to developing more robust modelling and sampling methodologies, a simple process‐based model for local‐scale dynamics of Atlantic salmon juveniles is developed from first principles by integrating contemporary understanding of self‐thinning, density‐dependent growth and dispersal. The aim is to present a readily understood structure to illustrate the links between spawning and stocking strategies, habitat, migration and fish production. Based on this structure, contemporary understanding of the more complex biological processes that affect density, growth and habitat are discussed in relation to some of the key requirements of managers, including stocking for rehabilitation, assessment of predation impact and development of strategies for sampling populations effectively when deriving habitat‐production models. A major conclusion is that more structured, integrated research is required to provide the basic variables needed to model links between local and global scale habitat and fish production effectively. Nevertheless, application of the current understanding of the biology of Atlantic salmon should be of great benefit to managers in extracting key information from field surveys.     

Habitat selection by juvenile Atlantic salmon: the interaction between physical habitat and abundance

The effect of physical river habitat variables on the distribution of juvenile Atlantic salmon Salmo salar L. in the Rivière de la Trinité, Québec, Canada, was examined using generalized additive modelling. A survey of Atlantic salmon fry and parr densities and habitat variables (flow velocity, water column depth and substratum size) was conducted in the summer months from 1984 to 1992. Clear patterns of habitat use existed: specific ranges of habitat variables were selected, with parr preferring greater velocities, depths and substratum sizes than fry. There was a large variation, however, in juvenile densities for given velocities, depths or substratum sizes, with this variation being greatest in optimal habitats. On examination of an individual year, interaction between the variables was found to explain some of the variation. On a year‐to‐year basis the juvenile Atlantic salmon population was found to exhibit an 'Ideal Free Distribution', which resulted in greatest variation in optimal habitats with year‐to‐year changes in population abundance.     

Changes in habitat availability for outmigrating juvenile salmon (Oncorhynchus spp.) following estuary restoration

The restoration of the Nisqually River Delta (Washington, U.S.A.) represents one of the largest efforts toward reestablishing the ecosystem function and resilience of modified habitat in the Puget Sound, particularly for anadromous salmonid species. The opportunity for outmigrating salmon to access and benefit from the expansion of available tidal habitat can be quantified by several physical attributes, which are related to the ecological and physiological responses of juvenile salmon. We monitored a variety of physical parameters to measure changes in opportunity potential from historic, pre‐restoration, and post‐restoration habitat conditions at several sites across the delta. These parameters included channel morphology, water quality, tidal elevation, and landscape connectivity. We conducted fish catch surveys across the delta to determine if salmon was utilizing restored estuary habitat. Overall major channel area increased 42% and major channel length increased 131% from pre‐ to post‐restoration conditions. Furthermore, the results of our tidal inundation model indicated that major channels were accessible up to 75% of the time, as opposed to 30% pre‐restoration. Outmigrating salmon utilized this newly accessible habitat as quickly as 1 year post‐restoration. The presence of salmon in restored tidal channels confirmed rapid post‐restoration increases in opportunity potential on the delta despite habitat quality differences between restored and reference sites.     

Effect of water temperature and density of juvenile salmonids on growth of young-of-the-year Atlantic salmon Salmo salar

A von Bertalanffy growth model for young-of the-year Atlantic salmon Salmo salar in a small French coastal stream was fitted using water temperatures and densities of juvenile salmonids (S. salar and brown trout Salmo trutta) as covariates influencing daily growth rate. The Bayesian framework was used as a template to integrate prior information from external data sets. The relative influence of the covariates on parr growth was quantified and results showed that growth of S. salar juveniles depended on both water temperatures and densities, but that most of the spatiotemporal variability of growth resulted from local spatiotemporal variations of 0+ age salmonid (S. salar and S. trutta) densities. Further analysis revealed that the fluctuations in young-of-the-year salmonid densities are likely to dominate the effects of potential future warming of water temperature due to climate change. It is concluded that factors that could affect salmonid densities might well have a greater effect on S. salar population dynamics than factors influencing water temperatures.     

Synthesis of habitat restoration impacts on young-of-the-year salmonids in boreal rivers

Reviews in Fish Biology and Fisheries - River restoration offers the potential to enhance biological integrity, often measured as fish population changes. We used a meta-analytical approach to...     

Nearshore fish habitat utilization and species associations in Lake Opinicon (Ontario,Canada)

Synopsis The bulk of Lake Opinicon fish biomass is concentrated in the physically diverse inshore areas. Quantitative analysis of the community compositions of the various inshore habitat types (weedy inlets, sandy shallows, rock shelf, gravel, etc.) showed that each supported a characteristic assemblage of fishes with a relatively constant species and year class composition. This was maintained throughout the season despite a drop in fish biomass in late summer when there was a progressive movement into the offshore waters.Weedbed areas supported the highest biomass, and greatest species and year class diversity. Thereafter, in declining order of richness, were rocky and sandy areas. A few fish species were restricted to single habitat types, e.g.Notropis heterodon to inshore weedbeds.Lepomis macrochirus, the commonest species in the lake was, by contrast, versatile and occurred in all inshore habitats. Commonly the numbers of a species in a habitat differed between day and night. Significant diel movements between habitats characterized two nocturnal feedersPomoxis nigromaculatus andIctalurus nebulosus.     

The spatial scale of density-dependent growth and implications for dispersal from nests in juvenile Atlantic salmon

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

The effect of habitat heterogeneity on the population density of juvenile Atlantic salmon Salmo salar L.

In each of eight sites in 2 years in Catamaran Brook and the Little Southwest Miramichi River, in New Brunswick, Canada, 36 boulders (median diameter = 0·20 m) were added to a 2 × 3 m quadrat in one treatment, all boulders were removed in another treatment, and one quadrat was left as a control. As predicted, adding boulders increased the density of salmonid fishes, primarily juvenile Atlantic salmon Salmo salar , by 2·8-fold, but had no significant effect on non-territorial fishes, primarily cyprinids and catostomids. Moreover, the effect of adding boulders was greatest for age 0+ year Atlantic salmon, intermediate for age 1+ year Atlantic salmon and had no effect on age 2+ year Atlantic salmon. The results suggest that adding boulders is an effective short-term technique for increasing the density of stream-dwelling salmonids.     

Movement and feeding ecology of recently emerged steelhead in Lake Ontario tributaries

Steelhead (Oncorhynchus mykiss) ascend several Lake Ontario tributaries to spawn and juveniles are often the most abundant salmonid where spawning is successful. Movement and diet of recently emerged subyearling steelhead were examined in three New York tributaries of Lake Ontario. Downstream movement occurred mainly at night and consisted of significantly smaller fry that were feeding at lower levels than resident fry. Fry fed at the highest rate during the day and chironomids and baetids were the main components of their diet. The diet composition of steelhead fry was closely associated with the composition of the benthos in Trout Brook but more similar to the composition of the drift in the other streams. Daily ration was similar among streams, ranging from 10.2 to 14.3%. These findings are consistent with previous findings on the ecology of steelhead fry, as well as fry of other salmonid species.     

Evaluating habitat effects on population status: influence of habitat restoration on spring-run Chinook salmon

1. A key element of conservation planning is the extremely challenging task of estimating the likely effect of restoration actions on population status. To compare the relative benefits of typical habitat restoration actions on Pacific salmon (Oncorhynchus spp.), we modelled the response of an endangered Columbia River Chinook salmon (O. tshawytscha) population to changes in habitat characteristics either targeted for restoration or with the potential to be degraded. 2. We applied a spatially explicit, multiple life stage, Beverton‐Holt model to evaluate how a set of habitat variables with an empirical influence on spring‐run Chinook salmon survivorship influenced fish population abundance, productivity, spatial structure and diversity. Using habitat condition scenarios – historical conditions and future conditions with restoration, no restoration, and degradation – we asked the following questions: (i) how is population status affected by alternative scenarios of habitat change, (ii) which individual habitat characteristics have the potential to substantially influence population status and (iii) which life stages have the largest impact on population status? 3. The difference in population abundance and productivities resulting from changes in modelled habitat variables from the ‘historical’ to ‘current’ scenarios suggests that there is substantial potential for improving population status. Planned restoration actions directed toward modelled variables, however, produced only modest improvements. 4. The model predicted that population status could be improved by additional restoration efforts directed toward further reductions in the percentage of fine sediments in the streambed, a factor that has a large influence on egg survival. Actions reducing fines were predicted to be especially effective outside the national forest that covers most of the basin. Scenarios that increased capacity by opening access to habitat in good condition also had a positive but smaller effect on spawner numbers. 5. Degradation in habitat quality, particularly in percent fine sediments, within stream reaches located in the national forest had great potential to further reduce this population’s viability. This finding supports current forest planning efforts to minimise road density and clear‐cut harvests and to return forest stand structure in dry regions to the historical condition that promoted frequent low‐intensity fires rather than catastrophic stand‐replacing fires, as these landscape factors have been shown to influence percent fine sediment in streams. 6. Together, these results suggest that planning focusing on protecting currently good habitat, reducing fine sediments to promote egg survival and increasing spawner capacity will be beneficial to endangered spring‐run Chinook population status.     

Size variability of juvenile Atlantic salmon: links to environmental conditions

Climate change models predict a 2 to 6° C increase in air temperature within the next 100 years in the Maritime Provinces of eastern Canada. Higher air temperatures are expected to contribute to increased water temperatures, alterations in stream flow conditions, and ultimately reductions in fish growth. Mean annual size-at-age of juvenile Atlantic salmon Salmo salar decreased in the Northwest Miramichi and Southwest Miramichi Rivers between 1971–1999. Lengths-at-age of juveniles were significantly correlated between the two rivers. For Atlantic salmon parr, stronger associations between inter-cohort fork length ( L _F) than intra-cohort L _F were observed, suggesting that environmental conditions in the current year of growth have the more significant effects on size of age 2 year parr than conditions encountered the previous year by age 1 year parr of the same cohort. Fork lengths of parr were significantly and negatively associated with spring air and water temperatures. In the Miramichi River, increases in air and water temperature as predicted from climate change models may adversely affect growth of juvenile Atlantic salmon parr, reducing the overall productivity of the Atlantic salmon populations in this region.     

Genetic changes in an Atlantic salmon population resulting from escaped juvenile farm salmon

The study was undertaken on three adjacent rivers in NW Ireland, on one of which an Atlantic salmon Salmo salar freshwater juvenile rearing unit is situated. Two markers which distinguished farm and wild populations were used. An Ava II-B RFLP in the ND1 region of mtDNA was at a frequency of 0.58 in the farm strain but absent in the wild populations. Allele E at minisatellite locus Ssa- A45/2/l was at a frequency of 0.91 in farm samples, but at a maximum of 0.41 in the populations in the two rivers adjacent to the one with the juvenile rearing unit. The farm strain showed a significant reduction in mean heterozygosity (0.281 ± 0.057), over three minisatellite loci examined, compared to wild samples (0.532 ± 0.063). The occurrence of farm genotypes and the independent occurrence of mtDNA and minisatellite markers in several parr samples from the river indicated that escaped juvenile salmon completed their life cycle, bred and interbred with native fish, upon their return to the river. Escaped fish homed accurately, as adults, to the site of escape, i.e. the area adjacent to the hatchery outflow in the upstream part of the river. Breeding of males in the lower part of the river was also indicated but this could have been due to mature male parr which had moved downstream. The return of adults of farm origin to the river to breed was indicated by the presence of the Ava II-B haplotype in adults netted in the estuary.     

Spatio-temporal effects of river regulation on habitat quality for Atlantic salmon fry

Many upland rivers in the Northern Hemisphere contain important habitat for Atlantic salmon (Salmo salar L.). Owing to their sensitivity to environmental change, salmon are often used as bio-indicators. In Scotland, rivers containing potentially suitable habitat for salmon fry are often also regulated for hydropower. Regulated flow regimes can differ substantially spatially and temporally. Thus, where river management may be needed to maintain, restore, and protect their ecological functioning, this needs to be based on evidence of such spatio-temporal effects. This study investigated the effects of different types of river regulation on the hydraulic characteristics of downstream river reaches and the inferred consequences for salmon fry using hydraulic habitat quality models. The study focussed on the River Lyon (390 km²), a tributary of the Tay (4587 km²), Scotland, UK. Hydraulic habitat variability was assessed for three reach-scale sites with contrasting flow regimes characterised by (a) releases from hydropower generation, (b) compensation flow and (c) partly re-naturalised flow conditions. For each site, high resolution Digital Terrain Models (DTMs) were developed from bathymetric surveys and 2D hydraulic models were used to assess hydraulic characteristics. Discharge time series were used to simulate hydraulic conditions for regulated and simulated natural flows. Depth and velocity data were extracted from the hydraulic models and used to infer habitat quality using a habitat model developed for Atlantic salmon fry in similar-sized Scottish rivers. Results showed the effects of regulation can vary substantially within reaches and between seasons. Comparison to natural flow regimes suggested that flow alteration has a variable influence on habitat quality depending on the type of regulation and time of year. This work has improved understanding of the effects of regulation on biophysical processes and may also be useful for managing trade-offs between management, restoration, and societal benefits.