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.     

Space invaders: Searching for invasive Smallmouth Bass (Micropterus dolomieu) in a renowned Atlantic Salmon (Salmo salar) river

Humans have the ability to permanently alter aquatic ecosystems and the introduction of species is often the most serious alteration. Non‐native Smallmouth Bass (Micropterus dolomieu) were identified in Miramichi Lake c. 2008, which is a headwater tributary to the Southwest Miramichi River, a renowned Atlantic Salmon (Salmo salar) river whose salmon population is dwindling. A containment programme managed by the Department of Fisheries and Oceans, Canada (DFO) was implemented in 2009 to confine Smallmouth Bass (SMB) to the lake. We utilized environmental DNA (eDNA) as a detection tool to establish the potential escape of SMB into the Southwest Miramichi River. We sampled at 26 unique sites within Miramichi Lake, the outlet of Miramichi Lake (Lake Brook), which flows into the main stem Southwest Miramichi River, and the main stem Southwest Miramichi River between August and October 2017. We observed n = 6 positive detections located in the lake, Lake Brook, and the main stem Southwest Miramichi downstream of the lake. No detections were observed upstream of the confluence of Lake Brook and the main stem Southwest Miramichi. The spatial pattern of positive eDNA detections downstream of the lake suggests the presence of individual fish versus lake‐sourced DNA in the outlet stream discharging to the main river. Smallmouth Bass were later confirmed by visual observation during a snorkeling campaign, and angling. Our results, both eDNA and visual confirmation, definitively show Smallmouth Bass now occupy the main stem of the Southwest Miramichi.     

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.     

Assessing the outcomes of stocking hatchery-reared juveniles in the presence of wild Atlantic salmon

Stocking of hatchery-reared juvenile Atlantic Salmon Salmo salar is a common enhancement and recovery strategy across jurisdictions, yet its impact remains uncertain. We investigate the potential effectiveness of stocking in the Miramichi River system where approximately 150,000 first-feeding fry are stocked annually in reaches where wild juveniles are present. Local site and landscape level characteristics were used to fit predictive models for wild parr densities measured as Percent Habitat Saturation (PHS) using Partial Least Squares Regression (PLSR). The observed PHS of stocked sites was found to be significantly lower than predicted, suggesting stocking has not been effective in increasing the PHS in the studied stocked sites. The results suggest that habitat and other density dependent effects limit productive capacity in this system, and consequently, may limit the effectiveness of stocking in other systems with natural production.     

Stream flow, salmon and beaver dams: roles in the structuring of stream fish communities within an anadromous salmon dominated stream

The current paradigm of fish community distribution is one of a downstream increase in species richness by addition, but this concept is based on a small number of streams from the mid-west and southern United States, which are dominated by cyprinids. Further, the measure of species richness traditionally used, without including evenness, may not be providing an accurate reflection of the fish community. We hypothesize that in streams dominated by anadromous salmonids, fish community diversity will be affected by the presence of the anadromous species, and therefore be influenced by those factors affecting the salmonid population. Catamaran Brook, New Brunswick, Canada, provides a long-term data set to evaluate fish community diversity upstream and downstream of an obstruction (North American beaver Castor canadensis dam complex), which affects distribution of Atlantic salmon Salmo salar. The Shannon Weiner diversity index and community evenness were calculated for sample sites distributed throughout the brook and over 15 years. Fish community diversity was greatest upstream of the beaver dams and in the absence of Atlantic salmon. The salmon appear to depress the evenness of the community but do not affect species richness. The community upstream of the beaver dams changes due to replacement of slimy sculpin Cottus cognatus by salmon, rather than addition, when access is provided. Within Catamaran Brook, location of beaver dams and autumn streamflow interact to govern adult Atlantic salmon spawner distribution, which then dictates juvenile production and effects on fish community. These communities in an anadromous Atlantic salmon dominated stream do not follow the species richness gradient pattern shown in cyprinid-dominated streams and an alternative model for stream fish community distribution in streams dominated by anadromous salmonids is presented. This alternative model suggests that community distribution may be a function of semipermeable obstructions, streamflow and the distribution of the anadromous species affecting resident stream fish species richness, evenness, biomass and production.     

Daylight responses to overhead cover in stream channels for fry of four salmonid species

Brown trout ( Salmo trutta ), Atlantic salmon ( Salmo salar ), brook trout ( Salvelinus fontinalis ) and lake trout ( Salvelinus namaycush ) fry entering the free-feeding stage, were tested for overhead cover preferences in stream channels at different temperatures and water velocities. Atlantic salmon showed strong preferences for overhead cover, brown trout moderate preferences, whereas lake trout had preferences only at high temperatures, i.e. 12.4–19.2°C. Brook trout showed no cover preferences. Temperature influenced cover preferences of Atlantic salmon and brown trout considerably. The fry tended to seek more cover at low temperatures, i.e. 6.0–8.3°C     

An analysis of the distribution of juvenile Atlantic salmon (Salmo salar) in nature as a function of relatedness using microsatellites

The major objective of this study was to test the hypothesis that juvenile Atlantic salmon kin occupy adjacent territories in their natural habitat in order to profit from the benefits associated with kin-biased behaviours, as has been observed under controlled laboratory conditions. Microsatellites were used to establish the relatedness of salmon fry (in their first summer of life) and parr (in their second and third summer of life) captured in adjacent territories. We did not observe a relationship between the proximity and the relatedness of either parr of the same cohort or fry in their natural habitat. Although many pairs of fry were identified as being related when sampled immediately after emergence, most family groups did not occupy adjacent territories. The high dispersal potential in rivers, the low occupation rate of the habitat and the incidence of half-sibs in nature most probably reduce the opportunity and advantage of kin-biased behaviour, in contrast to laboratory studies conducted in artificial, high-density conditions.     

Fine-scale population structure in Atlantic salmon from Maine's Penobscot River drainage

We report a survey of microsatellite DNAvariation in Atlantic salmon from theunimpounded lower reaches of Maine's PenobscotRiver. Our analysis indicates that Atlanticsalmon in the Penobscot River are distinct fromother populations that have little or nohistory of human-mediated repopulation,including two of its tributaries, Cove Brookand Kenduskeag Stream, another Maine river, theDucktrap, and Canada's Miramichi and Ganderrivers. Significant heterogeneity was detectedin allele frequency among all threesubpopulations sampled in the Penobscotdrainage. The high resolution of the 12-locussuite was quantified using maximum likelihoodassignment tests, which correctly identifiedthe source of 90.4–96.1% of individuals fromwithin the Penobscot drainage. Currentpopulations are clearly isolated from eachother, however we are unable to determine fromthe present data whether the populations inCove Brook and Kenduskeag Stream are recentlydiverged from populations stocked into thePenobscot River over the last century, or areaboriginal in origin. The degree of populationstructure identified in the Penobscot drainageis noteworthy in light of its lengthy historyof systematic restocking, the geographicproximity of the subpopulations, and the extentof the differentiation. Similar populationstructure on this extremely limited geographicscale could exist among Atlantic salmon runselsewhere in Maine and throughout the species'range and should be taken into account forfuture management decisions.     

Movements and habitat use by PIT-tagged Atlantic salmon parr in early winter: the influence of anchor ice

1. Movements and habitat use by Atlantic salmon parr in Catamaran Brook, New Brunswick, were studied using Passive Integrated Transponder technology. The fish were tagged in the summer of 1999, and a portable reading system was used to collect data on individual positions within a riffle‐pool sequence in the early winter of 1999. Two major freezing events occurred on November 11–12 (Ice 1) and November 18–19 (Ice 2) that generated significant accumulations of anchor ice in the riffle. 2. Individually tagged parr (fork length 8.4–12.6 cm, n = 15) were tracked from 8 to 24 November 1999. Over this period, emigration (40%) was higher from the pool than from the riffle. Of the nine parr that were consistently located, seven parr moved <5 m up‐ or downstream, and two parr moved more than 10 m (maximum 23 m). Parr moved significantly more by night than by day, and diel habitat shifts were more pronounced in the pool with some of the fish moving closer to the bank at night. 3. During Ice 2, there was relatively little movement by most of the parr in the riffle beneath anchor ice up to 10 cm in thickness. Water temperature was 0.16 °C above the freezing point beneath anchor ice, suggesting the existence of suitable habitats where salmon parr can avoid supercooling conditions and where they can have access to low velocity shelters. To our knowledge, these are the first data on habitat use by Atlantic salmon parr under anchor ice.     

No evidence of kin bias in dispersion of young‐of‐the‐year Atlantic salmon Salmo salar L. in a natural stream

Ninety‐one young‐of‐the‐year Atlantic salmon Salmo salar were captured using a non‐invasive snorkelling technique in a 38 m section of Catamaran Brook, New Brunswick, Canada, to test whether related fish settle closer to one another than unrelated fish. A maximum likelihood estimate of parentage relationships assessed by genotyping eight microsatellite loci revealed five half‐sibling families in the sample of fish. Related juvenile S. salar were not found closer to one another than unrelated fish in three analyses at two spatial scales: a comparison of the relatedness of focal fish to their nearest neighbour and to their four nearest neighbours, and a correlation of the pair‐wise relatedness and distance matrices for all fish in the sample. The lack of a kin‐biased dispersion pattern may be related to the lower density of fish or the scarcity of full‐siblings at the study site compared to laboratory conditions.     

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.     

Interhabitat migration of juvenile Atlantic salmon in a Newfoundland river system, Canada

Migrations of juvenile Atlantic salmon between habitats (both fluvial and lacustrine) were studied in a Newfoundland river system from May through September. Salmon parr showed poor site fidelity in fluvial habitats, and high rates of migration, especially in spring-early summer. Most habitat shifts were upstream from fluvial habitats to a lake at the head of a small tributary. In September, 10% of the salmon parr caught in the lake ( n =275) had been marked in the main stem of the river or in the tributary stream (total n =641). The abundance of parr in the lake increased in May-June, then declined gradually to September. Most of the lacustrine immigrants were 1+ parr. Mature males were found amongst the autumnal emigrants. Salmon parr in the lake grew larger than those in the river, and lacustrine smolts captured in the lake were larger than those caught at the mouth of the river.     

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.     

The distribution of salmonids in upland streams in relation to depth and gradient

The distribution of various age classes of salmon and trout was assessed in upland streams by electrofishing. Water depths and site gradients were measured and correlated to fish densities. The fry of both species were significantly more abundant in shallow water; up to 75·3% of salmon fry and 72·2% of trout fry were captured in sites of mean depth < 20 cm. Older trout were found mainly in the deeper areas, with a maximum of 7·4% captured in sites < 20 cm mean depth. Yearling fish were found in all the depth-ranges sampled, but with a tendency for higher numbers in mid-range depths. There were similar correlations in the abundance of each age class with the actual areas of shallow, mid-range and deep water habitat available within sites. Correlations of fish density with gradient indicated that trout were limited in their distribution to areas of lower flow, whereas salmon were not. Since depth and gradient were significantly negatively correlated, there was an apparent preference of trout for slightly deeper habitats than the equivalent year classes of salmon. The observed habitat segregation is discussed in terms of competition and selection.     

Seasonal variation in density of juvenile Atlantic salmon in fluvial shoreline habitats of a large subarctic river

The densities of Atlantic salmon fry (0+ years) and parr (1+ years and older) in shoreline habitats of the large River Teno watercourse and its tributary, the River Utsjoki generally fluctuated considerably, showing an increase from early summer towards late August and a subsequent decline towards autumn. The seasonal pattern of variation in density was more distinct for parr than for fry. In the period between late July and early September, parr density followed a sinusoidal curve, being highest in late August and lowest in early August and in September. Fry density had a weaker seasonal profile than parr, being highest in late August and in early September. Frequency distributions of the parr age groups (1+, 2+ and 3+ years) were mainly independent of the sampling month.     

Population structure of Atlantic salmon from the Conne River, Newfoundland as determined from microsatellite DNA

Variation at four microsatellite loci was examined for three populations of Atlantic salmon Salmo salar from the Conne River, Newfoundland. Samples of wild parr were collected from the mainstem Conne River during 4 years, and from tributaries Twillick Brook and Bernard Brook during 2 years. No significant temporal variation was observed in allele frequencies at the Ssal4, Ssal97, Ssa202, and Ssa289 loci. No difference in allele frequencies was observed between parr from Bernard and Twillick brooks at any locus, but allele frequencies of mainstem Conne River parr were significantly different from those of the tributaries at Ssal4 and Ssa202, indicative of differentiation among local populations. Atlantic salmon from the Conne River system were well differentiated from those in Nova Scotia, Canada and from those in Europe.     

Short-term study testing the resilience of an estuarine bivalve to macroalgal mats

Increased mortality of juvenile Atlantic salmon (Salmo salar L.), related to lowered levels of stored energy following the loss of ice cover during winter, has been observed after hydropower development in the subarctic River Alta, northern Norway. Drift samples were compared to examine if drift densities, and thus drift prey availabilities for juvenile salmon, were lower in the ice-free than the ice-covered area. In addition, juvenile salmon stomach contents were compared to benthos and drift in the ice-free area to examine salmon winter feeding habitat. Zooplankton, originating from the reservoir, dominated drift at the ice-free site but had lower densities at the downstream ice-covered site. Excluding zooplankton, Chironomidae comprised most of the remaining drift at both the ice-free and ice-covered site, followed by Ephemeroptera, Plecoptera and Simuliidae. No Trichoptera were found in the drift samples. There was no consistent diel periodicity in drift. Benthos was dominated by Chironomidae, followed by Ephemeroptera, Plecoptera and Trichoptera. Other invertebrates occurred in low numbers. Juvenile salmon demonstrated size-selective feeding and fed mainly on Ephemeroptera, followed by Trichoptera and Plecoptera. No zooplankton and few Chironomidae were found in the stomach samples. Stomach content was more similar to benthos than to drift, indicating a larger extent of benthic than drift feeding. No evidence was found for the hypothesis that lack of ice cover reduced the invertebrate drift or caused diel periodicity in the drift. Differences in drift between areas with and without ice could not account for the observed differences in mortality of juvenile salmon during the winter in these areas.     

Moon phase and nocturnal density of Atlantic salmon parr in the Sainte‐Marguerite River, Québec

Nocturnal underwater counts of Atlantic salmon Salmo salar parr were made on four consecutive occasions (two lunar cycles, samplings at both the full and new moon) at four 40 m long sites in the Sainte‐Marguerite River, Québec, Canada, between 30 June and 14 August 2003. Atlantic salmon parr counts did not differ significantly between moon phases. Cloud cover ranged from 0 to 100% during the study, and had no significant effect on parr counts. There were significantly more Atlantic salmon parr in the near shore than in the midstream areas. The findings of this study suggest that the sampling strategy of summer studies aimed at assessing population abundance or developing habitat quality models can be designed without taking moon phase or cloud cover into consideration, but it should account for the higher relative abundance of Atlantic salmon parr in the near shore areas as compared to areas closer to the middle of streams.     

Genetic studies on serum transferrins in Atlantic salmon

Published and unpublished data on genetic variation at the transferrin locus ( TF *) in Atlantic salmon from rivers in eastern North America sampled from 1968 to 1970 were reanalysed and compared with data for samples collected in 1998 from nine of the same rivers. Genetic differentiation among rivers was highly significant as was spatial differentiation among tributary samples within the Miramichi River system, the largest rivers studied. Comparison of allele frequencies in rivers also sampled in 1998 show no overall evidence of significant genetic change after 30 years, spanning 9 generations. The results strongly support the stability of the patterns of spatial genetic differentiation and support the occurrence in Atlantic salmon of reproductive isolation among rivers and among tributaries within large river systems.     

Influence de quelques paramètres du milieu d'incubation sur la survie d'alevins de saumon atlantique,Salmo salar L., en ruisseau expérimental. Influence of some Environmental Parameters upon Survival during Embryonic Development of Atlantic salmon,Salmo solar L., in an Experimental Stream Channel

The effect of some environmental parameters of the redd (substrate composition, interstitial dissolved oxygen concentration) upon survival of Atlantic salmon embryos was studied in a large artificial stream channel. Batches of 3000 eyed eggs were buried 0.25 m deep in the gravel substrate of 8 different channel sections, where natural or artificial sediment deposition took place. Upon emergence, fry were captured in drift nets or by electrofishing. Survival varied from 32 to 94 % in the different sections. It was strongly affected by volume of sediment less than 10 mm in particle size and more particularly by the fraction less than 0.2 mm, the main component of natural sediment deposition. Survival was less strongly determined by oxygen concentration variations except for values less than 2 mg/l obtained in the section with highest sediment deposition. Available volume of interstitial void space appeared to be crucial for good survival during larval development.