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.     

Genetic variation at enzyme loci in the southernmost European populations of Atlantic salmon

Genetic variation was studied at 8 allozyme loci in six severely endangered wild Spanish populations of Salmo salar located at the southernmost geographical limit of European Atlantic salmon. Low levels of variation were detected and no significant deviations from Hardy–Weinberg equilibrium were found.     

Spawning-strategy-dependent diets in two North American populations of Atlantic salmon Salmo salar

The diet of repeat-spawner Atlantic salmon Salmo salar was investigated using carbon and nitrogen stable-isotope values from the outer growth band of scales, which reflect the fish's consumption and growth during their most recent marine phase. Isotope values for S. salar displaying different spawning strategies were compared between and within the Miramichi and Nashwaak Rivers, New Brunswick, Canada and a Bayesian mixing model was used to infer dietary contributions from potential prey items. Significant differences in the stable-isotope values were found among spawning strategies and between rivers, indicating differences in diet and feeding area, consistent with hypotheses. Bayesian mixing model results inferred the main prey items consumed during marine feeding by S. salar to consist of hyperiid amphipods and capelin Mallotus villosus for repeat alternate spawners from both rivers, sandlance Ammodytes sp. for repeat consecutive spawners from the Miramichi River and amphipods for repeat consecutive spawners from the Nashwaak River. These results demonstrate the diversity of feeding tactics among S. salar spawning strategies from the same river and between populations from different rivers. Accounting for differences in prey availability and the subsequent impact on S. salar diet and spawner return rates (i.e., marine survival) will facilitate the application of ecosystem-based management practices, such as ensuring that fisheries for forage species do not indirectly adversely affect S. salar return rates.     

Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) in the western and eastern Atlantic diverged >600,000 years before present, with the two lineages isolated in different southern refugia during glacial maxima, driving trans‐Atlantic genomic and karyotypic divergence. Here, we investigate the genomic consequences of glacial isolation and trans‐Atlantic secondary contact using 108,870 single nucleotide polymorphisms genotyped in 80 North American and European populations. Throughout North America, we identified extensive interindividual variation and discrete linkage blocks within and between chromosomes with known trans‐Atlantic differences in rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post‐glacial trans‐Atlantic secondary contact, contrasting with low European ancestry genome‐wide (3%). Ssa08/Ssa29 showed greater intrapopulation diversity, suggesting a derived chromosome fusion polymorphism that evolved within North America. Evidence of potential selection on both genomic regions suggests that the adaptive role of rearrangements warrants further investigation in Atlantic salmon. Our study highlights how Pleistocene glaciations can influence large‐scale intraspecific variation in genomic architecture of northern species.     

Genetic divergence at the NAD +-dependent malic enzyme locus in Atlantic salmon from Europe and North America

The distribution of genetic variation for NAD+ malic enzyme ( ME* ) polymorphism in the Atlantic salmon was assessed in both anadromous and resident populations. The analysis revealed a major allelic divergence between North America and Europe. The *80 variant occurred in 39 of 40 North American samples, ranging in frequency from 0 to 0.515. In contrast, it was detected in only three fish from two of the 35 European locations analysed. Eleven fish from two rivers in north-west France had the * 110 variant. While heterogeneity among North American populations was significant, no regional differentiation was apparent and anadromous and resident salmon were not found to differ.     

Occurrence of Atlantic salmon parr in redds at spawning time

Several Atlantic salmon parr of different sizes were found alive in salmon redds under a 10–30 cm layer of stones at spawning time. Parr, both mature and immature, remain inactive in redds during daylight but show nocturnal activity.     

Allozyme variation in Atlantic salmon from the British Isles: associations with geography and the environment

Data on geographical variation in allele frequencies at enzyme coding loci in Atlantic salmon from the British Isles were collated from published and unpublished sources. Statistically significant differences in allele frequencies were found among samples both within and among river systems, suggesting that the Atlantic salmon in the British Isles is not a panmictic population and that even within major river systems it cannot be treated as a single genetic stock for fisheries management purposes. Although there was some evidence of regional differences in the frequency of some rare alleles, most single‐locus variation did not show strong geographic patterns, with the exception of the AAT‐4 * locus at which allele frequencies had a significant latitudinal cline. There was some evidence for the existence of genetically‐distinct celtic and boreal races of Atlantic salmon in the British Isles as previously has been suggested. Multiple regression analyses revealed associations between genetic variation and local environmental conditions ( i.e . between variation at MEP‐2 * and both temperature and local river gradient), providing additional evidence for adaptive population divergence in the species.     

Genetic variation in immune parameters and associations to survival in Atlantic salmon

Lysozyme activity, haemolytic activity, total level of IgM, and levels of antibodies against A-layer from Aeromonas salmonicida and O-antigen from Vibrio salmonicida , respectively, were determined in 77 full-sib groups of Atlantic salmon in order to evaluate their possible use as immune parameters for indirect selection to improve disease resistance. Fish from parallel full-sib groups had previously been challenged with Aeromonas salmonicida (causing furunculosis), Renibacterium salmoninarum (causing bacterial kidney disease, BKD) and Vibrio salmonicida (causing cold-water vibriosis). Heritabilities were estimated for each of the immune parameters and correlations between the least square means of the full-sib groups for the different immune parameters and survival rates in the parallel full-sib groups were determined. A significant genetic variation in lysozyme activity was found, as well as an apparent genetic association between low lysozyme activity and high survival rates. Low heritabilities and low univariate correlations with survival in the full-sib groups were estimated for all of the other immune parameters. An analysis of the multivariate associations between the full-sib mean values of the complete set of immune parameters, and survival rates in the parallel full-sib groups in each of the challenge tests, revealed that, at low levels of lysozyme activity and with low antibody titres against V. salmonicida O-antigen, increased IgM levels seemed to increase survival from furunculosis.     

Natural hybrids between Atlantic salmon, Salmo salar L., and trout, Salmo trutta L., in juvenile salmonid populations in south-west England

Electrophoretic analysis of juvenile salmonids from south-west England revealed the presence of natural hybrids between Atlantic salmon, Salmo salar L., and brown trout, Salmo rrurra L., within three of five rivers. Amongst 409 juvenile 'salmon', 1.2% were hybrids, and of 150 juvenile 'trout' sampled, 2.0% were natural hybrids. In one river, similar hybridization levels in 'salmon' parr samples were found in two successive years. Levels of hybridization are high when compared with most similar studies, especially others within the United Kingdom. Possible factors influencing this are discussed.     

Detection of QTL affecting harvest traits in a commercial Atlantic salmon population

Genetic variation in performance and quality traits measured at harvest has previously been demonstrated in Atlantic salmon aquaculture populations. To map major loci underlying this variation, we utilized data from 10 families from a commercial breeding programme. Significant QTL were detected affecting harvest weight and length traits on linkage group 1, and affecting waste weight on linkage group 5. In total, 11 of the 29 linkage groups examined showed at least suggestive evidence for a QTL. These data suggest that major loci affecting economically important harvest characteristics are segregating in commercial salmon populations.     

Temporal and spatial variation in growth of juvenile Atlantic salmon

Spatial and temporal variation in length‐at‐age and environmental factors affecting variation in growth rate of juvenile Atlantic salmon Salmo salar were studied using data from a long‐term study in the River Stjørdalselva, central Norway. Mean annual instantaneous growth rate among 1+ and 2+year juvenile Atlantic salmon varied between 0·59 and 1·50 g g⁻¹ year⁻¹ and mean instantaneous daily growth rate of young‐of‐the‐year (YOY) varied between 0·013 and 0·033 g g⁻¹ day⁻¹. Between year variation in growth was larger than the within year intra‐watercourse spatial variation. For YOY and 1+year Atlantic salmon, a major part of the observed between year variation in growth rates was explained by variation in mean daily water discharge and spring temperature. For 2+year juvenile Atlantic salmon, mean daily water discharge and cohort density were the only variables to significantly explain variation in growth rates. A large part of the within water‐course spatial variation could not be explained by temperature variations and juvenile Atlantic salmon in the uppermost areas of the river, experiencing the lowest ambient temperatures during the growth period, displayed the highest growth rates. Within the baselines set by temperature, biotic and abiotic factors connected to water flow regime and variation in food availability are suggested to be a major determinants of the temporal and spatial variation in juvenile Atlantic salmon growth rates.     

Amount and distribution of biochemical-genetic variation among wild populations and a hatchery stock of Atlantic salmon, Salmo salar L., from north-east Ireland

The effects of tributyltin (TBT) compounds on gill morphology were examined in the mummichog, Fundulus heteroclitus , in 96-h LC50 and 6-week sublethal exposures. Morphometry was used for the identification and quantification of effects with the light microscope. A 96-h LC50 of 17.2 μg 1 ¹ was determined. Morphometric analysis of gill tissues revealed hypertrophy of the lamellar epithelium in fish exposed to 17.2 μg 1–1. Relative diffusing capacity was significantly decreased (−41 %); ( P <0.05, ANOVA, Bonferroni t -test). At 35.6 μg 1⁻¹, TBT exposure resulted in a significant reduction (− 40%) in the volume of the lamellar blood channels. Both of these observations occurred in fish that showed signs of acute poisoning including loss of equilibrium. In fish exposed to sublethal concentrations of 0.105–2.000 μg TBT 1⁻¹ for 6 weeks, there were no pathological changes in the gill. There were no treatment-related changes in the surface morphology of the gills of fish from both experiments upon scanning electron microscopic examination. Although gill pathology was observed in acutely toxic exposures, it does not appear to be a major mechanism of TBT toxicity.     

Bimodal size distributions in wild juvenile Atlantic salmon populations and their relationship with age at smolt migration

A bimodal length distribution developed in an Atlantic salmon population planted as start-fed fry in a Norwegian stream. The earliest fish to smolt were from the upper modal group.     

Impact of naturally spawning captive-bred Atlantic salmon on wild populations: depressed recruitment and increased risk of climate-mediated extinction

The assessment report of the 4th International Panel on Climate Change confirms that global warming is strongly affecting biological systems and that 20–30% of species risk extinction from projected future increases in temperature. It is essential that any measures taken to conserve individual species and their constituent populations against climate-mediated declines are appropriate. The release of captive bred animals to augment wild populations is a widespread management strategy for many species but has proven controversial. Using a regression model based on a 37-year study of wild and sea ranched Atlantic salmon (Salmo salar) spawning together in the wild, we show that the escape of captive bred animals into the wild can substantially depress recruitment and more specifically disrupt the capacity of natural populations to adapt to higher winter water temperatures associated with climate variability. We speculate the mechanisms underlying this seasonal response and suggest that an explanation based on bio-energetic processes with physiological responses synchronized by photoperiod is plausible. Furthermore, we predict, by running the model forward using projected future climate scenarios, that these cultured fish substantially increase the risk of extinction for the studied population within 20 generations. In contrast, we show that positive outcomes to climate change are possible if captive bred animals are prevented from breeding in the wild. Rather than imposing an additional genetic load on wild populations by releasing maladapted captive bred animals, we propose that conservation efforts should focus on optimizing conditions for adaptation to occur by reducing exploitation and protecting critical habitats. Our findings are likely to hold true for most poikilothermic species where captive breeding programmes are used in population management.     

Determinants of hierarchical genetic structure in Atlantic salmon populations: environmental factors vs. anthropogenic influences

Disentangling the effects of natural environmental features and anthropogenic factors on the genetic structure of endangered populations is an important challenge for conservation biology. Here, we investigated the combined influences of major environmental features and stocking with non‐native fish on the genetic structure and local adaptation of Atlantic salmon (Salmo salar) populations. We used 17 microsatellite loci to genotype 975 individuals originating from 34 French rivers. Bayesian analyses revealed a hierarchical genetic structure into five geographically distinct clusters. Coastal distance, geological substrate and river length were strong predictors of population structure. Gene flow was higher among rivers with similar geologies, suggesting local adaptation to geological substrate. The effect of river length was mainly owing to one highly differentiated population that has the farthest spawning grounds off the river mouth (up to 900 km) and the largest fish, suggesting local adaptation to river length. We detected high levels of admixture in stocked populations but also in neighbouring ones, implying large‐scale impacts of stocking through dispersal of non‐native individuals. However, we found relatively few admixed individuals suggesting a lower fitness of stocked fish and/or some reproductive isolation between wild and stocked individuals. When excluding stocked populations, genetic structure increased as did its correlation with environmental factors. This study overall indicates that geological substrate and river length are major environmental factors influencing gene flow and potential local adaptation among Atlantic salmon populations but that stocking with non‐native individuals may ultimately disrupt these natural patterns of gene flow among locally adapted populations.     

Long‐term declines in body size and shifts in run timing of Atlantic salmon in Ireland

Records extending back from three to seven decades from Atlantic salmon Salmo salar fisheries on the Blackwater, Newport and Owenduff River systems in Ireland, were used to test the hypothesis that there have been progressive declines in size and associated shifts in run timing. They showed identical patterns in four respects: 1) peaks of catch, in spring (March to April) and summer (June to July), 2) the largest fish were caught in the spring, with declines in size over the summer and a slight increase in autumn, 3) marked declines over time in average size and in the proportion of the Atlantic salmon taken in spring and 4) reductions in size in most months at all three sites. Correlations were also detected in average fish mass among the rivers over time (especially the Owenduff and Newport systems), showing a slight rise from the late 1960s until the late 1970s, followed by a steep decline. Data from an electronic counter on the Blackwater showed a reduction in the abundance of early migrants. The early fish were apparently much more vulnerable to fishing than later migrants, so the catch records overstated the abundance of early fish. These long‐term declines in size, which have been noted elsewhere, may be due to other factors in addition to changes in marine productivity. Specifically, reduction in the abundance of large, spring‐running Atlantic salmon may be due to selection resulting from heavy angler exploitation.     

Protein digestion, growth and food conversion in Atlantic salmon and Arctic charr with different trypsin-like isozyme patterns

Protein digestibility and food conversion were determined in groups of Atlantic salmon ( Salmo salar L.) and Arctic charr ( Salvelinus alpinus L.) with or without the trypsin-like isozyme TRP-2*92 . Determinations were made at two salinities, 0 and 27 ppt; at two temperatures, 6 and 10° C and on large (200 g) and small (30–90 g) fish. The overall digestibility of protein was found to be 81.4±0.2% and was unaffected by the presence of the isozyme or the other variables. The feed conversion ratio of Atlantic salmon possessing TRP-2*92 was observed to be significantly lower with significantly higher specific growth rate than in fish without this isozyme.     

Food partitioning between coexisting Atlantic salmon and brook trout in the Sainte‐Marguerite River ecosystem, Quebec

Food resource partitioning between similar‐sized, sympatric Atlantic salmon Salmo salar and brook trout Salvelinus fontinalis was examined as a possible mechanism enabling their coexistence in a stream (Allaire) of the Sainte‐Marguerite River ecosystem, Quebec, Canada. Fish stomach contents and invertebrate drift were collected concurrently during three diel cycles in August to September 1996. The food and feeding habits of an allopatric brook trout population in a nearby stream (Epinette) were studied for comparison. The diel feeding rhythms of the two coexisting fish species were similar. The composition of their diet, however, showed significant differences. Atlantic salmon predominantly (60–90%) fed on aquatic insects, mainly Ephemeroptera (35–60% of the diet). The brook trout mostly (50–80%) fed upon the allochthonous terrestrial insects (mainly adults of Coleoptera, Hymenoptera and Diptera) which comprised 5–40% of the stream drift. The allopatric brook trout fed opportunistically on the more abundant aquatic insects and terrestrial insects rarely formed 25% of its diet. The allopatric trout fed nearly twice as much as the sympatric brook trout during a day. The results suggest that the differences in feeding by brook trout in the two streams (with and without Atlantic salmon) are the result of inter‐specific interaction with Atlantic salmon and are not related to the differences in food availability between the two streams. Food resource partitioning between Atlantic salmon and brook trout may be viewed as an adaptive response resulting in a greater exploitation of available resources and coexistence.     

Residence time of the sea louse, Lepeophtheirus salmonis K., on Atlantic salmon, Salmo salar L., after immersion in fresh water

Returning adult salmon caught at the mouth of the River Dee, Aberdeenshire, were transferred to tanks in the laboratory. For fish placed in fresh water, sea lice remained attached for up to 6 days, though most lice were lost in the first 48 hours. Few lice were lost from salmon maintained in sea water. The experiments were conducted in water within a temperature range of 12·8 to 16° C, equivalent to summer river temperatures in the Aberdeenshire Dee.