Spatial and temporal genetic structure of a river‐resident Atlantic salmon (Salmo salar) after millennia of isolation

The river‐resident Salmo salar (“småblank”) has been isolated from other Atlantic salmon populations for 9,500 years in upper River Namsen, Norway. This is the only European Atlantic salmon population accomplishing its entire life cycle in a river. Hydropower development during the last six decades has introduced movement barriers and changed more than 50% of the river habitat to lentic conditions. Based on microsatellites and SNPs, genetic variation within småblank was only about 50% of that in the anadromous Atlantic salmon within the same river. The genetic differentiation (F_ST) between småblank and the anadromous population was 0.24. This is similar to the differentiation between anadromous Atlantic salmon in Europe and North America. Microsatellite analyses identified three genetic subpopulations within småblank, each with an effective population size N_e of a few hundred individuals. There was no evidence of reduced heterozygosity and allelic richness in contemporary samples (2005–2008) compared with historical samples (1955–56 and 1978–79). However, there was a reduction in genetic differentiation between sampling localities over time. SNP data supported the differentiation of småblank into subpopulations and revealed downstream asymmetric gene flow between subpopulations. In spite of this, genetic variation was not higher in the lower than in the upper areas. The meta‐population structure of småblank probably maintains genetic variation better than one panmictic population would do, as long as gene flow among subpopulations is maintained. Småblank is a unique endemic island population of Atlantic salmon. It is in a precarious situation due to a variety of anthropogenic impacts on its restricted habitat area. Thus, maintaining population size and avoiding further habitat fragmentation are important.     

Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high‐resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)‐based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine‐scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (F_ST = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late‐maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence.     

Relative production of Atlantic salmon from fluvial and lacustrine habitats estimated from analyses of scale characteristics

Empirical and back-calculated growth of Atlantic salmon parr were compared between fish reared in fluvial and lacustrine habitats of Conne River, Newfoundland. Length at age was significantly higher for lacustrine parr. Various classification and maximum likelihood estimators indicated that 75% or more of the fish used lakes for rearing. Lacustrine use is another aspect of the inherent variability and plasticity of Atlantic salmon life-history traits. As most Newfoundland river systems include lakes, estimates of regional spawning targets and potential smolt production will need to take lake habitat into account.     

The importance of stocking age in the enhancement of River Kymijoki salmon (Salmo salar)

Hatchery‐reared Atlantic salmon parr and smolts are regularly released into the River Kymijoki, Southern Finland, to enhance the local river and coastal fisheries. In 1988–1994, a series of micro‐ and Carlin‐tagging experiments were carried out to examine the influence of stocking age on the stocking results. Five age groups were compared: 1‐year and 2‐year‐old smolts, and 1‐summer, 1‐year and 2‐summer‐old parr. The aim was to determine the most profitable way of producing salmon for fishing in the River Kymijoki. Stocking age had a strong influence on the stocking results, measured as the proportion of adult recoveries. The most favourable results were obtained using 2‐year‐old smolts (survival index 100), followed by 1‐year‐old smolts (52), 2‐summer‐old parr (51), 1‐year‐old parr (37) and 1‐summer‐old parr (24). Available data on rearing costs suggest that 2‐year‐old smolts were also the most economically profitable choice, followed by 1‐year‐old parr, 1‐year‐old smolts and 1‐summer‐old parr. The most expensive way of producing salmon was by stocking 2‐summer‐old parr.     

Genetic variation in threshold reaction norms for alternative reproductive tactics in male Atlantic salmon, Salmo salar

Alternative reproductive tactics may be a product of adaptive phenotypic plasticity, such that discontinuous variation in life history depends on both the genotype and the environment. Phenotypes that fall below a genetically determined threshold adopt one tactic, while those exceeding the threshold adopt the alternative tactic. We report evidence of genetic variability in maturation thresholds for male Atlantic salmon (Salmo salar) that mature either as large (more than 1 kg) anadromous males or as small (10-150 g) parr. Using a common-garden experimental protocol, we find that the growth rate at which the sneaker parr phenotype is expressed differs among pure- and mixed-population crosses. Maturation thresholds of hybrids were intermediate to those of pure crosses, consistent with the hypothesis that the life-history switch points are heritable. Our work provides evidence, for a vertebrate, that thresholds for alternative reproductive tactics differ genetically among populations and can be modelled as discontinuous reaction norms for age and size at maturity.     

Allozyme heterozygosity, date of first feeding and life history strategy in Atlantic salmon

The relations between allozyme heterozygosity, relative date of first feeding and life history strategy in juvenile Atlantic salmon Salmo salar were examined using eggs obtained from a 400 family cross (20 male × 20 female adult Atlantic salmon). Multilocus heterozygosity, through its positive associations with the timing of first feeding and growth rate, was correlated with life history strategy in juvenile Atlantic salmon, albeit under genotype × environmental (temperature, food availability) regulation. Under hatchery conditions, a 10 day difference was observed in the relative date of first feeding between early and late first feeding Atlantic salmon. Early first feeding Atlantic salmon exhibited a significantly higher mean heterozygosity, grew faster at ambient water temperature (April to November) and a significantly higher proportion adopted the early freshwater maturation (age 0+ years, male fish) or early migrant (age 1+ years, mainly female fish) strategies compared to late first feeding Atlantic salmon. Elevated water temperatures over the winter (December to April, >10·5° C) provided additional growth opportunity allowing previously mature male parr (mainly early first feeders) and lower modal group parr (mainly late first feeders) to adopt the early migrant strategy by the following spring.     

Effect of hatchery environment on cranial morphology and developmental stability of Atlantic salmon (Salmo salar L.) from North‐West Russia

The study addresses the effect of hatchery rearing on morphological variation and developmental stability of Atlantic salmon parr from North‐West Russia. Totally, we collected nine samples. Four wild samples were collected from each of the rivers Kola, Umba, Keret’ and Shuia. Five samples of hatchery‐reared parr were the first‐generation progeny of wild adults from these rivers reared separately at the four hatcheries (one hatchery was represented by two samples). Ten meristic and 48 morphometric cranial characters were analysed. We studied the morphological divergence between wild and hatchery fishes of the same river of origin. To analyze developmental stability we used fluctuating asymmetry (random deviations from perfect bilateral symmetry). It was found that hatchery‐reared parr significantly differ from wild parr in both meristic characters and the shape of cranial bones. Different hatcheries caused similar effect on morphological variation in all populations. Fluctuating asymmetry in morphometric characters was significantly higher in hatchery fish than in wild from the Shuia River, indicating a higher level of developmental instability. However, wild parr from the Keret’ River had significantly higher fluctuating asymmetry than cultivated parr of the same origin, possible due to a high infection pressure of the parasite Gyrodactylus salaris Malmberg which has led to significant decline of the wild salmon population in this river, or from genetic changes caused by cultivation. The obtained results indicate a notable effect of hatchery environment on Atlantic salmon’s phenotype.     

Influence of size, winter duration and density on sexual maturation of Atlantic salmon (Salmo salar) juveniles in Little Codroy River (southwest Newfoundland)

Factors affecting sexual maturation of Atlantic salmon ( Salmo salar L.) juveniles in fresh water were analysed under wild conditions in Little Codroy River (southwest Newfoundland). Large size after the first year of life and short winters favoured maturation of age 1 + male parr. Incidence of maturing 1+ males was greater where high densities of parr (>0.2 individuals m ²; fish >6cm fork length) were recorded in the second season of growth. These results were discussed according to current knowledge on early maturation in Atlantic salmon.     

The effect of temperature on growth and early maturation in a wild population of Atlantic salmon parr

Atlantic salmon Salmo salar parr exposed to heated water effluent were larger than parr living upstream of the discharge. There was no effect, however, of temperature on the incidence of male parr maturation, despite the link between growth and maturation found in other studies. Mature parr upstream of the effluent were smaller than mature parr downstream of it, suggesting a higher size threshold for maturation in those parr exposed to the heated water. The small distance between upstream and downstream sampling sites probably precluded genetic differences between the parr, thus implying an environmental influence on the threshold size above which male parr matured.     

Divergence in smolt production from the stocking of 1-summer-old and 1-year-old Atlantic salmon parr in a northern Baltic river

One‐year‐old and 1‐summer‐old salmon parr have been stocked in the Simojoki, a northern Baltic river, to protect the natural salmon stock from extinction. This enhancement practice was studied during a 5‐year stocking period, when an average of 14.3 1‐summer‐old parr and 5.4 1‐year‐old parr was needed to produce one sea running smolt. The mean yield from stocking was 70 smolts per 1000 stocked 1‐summer‐old parr and 186 smolts per 1000 stocked 1‐year‐old parr. The mean cost of smolts produced by stocking 1‐year‐old and 1‐summer‐old parr was 1.2 and 2.6 times the cost of producing one 50 g smolt in the hatchery, respectively. There was a negative relationship between density of wild parr and length of smolts stocked as 1‐summer‐old parr in the river, but no relationship between wild parr density and length of smolts stocked as 1‐year‐old parr. This indicated that 1‐summer‐old parr were more susceptible than the older parr to competition with wild parr. Considering production costs and smolt yield, stocking of 1‐year‐old parr appeared to be more profitable than that of 1‐summer‐old parr in the enhancement of the endangered salmon stock.     

Infection of Atlantic salmon, Salmo salar L., by Gyrodactylus salaris, Malmberg 1957, in the River Lakselva, Misvær in northern Norway

Gyrodacrylus salaris was most probably introduced to the River Lakselva in 1975 through stocking of Atlantic salmon from an infected hatchery. The parasite population grew rapidly, and the parasite spread throughout the entire watercourse during the summer of 1976. This epidemic situation led to mortality among the young Atlantic salmon, and the density of salmon parr was heavily reduced from 1976 to 1977. The density of salmon parr has remained close to zero since then, while there are no apparent trends toward decrease or increase in the density of brown trout. In spite of the reduced density of young salmon, a new epidemic has developed each year among the few young 0+ and 1+ Atlantic salmon present in the river. Results from successive sampling during the summer of 1987, 1988 and 1989 indicate that most of the presmolt salmon are attacked during their first summer or autumn of life. The infection develops into an epidemic during the first autumn, winter or the next summer. The build-up of the parasite burden on the fish leads in turn to mortality. Norwegian Atlantic salmon probably have no resistance against G. salaris, since the parasite has recently been introduced to Norwegian rivers.     

Relative ventricular weight of wild Atlantic salmon parr in relation to sex, gonad maturation and migratory activity

Relative ventricular weight (RVW, ventricular weight/body weight · 100) was measured for five groups of Atlantic salmon parr from the Girnock Burn in Scotland. The mean RVW was: mature males, 0.087; immature resident males, 0.054; immature resident females, 0.056; immature migrant males, 0.056; immature migrant females, 0.053. For a group of mature male parr from the R. Nith, Galloway, Scotland, the mean RVW was 0.108. There were no significant differences in the RVW between groups of immature fish. The RVW of each group of mature male parr was significantly greater than those of each, group of immature parr. Condition indices (weight/length³) were closely similar between all groups of parr. The functional significance of plasticity in ventricular weight is discussed in relation to life histories of Atlantic salmon.     

Nature versus nurture? Consequences of short captivity in early stages

Biological changes occurring as a consequence of domestication and/or captivity are not still deeply known. In Atlantic salmon (Salmo salar), endangered (Southern Europe) populations are enhanced by supportive breeding, which involves only 6 months of captive rearing following artificial spawning of wild‐collected adults. In this work, we assess whether several fitness‐correlated life‐history traits (migratory behavior, straying rate, age at maturity, and growth) are affected by early exposure to the captive environment within a generation, before reproduction thus before genetic selection. Results showed significant differences in growth and migratory behavior (including straying), associated with this very short period of captivity in natural fish populations, changing even genetic variability (decreased in hatchery‐reared adults) and the native population structure within and between rivers of the species. These changes appeared within a single generation, suggesting very short time of captivity is enough for initiating changes normally attributed to domestication. These results may have potential implications for the long‐term population stability/viability of species subjected to restoration and enhancement processes and could be also considered for the management of zoo populations.     

The use of genetic marking to assess the reproductive success of mature male Atlantic salmon parr (Salmo salar, L.) under natural spawning conditions

The reproductive success of mature male Atlantic salmon parr ( Salmo salar ) under natural spawning conditions was estimated using the polymorphism at the MEP - 2 * locus as a genetic marker. The percentage of eggs per redd fertilized by parr varied considerably over the five redds examined (0·9–27.7%, mean 10·8%), but a gametic contribution from mature parr was detected in each case. Parr reproductive success has important implications for the population structure and evolution of the Atlantic salmon through its effect on gene flow.     

Farmed Atlantic salmon Salmo salar L. parr may reduce early survival of wild fish

The study examined the density‐mediated effects on growth, survival and dispersal of wild and farmed Atlantic salmon Salmo salar offspring in the period immediately following emergence, using a substitutive design. In small confined stream channels, wild parr coexisting with farmed parr had a significantly poorer survival, than wild parr alone. Density did not affect this relationship. In larger unconfined stream channels, wild parr coexisting with farmed parr entered a downstream trap in higher numbers than wild parr in allopatry. The results suggests that during the earliest life stages, farmed S. salar can outcompete wild S. salar, resulting in a reduced survival of wild S. salar.     

Reproductive Strategies Explain Genetic Diversity in Atlantic Salmon, Salmo salar

Synopsis We investigated the relationship between conservation status and genetic variability in European and North American Atlantic salmon, Salmo salar, populations, many of which have suffered severe bottlenecks. A negative north--south cline exists for the status of population conservation in this species. A literature review of genetic variability and demographic parameters of wild Atlantic salmon populations resulted in no statistical associations between population conservation status and genetic variation at enzyme or VNTR loci. We found however, a negative relationship between male parr maturation rates and geographical latitude for both American and European populations. The increase in effective population size due to participation by mature male parr and the increased proportions of these males in smaller (southern) populations could explain the lack of expected relationship between genetic variation and conservation status.     

Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon

The high level of escapes from Atlantic salmon farms, up to two million fishes per year in the North Atlantic, has raised concern about the potential impact on wild populations. We report on a two-generation experiment examining the estimated lifetime successes, relative to wild natives, of farm, F(1) and F(2) hybrids and BC(1) backcrosses to wild and farm salmon. Offspring of farm and "hybrids" (i.e. all F(1), F(2) and BC(1) groups) showed reduced survival compared with wild salmon but grew faster as juveniles and displaced wild parr, which as a group were significantly smaller. Where suitable habitat for these emigrant parr is absent, this competition would result in reduced wild smolt production. In the experimental conditions, where emigrants survived downstream, the relative estimated lifetime success ranged from 2% (farm) to 89% (BC(1) wild) of that of wild salmon, indicating additive genetic variation for survival. Wild salmon primarily returned to fresh water after one sea winter (1SW) but farm and 'hybrids' produced proportionately more 2SW salmon. However, lower overall survival means that this would result in reduced recruitment despite increased 2SW fecundity. We thus demonstrate that interaction of farm with wild salmon results in lowered fitness, with repeated escapes causing cumulative fitness depression and potentially an extinction vortex in vulnerable populations.     

Atlantic salmon straying from the River Imsa

Mean estimated straying rate for Atlantic salmon Salmo salar L. leaving the River Imsa as smolts during 1976–1999 was 15% for hatchery fish and 6% for wild conspecifics. Hatchery Atlantic salmon selected for production traits during four or more generations strayed >50%. The straying rate was higher for Atlantic salmon staying 2 rather than 1 year at sea before attaining maturity. For spawning, 96% of the strays entered streams within 420 km from the River Imsa, and c . 80% entered streams within 60 km of the mouth of the River Imsa, whether the fish were wild or hatchery released. Within the 60 km zone, the number of strays caught in a river increased with the Atlantic salmon catch in that river, but there was no significant relationship between straying rate and water discharge or distance from the river to the River Imsa. The observed straying rate of hatchery Atlantic salmon decreased with increasing number of fish entering the River Imsa. Sexual maturation as parr did not influence the tendency to stray. The results suggest that the establishment of temporary zones, free of fish farms, outside important Atlantic salmon rivers by the fisheries authorities in Norway should be large, whole fjords, to be effective.     

Metabolic recovery in Atlantic salmon fry and parr following forced activity

Atlantic salmon Salmo salar fry and parr were subjected to 5 min of forced activity and the subsequent changes in oxygen consumption and ammonia excretion rates were evaluated over a 24 h period. In a second experiment, individual Atlantic salmon fry and parr were freeze‐clamped in liquid nitrogen, before, immediately following a 5 min activity period, or after periods of recovery up to 2 h. Samples were analysed for whole body phosphocreatine (PCr), ATP and lactate. Five minutes of forced activity resulted in significant increases in both oxygen consumption and ammonia excretion rates. Changes in the oxygen consumption rates were greater in the parr compared with the fry. In contrast, the post‐exercise ammonia excretion rates were nearly twice as high for the fry compared with the parr. Exercise also caused a marked decrease in PCr levels (c. 47 and 65% in fry and parr, respectively), no change in ATP levels and a significant increase in lactate levels in Atlantic salmon fry and parr. Recovery of PCr occurred quickly (between 15 and 30 min) in fry and parr. Although the post‐activity levels of lactate were lower in fry (c. 3 μmol g^?1) compared with parr (c. 14 μmol g^?1), lactate levels returned to control levels within 60 min in fry, but it took >2 h for this metabolite to recover in parr. Compared with parr, these findings show that Atlantic salmon fry possess a reduced anaerobic capacity, and these results are consistent with the theoretical and experimental evidence that smaller fish support burst swimming through aerobic processes.     

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.