Genetic assessment of Atlantic salmon Salmo salar and sea trout Salmo trutta stocking in a Baltic Sea river

Microsatellite DNA variation was used to assess the outcome of stocking Atlantic salmon Salmo salar and migratory trout Salmo trutta in River Sävarå, N Sweden. No information on pre‐stocking genetic composition of S. salar and S. trutta in River Sävarå was available. In 2 year‐classes of S. salar smolt, microsatellite data indicated that post‐stocking genetic composition differed markedly (F_ST= 0·048) from the main donor strain, Byskeälven S. salar, and from other Gulf of Bothnia S. salar stocks (F_ST 0·047 and 0·132). The STRUCTURE programme failed to detect any substructuring within Sävarå salmon. It was concluded that only minor introgression estimated to a proportion of 0·11 (95% CI 0·07–0·16) has occurred in S. salar. Salmo trutta showed overall low differentiation among populations with maximum F_ST of 0·03 making analysis more cumbersome than in S. salar. Still, the SävaråS. trutta deviated significantly from potential donor populations, and STRUCTURE software supported that majority of trout in Sävarå formed a distinct genetic population. Admixture was more extensive in S. trutta and estimated to 0·17 (95% CI 0·10–0·25).     

The origins of Atlantic salmon (Salmo salar L.) recolonizing the River Mersey in northwest England

By the 1950s, pollution had extirpated Atlantic salmon in the river Mersey in northwest England. During the 1970s, an extensive restoration program began and in 2001, an adult salmon was caught ascending the river. Subsequently, a fish trap was installed and additional adults are now routinely sampled. In this study, we have genotyped 138 adults and one juvenile salmon at 14 microsatellite loci from across this time period (2001–2011). We have used assignment analysis with a recently compiled pan‐European microsatellite baseline to identify their most probable region of origin. Fish entering the Mersey appear to originate from multiple sources, with the greatest proportion (45–60%, dependent on methodology) assigning to rivers in the geographical region just north of the Mersey, which includes Northwest England and the Solway Firth. Substantial numbers also appear to originate from rivers in western Scotland, and from rivers in Wales and Southwest England; nonetheless, the number of fish originating from proximal rivers to the west of the Mersey was lower than expected. Our results suggest that the majority of salmon sampled in the Mersey are straying in a southerly direction, in accordance with the predominantly clockwise gyre present in the eastern Irish Sea. Our findings highlight the complementary roles of improving water quality and in‐river navigability in restoring salmon to a river and underlines further the potential benefits of restoration over stocking as a long‐term solution to declining fish stocks.     

Characterization and PCR multiplexing of novel highly variable tetranucleotide Atlantic salmon (Salmo salar L.) microsatellites

Seven novel and highly variable tetranucleotide microsatellite markers, and conditions for multiplexing and simultaneous genotyping six of these in a single run, are described for Atlantic salmon. These provide a highly informative and cost‐effective set of molecular markers for genetic studies on cultured and wild populations of the species. The primers sets showed cross‐species amplification of appropriately sized amplified products in a number of other salmonid species and suggests the primer sets may have wider application.     

Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland

Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly, suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition, we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography, and thus, knowledge of landscape features (for example, as characterized within Geographical Information Systems) has the potential to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.     

Genetic variation in haemolytic activity in Atlantic salmon (Salmo salar L.)

Spontaneous and antibody-dependent haemolytic activity against sheep red blood cells (SRBC) has been studied in serum from Atlantic salmon, Salmo salar L. Considerable increase in haemolytic activity was detected when SRBC were sensitized with haemolysin produced in Atlantic salmon. Haemolytic activity was sensitive both to divalent cations and to heat treatment. Significant reduction in haemolytic activity was detected after absorption with SRBC, indicating the presence of natural antibody against SRBC in Atlantic salmon serum. Persistent haemolytic activity of unsensitized SRBC in serum absorbed to remove natural antibodies was found, which suggests the activation of the alternative complement pathway, while the observed increased haemolytic activity in the presence of specific antibody against SRBC suggests activation of the classical complement pathway. Spontaneous and antibody-dependent haemolytic activity were both analysed in absorbed and non-absorbed sera in a family material of Atlantic salmon. The material consisted of 574 fish belonging to 57 fullsib groups within 20 paternal halfsib groups. Fish with signs of sexual maturity generally showed reduced haemolytic activity. Statistically significant effect of sire on the spontaneous haemolytic activity of both absorbed and nonabsorbed serum, and on antibody-dependent activity, provides evidence of significant additive genetic variation in both the alternative and the classical complement activation in Atlantic salmon. Neither on a phenotypical nor on a family basis were the two traits statistically correlated. The estimated heritabilities were 0.2–0.3 with a standard error of approximately 0.1.     

Use of differential expression data for identification of novel immune relevant expressed sequence tag-linked microsatellite markers in Atlantic salmon (Salmo salar L.)

Despite the large number of genes contributing to the immune response, wildlife immunogenetic studies have tended to focus mostly on the major histocompatibility complex-related genes. Here, we utilized previously published microarray and competitive RNA hybridization information to identify 3750 immune relevant Atlantic salmon (Salmo salar) expressed sequence tags. We then identified those expressed sequence tags containing microsatellites and subsequently designed 48 primer pairs and tested them for polymorphism in Atlantic salmon. Altogether, 16 polymorphic markers were characterized, with allele numbers ranging from two to 18, and these 16 loci were further tested in five other salmonid species.     

Ecological determinants and temporal stability of the within-river population structure in Atlantic salmon (Salmo salar L.)

A gene diversity analysis was performed using microsatellite loci in order to (i) describe the extent and pattern of population structure in Atlantic salmon (Salmo salar L.) within a river system; (ii) establish the importance of quantifying the signal:noise ratio in accurately estimating population structure; and (iii) assess the potential usefulness of two evolutionary models in explaining within-river population structure from the ecological and habitat characteristics of Atlantic salmon. We found weak, yet highly significant microscale spatial patterning after accounting for variance among temporal replicates within sites. Lower genetic distances were observed among temporal samples at four sampling sites whereas no evidence for temporal stability was observed at the other three locations. The component of genetic variance attributable to either temporal instability and/or random sampling errors was almost three times more important than the pure spatial component. This indicates that not considering signal:noise ratio may lead to an important overestimation of genetic substructuring in situations of weak genetic differentiation. This study also illustrates the usefulness of the member-vagrant hypothesis to generate a priori predictions regarding the number of subpopulations that should compose a species, given its life-history characteristics and habitat structure. On the other hand, a metapopulation model appears better suited to explain the extent of genetic divergence among subpopulations, as well as its temporal persistence, given the reality of habitat patchiness and environment instability. We thus conclude that the combined use of both models may offer a promising avenue for studies aiming to understand the dynamics of genetic structure of species found in unstable environments.     

Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship,population structure,and mixed‐fishery analyses

Eleven microsatellite DNA loci were identified and characterized for Atlantic salmon (Salmo salar) collected from the Penobscot River, Maine, USA and the River Nith, Scotland, UK. The markers revealed high levels of genetic diversity (seven to 48 alleles per locus), heterozygosity (to 100%), and allelic heterogeneity (all comparisons). Considerable differentiation was observed as the genetic distance (chord) between the two collections was 0.680 and the pairwise F_ST, 0.12, was highly significant. These findings are consistent with patterns of continental‐level differentiation observed previously using an alternate suite of microsatellite loci. Locus‐by‐locus analyses of molecular variance suggested that most markers were suitable for delineating kinships and population genetic structure.     

Stability of population structure and genetic diversity across generations assessed by microsatellites among sympatric populations of landlocked Atlantic salmon (Salmo salar L.)

It may often be necessary to perform genetic analyses of temporal replicates to estimate the significance of spatial variation independently from that of temporal variation in order to ensure the reliability of estimates of a defined population structure. Nevertheless, temporal studies of genetic diversity remain scarce in the literature relative to the plethora of empirical studies of population structure. In vertebrates, a limited number of studies have specifically assessed the temporal stability of population structure for more than one generation. In this study, we performed a microsatellite analysis of DNA obtained from archived scales to compare the population structure among four sympatric landlocked populations of Atlantic salmon ( Salmo salar ) over a time frame of three to five generations. The same patterns of allele frequency distribution, θ, R _ST and genetic distance estimates were observed among populations for two time periods, confirming the temporal stability of the population structure. Despite population declines and stocking during this period, no statistically significant changes in intrapopulation genetic diversity were apparent. This study illustrates the feasibility and usefulness of microsatellite analysis of temporal samples, not only to infer changes of intrapopulation genetic diversity, but also to assess the stability of population structure over a time frame of several generations.     

The effects of handling on flounder (Platichthys flesus L.) and Atlantic salmon (Salmo salar L.)

The effect of 9 min of net confinement on two marine teleost species, the flounder and the Atlantic salmon, was investigated in order to gauge how different species respond to the same stress stimulus. Net confinement in both species induced significant elevations in plasma cortisol, glucose, lactate, osmolality, and monovalent ion levels; the responses to net confinement in salmon were generally of a greater magnitude. In both species, handling induced significant alterations in PFFA levels though there were marked species differences in the qualitative and quantitative aspects of this response. Plasma protein levels were significantly elevated only in the flounders. In general, the two species responded similarly to the net confinement with differences only in the absolute levels and durations of the responses.     

Spawning success in Atlantic salmon (Salmo salar L.): a long-term DNA profiling-based study conducted in a natural stream

Spawning success of Atlantic salmon (Salmo salar L.) was investigated, under near-natural conditions, in the Girnock Burn, an 8-km long tributary of the River Dee in Scotland. Employing minisatellite-based DNA profiling, mating outcomes were resolved over three spawning seasons by assigning parentage to progeny samples removed from spawning nests ('redds'). While individual spawning patterns differed markedly, consistent trends were present over the 3 years studied. Multiple spawning was found to be prevalent. More than 50% of anadromous spawners of both sexes contributed to more than one redd. Up to six redds for a single female and seven for a single male were detected. Both sexes ranged extensively. Distance between redds involving the same parent varied from a few metres to > 5 km. Distances > 1 km were common. Both males and females ranged to a similar extent. Range limit was not correlated to fish size. Pairs were not monogamous, both males and females mating with different partners at different sites. Size assortative mating was apparent among 1991 spawners but was not detected for 1992 or 1995. Redd superimposition was found to be common (17-22% of redds over the 3 years), although it was not correlated to the number of anadromous spawners present. High levels of nonanadromous mature parr mating success (40-50% of total progeny sampled) were recorded, and these likely contribute greatly to the effective population size. The relevance of these findings at the individual and population level is discussed, with particular reference to management implications.     

Effects of sexual maturation, castration, and androgen implants on growth in one- and two-year-old parr in a Baltic Atlantic salmon (Salmo salar L.) stock

The effects of maturation, castration, and androgen implants on growth in 1- and 2-year-old Baltic salmon ( Salmo salar L.) were studied in a stock originating from the Umeälven (Ume river) in northern Sweden. 1 + male parr that later matured were larger than non-maturing parr in the spring. Later in the summer, during the period of gonadal growth, the growth rate of maturing parr was depressed compared to that of non-maturing males. Implantation of capsules with 11-ketoandrostenedione (OA) or testosterone (T) in sexually immature 1-year-old fish, accelerated the specific growth rate in spring and early summer, particularly considering growth in weight, resulting in an increase in the condition factor. In contrast, the growth rate was depressed from late June onwards, the period when the gonads normally develop in 1 + parr. T, but not OA, also promoted sexual maturation. Castration or OA treatment did not affect total summer growth in 2-year-old salmon. This study suggests a causal relationship between androgens and the growth pattern observed in maturing 1 + male parr.     

Seasonal and spatial microhabitat selection and segregation in young Atlantic salmon, Salmo salar L., and brown trout, Salmo trutta L., in a Norwegian river

Seasonal microhabitat selection by sympatric young Atlantic salmon and brown trout was studied by diving. Both species, especially Atlantic salmon, showed seasonal variation with respect to surface and mean water velocities and depth. This variation is partly attributed to varying water flows and water temperatures. In winter the fish sought shelter in the substratum. A spatial variation in habitat use along the river due to different habitat availabilities was observed. Both species occupied habitats within the ranges of the microhabitat variables, rather than selecting narrow optima. It is hypothesized that the genetic basis allows a certain range to the behavioural response. Microhabitat segregation between the two species was pronounced, with brown trout inhabiting the more slow-flowing and partly more shallow stream areas. Atlantic salmon tolerated a wider range of water velocities and depths. Habitat suitability curves were produced from both species. It is suggested that habitat suitability curves that are based on observations of fish occupancy of habitat at median or base flow may not be suitable in habitat simulation models, where available habitat is projected at substantially greater water flows.     

Allelic and haplotypic diversity at the major histocompatibility class II within domesticated Australian Atlantic salmon (Salmo salar L.)

Variation within the major histocompatibility (MH) class II alpha gene ( Sasa-DAA ) was compared between domesticated Australian Atlantic salmon and their ancestral Canadian population. The level of Sasa-DAA and MH class II beta gene ( Sasa-DAB ) sequence variation was also examined within the Australian population and compared with that published for European Atlantic salmon populations. In contrast to variation previously reported for non-coding microsatellite loci, a high level of MH class II allelic variation has been maintained within the domesticated Australian populations. Furthermore, a high level of Sasa-DAA and Sasa-DAB allele sequence diversity was also observed and exceeded that reported for other cultured Atlantic salmon populations. The number of Sasa-DAB allele sequences (14) surpassed the number of Sasa-DAA allele sequences (9) to produce 14 unique class II haplotypes. We conclude that the Australian Atlantic salmon populations show high MH class II allelic and haplotypic variation compared with both its ancestral Canadian population and other cultured Atlantic salmon populations.     

Isolation and characterization of variable (GT)n repetitive sequences from Atlantic salmon, Salmo salar L.

Microsatellites are islands of long repeats of mono-, di- or trinucleotides evenly distributed in the eukaryotic genome with an average distance of 50–100 kb. They display a high degree of length polymorphism and heterozygosity at individual loci, making them highly useful as markers in the development of genomic maps of eukaryotes. In the present work, we examined the dinucleotide repeat motif (dG-dT)_n in the Atlantic salmon, Salmo salar L., genome. The frequency of (dG-dT)_n microsatellites in salmon correlates well with earlier published estimations. Cloning and sequencing of 45 salmon microsatellites revealed perfect and imperfect repeats, but no compound microsatellites. The distribution of number of repeat units in salmon microsatellites differ significantly from that of higher vertebrates. Salmon tends to have more long repeat stretches and less intermediate length repeats.     

Patterns of growth and smolting in autumn migrants from a Scottish population of Atlantic salmon, Salmo salar L.

In late November 1990 salmon parr, Salmo salar L., from the Girnock Burn in northern Scotland were either caught on their feeding territories (n=25) or trapped during downstream migration (n= 18). They were then housed in a laboratory rearing tank and their food intake and growth rates were tracked, until their smolting status was ascertained in the following May. Female fish were predominant in both groups; although the range of ages was the same, the total age of migrants was 2+ while that of residents was 1+. In November, compared to resident fish of the same year class, migrants were larger, heavier and in better condition. Although growth rates dropped during the winter in both groups before increasing in spring, migrants ate more and consistently grew faster than residents. In seawater tolerance tests conducted in May, more residents than migrants failed to adapt. These results confirm the suggestion that autumn migrants smolt in the following spring and suggest that they represent the faster-growing component of their cohort.