Review of NRA tracking projects on salmon, Salmo salar L., and sea trout, Salmo trutta L

The report briefly outlines the programme of the National Rivers Authority (NRA), placing the Fisheries programme in the context of the work of the NRA as a whole, and viewing the tracking work against the broader requirements of the NRA Fisheries research programme. All regions of England and Wales are considered. Two techniques currently exist for studying the detailed timing and extent of movements of adult salmon: tracking of individually identifiable fish, and counting the numbers of fish moving past a fixed point in the river. The development of tracking techniques and the integrated use of tracking and fish counters is briefly reviewed in Section 3. Further details of these techniques are given in Appendices. Section 4 summarises and assesses completed and current NRA tracking studies. Section 5 discusses the scientific content of these studies in relation to similar work carried out elsewhere in the UK. The NRA programme of tracking studies is evaluated in Section 6. Section 7 discusses future fisheries projects and Section 8 details the future development of tracking techniques. Finally, recommendations arising out of this review are summarised in Section 9.

An evaluation of the survival of Atlantic salmon (Salmo salar L.)fry stocked in eight streams in the North West of England.

Eight streams from the North West of England were stocked with Atlantic salmon (Salmo salar L.) fed fry at densities ranging from 1 to 4/m2 over a period of up to three years to evaluate survival to the end of the first an d second growing periods and hence assess the value of stocking as a management practice. Survival to the end of the first growin g period (mean duration of 108 days) was found to vary between 7.8 and 41.3% with a mean of 22% and CV of 0.44. Survival from the end of the first growing period to the end of the second growing period (mean duration of 384 days) ranged from 19.9 to 34.1% with a mean of 26.3% and CV of 0.21. Survival was found to be positively related to 0+ trout density (P < 0.05) and negatively related to altitude (P < 0.05). A comparison of the raw survival data (non standardised with respect to duration of experiments) with that from other studies in relation to stocking densities revealed a negative relationship between fry survival and stocking density (P < 0.05). Densities in excess of 5/m2 tended to result in lower levels of survival. Post stocking fry dispersal patterns were examined for the 1991 data. On average 86.7% of the number of fry surviving remained within the stocked zone by the end of the first growing period. With the exception of one stream there was little in the way of dispersal beyond the stocked zone. The dispersal pattern approximated to the normal distribution (P < 0.05). It was estimated that stocking can result in a net gain of fish to a river system compared with natural productivity, however the numerical significance of this gain and its cost effectiveness need to be determined on a river specific basis.

Use of biological reference points for the conservation of atlantic salmon (Salmo salar L.)in the River Lune, North West England.

This paper deals with the development and use of biological reference points for salmon conservation on the River Lune, England. The Lune supports recreational and net fisheries with annual catches in the region of 1,000 and 1356 salmon respectively. Using models transported from other river systems, biological reference points exclusive to the Lune were developed; specifically the number of eggs deposited and carrying capacity estimates for age 0+ and 1+ parr. The conservation limit was estimated at 11.9 million eggs and between 1989 and 1998 was exceeded in two years. Comparison of juvenile salmon densities in 1991 and 1997 with estimates of carrying capacity indicated that 0+ and 1+ parr densities were at around 60 % of carrying capacity and may relate to the number of eggs deposited in 1990 and 1996 being approximately 70% of the target value. The paper discusses the management actions taken in order to ensure that the management target of the conservation limit being met four years out of five is delivered. It also discusses the balance between conservation and exploitation and the socio-economic decisions made in order to ensure parity of impacts on the rod and net fisheries. The regulations have been enforced since 1999 and the paper concludes with an assessment of the actions taken to deliver the management targets, over the last five years.

Use of telemetric tracking to examine environmental influences on catch/effort indices. A case study of Atlantic Salmon (Salmo salar L.)in the R. Tywi, S. Wales

A case study of Atlantic Salmon runs into the R. Tyvi (S. Wales) is presented. Radio tracking of over 200 salmon in 1988 and 1989 has demonstrated that flow is an important factor in modifying both run timing and migratory success. Entry of salmon into the river is typically in response to flow events, and periods of low falling flows delay entry and may directly result in reduced runs into the river. Delayed entry may also increase the proportion of the run migrating after the end of both rod and net fishing seasons. The implications of these results for net and rod catch and catch/effort data are discussed, using both statutory reported catch data and data from specific catch/effort studies. Flow is demonstrated to be a dominant factor in determining the within-season distribution of rod catch and catch/effort during low-flow years. Estuarial seine net catch and catch/effort tend to be controlled more by time of return than by flow although low flows may delay runs. Annual reported rod catch is correlated with flow, which controls in season availability, catchability and consequently the amount of fishing effort. Use of catch or catch/effort data should take account of inter-year variations in flow and other environmental factors. Although catch and catch/effort are valuable indicators of fishery performance, they are inadequate to represent changing stock levels.

Diurnal and nocturnal temperatures for Atlantic salmon postsmolts (Salmo salar L.) during their early marine life

Data storage tags (DSTs) were applied to Atlantic salmon (Salmo salar L.) smolts during their seaward migration in the spring of 2002 at a fish counting fence on Campbellton River, Newfoundland. Our objectives were to discover whether or not salmon smolts could carry DSTs and survive, whether or not useful data on thermal habitat could be obtained and interpreted, and whether or not salmon smolts moved vertically in the water column. Data were downloaded from 15 of the recovered tags and revealed the hourly water temperatures experienced by the fish for periods of 3 to 71 days. The data on the DSTs were analyzed for temperature patterns in relation to migration behavior and diurnal movement of the fish. While in the sea, the DSTs recorded night temperatures of 12.5°C, which were higher than day temperatures of 11.6°C; the record from moored recorders, however, indicated that sea temperatures actually declined at night. It is hypothesized that posts-molts avoid avian predators during daylight hours by positioning themselves deeper in the water column and that they were pursuing prey during the deeper vertical descents or ascents noted during the periods of more rapid changes in temperature.

The study of molecular variation in Atlantic salmon (Salmo salar L.) and brown trout (Salmo trutta L.)

Polymorphic microsatellite DNA loci were used here in three studies, one on Salmo salar and two on S. trutta. In the case of S. salar, the survival of native fish and non-natives from a nearby catchment, and their hybrids, were compared in a freshwater common garden experiment and subsequently in ocean ranching, with parental assignment utilising microsatellites. Overall survival of non-natives was 35% of natives. This differential survival was mainly in the oceanic phase. These results imply a genetic basis and suggest local adaptation can occur in salmonids across relatively small geographic distances which may have important implications for the management of salmon populations. In the first case study with S trutta, the species was investigated throughout its spread as an invasive in Newfoundland, eastern Canada. Genetic investigation confirmed historical records that the majority of introductions were from a Scottish hatchery and provided a clear example of the structure of two expanding waves of spread along coasts, probably by natural straying of anadromous individuals, to the north and south of the point of human introduction. This study showed a clearer example of the genetic anatomy of an invasion than in previous studies with brown trout, and may have implications for the management of invasive species in general. Finally, the genetics of anadromous S. trutta from the Waterville catchment in south western Ireland were studied. Two significantly different population groupings, from tributaries in geographically distinct locations entering the largest lake in the catchment, were identified. These results were then used to assign very large rod caught sea trout individuals (so called “specimen” sea trout) back to region of origin, in a Genetic Stock Identification exercise. This suggested that the majority of these large sea trout originated from one of the two tributary groups. These results are relevant for the understanding of sea trout population dynamics and for the future management of this and other sea trout producing catchments. This thesis has demonstrated new insights into the population structuring of salmonids both between and within catchments. While these chapters look at the existence and scale of genetic variation from different angles, it might be concluded that the overarching message from this thesis should be to highlight the importance of maintaining genetic diversity in salmonid populations as vital for their long-term productivity and resilience.

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.

Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).

Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.

Complex pattern of genetic structuring in the Atlantic salmon (Salmo salar L.) of the River Foyle system in northwest Ireland: disentangling the evolutionary signal from population stochasticity

Little is known about the microevolutionary processes shaping within river population genetic structure of aquatic organisms characterized by high levels of homing and spawning site fidelity. Using a microsatellite panel, we observed complex and highly significant levels of intrariver population genetic substructure and Isolation-by-Distance, in the Atlantic salmon stock of a large river system. Two evolutionary models have been considered explaining mechanisms promoting genetic substructuring in Atlantic salmon, the member-vagrant and metapopulation models. We show that both models can be simultaneously used to explain patterns and levels of population structuring within the Foyle system. We show that anthropogenic factors have had a large influence on contemporary population structure observed. In an analytical development, we found that the frequently used estimator of genetic differentiation, F-ST, routinely underestimated genetic differentiation by a factor three to four compared to the equivalent statistic Jost's D-est (Jost 2008). These statistics also showed a near-perfect correlation. Despite ongoing discussions regarding the usefulness of "adjusted" F-ST statistics, we argue that these could be useful to identify and quantify qualitative differences between populations, which are important from management and conservation perspectives as an indicator of existence of biologically significant variation among tributary populations or a warning of critical environmental damage.

Rapid temperature-dependent wound closure following adipose fin clipping of Atlantic salmon Salmo salar L.

Three groups of Atlantic salmon were kept at a constant temperature of 4, 10 and 14 °C. The adipose fins were removed; six fish/group were sampled at 11 subsequent time points post-clipping. Samples were prepared for histopathological examination to study the course of re-epithelization. A score sheet was developed to assess the regeneration of epidermal and dermal cell types. Wounds were covered by a thin epidermal layer between 4 and 6 h post-clipping at 10 and 14 °C. In contrast, wound closure was completed between 6 and 12 h in fish held at a constant temperature of 4 °C. By 18 h post-clipping, superficial cells, cuboidal cells, prismatic basal cells and mucous cells were discernible in all temperature groups, rapidly progressing towards normal epidermal structure and thickness. Within the observation period, only minor regeneration was found in the dermal layers. A positive correlation between water temperature and healing rates was established for the epidermis. The rapid wound closure rate, epidermal normalization and the absence of inflammatory reaction signs suggest that adipose fin clipping under anaesthesia constitutes a minimally invasive method that may be used to mark large numbers of salmon presmolts without compromising fish welfare.

Effect of temperature and diet on wound healing in Atlantic salmon (Salmo salar L.).

Compromised skin integrity of farmed Atlantic salmon, commonly occurring under low temperature and stressful conditions, has major impacts on animal welfare and economic productivity. Even fish with minimal scale loss and minor wounds can suffer from secondary infections, causing downgrading and mortalities. Wound healing is a complex process, where water temperature and nutrition play key roles. In this study, Atlantic salmon (260 g) were held at different water temperatures (4 or 12 °C) and fed three different diets for 10 weeks, before artificial wounds were inflicted and the wound healing process monitored for 2 weeks. The fish were fed either a control diet, a diet supplemented with zinc (Zn) or a diet containing a combination of functional ingredients in addition to Zn. The effect of diet was assessed through subjective and quantitative skin histology and the transcription of skin-associated chemokines. Histology confirmed that wound healing was faster at 12 °C. The epidermis was more organised, and image analyses of digitised skin slides showed that fish fed diets with added Zn had a significantly larger area of the epidermis covered by mucous cells in the deeper layers after 2 weeks, representing more advanced healing progression. Constitutive levels of the newly described chemokines, herein named CK 11A, B and C, confirmed their preferential expression in skin compared to other tissues. Contrasting modulation profiles at 4 and 12 °C were seen for all three chemokines during the wound healing time course, while the Zn-supplemented diets significantly increased the expression of CK 11A and B during the first 24 h of the healing phase.

Efecto de la incorporación de γ-tocoferol en dietas para salmón Atl��ntico (Salmo Salar L.) sobre la composición y metabolismo lipídico

El aceite de pescado ha sido la principal fuente de grasa incluida en la dieta de salmón Atl��ntico ya que su uso optimiza el crecimiento y aporta grandes cantidades de ácidos grasos poliinsaturados (PUFA) omega 3, principalmente los ácidos eicosapentaenoico (EPA) y docosahexaenoico (DHA). En los años 90 se utilizaba un 24% de aceite de pescado en los piensos para salmón, sin embargo la escasez del recurso y la presión comercial sobre su demanda por parte de distintos sectores ha dado lugar a una progresiva reducción de su inclusión teniendo la industria como objetivo llegar a utilizar en 2020 tan sólo un 8%. Al reducir los niveles de aceite de pescado disminuye el contenido de EPA y DHA aportado, por lo que se hace necesario diseñar estrategias que permitan maximizar la retención de EPA y DHA en los tejidos del animal. De esta forma, la optimización del uso de antioxidantes para prevenir la peroxidación lipídica de los ácidos grasos poliinsaturados de cadena larga (LC-PUFA), puede ser una estrategia a seguir. Entre los antioxidantes empleados en acuicultura destaca la vitamina E. Aunque el α-tocoferol es el isómero principal de la vitamina E, estudios recientes sugieren que el γ-tocoferol presenta igualmente una potente actividad antioxidante. Sin embargo, hasta la fecha no hay muchos estudios con salmón Atl��ntico empleando γ-tocoferol como principal isómero añadido en la dieta. Además de su función como antioxidante, en investigaciones recientes la vitamina E ha mostrado capacidad para inducir de manera directa o indirecta la expresión de genes que codifican enzimas implicadas en el metabolismo de los ácidos grasos. Con esta perspectiva el presente trabajo tiene como principal objetivo determinar si la incorporación de 300 ppm de γ-tocoferol a la dieta del salmón da lugar a una mayor capacidad antioxidante en los tejidos del animal, disminuyendo la oxidación lipídica in vivo y afectando tanto a la composición como al metabolismo lipídico. Un total de 180 esguines de salmón Atl��ntico (Salmo Salar) con un peso inicial de 137,4 ± 1g fueron distribuidos al azar y uniformemente en 6 tanques y fueron alimentados con una de las tres dietas experimentales. Se aportó agua salada a los tanques y la temperatura se mantuvo a 12°C. Las dietas experimentales se formularon para tener: bajo contenido en EPA y DHA (CB); alto en EPA y DHA (CA); y con bajos niveles de EPA y DHA pero con un suplemento de 300 ppm de γ-tocoferol como antioxidante (CB+γtoc). Las dietas fueron suministradas en tanques duplicados durante 14 semanas. Al final del experimento, se sacrificaron 4 peces de cada tanque y se tomaron muestras de hígado y filete izquierdo para realizar el análisis de ácidos grasos y de expresión génica. A pesar de que los peces alimentados con la dieta CB+γtoc presentaron 3 veces más concentración de γ-tocoferol en los tejidos, la administración de esta dieta no tuvo un efecto significativo (P>0.05) sobre la composición de EPA, DHA y ácido araquidónico (ARA) en los tejidos del salmón. Los resultados del análisis de expresión de genes mostraron que la incorporación de 300 ppm de γ-tocoferol dio lugar a una cierta inhibición del metabolismo lipídico tanto de genes relacionados con la β-oxidación como de aquellos relacionados con la síntesis de LC-PUFA. En cuanto al sistema de defensa antioxidante GPx4, los resultados indicaron que no hubo efecto estimulatorio del γ-tocoferol sobre el mismo. Sin embargo, se observó un aumento de omega 3 totales (P<0.05) en el músculo del animal. La incorporación de 300 ppm de γ-tocoferol tuvo un efecto limitado sobre la composición lipídica y un efecto inhibitorio del metabolismo lipídico a nivel de expresión.

Atlantic Salmon (Salmo salar L.) as a Marine Functional Source of Gamma-Tocopherol

Gamma tocopherol (gT) exhibits beneficial cardiovascular effects partly due to its anti-inflammatory activity. Important sources of gT are vegetable oils. However, little is known to what extent gT can be transferred into marine animal species such as Atlantic salmon by feeding. Therefore, in this study we have investigated the transfer of dietary gT into salmon. To this end, fish were fed a diet supplemented with 170 ppm gT for 16 weeks whereby alpha tocopherol levels were adjusted to 190 ppm in this and the control diet. Feeding gT-rich diets resulted in a three-fold increase in gT concentrations in the liver and fillet compared to non-gT-supplemented controls. Tissue alpha tocopherol levels were not decreased indicating no antagonistic interaction between gamma- and alpha tocopherol in salmon. The concentration of total omega 3 fatty acids slightly increased in response to dietary gT. Furthermore, dietary gT significantly decreased malondialdehyde in the fillet, determined as a biomarker of lipid peroxidation. In the liver of gT fed salmon we observed an overall down-regulation of genes involved in lipid homeostasis. Additionally, gT improved the antioxidant capacity by up-regulating Gpx4a gene expression in the pyloric caeca. We suggest that Atlantic salmon may provide a marine functional source capable of enriching gT for human consumption.