Does fin damage allow discrimination among wild,escaped and farmed Sparus aurata (L.) and Dicentrarchus labrax (L.)?

The present study compares fin damages in gilthead seabream (Sparus aurata) and European seabass (Dicentrarchus labrax) according to their wild, escaped or farmed origins. In addition, the potential applicability of fin condition indices (Fin Erosion Index ‘FEI’ and Fin Splitting Index ‘FSI’) as identification tools is discussed. Farmed seabream fins evidenced more erosion and splitting (FEI ± SD: 2.1 ± 0.3; FSI ± SD: 1.9 ± 0.6) than wild seabream fins (FEI: 0.8 ± 0.6; FSI: 1.2 ± 0.9), a result of farming conditions in open‐sea cages. Escaped seabream fin erosion was between that of farmed and wild seabream (FEI: 1.6 ± 0.4), which could indicate that fins in farmed fish recover over time from farming abrasions once they are in the wild. However, the fins of escaped seabream seem to be weaker than those of the wild fish, and therefore might be more susceptible to suffer other types of erosion such as splitting or nipping (FSI: 2.3 ± 0.7). No significant differences were found in seabass FEI according to their origins, although wild seabass presented significantly more split caudal fins (FSI: 3.3 ± 2.8) than the farmed seabass (FSI: 1.2 ± 1.1) and escapees (FSI: 2.5 ± 1.6). Therefore, FEI for seabream could be used as tools not only to distinguish between wild and farmed fish, but also to identify recent escapees, improving further assessments on the contribution of seabream escapees in fishery landings. However, the healing potential of damaged fins must be considered for the proper identification of escapees. Use of fin condition indices from both species could be helpful for aquaculture management, to assess fish welfare in fish farms stocks, and improve the knowledge of handling, stock densities and open‐sea cage environment conditions.     

Genetic screening of farmed Atlantic salmon escapees demonstrates that triploid fish display reduced migration to freshwater

Each year, hundreds of thousands of farmed Atlantic salmon escape from fish farms into the wild. Some of these escapees enter freshwater, and manage to interbreed with native populations. To hinder further genetic introgression in native populations, the use of sterile triploid salmon within commercial aquaculture is being examined. However, if triploid escapees migrate into freshwater, they may still have ecological impacts on local populations. In the present study, we used microsatellite DNA genotyping to determine the ploidy of 3794 farmed escapees captured in 17 Norwegian rivers in the period 2007–2014. Although a previous study has reported an average of 2 % triploids in Norwegian fish farms during this exact period, here, we only observed 7 (0.18 %) triploids among the escapees captured in freshwater. In addition, we identified three trisomic escapees. For the triploids where the within-river capture location was determined, they were only observed in the lower reaches and not on the spawning grounds. It is concluded that propensity for triploid Atlantic salmon to migrate into freshwater following escape from a fish farm is significantly lower than for normal diploid salmon escapees. Therefore, commercial production of triploids should not only be seen as an effective way of stopping genetic introgression, it will also significantly reduce the numbers of escapees entering rivers, which in turn limits ecological interactions and potential disease transmission.     

Genetic diversity within and among Atlantic cod (Gadus morhua) farmed in marine cages: a proof-of-concept study for the identification of escapees

This study presents a molecular genetic characterization of Atlantic cod reared in commercial marine farms. Samples consisted of approximately 47 fish collected from nine cages located on four farms throughout Norway. In addition, 28 farmed escapees were recaptured in the sea (443 fish in total). Nine microsatellite loci and the Pan I gene were analysed, revealing a total of 181 alleles. Each sample contained 43–63% of total allelic variation. Comparing variation with published data for wild cod indicates that lower genetic variation exists within single cages than in wild populations. Significant linkage disequilibrium was observed amongst pairs of loci in all samples, suggesting a low number of contributing parental fish. Global F_ST was 0.049, and the highest pairwise F_ST value (pooled loci) was 0.085. For single loci, the Pan I gene was the most diagnostic, displaying a global F_ST of 0.203. Simulations amongst the samples collected on farms revealed an overall correct self-assignment percentage of 75%, demonstrating a high probability of identifying individuals to their farm of origin. Identification of the 28 escapees revealed a single cage as the most likely source of origin for half of the escapees, whilst the remaining fish were assigned to a mixture of samples, suggesting more than one source of escapees.     

Escape of farmed tilapiines into the wild and entry of wild forms in fishponds,and the possible interactions between wild and farmed tilapiines from a sample of smallholder farms in Central Uganda

Seven smallholder fishponds in central Uganda were studied between 2000 and 2001 to investigate the interaction of farmed tilapiines with their wild conspecifics. Emphasis was on the features that facilitate escape of fish and/or entry of fish into the farms and interactions between the farmed and the wild. These included number of species, source of seed, connection between pond and natural watercourses, purpose of the farm, destination of cultured fish and interaction between farmed and wild fish. Fishponds had no screens against entry of wild fish into the farm or escape of farmed fish into the wild and occurred within wetlands close to natural watercourses. Ponds stocked with one fish species were found to have multispecies with some individuals that were apparently intermediate morphs between the species. Fry produced within the growout fishponds was shared with other farmers within and outside the watersheds. This study showed that smallholder farms with little or no control of escape or entry of fish out and into the fishponds, and little or no management present circumstances that facilitate continued movement of tilapiines within and across watersheds in Ugandan waters. The study also indicated possible genetic interaction between farmed and their wild conspecifics through interactions within fishponds.     

The status of farmed fish hearts: an alert to improve health and production in three Mediterranean species

The heart ventricles of farmed gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and Senegalese sole (Solea senegalensis) have been examined and we compared them to the corresponding fish from wild populations. These results can help to understand the differences in farmed fish hearts and in the myocardial structure that this condition of growth can produce. Several parameters were measured in the two groups. Numerical comparisons included heart mass, cardiac and ventricular index, ventricle height:width ratio, width and alignment of bulbus arteriosus, ventricular angles and compacta thickness. We confirm that the normal shape of wild fish hearts can be modified as a result from the adaptation to different environments. These changes can modify the structure of myocardium and compromise the cardiac function in farmed species. The ventricle of farmed fish present differences in shape, were misaligned, rounder, with a wider bulbus and thinner compact layer. Further studies are necessary to reveal functional significance and possible causes of these abnormal hearts and improve the cardiac welfare of Mediterranean species in culture as a way of ensuring a level of production compatible with economic benefits.     

Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both selective breeding and population genomic research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding programmes increasingly underpin stock supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, particularly for traits practically impossible to measure on selection candidates, such as disease resistance and fillet characteristics. The aim of our study was to design a combined-species 60 K SNP array for European seabass and gilthead seabream, and to test its performance on farmed and wild populations from numerous locations throughout the species range. To achieve this, high coverage Illumina whole-genome sequencing of pooled samples was performed for 24 populations of European seabass and 27 populations of gilthead seabream. This resulted in a database of ~20 million SNPs per species, which were then filtered to identify high-quality variants and create the final set for the development of the ‘MedFish’ SNP array. The array was then tested by genotyping a subset of the discovery populations, highlighting a high conversion rate to functioning polymorphic assays on the array (92% in seabass; 89% in seabream) and repeatability (99.4–99.7%). The platform interrogates ~30 K markers in each species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to have high functional effects on proteins. The array was demonstrated to be effective at detecting population structure across a wide range of fish populations from diverse geographical origins, and to examine the extent of haplotype sharing among Mediterranean farmed fish populations. In conclusion, the new MedFish array enables efficient and accurate high-throughput genotyping for genome-wide distributed SNPs for each fish species, and will facilitate stock management, population genomics approaches, and acceleration of selective breeding through genomic selection.     

Detection of farm fox and hybrid genotypes among wild arctic foxes in Scandinavia

In Scandinavia, farmed arctic foxes frequently escape from farms, raising concern about hybridization with the endangered wild population. This study was performed to find a genetic marker to distinguish escaped farm foxes from wild Scandinavian foxes. Microsatellite and mitochondrial control region variation were analyzed in 41 farm foxes. The results were compared with mitochondrial and microsatellite data from the wild population in Scandinavia. The farm foxes were genetically distinct from the wild foxes (F _ST=0.254, P < 0.00001) and all farm foxes had a single control region haplotype different from those observed in the wild population. We developed a method based on Restriction Fragment Length Polymorphism (RFLP) on the mitochondrial control region to differentiate between farmed and wild arctic foxes. This test was subsequently successfully used on 25 samples from free-ranging foxes, of which four had a suspected farm origin. All four of the suspected foxes, and none of the others, carried the farm fox haplotype. Three of these were successfully genotyped for all eleven microsatellite loci. A population assignment test and a Bayesian Markov Chain Monte Carlo analysis indicated that two of these individuals were escaped farm foxes, and that the third possibly was a hybrid between a farmed and a wild arctic fox.     

An Industry-Scale Mass Marking Technique for Tracing Farmed Fish Escapees

Farmed fish escape and enter the environment with subsequent effects on wild populations. Reducing escapes requires the ability to trace individuals back to the point of escape, so that escape causes can be identified and technical standards improved. Here, we tested if stable isotope otolith fingerprint marks delivered during routine vaccination could be an accurate, feasible and cost effective marking method, suitable for industrial-scale application. We tested seven stable isotopes, ¹³⁴Ba, ¹³⁵Ba, ¹³⁶Ba, ¹³⁷Ba, ⁸⁶Sr, ⁸⁷Sr and ²⁶Mg, on farmed Atlantic salmon reared in freshwater, in experimental conditions designed to reflect commercial practice. Marking was 100% successful with individual Ba isotopes at concentrations as low as 0.001 µg. g^-1 fish and for Sr isotopes at 1 µg. g^-1 fish. Our results suggest that 63 unique fingerprint marks can be made at low cost using Ba (0.0002 – 0.02 $US per mark) and Sr (0.46 – 0.82 $US per mark) isotopes. Stable isotope fingerprinting during vaccination is feasible for commercial application if applied at a company level within the world’s largest salmon producing nations. Introducing a mass marking scheme would enable tracing of escapees back to point of origin, which could drive greater compliance, better farm design and improved management practices to reduce escapes.     

Gonadal maturation in the blackspot seabream Pagellus bogaraveo: a comparison between a farmed and a wild broodstock

The blackspot seabream Pagellus bogaraveo (Brünnich, 1768) has been regarded as a possible alternative to traditionally cultured Mediterranean species such as seabream and seabass, due to its high market value and good adaptation to captivity. Broodstock establishment and management represent the first step towards reliable production of eggs and fry, which is required to develop aquaculture of this new species. Two different broodstocks were tested for gonadal maturation and spawning, one constituting of wild fish caught as juveniles and reared in tanks until sexual maturity (4 years), and one assembled from wild adult fish caught during or just before the reproductive season. All fish were maintained under the same rearing conditions and fed the same diet. Gonadal stripping and biopsies were performed weekly to monitor maturation in both males and females. Ovarian samples were staged for maturity on the basis of follicular diameter and migration of germinal vesicle. Sperm samples were tested for density (number of spermatozoa ml⁻¹) and motility. The fish reared in captivity reached ovarian maturity during the breeding season of the wild stock. Eggs were obtained by stripping from both farmed and wild specimens, but appeared degenerated as a result of being retained too long in the ovarian cavity due to the absence of spontaneous spawning. Spermiation was prolonged in the farmed fish, but appeared to be blocked in the wild breeders after first sampling. However, the sperm was very viscous and the motile spermatozoa did not exceed 10%.     

Welfare status of cultured seabass (Dicentrarchus labrax L.) and seabream (Sparus aurata L.) assessed by blood parameters and tissue characteristics

Seabass (SBS) and seabream (SBM) juveniles were reared with the goal of obtaining three different final densities (SINT = 40 kg m^?3; INT = 20 kg m^?3; SEM = 0.2 kg m^?3) to ascertain the effects thereof on the welfare of the fish. Significant blood metabolites and hepatic glycogen were determined every 3 months and at harvest. Trials lasted 18 months in seabass and 17 months in seabream. At the end of experiment the main biometric productive parameters and quality of body composition were also recorded. Regarding intensively reared seabass (SINT‐SBS, INT‐SBS), the plasma triglycerids, total cholesterol and transaminases (AST, ALT) were always significantly higher than in semi‐intensively maintained fish (SEM‐SBS). At the final sampling in the SINT‐SBS batch, the total protein and glucose were also markedly increased. Conversely, at harvest the liver glycogen content decreased in SINT‐SBS (34 ± 8 mg g^?1 liver) with respect to INT‐SBS (57 ± 12 mg g^?1 liver) and SEM‐SBS (63 ± 11 mg g^?1 liver). No differences among groups were observed for creatine kinase (CK) and lactate dehydrogenase (LDH). With regard to seabream, SINT‐SBM and INT‐SBM constantly showed plasma triglycerids and total cholesterol as being significantly higher when compared to SEM‐SBM. In the final two blood samplings, SINT‐SBM exhibited the most elevated values for LDH. At harvest, AST, ALT, total protein and glucose markedly increased in SINT‐SBM, whereas liver glycogen content was reduced (22.5 ± 9 mg g^?1 liver), more than in INT‐SBM (70 ± 16 mg g^?1 liver) and SEM‐SBM (75 ± 20 mg g^?1 liver). In both seabass and seabream, body composition was very similar in the different stocking densities, except for total cholesterol. Total n‐3 polyunsaturated fatty acid (PUFA) in seabream was significantly different from fish of the semi‐intensive groups; however, nutritional values and fatty acid profiles were equally good. The intermediate final density of seabass and seabream at 20 kg m^?3 seemed to give the best results in terms of their well being when compared to fish reared at 40 kg m^?3. The absence of differences in blood metabolites and hepatic glycogen levels between the intensive batch and the semi‐intensive groups until harvest was a reference to the positive status of the fish. A density of 20 kg m^?3 can be considered acceptable for farm strategy planning for raising healthy on‐growing seabass and seabream juveniles.     

Three Decades of Farmed Escapees in the Wild: A Spatio-Temporal Analysis of Atlantic Salmon Population Genetic Structure throughout Norway

Each year, hundreds of thousands of domesticated farmed Atlantic salmon escape into the wild. In Norway, which is the world’s largest commercial producer, many native Atlantic salmon populations have experienced large numbers of escapees on the spawning grounds for the past 15–30 years. In order to study the potential genetic impact, we conducted a spatio-temporal analysis of 3049 fish from 21 populations throughout Norway, sampled in the period 1970–2010. Based upon the analysis of 22 microsatellites, individual admixture, F_ST and increased allelic richness revealed temporal genetic changes in six of the populations. These changes were highly significant in four of them. For example, 76% and 100% of the fish comprising the contemporary samples for the rivers Vosso and Opo were excluded from their respective historical samples at P = 0.001. Based upon several genetic parameters, including simulations, genetic drift was excluded as the primary cause of the observed genetic changes. In the remaining 15 populations, some of which had also been exposed to high numbers of escapees, clear genetic changes were not detected. Significant population genetic structuring was observed among the 21 populations in the historical (global F_ST = 0.038) and contemporary data sets (global F_ST = 0.030), although significantly reduced with time (P = 0.008). This reduction was especially distinct when looking at the six populations displaying temporal changes (global F_ST dropped from 0.058 to 0.039, P = 0.006). We draw two main conclusions: 1. The majority of the historical population genetic structure throughout Norway still appears to be retained, suggesting a low to modest overall success of farmed escapees in the wild; 2. Genetic introgression of farmed escapees in native salmon populations has been strongly population-dependent, and it appears to be linked with the density of the native population.     

Movements and dispersal of farmed Atlantic salmon following a simulated-escape event

One of the major challenges for understanding the ecological impact of escaped farmed Atlantic salmon (Salmo salar L.) is predicting their dispersal patterns after an escape event. Here, we quantify the behaviour of escaped farmed salmon using a simulated-escape experiment within a Norwegian fjord system. Thirty-seven individuals were tagged with acoustic transmitters and their spatial distribution, horizontal movements and diving behaviour was monitored throughout the fjord and accompanying rivers using 29 acoustic receivers. A rapid movement away from the release site occurred. There was no movement into the rivers feeding the fjord and there was no preference for residence at the fish farms: nearly a third of the individuals had a final detection in the outer part of the fjord and no detections occurred from approximately 2 months after release. As it is unlikely that all fish died or remained undetected within the study area it is reasonable to assume that a substantial proportion of the fish moved out of the fjord system. If a recapture program is not implemented immediately after an escape event, we recommend spreading potential recapture efforts over a relatively large area.     

Twelve new microsatellite markers for gilted seabream (Sparus aurata L.): characterization,polymorphism and linkage

Twelve new microsatellite markers were isolated from the gilted seabream Sparus aurata L., a seawater fish distributed throughout the Mediterranean Sea and on the East Atlantic Coast and exploited in both fisheries and aquaculture. Characterization in 16 individuals from a hatchery population from France reveals three to 17 alleles and a mean expected heterozygosity of 0.752. Inheritance and linkage were assessed in a bi‐parental cross, and using polymorphism and linkage information, two PCR‐multiplex were developed for routine analysis of Sparus aurata populations.     

The European sea bass: a key marine fish model in the wild and in aquaculture

The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype‐by‐environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large‐scale aquaculture productions.     

The Impact of Escaped Farmed Atlantic Salmon (Salmo salar L.) on Catch Statistics in Scotland

In Scotland and elsewhere, there are concerns that escaped farmed Atlantic salmon (Salmo salar L.) may impact on wild salmon stocks. Potential detrimental effects could arise through disease spread, competition, or inter-breeding. We investigated whether there is evidence of a direct effect of recorded salmon escape events on wild stocks in Scotland using anglers' counts of caught salmon (classified as wild or farmed) and sea trout (Salmo trutta L.). This tests specifically whether documented escape events can be associated with reduced or elevated escapes detected in the catch over a five-year time window, after accounting for overall variation between areas and years. Alternate model frameworks were somewhat inconsistent, however no robust association was found between documented escape events and higher proportion of farm-origin salmon in anglers' catch, nor with overall catch size. A weak positive correlation was found between local escapes and subsequent sea trout catch. This is in the opposite direction to what would be expected if salmon escapes negatively affected wild fish numbers. Our approach specifically investigated documented escape events, contrasting with earlier studies examining potentially wider effects of salmon farming on wild catch size. This approach is more conservative, but alleviates some potential sources of confounding, which are always of concern in observational studies. Successful analysis of anglers' reports of escaped farmed salmon requires high data quality, particularly since reports of farmed salmon are a relatively rare event in the Scottish data. Therefore, as part of our analysis, we reviewed studies of potential sensitivity and specificity of determination of farmed origin. Specificity estimates are generally high in the literature, making an analysis of the form we have performed feasible.     

Escapees of potentially invasive fishes from an ornamental aquaculture facility: the case of topmouth gudgeon Pseudorasbora parva

Accidental escapees from aquacultural facilities are an ongoing problem facing scientists, conservationists, policy makers and naturalists throughout the world. The topmouth gudgeon Pseudorasbora parva , a small cyprinid native to Southeast Asia, was introduced to Romanian waters in 1960 via the aquaculture trade and has since spread throughout Europe. It first appeared in England in an ornamental fish farm near Romsey in Hampshire. The aim of the present study was to quantify the dispersal of this potentially highly invasive species from an ornamental fish farm into the wild. In order to measure the dispersal of escapees, intensive electrofishing surveys were carried out between June and September 2003 in the catchment downstream of the fish farm. The distribution of topmouth gudgeon in the catchment was found to be limited and patchy. The presence of small individuals suggests that the species has successfully established itself in the wild, but this remains to be confirmed. The results were examined in light of invasion theory principles of biological resistance and ecological fitness.     

Contrasting Fish Behavior in Artificial Seascapes with Implications for Resources Conservation

Artificial reefs are used by many fisheries managers as a tool to mitigate the impact of fisheries on coastal fish communities by providing new habitat for many exploited fish species. However, the comparison between the behavior of wild fish inhabiting either natural or artificial habitats has received less attention. Thus the spatio-temporal patterns of fish that establish their home range in one habitat or the other and their consequences of intra-population differentiation on life-history remain largely unexplored. We hypothesize that individuals with a preferred habitat (i.e. natural vs. artificial) can behave differently in terms of habitat use, with important consequences on population dynamics (e.g. life-history, mortality, and reproductive success). Therefore, using biotelemetry, 98 white seabream (Diplodus sargus) inhabiting either artificial or natural habitats were tagged and their behavior was monitored for up to eight months. Most white seabreams were highly resident either on natural or artificial reefs, with a preference for the shallow artificial reef subsets. Connectivity between artificial and natural reefs was limited for resident individuals due to great inter-habitat distances. The temporal behavioral patterns of white seabreams differed between artificial and natural reefs. Artificial-reef resident fish had a predominantly nocturnal diel pattern, whereas natural-reef resident fish showed a diurnal diel pattern. Differences in diel behavioral patterns of white seabream inhabiting artificial and natural reefs could be the expression of realized individual specialization resulting from differences in habitat configuration and resource availability between these two habitats. Artificial reefs have the potential to modify not only seascape connectivity but also the individual behavioral patterns of fishes. Future management plans of coastal areas and fisheries resources, including artificial reef implementation, should therefore consider the potential effect of habitat modification on fish behavior, which could have key implications on fish dynamics.