Neoparameoba perurans causes Amoebic Gill Disease (AGD), a major parasitic disease of marine-phase Atlantic salmon and rainbow trout worldwide. Treatment options are limited to freshwater baths, which are costly at scale and exhibit only limited long-term efficacy. N. perurans contains an obligate eukaryotic symbiont, Perkinsela-like organism (PLO). PLO belongs to the class Kinetoplastida, which includes medically and veterinary important parasites such as Trypanosoma and Leishmania. As such, we hypothesised that trypanocidal drugs developed against other kinetoplastids might also affect N. perurans, potentially through disruption of its PLO symbiont, and used this hypothesis as a rationale for prioritising a focused panel of candidate compounds for screening. A holographic motility-based cytotoxicity assay was established to identify promising candidates in vitro, followed by controlled host tolerance testing and finally a field efficacy sea trial using naturally AGD-exposed site in the west of Ireland. Several compounds showed activity in vitro, especially miltefosine (EC50 1.84 uM, amoebicidal) and isometamidum (EC50 4.63 uM, amoebostatic). In vivo (two intramuscular injections, two weeks apart), miltefosine (Odds Ratio (OR) 0.62), isometamidum (OR 0.61) and benznidazole (OR 0.64) significantly improved gill score over four weeks, with miltefosine showing the largest effect size. Gill parasitaemia, measured via qPCR, was not reduced. Instead, two compounds increased apparent amoeba loads. This work support trypanocidal as potential AGD treatments in the field, although optimisation of dosing, delivery and mode of action requires further study.

Vitamin D is a crucial micronutrient for vertebrate health that affects musculoskeletal function and likely modulates immune responses in tissues such as the skin. Infectious diseases are a critical concern in Atlantic salmon aquaculture due to the potential economic impact of stock losses, risks to fish welfare, and environmental sustainability. Since the skin is the first line of immunological defence, its ability to mediate host-pathogen interactions may be influenced by dietary vitamin D. This study examined the transcriptomic response of salmon skin after six months of dietary vitamin D supplementation, with an emphasis on immune-related gene expression. A total of 151 differentially expressed genes were identified, 27 of which are linked to inflammation, antigen presentation, and both innate and adaptive immunity. These results indicate that vitamin D could modulate cutaneous immune responses by reducing inflammation and enhancing innate defences, potentially improving resistance to many skin-associated salmon pathogens.

Seaweeds are increasingly being incorporated into animal diets to address the challenge of intensifying food production while minimizing ecological impacts. Although seaweeds represent promising natural resources for developing economically and environmentally sustainable feeds, especially in aquaculture, the consequences of ingesting seaweed for the animals themselves are often unclear. Therefore, this study examined how the inclusion of the brown seaweed Alaria esculenta affects body condition, skeletal muscle growth, and gene expression across three tissues in Atlantic salmon (Salmo salar). Dietary inclusion of A. esculenta was found to significantly enhance juvenile S. salar body condition. Then, using a novel application of contrast-enhanced soft tissue computed tomography, it was demonstrated that seaweed positively influenced the muscle cross-sectional area of the commercially valuable filet muscle. Transcriptomic analysis further revealed that dietary seaweed altered the expression of hundreds of genes, including several involved in muscle and immune function across the three tissues. These integrative findings indicate that A. esculenta enhances salmon muscle growth and influences the molecular underpinnings of fish health, collectively supporting the utility of seaweed as a sustainable win-win functional food.

Standard metabolic rate (SMR) influences growth, behaviour and energy use in fish, yet its relationship with gut microbiota remains unclear. Here, we combined physiological measurements with 16S rRNA sequencing of foregut and hindgut tissue to test whether gut microbial communities differ with metabolic phenotype in juvenile Atlantic salmon. High-SMR fish showed greater growth efficiency and lower body water content than low-SMR fish, indicating higher fat levels. In contrast, microbial differences were most evident in the foregut, where low-SMR fish exhibited significantly higher alpha diversity. Microbial beta-diversity analyses revealed clear segregation among metabolic groups, and distance-based redundancy analysis showed that both SMR and body mass strongly explained variation in foregut microbial composition. Correlation analysis identified a negative association between SMR and members of the Rhodobacteraceae family, which were consistently more abundant in the foregut of low-SMR fish. Together, these findings indicate that the metabolic phenotype is associated with distinct patterns of energy utilisation and gut microbiota composition, suggesting that foregut microbial communities may contribute to individual differences in metabolic strategy.

The movement of individuals from one breeding site to another (i.e. breeding dispersal) can have important consequences for fitness and population genetics. Whilst closely related species are expected to be phenotypically similar in many respects, they can nevertheless exhibit important differences in behaviour and ecology that can have repercussions for population structure. Here we use genetic information (microsatellite data) collected on two sister species – Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) – that overlap in their spawning and freshwater rearing habitats within a small (ca. 100 km2) catchment in western Ireland. We first explore differences in the spatial extent of within-season breeding dispersal. To do so, we combine sibship reconstruction analysis with distances between siblings’ sampling locations and introduce the ratio of half-sibling to full-sibling pair distances as a novel proxy measure for breeding dispersal (IBD). We then use a range of population genetic analyses to assess the genetic structure of both species. The IBD value was 1.8 times higher in Atlantic salmon than in brown trout, and distances between breeding sites were much greater in salmon (typically within 4 kilometres) than in trout (typically within 600 metres). No genetic structure was detected in Atlantic salmon. In contrast, fine-scale genetic structuring was observed in the brown trout data with at least two genetic clusters being detected, confirming similar patterns reported in previous studies. Our results support the hypothesis that Atlantic salmon engage in more spatially extensive breeding dispersal behaviour than brown trout, which in turn may explain why trout but not salmon exhibit population genetic structure in this system. Collectively, our findings showcase how the same genetic data can be used to gain complementary insights into the movement behaviours of individuals and the genetic structuring of populations, with implications for conservation management. They furthermore emphasise a hitherto overlooked role for intra-seasonal breeding dispersal in shaping spatial genetic connectivity in polygamous species.

We undertook a common garden experiment in the Burrishoole catchment, western Ireland, to test for heritable life-history differences among neighboring brown trout (Salmo trutta L.) populations that exhibit neutral genetic divergence. Experimental crosses were made using either local females (obtained from a below-waterfalls section of the Rough River within the Burrishoole) or females from the Erriff River-a neighboring catchment that currently produces a stronger run of anadromous migrants than the Burrishoole. Each female was mated to three different types of males: Rough Below-Falls, Rough Above-Falls (resident males obtained from above the waterfalls), and Erriff. Offspring from the resulting six crosses were introduced as unfed fry into a stretch of the Rough River bounded upstream by the waterfalls and downstream by a Wolf-type fish trap (Rough River Downstream Trap, RRDT). Genetic parentage analysis (16 microsatellite markers) was then used to assign offspring sampled at various time points and locations back to cross type. No differences in parr survival rates (electrofishing in the Rough River) were found among the crosses, but parr moving downstream (intercepted at the RRDT) were skewed toward the Erriff female × Erriff male cross, with a deficit assigning to the Rough Below-Falls female × Rough Above-Falls male cross. Smolts leaving fresh water (sampled at two sea-entry traps) were assigned disproportionately to crosses involving one or two Erriff parents. Offspring from pure Burrishoole crosses were more likely to become putative spawners than those from crosses involving one or two Erriff parents, pointing toward possible local adaptation. These results are consistent with heritable variation in migratory tendencies-a key aspect of intraspecific biodiversity that warrants protection-and with previous suggestions that the Burrishoole system may have evolved recently toward reduced anadromy following a novel and catastrophic anthropogenic change.

BACKGROUND:In aquaculture, several functional mushrooms have been efficiently used as prebiotics, impacting gut microbiota, increasing growth, and delivering antioxidant advantages to a variety of finfish species. However, the potential of Boletus edulis, the 'porcini' or 'penny bun' to influence the gut microbiota of Salmo salar has yet to be studied. Here, we investigated the prebiotic effect of Boletus edulis extract (BEE) on the gut microbiota of farmed Atlantic salmon via an in vitro gut model (SalmoSim). RESULTS:Notable changes in the production of short-chain fatty acids and microbial diversity were observed upon the addition of BEE. In particular, increased fiber fermentation was suggested by the decreasing concentrations of ammonia and increasing levels of acetate and propionate. Moreover, the 10% BEE improved the absorption of amino acids and increased the digestibility of crude protein, promoting a more diverse microbial community and reducing the accumulation of nitrogenous waste. CONCLUSIONS:The results of the present study revealed that the addition of BEE efficiently altered the gut microbiota, increasing microbial diversity, supporting beneficial short-chain fatty acid synthesis, and improving nutritional absorption in Atlantic salmon.

BACKGROUND:Accounting for isoforms is likely key to understanding muscle transcriptomic divergence. Muscles offer classic examples of tissues where changes in isoforms alter function and structure in response to stimuli like increased exercise or novel nutrient regimes. To determine how an essential micronutrient alters muscle isoform production, we examined how vitamin D supplementation influences transcription at multiple hierarchical levels across four Atlantic salmon (Salmo salar) muscle tissues. Specifically, we investigated whether analyses of differential transcript expression (DTE), differential transcript usage (DTU), and alternative splicing (DAS) recovered different responses to vitamin D compared to differential gene expression (DGE) alone. RESULTS:Vitamin D modulates salmon muscle transcription at the level of the gene, transcript, and splice junctions in all four muscle tissues. However, the strongest effects at all levels were found in the heart. There was little overlap among significant genes found at the gene, transcript, and splicing levels and the distribution of isoforms per significant gene varied across DGE, DTE, and DTU, indicating that each method tends to identify unique sets of genes. For example, we found that several myosin light chain kinase isoforms were particularly impacted by vitamin D in the heart, but many of the genes exhibited isoforms that were differentially expressed in opposing directions and were thus masked in DGE analysis. We also identified myofibrillar genes that are impacted by vitamin D at all levels of gene regulation, demonstrating that vitamin D impacts many structural proteins that are directly involved in striated muscle contractions. CONCLUSIONS:Vitamin D influences several muscle tissue types across multiple levels of transcriptomic divergence. Further, the limited overlap among significant genes found at the gene, transcript, and splicing levels suggests examining only DGE can mask important genes that show differential effects at other levels. Myofibrillar gene isoforms that directly influence muscle contractions in critical organs like the heart could provide an especially fruitful avenue of additional investigation into the transcriptional impacts of vitamin D. Together, these findings clarify how vitamin D influences muscle differentiation, health, and function.

Vitamin D is essential to muscle health but could affect different muscle tissues in distinct ways. In humans, vitamin D is primarily synthesized in the skin via sun exposure but can also be obtained through ingesting foods that are fortified (e.g., milk) or naturally high in vitamin D (e.g., salmon). Like humans, salmon vitamin D content can vary considerably and can be altered through dietary consumption of vitamin D. We experimentally determined how vitamin D manipulation alters gene expression in four salmon muscle tissues: skeletal, craniofacial, smooth, and cardiac. Vitamin D induced changes in expression were exceptionally profound in the heart, where there were also several gene duplicates expressed unidirectionally. Five genes were differentially expressed in multiple muscles and many genes impacted by our vitamin D treatments in salmon show extensive evolutionary conservation as they are influenced by vitamin D titers in mammals, including humans. Salmon could provide a powerful model for understanding how variation in vitamin D impacts all vertebrates.

Studies of fish behaviour and ecology create opportunities for studying piscivores that have been underutilised. A leading example is the widespread use by fish biologists of Passive Integrated Transponder (PIT) tagging for identifying individuals, tracking movements, and estimating population sizes. PIT tags have high physical durability and long electronic lifespans. In consequence, if a piscivore swallows a tagged fish, the tag will almost certainly be excreted intact and subsequently detectable at the location of excretion for years. Accessible nesting or roosting colonies of piscivorous birds adjacent to fish PIT-tagging study sites thus present a potentially rich source of information on feeding habits. However, when such PIT tag surveys are conducted, they typically focus on the biology of the prey and not the predator. Here, we make opportunistic use of a PIT-tagging study of young Salmo spp. salmonids in Ireland to investigate the biology of a widespread and familiar avian piscivore, the Grey Heron Ardea cinerea. We scanned the ground underneath an accessible heronry for tags known to have been fitted to their carriers over four days in May 2019 in an intensively monitored river from which emigration is only possible via a fish trap. We found 48 focal tags in the heronry out of 594 tagged fish. Tags in the heronry were significantly biased towards smaller individuals and S. salar. Data on unpredated fish implies that all putative predation events occurred at least 10.8 km from the heronry despite there being foraging habitat less than 150 m from the colony, and that the majority occurred before the end of June in the year of tagging. We discuss our results in the context of the relatively limited information on breeding-season foraging activity for Grey Herons, optimal foraging considerations and ways to refine the use of PIT tagging of fish for studying piscivores.

Vitamin D is a key micronutrient in vertebrate health that influences musculoskeletal function and likely modulates immune responses in tissues such as the skin. In aquaculture, Atlantic salmon ( Salmo salar ) are particularly vulnerable to skin pathogens, notably the ectoparasitic salmon louse ( Lepeophtheirus salmonis ). As the skin represents the first line of immunological defence, its capacity to mediate host-pathogen interactions may be influenced by dietary vitamin D. This study investigated the transcriptomic response of salmon skin following six months of dietary vitamin D supplementation, with a focus on immune-related gene expression. A total of 113 differentially expressed genes (DEGs) were identified, 46 of which are implicated in inflammation, immune signalling, and both innate and adaptive immunity. These DEGs were further compared to published RNA-seq data of salmon skin challenged with L. salmonis . Notably, while pro-inflammatory genes were regulated in opposing directions, heat shock proteins, lysozyme and antimicrobial peptides were consistently upregulated under both conditions. These findings suggest that vitamin D may modulate cutaneous immune responses by dampening inflammation and enhancing innate defences, potentially improving resistance to skin-associated pathogens such as salmon lice. ### Competing Interest Statement The authors have declared no competing interest. Science Foundation Ireland Frontiers for the Future grant, 21/FFP-P/10171 Science Foundation Ireland, https://ror.org/0271asj38, SFI/15/IA/3028 Biotechnology and Biological Science Research Council (UK), 16/BBSRC/3316 Marine Institute, https://ror.org/05581wm82, RESPI/FS/20/01

BackgroundThe development, progression, and dissemination of antimicrobial resistance (AMR) are determined by interlinked human, animal, and environmental drivers, which pose severe risks to human and livestock health. Conjugative plasmid transfer drives the rapid dissemination of AMR among bacteria. In addition to the judicious use and implementation of stewardship programs, mitigating the spread of antibiotic resistance requires an understanding of the dynamics of AMR transfer among microbial communities, as well as the role of various microbial taxa as potential reservoirs that promote long-term AMR persistence. Here, we employed Hi-C, a high-throughput, culture-free technique, combined with qPCR, to monitor carriage and transfer of a multidrug-resistent (MDR) plasmid within an Atlantic salmon in vitro gut model during florfenicol treatment, a benzenesulfonyl antibiotic widely deployed in fin-fish aquaculture.ResultsMicrobial communities from the pyloric ceaca of three healthy adult farmed salmon were inoculated into three bioreactors simulating the teleost gut, which were developed for the SalmoSim gut system. The model system was then inoculated with the Escherichia coli strain ATCC 25922 carrying the plasmid pM07-1 and treated with florfenicol at a concentration of 150 mg/L in fish feed media for 5 days prior to the washout/recovery phase. Hi-C and metagenomic sequencing identified numerous transfer events, including those involving gram-negative and gram-positive taxa, and, crucially, the transfer and persistence of the plasmid continued once florfenicol treatment was withdrawn.ConclusionsOur findings highlight the role of the commensal teleost gut flora as a reservoir for AMR even once antimicrobial selective pressure has been withdrawn. Our system also provides a model to study how different treatment regimens and interventions may be deployed to mitigate AMR persistence.

The deliberate release of captive-bred individuals, the accidental escape of domesticated strains, or the invasion of closely related conspecifics into wild populations can all lead to introgressive hybridization, which poses a challenge for conservation and wildlife management. Rates of introgression and the magnitude of associated demographic impacts vary widely across ecological contexts. However, the reasons for this variation remain poorly understood. One rarely considered phenomenon in this context is soft selection, wherein relative trait values determine success in intraspecific competition for a limiting resource. Here we develop an eco-genetic model explicitly focussed on understanding the influence of such competitive interactions on the eco-evolutionary dynamics of wild populations experiencing an influx of foreign/domesticated individuals. The model is applicable to any taxon that experiences natural or human-mediated inputs of locally maladapted genotypes ('intrusion'), in addition to phenotype-dependent competition for a limiting resource (e.g. breeding sites, feeding territories). The effects of both acute and chronic intrusion depended strongly on the relative competitiveness of intruders versus locals. When intruders were competitively inferior, density-dependent regulation limited their reproductive success (ability to compete for limited spawning sites), which prevented strong introgression or population declines from occurring. In contrast, when intruders were competitively superior, this amplified introgression and led to increased maladaptation of the admixed population. This had negative consequences for population size and population viability. The results were sensitive to the intrusion level, the magnitude of reproductive excess, trait heritability and the extent to which intruders were maladapted relative to locals. Our findings draw attention to under-appreciated interactions between phenotype-dependent competitive interactions and maladaptive hybridization, which may be critical to determining the impact captive breeding programmes and domesticated escapees can have on otherwise self-sustaining wild populations.

Migration in animals and associated adaptations to contrasting environments are underpinned by complex genetic architecture. Here, we explore the genomic basis of facultative anadromy in brown trout (Salmo trutta), wherein some individuals migrate to sea while others remain resident in natal rivers, to better understand how alternative migratory tactics (AMTs) are maintained evolutionarily. To identify genomic variants associated with AMTs, we sequenced whole genomes for 194 individual trout from five anadromous-resident population pairs, situated above and below waterfalls, in five different Irish rivers. These waterfalls act as natural barriers to upstream migration and hence we predicted that loci underpinning AMTs should be under similar divergent selection across these replicate pairs. A sliding windows based analysis revealed a highly polygenic adaptive divergence between anadromous and resident populations, encompassing 329 differentiated genomic regions. These regions were associated with 292 genes involved in various processes crucial for AMTs, including energy homeostasis, reproduction, osmoregulation, immunity, circadian rhythm and neural function. Furthermore, examining patterns of diversity we were able to link specific genes and biological processes to putative AMT trait classes: migratory-propensity, migratory-lifestyle and residency. Importantly, AMT outlier regions possessed higher genetic diversity than the background genome, particularly in the anadromous group, suggesting balancing selection may play a role in maintaining genetic variation. Overall, the results from this study provide important insights into the genetic architecture of migration and the evolutionary mechanisms shaping genomic diversity within and across populations.

Climate change is restructuring biodiversity on multiple scales and there is a pressing need to understand the downstream ecological and genomic consequences of this change. Recent advancements in the field of eco-evolutionary genomics have sought to include evolutionary processes in forecasting species' responses to climate change (e.g., genomic offset), but to date, much of this work has focused on terrestrial species. Coastal and offshore species, and the fisheries they support, may be even more vulnerable to climate change than their terrestrial counterparts, warranting a critical appraisal of these approaches in marine systems. First, we synthesize knowledge about the genomic basis of adaptation in marine species, and then we discuss the few examples where genomic forecasting has been applied in marine systems. Next, we identify the key challenges in validating genomic offset estimates in marine species, and we advocate for the inclusion of historical sampling data and hindcasting in the validation phase. Lastly, we describe a workflow to guide marine managers in incorporating these predictions into the decision-making process.

When verifying the validity of the exponential-decay law through 137 precise decay rate measurement series at various nuclear laboratories, minor violations have been observed in the shape of annual cycles in the residuals with different amplitudes and phase shifts. The timing and amplitude of these deviations have been compared with local weather data and it appears that ambient humidity is highly correlated with the observed instabilities in these radioactivity measurements. In fact, when compensating the residuals for a linear relationship with absolute humidity in air, most of the annual cycles are no longer statistically significant. As a result, the validity of the exponential-decay law can now be demonstrated with even higher fidelity.

Interspecific introgression is a potentially important source of novel variation of adaptive significance. Although multiple cases of adaptive introgression are well documented, broader generalizations about its targets and mechanisms are lacking. Multiallelic balancing selection, particularly when acting through rare allele advantage, is an evolutionary mechanism expected to favor adaptive introgression. This is because introgressed alleles are likely to confer an immediate selective advantage, facilitating their establishment in the recipient species even in the face of strong genomic barriers to introgression. Vertebrate major histocompatibility complex genes are well-established targets of long-term multiallelic balancing selection, so widespread adaptive major histocompatibility complex introgression is expected. Here, we evaluate this hypothesis using data from 29 hybrid zones formed by fish, amphibians, squamates, turtles, birds, and mammals at advanced stages of speciation. The key prediction of more extensive major histocompatibility complex introgression compared to genome-wide introgression was tested with three complementary statistical approaches. We found evidence for widespread adaptive introgression of major histocompatibility complex genes, providing a link between the process of adaptive introgression and an underlying mechanism. Our work identifies major histocompatibility complex introgression as a general mechanism by which species can acquire novel, and possibly regain previously lost, variation that may enhance defense against pathogens and increase adaptive potential.

Global warming has been implicated in widespread demographic changes in Atlantic salmon Salmo salar populations, but projections of life-history responses to future climate change are lacking. Here, we first exploit multiple decades of climate and biological data from the Burrishoole catchment in the west of Ireland to model statistical relationships between atmospheric variables, water temperature, and freshwater growth of juvenile Atlantic salmon. We then use this information to project potential changes in juvenile growth and life-history scheduling under three shared socioeconomic pathway and representative concentration pathway scenarios from 1961 to 2100, based on an ensemble of five climate models. Historical water temperatures were well predicted with a recurrent neural network, using observation-based atmospheric forcing data. Length-at-age was in turn also well predicted by cumulative growing degree days calculated from these water temperatures. Most juveniles in the Burrishoole population migrated to sea as 2-year-old smolts, but our future projections indicate that the system should start producing a greater proportion of 1-year-old smolts, as increasingly more juveniles cross a size-based threshold in their first summer for smoltification the following spring. Those failing to cross the size-based threshold will instead become 2-year-old smolts, but at a larger length relative to 2-year-old smolts observed currently, owing to greater overall freshwater growth opportunity. These changes in age- and size-at-seaward migration could have cascading effects on age- and size-at-maturity and reproductive output. Consequently, the seemingly small changes that our results demonstrate have the potential to cause significant shifts in population dynamics over the full life cycle. This workflow is highly applicable across the range of the Atlantic salmon, as well as to other anadromous species, as it uses openly accessible climate data and a length-at-age model with minimal input requirements, fostering improved general understanding of phenotypic and demographic responses to climate change and management implications.

The deliberate release of captive-bred individuals, the accidental escape of domesticated strains, or the invasion of closely related conspecifics into wild populations can all lead to introgressive hybridisation, which poses a challenge for conservation and wildlife management. Rates of introgression and the magnitude of associated demographic impacts vary widely across ecological contexts. However, the reasons for this variation remain poorly understood. One rarely considered phenomenon in this context is soft selection, wherein relative trait values determine success in intraspecific competition for a limiting resource. Here we develop an eco-genetic model explicitly focussed on understanding the influence soft selection has on the eco-evolutionary dynamics of wild populations experiencing intrusion from foreign/domesticated individuals. While based on a generalised salmonine lifecycle, the model is applicable to any taxon that experiences incursion from locally maladapted genotypes, in addition to phenotype-dependent competition for a limiting resource (e.g., breeding sites, feeding territories). The effects of both acute and chronic intrusion depended strongly on the relative competitiveness of intruders versus locals. When intruders were competitively inferior, soft selection limited their reproductive success (ability to compete for limited spawning sites), which prevented strong introgression or population declines from occurring. In contrast, when intruders were competitively superior, this amplified introgression and led to increased maladaptation of the admixed population. This had negative consequences for population size and population viability. The results were sensitive to the intrusion level, the magnitude of reproductive excess, trait heritability, and the extent to which intruders were maladapted relative to locals. Our findings draw attention to under- appreciated interactions between soft selection and maladaptive hybridisation, which may be critical to determining the impact captive breeding programmes and domesticated escapees can have on otherwise self-sustaining wild populations.

International wild Atlantic salmon management priorities have moved from exploitation to conservation since the 1990s, recognizing the need to protect diversity and abundance at individual river levels amid widespread declines. Here we review international salmon-stock assessments and describe a simple, transferable catch-advice framework, established for management of fisheries that conforms to international obligations. The risk assessment approach, applied at the river scale, jointly incorporates uncertainty in estimated and forecasted returning salmon numbers with the level of uncertainty around spawning requirements (Conservation Limits). Outputs include quantification of risk of stocks not attaining conservation limits (CL) and surpluses above CL on stocks able to support sustainable exploitation via total allowable catches (TAC), with monitoring by rod catch or fish counter. Since management implementation and cessation of at-sea mixed-stock fisheries, there has been a deterioration in the performance of many individual stocks, without any sustained increase in fisheries open to harvest. Given declines in mid-latitude Atlantic salmon populations over 30 years, the novel framework presented provides an approach to protect stocks failing to meet spawning thresholds while supporting sustainable exploitation of those achieving them. On-going management policy of adopting scientific advice and allowing exploitation only on stocks exceeding CLs is central to the objective of protecting salmon stocks.