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Stocking of hatchery produced fish is common practise to mitigate declines in natural populations and may have unwanted genetic consequences. Here we describe a novel phenomenon arising where broodstock used for stocking may be introgressed with farmed individuals. We test how stocking affects introgression in a wild population of Atlantic salmon (Salmo salar) by quantifying how the number of adult offspring recaptured in a stocked river depend on parental introgression. We found that hatchery conditions favour farmed genotypes such that introgressed broodstock produce up to four times the number of adult offspring compared to non-introgressed broodstock, leading to increased introgression in the recipient spawning population. Our results provide the first empirical evidence that stocking can unintentionally favour introgressed individuals and through selection for domesticated genotypes compromise the fitness of stocked wild populations.

The Ryman-Laikre （R-L） effect is an increase in inbreeding and a reduction in total effective population size （NET） in a combined captive-wild system, which arises when a few captive parents produce large numbers of offspring. To facilitate evaluation of the R-L effect for scenarios that are relevant to marine stock enhancement and aquaculture, we extended the original R-L formula to explicitly account for several key factors that determine NeT, including the numbers of captive and wild adults, the ratio of captive to wild Ne/N （β）, productivity of captive and wild breeders, and removal of individuals from the wild for captive breeding. We show how to provide quantitative answers to questions such as： What scenarios lead to no loss of effective size？ What is the maximum effective size that can be achieved？ and What scenarios insure that NeTWill be no smaller than a specified value？ Important results include the following： （1） For large marine populations, the value of β becomes increasingly important as the captive contribution increases. Captive propagation will sharply reduce NeT unless the captive contribution is very small or β is very large （～10^3 or higher）. （2） Very large values of β are only possible if wild Ne/N is tiny. Therefore, large wild populations undergoing captive enhancement at even modest levels will suffer major reductions in effective size unless wild Ne is a tiny fraction of the census size （about 10 4 or lower）.

Interbreeding between domesticated and wild animals occurs in several species. This gene flow has long been anticipated to induce genetic changes in life-history traits of wild populations, thereby influencing population dynamics and viability. Here, we show that individuals with high levels of introgression (domesticated ancestry) have altered age and size at maturation in 62 wild Atlantic salmon Salmo salar populations, including seven ancestral populations to breeding lines of the domesticated salmon. This study documents widespread changes to life-history traits in wild animal populations following gene flow from selectively bred, domesticated conspecifics. The continued high abundance of escaped, domesticated Atlantic salmon thus threatens wild Atlantic salmon populations by inducing genetic changes in fitness-related traits. Our results represent key evidence and a timely warning concerning the potential ecological impacts of the globally increasing use of domesticated animals. Gene flow between wild and farmed salmon is known to be widespread. Here, the authors show that introgression with domestic conspecifics has demographic consequences for wild Atlantic salmon by altering fitness-related life history traits.

Domestication involves adapting animals to the human-controlled environment. Genetic changes occurring during the domestication process may manifest themselves in phenotypes that render domesticated animals maladaptive for life in the wild. Domesticated Atlantic salmon frequently interbreed with wild conspecifics, and their offspring display reduced survival in the wild. However, the mechanism(s) contributing to their lower survival in the wild remains a subject of conjecture. Here, we document higher susceptibility to predation by brown trout in fast-growing domesticated salmon, as compared to their slow-growing wild conspecifics, demonstrating that directional selection for increased growth comes at a cost of decreased survival when under the risk of predation, as predicted by the growth/predation risk trade-off. Despite earlier documentation of altered risk-taking behavior, this study demonstrates for the first time that domestication of Atlantic salmon has lead to increased predation susceptibility, and that this consitutes a mechanism underpinning the observed survial differences in the wild.

Structural variants (SVs) are a major source of genetic and phenotypic variation, but remain challenging to accurately type and are hence poorly characterized in most species. We present an approach for reliable SV discovery in non-model species using whole genome sequencing and report 15,483 high-confidence SVs in 492 Atlantic salmon (Salmo salar L.) sampled from a broad phylogeographic distribution. These SVs recover population genetic structure with high resolution, include an active DNA transposon, widely affect functional features, and overlap more duplicated genes retained from an ancestral salmonid autotetraploidization event than expected. Changes in SV allele frequency between wild and farmed fish indicate polygenic selection on behavioural traits during domestication, targeting brain-expressed synaptic networks linked to neurological disorders in humans. This study offers novel insights into the role of SVs in genome evolution and the genetic architecture of domestication traits, along with resources supporting reliable SV discovery in non-model species.

The lack of a fitness‐based theory of micronutrient allocation to specific tissues hinders understanding of the ultimate causes of mass juvenile mortality due to thiamine (vitamin B1) deficiency, which is an emerging threat to marine and coastal ecosystems worldwide. We modeled the optimal allocation of thiamine in salmon to somatic and reproductive tissues to investigate correlations between tissue thiamine levels, adult mortality, juvenile recruitment, and excretion rates that change with thiamine concentration. The model showed a positive correlation between thiamine levels in gonads and muscles, with a slope that increased with time. This was driven by a constrained thiamine input in salmon, but a negative or no correlation was found in scenarios with high thiamine input. These predictions were confirmed by analysis of empirical data from Atlantic salmon (Salmo salar) populations that differ in the occurrence of episodic thiamine deficiency. A positive correlation was indicative of low thiamine input, regardless of how juvenile recruitment and adult survival increased with thiamine concentration. The model output suggests that renal (i.e., kidney) reuptake is fundamental to understanding micronutrient allocation strategies. Measuring correlations between micronutrient concentrations in reproductive and somatic tissues of adults may help to detect early signs of thiamine deficiency before mass mortality of juveniles occurs. This can complement the previously suggested tissue concentrations and food web indicators. Future studies should try to distinguish and quantify the factors that alter the net thiamine input in salmonids and the subsequent allocation to offspring. Particular attention should be given to changes in thiamine uptake from the diet, including intestinal uptake mechanisms and effects of thiaminase activity. Additionally, more information is needed on internal factors that reduce thiamine availability, such as thiamine degradation as an antioxidant during lipid metabolism, and other physiological factors that can potentially increase thiamine loss, including allocation mechanisms and renal processes. The lack of a fitness‐based theory for micronutrient allocation hinders understanding of juvenile mortality due to thiamine deficiency, a threat to organisms in aquatic ecosystems. Our model showed that thiamine levels in gonads and muscles correlate positively, indicating low thiamine input, and this was confirmed by empirical data from Atlantic salmon. Renal reuptake is crucial for understanding micronutrient strategies, and measuring tissue correlations can detect early thiamine deficiency signs.

The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of gene flow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of 2 years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort). This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity. aquaculture, Atlantic salmon, farmed salmon, genetic introgression, Salmo salar, survival

Thiamine deficiency is an ongoing issue across the Northern Hemisphere, causing reproductive failure in multiple salmonid populations. In the Baltic Sea, a large brackish water system in northern Europe, previous research has suggested that this deficiency is associated with lipid‐rich diets with a high proportion of docosahexaenoic acid (DHA, 22:6n‐3). The mechanism proposed is that a diet abundant in highly unsaturated fatty acids, such as DHA, depletes thiamine as an antioxidant defense in adult salmonids, rather than allocating thiamine to the offspring. In light of this existing hypothesis, we here explore the relationship between diet history and the related fatty acid (FA), profiles, and thiamine status of Atlantic salmon (Salmo salar L.) in three systems: the Baltic Sea, the North Atlantic Ocean, and Lake Vänern. Atlantic salmon inhabiting each system is known to have unique feeding histories and thiamine status. Our results showed that despite extensive sampling effort and distinct FA profiles, indicative of their diverse diets, there were no correlations between any FAs, including DHA, and the thiamine status of these populations. This finding does not support the above‐mentioned hypothesis that diets rich in easily oxidized FAs would lead to lower thiamine concentrations in salmon tissues. Additionally, we found that changes in the salmon FA profiles throughout their life cycle are consistent for both low‐thiamine populations from the Baltic Sea and medium‐thiamine populations from North Atlantic Ocean, suggesting that these changes might not be involved in thiamine deficiency development. Thiamine deficiency, linked to reproductive failure in salmonids, is a significant issue in the Northern Hemisphere, with previous research suggesting it is caused by lipid‐rich diets high in docosahexaenoic acid (DHA). However, our study across three distinct systems—the Baltic Sea, the North Atlantic Ocean, and Lake Vänern—found no correlation between fatty acid (FA) profiles, including DHA, and thiamine status, contradicting the hypothesis that diets rich in easily oxidized FAs lead to lower thiamine concentrations. Furthermore, changes in salmon FA profiles throughout their life cycle were consistent across both low‐thiamine and medium‐thiamine populations, suggesting these changes do not contribute to thiamine deficiency development.

The farming of salmon and other marine finfish in open net pens continues to increase along the world's coastlines as the aquaculture industry expands to meet human demand. Farm fish are known to escape from pens in all salmon aquaculture areas. Their escape into the wild can result in interbreeding and competition with wild salmon and can facilitate the spread of pathogens, thereby placing more pressure on already dwindling wild populations. Here we assess the ecological, genetic, and socioeconomic impacts of farm salmon escapes, using a risk-assessment framework. We show that risks of damage to wild salmon populations, ecosystems, and society are large when salmon are farmed in their native range, when large numbers of salmon are farmed relative to the size of wild populations, and when exotic pathogens are introduced. We then evaluate the policy and management options for reducing risks and discuss the implications for farming other types of marine finfish.

Background: Invasive species represent a major challenge for the conservation of biodiversity. The invasive ectoparasitic fluke Gyrodactylus salaris is considered one of the major threats to the Atlantic salmon (Salmo salar), and the parasite has so far been detected in 50 rivers in Norway. Aims: We investigate environmental DNA (eDNA) as a tool for detecting and assessing relative abundance of G. salaris and Atlantic salmon, upstream and downstream of a recently constructed artificial migration barrier in the River Driva in Norway. In addition, we also use eDNA to assess abundance of the less pathogenic G. derjavinoides and its main host, the brown trout (S. trutta). Material & Methods: We filtered 1 L and 10 L of water through a 0.45 μm cellulose filter and a 2.0 μm glass fiber filter, respectively, at nine different localities along the river. Concentrations of eDNA were assessed using droplet digital PCR (ddPCR) and compared to parasite abundance based on conventional methodology using electrofishing and the counting of individual parasites on juvenile salmon. Results: All four species could successfully be detected from water samples using two different protocols varying in sample volumes, filter types, and DNA‐isolation methods. However, eDNA‐occupancy modeling revealed that the probability of detecting the two gyrodactylid species was higher when filtering 10 L water through a 2.0 μm glass fiber filter (p > .99) than when filtering 1 L water through a 0.45 μm cellulose filter (p = .48–.78). The eDNA concentrations of the two fish species were markedly higher below the migration barrier, reflecting the expected higher biomass of fish. For the two gyrodactylid parasites, eDNA concentrations showed a peak upstream of the migration barrier and decreased below the migration barrier. The observed pattern was consistent with parasite abundance based on conventional methodology. Discussion: Assessing abundance in rivers using eDNA is challenging and potentially influenced by downstream accumulation and dilution from tributaries, but our results suggest that G. salaris eDNA concentrations were indicative of parasite abundance. Conclusion: We conclude that eDNA is an efficient way of monitoring gyrodactylid parasites and their salmonid hosts, and we suggest that eDNA should be incorporated into future monitoring of G. salaris.