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Escaped farmed Atlantic salmon Salmo salar interbreeding with wild conspecifics represents a threat to the genetic integrity and viability of wild populations. Therefore, it is necessary to accurately quantify escapees in riverine systems to monitor and mitigate interactions with wild conspecifics. Drift diving surveys are presently used in Norway to quantify the number of wild and escaped farmed salmon in rivers. However, limited information is available on the validity of the method for distinguishing escapees from wild conspecifics. Comparing the proportion of escapees calculated from drift diving (mean = 8.5%) and net captures (mean = 8.6%), we found that drift diving was well correlated with net captures (adj. r2 = 0.79). Furthermore, scale analysis from an independent data set demonstrated a 98% true positive rate when identifying and capturing farmed escapees during drift diving. The results of this study indicate that drift diving is an accurate and robust method for quantifying escaped farmed salmon, at least in rivers where observation conditions are adequate for snorkeling. In general, drift diving can be a valuable tool for stakeholders to quickly assess broad spatial extents with limited time and resources.

Abstract Background Single nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico. Results Most of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM). Conclusions Genome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.

When haemoglobin genotyping was implemented in the early 1960s to investigate population genetic structure in Atlantic cod ( Gadus morhua ), it became one of the first molecular genetic markers deployed in fisheries research worldwide. However, its suitability was questioned due to its potential for selection. While the issue of neutrality concerned the first population geneticists, markers under selection are now routinely used to study population genetic structure. Here, we revisited haemoglobin genotyping half a decade later to analyse >6000 mature Atlantic cod from 73 spawning locations throughout Norway's approximately 2500 km coastline. A latitudinal gradient in allele frequencies, with a decrease in the HbI-2 allele towards the south, was observed. Our observed HbI-2 frequencies were consistently slightly lower than data from the 1960s, potentially reflecting adaptive changes to increasing sea temperatures. However, despite this difference, the observed north-south pattern in allele frequencies observed here and in the historical studies overlapped, aligning with current knowledge of population genetic structure in this species. We therefore conclude that this once questioned marker, which provided the first molecular genetic insights into genetic structure in Atlantic cod, provides knowledge consistent with the isolation by distance pattern revealed through decades of research in this species in this region., Competing Interests: We declare we have no competing interests., (© 2025 The Authors.)

In commercial aquaculture, the production of triploid fish is currently the most practical approach to prevent maturation and farm-to-wild introgression following escapes. However, triploids often exhibit poor welfare, and the underlying mechanisms remain unclear. Inheritance issues associated with sub-optimal hydrostatic pressure treatments used to induce triploidy, or the genetic background of parental fish, have been speculated to contribute. We tested this by quantifying the frequency and type of chromosomal aberrations in Atlantic salmon subjected to a gradient of sub-optimal pressure treatments (Experiment 1) and from multiple mothers (Experiment 2). From these experiments, we genotyped a subsample of ~900 eyed eggs and all ~3300 surviving parr across ~20 microsatellites. In contrast to the low frequency of chromosomal aberrations in the diploid (no hydrostatic pressure) and triploid (full 9500 PSI treatment) controls, eyed eggs subjected to sub-optimal pressure treatments (6500-8500 PSI) had a higher incidence of chromosomal aberrations such as aneuploidy and uniparental disomy, corresponding to lower triploidization success and higher egg mortality rates. We also observed maternal effects on triploidization success and incidence of chromosomal aberrations, with certain half-sibling families exhibiting more aberrations than others. Chromosomal aberrations were rare among surviving parr, suggesting a purge of maladapted individuals during early development. This study demonstrates that sub-optimal hydrostatic pressure treatments and maternal effects not only influence the success of triploidization treatments, but may also affect the incidence of chromosomal aberrations and early mortality. The results have important implications for aquaculture breeding programs and their efforts to prevent farm-to-wild introgression., Competing Interests: Competing interests: The authors declare no competing interests. Ethical approval: The experimental protocol was approved by the Norwegian Food Safety Authority (permit number 28350), and all welfare and use of experimental animals was performed in strict accordance with the Norwegian Animal Welfare Act. In addition, all personnel involved in this experiment had undergone training approved by the Norwegian Food Safety Authority, which is mandatory for all personnel., (© 2024. The Author(s).)

Sustainable fisheries management is important for the continued harvest of the world's marine resources, especially as they are increasingly challenged by a range of climatic and anthropogenic factors. One of the pillars of sustainable fisheries management is the accurate identification of the biological units, i.e., populations. Here, we developed and implemented a genetic baseline for Atlantic herring harvested in the Norwegian offshore fisheries to investigate the validity of the current management boundaries. This was achieved by genotyping > 15,000 herring from the northern European seas, including samples of all the known populations in the region, with a panel of population-informative SNPs mined from existing genomic resources. The final genetic baseline consisted of ~1000 herring from 12 genetically distinct populations. We thereafter used the baseline to investigate mixed catches from the North and Norwegian Seas, revealing that each management area consisted of multiple populations, as previously suspected. However, substantial numbers (up to 50% or more within a sample) of herring were found outside of their expected management areas, e.g., North Sea autumn-spawning herring north of 62° N (average = 19.2%), Norwegian spring-spawning herring south of 62° N (average = 13.5%), and western Baltic spring-spawning herring outside their assumed distribution area in the North Sea (average = 20.0%). Based upon these extensive observations, we conclude that the assessment and management areas currently in place for herring in this region need adjustments to reflect the populations present. Furthermore, we suggest that for migratory species, such as herring, a paradigm shift from using static geographic stock boundaries towards spatial dynamic boundaries is needed to meet the requirements of future sustainable management regimes., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Author(s). Evolutionary Applications published by John Wiley & Sons Ltd.)

Polyploidy occurs naturally across eukaryotic lineages and has been harnessed in the domestication of many crops and vertebrates. In aquaculture, triploidy can be induced as a biocontainment strategy, as it creates a reproductive barrier preventing farm-to-wild introgression, which is currently a major conservation issue for the industry. However, recent work suggests that triploidisation protocols may, on occasion, produce 'failed triploids' displaying diploidy, aneuploidy and aberrant inheritance. The potentially negative consequences for conservation and animal welfare motivate the need for methods to evaluate the success of ploidy-manipulation protocols early in the production process. We developed a semi-automated version of the MAC-PR (microsatellite DNA allele counting - peak ratios) method to resolve the allelic configuration of large numbers of individuals across a panel of microsatellite markers that can be used to infer ploidy, pedigree and inheritance aberrations. We demonstrate an application of the approach using material from a series of Atlantic salmon (Salmo salar) breeding experiments where ploidy was manipulated using a hydrostatic pressure treatment. We validated the approach to infer ploidy against blood smears, finding a > 99% agreement between these methods, and demonstrate its potential utility to infer ploidy as early as the embryonic stage. Furthermore, we present tools to assign diploid and triploid progeny to families and to detect aberrant inheritance, which may be useful for breeding programmes that utilise ploidy manipulation techniques. The approach adds to the ploidy verification toolbox. The increased precision in detecting ploidy and inheritance aberrations will facilitate the ability of triploidisation programmes to prevent farm-to-wild introgression., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors., (© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Introgression of non-native conspecifics changes the genetic composition of wild populations, potentially leading to loss of local adaptations and fitness declines. However, long-term data from wild populations are still relatively few. Here, we studied the effects of introgression in a Danish brown trout ( Salmo trutta , L.) population, subjected to intensive stocking with domesticated hatchery fish of non-native origin. We used wild-caught genetically wild and admixed trout as well as fish from the partly domesticated hatchery strain used for stocking the river up until ~15 years prior to this study, to produce 22 families varying in hatchery/wild admixture. Following a replicated common-garden experiment conducted in fish tanks from first feeding through 23 weeks at 7, 12, and 16°C, we observed a significant positive relationship between family admixture and fish size upon termination, an effect observed through all levels of admixture. Furthermore, the admixture effect was most distinct at the higher rearing temperatures. Although the hatchery strain used for stocking had been in culture for ~7 generations, it had not been deliberately selected for increased growth. These data thus demonstrate: (i) that growth had increased in the hatchery strain even in the absence of deliberate directional selection for this trait, (ii) that the increasing effect of admixture by temperature could represent inadvertent selection for performance in the hatchery strain at higher temperatures, and most significantly, (iii) that despite undergoing up to five generations of natural selection in the admixed wild population, the genetically increased growth potential was still detectable and thus persistent. Our findings suggest that altered growth patterns and potentially their cascading effects are of importance to the severity of hatchery/wild introgression, especially under changing-climate scenarios and are of general significance to conservation practitioners seeking to evaluate long-term effects of intra-specific hybridization including under recovery., Competing Interests: Authors declare no conflicts of interest., (© 2024 The Author(s). Evolutionary Applications published by John Wiley & Sons Ltd.)

Disease interactions between farmed and wild populations have been poorly documented for most aquaculture species, in part due to the complexities to study this. Here, we tested 567 farmed Atlantic salmon escapees, captured in a Norwegian river during 2014-2018, for five viral infections that are prevalent in global salmonid aquaculture. Over 90% of the escapees were infected with one or more viruses. Overall prevalences were: 75.7% for piscine orthoreovirus (PRV-1), 43.6% for salmonid alphavirus (SAV), 31.2% for piscine myocarditis virus (PMCV), 1.2% for infectious pancreatic necrosis virus (IPNV) and 0.4% for salmon anaemia virus (ISAV). A significantly higher prevalence of PMCV infection was observed in immature compared to mature individuals. The prevalence of both SAV and PMCV infections was higher in fish determined by fatty acid profiling to be 'recent' as opposed to 'early' escapees that had been in the wild for a longer period of time. This is the first study to establish a time-series of viral infection status of escapees entering a river with a native salmon population. Our results demonstrate that farmed escapees represent a continuous source of infectious agents which could potentially be transmitted to wild fish populations., (© 2024 The Authors. Journal of Fish Diseases published by John Wiley & Sons Ltd.)

Elucidating the effects of domesticated organisms escaping into the natural environment represents a topic of importance in both evolutionary and conservation biology. However, when excluding the abundant data on salmonids, there is a lack of knowledge on this topic for marine fish aquaculture, which continues to expand globally. In order to bridge this empirical gap, we investigated a suspected escape of sexually mature domesticated Atlantic cod from a commercial marine fish farm in northern Norway. This involved genotyping samples of fish from cages on the farm, putatively identified escapees and wild cod captured in the region and samples of recently spawned eggs collected in the sea. Genetic analyses confirmed a farmed ancestry of the suspected escapees, and significantly, 27% of the sampled cod eggs. Furthermore, statistical analyses revealed a strong reduction in genetic variation in all samples of the farmed cod, including low effective population size and high degree of siblingship. These results thus document the escape of sexually mature adult cod and the release of fertilized domesticated cod eggs into the natural environment. Although it is possible that some of the mature escapees spawned post-escape, the fact that only a single egg of potential hybrid farmed × wild origin was identified, together with the high number of mature cod in the farm, points to within cage spawning as the primary source of these eggs. This suggestion is supported by oceanic particle-drift modelling, verifying that transport of eggs between the farm and the egg sampling locations was plausible. This study represents a rare documentation of interaction between domesticated and wild populations for a marine fish, pointing towards potential impacts on the local wild population., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

In Atlantic salmon, age at maturation is a life history trait governed by a sex-specific trade-off between reproductive success and survival. Following environmental changes across large areas of the Northeast Atlantic, many populations currently display smaller size at age and higher age at maturation. However, whether these changes reflect rapid evolution or plasticity is unknown. Approximately 1500 historical and contemporary salmon from the river Etne in Western Norway, genotyped at 50,000 SNPs, revealed three loci associated with age at maturation. These included vgll3 and six6 which collectively explained 36%-50% of the age at maturation variation in the 1983-1984 period. These two loci also displayed sex-specific epistasis, as the effect of six6 was only detected in males bearing two copies of the late maturation allele for vgll3. Strikingly, despite allelic frequencies at vgll3 remaining unchanged, the combined influence of these genes was nearly absent in all samples from 2013 to 2016, and genome-wide heritability strongly declined between the two time-points. The difference in age at maturation between males and females was upheld in the population despite the loss of effect from the candidate loci, which strongly points towards additional causative mechanisms resolving the sexual conflict. Finally, because admixture with farmed escaped salmon was excluded as the origin of the observed disconnection between gene(s) and maturation age, we conclude that the environmental changes observed in the North Atlantic during the past decades have led to bypassing of the influence of vgll3 and six6 on maturation through growth-driven plasticity., (© 2023 John Wiley & Sons Ltd.)

The environment gametes perform in just before fertilization is increasingly recognized to affect offspring fitness, yet the contributions of male and female gametes and their adaptive significance remain largely unexplored. Here, we investigated gametic thermal plasticity and its effects on hatching success and embryo performance in Atlantic salmon ( Salmo salar ). Eggs and sperm were incubated overnight at 2°C or 8°C, temperatures within the optimal thermal range of this species. Crosses between warm- and cold-incubated gametes were compared using a full-factorial design, with half of each clutch reared in cold temperatures and the other in warm temperatures. This allowed disentangling single-sex interaction effects when pre-fertilization temperature of gametes mismatched embryonic conditions. Pre-fertilization temperature influenced hatch timing and synchrony, and matching sperm and embryo temperatures resulted in earlier hatching. Warm incubation benefited eggs but harmed sperm, reducing the hatching success and, overall, gametic thermal plasticity did not enhance offspring fitness, indicating vulnerability to thermal changes. We highlight the sensitivity of male gametes to higher temperatures, and that gamete acclimation may not effectively buffer against deleterious effects of thermal fluctuations. From an applied angle, we propose the differential storage of male and female gametes as a tool to enhance sustainability within the hatcheries., Competing Interests: We declare we have no competing interests., (© 2023 The Authors.)

Iteroparity represents an important but often overlooked component of life history in anadromous Atlantic salmon. Here, we combined individual DNA profiling and scale reading to identify repeat spawners among ~8000 adult salmon captured in a fish trap in the river Etne, Norway, in the period 2015-2019. Additionally, 171 outward migrating kelts were captured in the spring of 2018-2020 and identified using molecular methods to estimate weight loss since ascending the river to spawn. The overall frequency of repeat spawners identified using molecular methods and scale reading combined was 7% in females and 3% in males (5% in total). Most of these (83%) spent one full year reconditioning at sea before returning for their second spawning, with a larger body size compared with their size at first spawning, gaining on average 15.9 cm. A single female migrating back into the river for a fifth breeding season was also identified. On average, kelts lost 40% bodyweight in the river, and more female than male kelts were captured during outward migration. The date of arrival in the upstream fish trap was significantly but moderately correlated between maiden and second entry to the river for alternate and consecutive spawners. The estimated contribution from repeat spawners to the total number of eggs deposited in the river each year varied between 2% and 17% (average 12%). Molecular-based methods marginally underestimated the number of repeat spawners compared with scale reading (5% vs 7%) likely due to a small number of returning spawners not being trapped and sampled. Differences between the methods were most evident when classifying the spawning strategy (alternate or consecutive-year repeat spawners), where the scale method identified proportionally more consecutive-year repeat spawners than the molecular method. This unique data set reveals previously unstudied components of this life history strategy and demonstrates the importance of repeat spawners in population recruitment., Competing Interests: The authors declare no conflict of interest., (© 2023 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Resistance toward the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse ( Lepeophtheirus salmonis salmonis ), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000-2002 "pre-resistance") and contemporary (2014-2017 "post-resistance") samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as "neutral" controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000-2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes, respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual . No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and that long-distance dispersion of resistance is rapid due to high level of genetic connectivity that is observed in this species., (© 2023 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4,393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations. Both approaches identified extensive population genetic structuring with a major split between the East and West Atlantic and a distinct Baltic Sea population, as well as further differentiation of lumpfish from the English Channel, Iceland, and Greenland. The discriminatory loci displayed ~2-5 times higher divergence than the genome wide approach, revealing further evidence of local population substructures. Lumpfish from Isfjorden in Svalbard were highly distinct but resembled most fish from Greenland. The Kattegat area in the Baltic transition zone, formed a previously undescribed distinct genetic group. Also, further subdivision was detected within North America, Iceland, West Greenland, Barents Sea, and Norway. Although lumpfish have considerable potential for dispersal and gene-flow, the observed high levels of population structuring throughout the Atlantic suggests that this species may have a natal homing behavior and local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for exploitation of lumpfish stocks and in decisions related to sourcing and moving lumpfish for cleaner fish use in salmonid aquaculture., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Jansson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Gene flow between wild and domestic populations has been repeatedly demonstrated across a diverse range of taxa. Ultimately, the genetic impacts of gene flow from domestic into wild populations depend both on the degree of domestication and the original source of the domesticated population. Atlantic salmon, Salmo salar , used in North American aquaculture are ostensibly of North American origin. However, evidence of European introgression into North American aquaculture salmon has accumulated in recent decades, even though the use of diploid European salmon has never been approved in Canada. The full extent of such introgression as well as the potential impacts on wild salmon in the Northwest Atlantic remains uncertain. Here, we extend previous work comparing North American and European wild salmon ( n  = 5799) using a 220 K SNP array to quantify levels of recent European introgression into samples of domestic salmon, aquaculture escapees, and wild salmon collected throughout Atlantic Canada. Analysis of North American farmed salmon ( n  = 403) and escapees ( n  = 289) displayed significantly elevated levels of European ancestry by comparison with wild individuals ( p  < 0.001). Of North American farmed salmon sampled between 2011 and 2018, ~17% had more than 10% European ancestry and several individuals exceeded 40% European ancestry. Samples of escaped farmed salmon similarly displayed elevated levels of European ancestry, with two individuals classified as 100% European. Analysis of juvenile salmon collected in rivers proximate to aquaculture locations also revealed evidence of elevated European ancestry and larger admixture tract in comparison to individuals collected at distance from aquaculture. Overall, our results demonstrate that even though diploid European salmon have never been approved for use in Canada, individuals of full and partial European ancestry have been in use over the last decade, and that some of these individuals have escaped and hybridized in the wild., Competing Interests: The authors declare no conflict of interest., (© 2022 Her Majesty the Queen in Right of Canada and the Authors. Evolutionary Applications published by John Wiley & Sons Ltd. Reproduced with the permission of the Minister of Fisheries and Oceans Canada.)

Identifying how physical and biotic factors shape genetic connectivity among populations in time and space is essential to our understanding of the evolutionary trajectory as well as the management of marine species. Atlantic cod is a widespread and commercially important marine species displaying several ecotypes with different life history strategies. Using three sets of SNPs: neutral, informative, and genome-inversion linked, we studied population genetic structure of ~2500 coastal Atlantic cod (CC) from 40 locations along Norway's 2500 km coastline, including nine fjords. We observed: (1) a genetic cline, suggesting a mechanism of isolation by distance, characterized by a declining F ST between CC and North East Arctic Cod (NEAC-genetically distinct migratory ecotype) with increasing latitude, (2) that in the north, samples of CC from outer-fjord areas were genetically more similar to NEAC than were samples of CC from their corresponding inner-fjord areas, (3) greater population genetic differentiation among CC sampled from outer-fjord areas along the coast, than among CC sampled from their corresponding inner-fjord areas, (4) genetic differentiation among samples of CC from both within and among fjords. Collectively, these results permit us to draw two main conclusions. First, that differences in the relative presence of the genetically highly distinct, migratory ecotype NEAC, declining from north to south and from outer to inner fjord, plays the major role in driving population genetic structure of the Norwegian CC. Second, that there is limited connectivity between CC from different fjords. These results suggest that the current management units implemented for this species in Norway should be divided into smaller entities. Furthermore, the situation where introgression from one ecotype drives population genetic structure of another, as is the case here, may exist in other species and geographical regions, thus creating additional challenges for sustainable fisheries management., Competing Interests: None declared., (© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

The release of domesticated conspecifics into the natural environment, whether deliberate or accidental, has the potential to alter the genetic integrity and evolutionary trajectory of wild populations. This widespread challenge is of particular concern for wild Atlantic salmon. By investigating phenotypic differences between the offspring of domesticated, hybrid, and wild Atlantic salmon released into the natural environment, earlier studies have documented the short-term consequences of introgression from domesticated fish into wild salmon populations. However, few studies have investigated the joined product of introgression and natural selection after several generations. Here, we investigated the phenotypic response of an Atlantic salmon population that has been subjected to an average of 24% genetic admixture by domesticated conspecifics escaping from fish farms over three decades (approximately 6-7 generations). Individual levels of admixture were positively correlated with increased size at the smolt and adult stages for both sexes, a decrease in the age of male smolts, and a decrease in the age at maturity for males. These life history changes are presumably the consequence of the well-documented directional selection for increased growth in domesticated salmon and are likely maladaptive. However, the most novel result of this study is that admixture was positively linked with delayed date of return to the river, with highly admixed fish arriving up to 26 days later than nonadmixed fish. Potentially, this phenological change provides admixed individuals with a survival advantage in the later phase of the life cycle as it reduces their period of exposure to selection through rod and line angling. We, therefore, conclude that while gene flow from domesticated conspecifics changes life history and phenological traits of wild Atlantic salmon populations, most of which are likely to be maladaptive, when pressured by additional anthropogenic challenges, some changes may confer a fitness advantage for a short part of the life cycle., Competing Interests: The authors declare no conflict of interest., (© 2022 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13,081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including apparent downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite repeated development of resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Populations may counteract lasting temperature changes or recurrent extremes through plasticity or adaptation. However, it remains underexplored how outbreeding, either naturally, unintentionally, or facilitated, may modify a local response potential and whether genotype-by-environment interactions or between-trait correlations can restrict this potential. We quantified population differences and outbreeding effects, within-population genetic variation, and plasticity of these, for thermal performance proxy traits using 32 pedigreed wild, domesticated, and wild-domesticated Atlantic salmon families reared under common-garden conditions. Following exposure to ambient cold (11.6 °C) or ~4° and ~8° warmer summer temperatures, populations differed notably for body length and critical thermal maximum (CT max ) and for thermal plasticity of length, condition, and CT max , but not for haematocrit. Line-cross analysis suggested mostly additive and some dominant outbreeding effects on means and solely additive outbreeding effects on plasticity. Heritability was detected for all traits. However, with increasing acclimation temperature, differences in CT max between populations and CT max heritability diminished, and CT max breeding values re-ranked. Furthermore, CT max and body size were negatively correlated at the genetic and phenotypic levels, and there was indirect evidence for a positive correlation between growth potential and thermal performance breadth for growth. Thus, population differences (including those between wild and domesticated populations) in thermal performance and plasticity may present a genetic resource in addition to the within-population genetic variance to facilitate, or impede, thermal adaptation. However, unfavourable genotype-by-environment interactions and negative between-trait correlations may generally hamper joint evolution in response to an increase in average temperature and temporary extremes., (© 2021. The Author(s), under exclusive licence to The Genetics Society.)

Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits. However, the impact of domestication on eye size has not been studied. We measured body size corrected eye size in 4000 salmon from six common garden experiments conducted under artificial and natural conditions, in freshwater and saltwater environments, in two countries. Within these common gardens, offspring of domesticated and wild parents were crossed to produce 11 strains, with varying genetic backgrounds (wild, domesticated, F1 hybrids, F2 hybrids and backcrosses). Size-adjusted eye size was influenced by both genetic and environmental factors. Domesticated fish reared under artificial conditions had smaller adjusted eye size when compared to wild fish reared under identical conditions, in both the freshwater and marine environments, and in both Irish and Norwegian experiments. However, in parr that had been introduced into a river environment shortly after hatching and sampled at the end of their first summer, differences in adjusted eye size observed among genetic groups were of a reduced magnitude and were nonsignificant in 2-year-old sea migrating smolts sampled in the river immediately prior to sea entry. Collectively, our findings could suggest that where natural selection is present, individuals with reduced eye size are maladapted and consequently have reduced fitness, building on our understanding of the mechanisms that underlie a well-documented reduction in the fitness of the progeny of domesticated salmon, including hybrid progeny, in the wild., Competing Interests: The authors declare no competing interests., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Background: In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts., Results: Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents., Conclusions: The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system., (© 2021. The Author(s).)

Nothing lasts forever, including the effect of chemicals aimed to control pests in food production. As old pesticides have been compromised by emerging resistance, new ones have been introduced and turned the odds back in our favour. With time, however, some pests have developed multi-pesticide resistance, challenging our ability to control them. In salmonid aquaculture, the ectoparasitic salmon louse has developed resistance to most of the available delousing compounds. The discovery of genetic markers associated with resistance to organophosphates and pyrethroids made it possible for us to investigate simultaneous resistance to both compounds in approximately 2000 samples of salmon lice from throughout the North Atlantic in the years 2000-2016. We observed widespread and increasing multiresistance on the European side of the Atlantic, particularly in areas with intensive aquaculture. Multiresistant lice were also found on wild Atlantic salmon and sea trout, and also on farmed salmonid hosts in areas where delousing chemicals have not been used. In areas with intensive aquaculture, there are almost no lice left that are sensitive to both compounds. These results demonstrate the speed to which this parasite can develop widespread multiresistance, illustrating why the aquaculture industry has repeatedly lost the arms race with this highly problematic parasite., (© 2021 The Authors.)

The parasitic salmon louse represents one of the biggest challenges to environmentally sustainable salmonid aquaculture across the globe. This species also displays a high evolutionary potential, as demonstrated by its rapid development of resistance to delousing chemicals. In response, farms now use a range of non-chemical delousing methods, including cleaner fish that eat lice from salmon. Anecdotal reports suggest that in regions where cleaner fish are extensively used on farms, lice have begun to appear less pigmented and therefore putatively less visible to cleaner fish. However, it remains an open question whether these observations reflect a plastic (environmental) or adaptive (genetic) response. To investigate this, we developed a pigment scoring system and conducted complimentary experiments which collectively demonstrate that, a) louse pigmentation is strongly influenced by environmental conditions, most likely light, and b) the presence of modest but significant differences in pigmentation between two strains of lice reared under identical conditions. Based on these data, we conclude that pigmentation in the salmon louse is strongly influenced by environmental conditions, yet there are also indications of underlying genetic control. Therefore, lice could display both plastic and adaptive responses to extensive cleaner fish usage where visual appearance is likely to influence survival of lice., Competing Interests: The authors declare that they have no conflict of interest., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse ( Symphodus melops ) escapees and admixed individuals in wild populations in western Norway. Applying this panel to ~2000 individuals, escapees and hybrids were found to constitute up to 20% of the local population at the northern edge of the species' distribution. The introduction of southern genetic material at the northern edge of the species distribution range has altered the local genetic composition and could obstruct local adaptation and further range expansion. Surprisingly, in other parts of the species distribution where salmon farming is also common, few escapees and hybrids were found. Why hybridization seems to be common only in the far north is discussed in the context of demographic and transport history. However, the current lack of reporting of escapes makes it difficult to evaluate possible causes for why some aquaculture-dense areas have more escapees and hybrids than others. The results obtained in this study, and the observed high genomic divergence between the main export and import regions, puts the sustainability of mass translocation of nonlocal wild wrasse into question and suggests that the current management regime needs re-evaluation., Competing Interests: None declared., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; that is, Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat, and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant F ST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbor-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation ( F ST ) between marine and brackish sprat is larger in the comparison Norway-Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, that is, 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen., Competing Interests: None declared., (© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Background: Farmed Atlantic salmon are one of the most economically significant global aquaculture products. Early sexual maturation of farmed males represents a significant challenge to this industry and has been linked with the vgll3 genotype. However, tools to aid research of this topic, such as all-male and clonal fish, are still lacking. The present 6-year study examined if all-male production is possible in Atlantic salmon, a species with heteromorphic sex chromosomes (males being XY, females XX), and if all-male fish can be applied to further explore the vgll3 contribution on the likelihood of early maturation., Results: Estrogen treatment of mixed sex yolk sac larvae gave rise to one sexually mature hermaphrodite with a male genotype (XY) that was used to produce both self-fertilized offspring and androgenetic double haploid (dh) offspring following egg activation with UV treated sperm and pressure shock to block the first mitotic division. There were YY supermales among both offspring types, which were crossed with dh females. Between 1 and 8% of the putative all-male offspring from the eight crosses with self-fertilized supermales were found to have ovaries, and 95% of these phenotypic females were also genetically female. None of the offspring from the one dh supermale cross had ovaries. When assessing the general contribution of the vgll3 locus on the likelihood of early post-smolt sexual maturation (jacking) in the all-male populations we found individuals that were homozygous for the early maturing genotype (97%) were more likely to enter puberty than individuals that were homozygous for the late maturing genotype (26%). However, the likelihood of jacking within individuals with an early/late heterozygous genotype was higher when the early allele came from the dam (94%) compared to the sire (45%)., Conclusions: The present results show that supermale Atlantic salmon are viable and fertile and can be used as a research tool to study important aspects of sexual maturation, such as to further explore the sex dependent parental genetic contribution to age at puberty in Atlantic salmon. In addition, we report the production of viable double haploid supermale fish.

Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan I AA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection., Competing Interests: We declare we have no competing interests., (© 2020 The Authors.)

Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are among the best studied fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome ( sdY ) has been identified. However, sdY displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of recent transposition events in this species. We hypothesized the existence of an autosomal copy of sdY , causing apparent discordance between phenotypic and genetic sex, that is transmitted in accordance with autosomal inheritance. To test this, we developed a qPCR methodology to detect the total number of sdY copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2,025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomal copies of sdY in addition to the Y-specific copy present in males. Patterns across families were highly consistent with autosomal inheritance. These autosomal sdY copies appear to have lost the ability to function as a sex determining gene and were only occasionally assigned to the actual sex chromosome in any of the affected families., (Copyright © 2020 Ayllon, Solberg, Besnier, Fjelldal, Hansen, Wargelius, Edvardsen and Glover.)

Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies., Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global F ST among these populations was 0.015-0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (F ST  > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species' Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean F ST&#95;173&#95;loci  = 0.065, F ST&#95;69&#95;loci  = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin., Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.

Livestock domestication has long been a part of agriculture, estimated to have first occurred approximately 10 000 years ago. Despite the plethora of traits studied, there is little understanding of the possible impacts domestication has had on internal organs, which are key determinants of survival. Moreover, the genetic basis of observed associated changes in artificial environments is still puzzling. Here we examine impacts of captivity on two organs in Atlantic salmon ( Salar salar ) that have been domesticated for approximately 50 years: heart and liver, in addition to growth. We studied multiple families of wild, domesticated, F 1 and F 2 hybrid, and backcrossed strains of S. salar in replicated common garden tanks during the freshwater and marine stages of development. Heart and liver weight were investigated, along with heart morphology metrics examined in just the wild, domesticated and F 1 hybrid strains (heart height and width). Growth was positively linked with the proportion of the domesticated strain, and recombination in F 2 hybrids (and the potential disruption of co-adapted gene complexes) did not influence growth. Despite the influence of domestication on growth, we found no evidence for domestication-driven divergence in heart or liver morphology. However, sexual dimorphism was detected in heart morphology, and after controlling for body size, females exhibited significantly larger heart weight and heart width when compared with males. Wild females also had an increased heart height when compared with wild males, and this was not observed in any other strain. Females sampled in saltwater showed significantly larger heart height with rounder hearts, than saltwater males. Collectively, these results demonstrate an additive basis of growth and, despite a strong influence of domestication on growth, no clear evidence of changes in heart or liver morphology associated with domestication was identified., Competing Interests: The authors declare no competing interests., (© 2020 The Authors.)

To avoid negative environmental impacts of escapees and potential inter-breeding with wild populations, the Atlantic salmon farming industry has and continues to extensively test triploid fish that are sterile. However, they often show differences in performance, physiology, behavior and morphology compared to diploid fish, with increased prevalence of vertebral deformities and ocular cataracts as two of the most severe disorders. Here, we investigated the mechanisms behind the higher prevalence of cataracts in triploid salmon, by comparing the transcriptional patterns in lenses of diploid and triploid Atlantic salmon, with and without cataracts. We assembled and characterized the Atlantic salmon lens transcriptome and used RNA-seq to search for the molecular basis for cataract development in triploid fish. Transcriptional screening showed only modest differences in lens mRNA levels in diploid and triploid fish, with few uniquely expressed genes. In total, there were 165 differentially expressed genes (DEGs) between the cataractous diploid and triploid lens. Of these, most were expressed at lower levels in triploid fish. Differential expression was observed for genes encoding proteins with known function in the retina (phototransduction) and proteins associated with repair and compensation mechanisms. The results suggest a higher susceptibility to oxidative stress in triploid lenses, and that mechanisms connected to the ability to handle damaged proteins are differentially affected in cataractous lenses from diploid and triploid salmon., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Challenging long-held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor genetic units can occur. Atlantic cod ( Gadus morhua ) is an economically and ecologically important marine species across the North Atlantic. The application of new genomic resources, including SNP arrays, allows us to detect and explore novel structure within specific cod management units. In Norwegian waters, coastal cod (i.e. those not undertaking extensive migrations) are divided into two arbitrary management units defined by ICES: one between 62° and 70°N (Norwegian coastal cod; NCC) and one between 58° and 62°N (Norwegian coastal south; NCS). Together, these capture a fishery area of >25,000 km 2 containing many spawning grounds. To assess whether these geographic units correctly represent genetic stocks, we analysed spawning cod of NCC and NCS for more than 8,000 SNPs along with samples of Russian White Sea cod, north-east Arctic cod (NEAC: the largest Atlantic stock), and outgroup samples representing the Irish and Faroe Sea's. Our analyses revealed large differences in spatial patterns of genetic differentiation across the genome and revealed a complex biological structure within NCC and NCS. Haplotype maps from four chromosome sets show regional specific SNP indicating a complex genetic structure. The current management plan dividing the coastal cod into only two management units does not accurately reflect the genetic units and needs to be revised. Coastal cod in Norway, while highly heterogenous, is also genetically distinct from neighbouring stocks in the north (NEAC), west (Faroe Island) and the south. The White Sea cod are highly divergent from other cod, possibly yielding support to the earlier notion of subspecies rank., (© 2020 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Background: In several fish species homozygous and heterozygous clonal lines have been produced using gynogenetic and androgenetic techniques. These lines are standardized and can be reproduced over generations. In rainbow trout such lines have existed for decades and has become important research tools in genome studies as well as in studies of commercially important traits. The Atlantic salmon is one of the best studied fish species globally, but all experiments are done on fish of wild or domesticated origin and access to standardized immortal fish lines would be of great benefit. Here, we describe the protocols developed to produce mitotic gynogenes, and from these the first clonal lines in Atlantic salmon., Results: Atlantic salmon eggs fertilized with UV irradiated sperm combined with a pressure shock applied at 4700-4800 minC at 8 °C gave all homozygous (doubled haploid) gynogenetic progeny with high survival. From the six first maturing females, five all homozygous clonal lines were produced by meiotic gynogenesis and were verified as clonal and identical to their mother with microsatellite markers., Conclusions: We have now produced the first documented cloned Atlantic salmon lines. This work demonstrates the potential for production of further Atlantic salmon clonal lines, potentially with distinct characteristics. Such lines will provide an important resource for further elucidation of phenotypic and genetic traits in this globally important species.

Background: Triploid organisms have three sets of chromosomes. In Atlantic salmon, hydrostatic pressure treatment of newly fertilized eggs has been extensively used to produce triploids which are functionally sterile due to their unpaired chromosomes. These fish often perform poorly on commercial farms, sometimes without explanation. Inheritance patterns in individuals subjected to pressure treatment have not been investigated in Atlantic salmon thus far. However, work on other species suggests that this treatment can result in aberrant inheritance. We therefore studied this in Atlantic salmon by genotyping 16 polymorphic microsatellites in eyed eggs and juveniles which had been subjected to pressure-induction of triploidy. Communally reared juveniles including fish subjected to pressure-induction of triploidy and their diploid siblings were included as a control., Results: No diploid offspring were detected in any of the eggs or juveniles which were subjected to hydrostatic pressure; therefore, the induction of triploidy was highly successful. Aberrant inheritance was nevertheless observed in 0.9% of the eggs and 0.9% of the juveniles that had been subjected to pressure treatment. In the communally reared fish, 0.3% of the fish subjected to pressure treatment displayed aberrant inheritance, while their diploid controls displayed 0% aberrant inheritance. Inheritance errors included two eyed eggs lacking maternal DNA across all microsatellites, and, examples in both eggs and juveniles of either the maternal or paternal allele lacking in one of the microsatellites. All individuals displaying chromosome aberrations were otherwise triploid., Conclusions: This is the first study to document aberrant inheritance in Atlantic salmon that have been subjected to pressure-induction of triploidy. Our experiments unequivocally demonstrate that even when induction of triploidy is highly successful, this treatment can cause chromosome aberrations in this species. Based upon our novel data, and earlier studies in other organisms, we hypothesize that in batches of Atlantic salmon where low to modest triploid induction rates have been reported, aberrant inheritance is likely to be higher than the rates observed here. Therefore, we tentatively suggest that this could contribute to the unexplained poor performance of triploid salmon that is occasionally reported in commercial aquaculture. These hypotheses require further investigation.

Capture and long-distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetic structure of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain, using 82 SNP markers. We detected two very distinct genetic groups in Scandinavia, northwestern and southeastern. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat discontinuity for this rocky shore associated benthic egg-laying species. Wrasse from Galicia were highly differentiated from all Scandinavian locations, but more similar to northwestern than southeastern locations. Distinct genetic differences were observed between sympatric spotty and plain phenotypes in Galicia, but not in Scandinavia. The mechanisms underlying the geographic patterns between phenotypes are discussed, but not identified. We conclude that extensive aquaculture-mediated translocation of ballan wrasse from Sweden and southern Norway to western and middle Norway has the potential to mix genetically distinct populations. These results question the sustainability of the current cleaner fish practice., Competing Interests: None declared., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

Background: Domestication is the process by which organisms become adapted to the human-controlled environment. Since the selection pressures that act upon cultured and natural populations differ, adaptations that favour life in the domesticated environment are unlikely to be advantageous in the wild. Elucidation of the differences between wild and domesticated Atlantic salmon may provide insights into some of the genomic changes occurring during domestication, and, help to predict the evolutionary consequences of farmed salmon escapees interbreeding with wild conspecifics. In this study the transcriptome of the offspring of wild and domesticated Atlantic salmon were compared using a common-garden experiment under standard hatchery conditions and in response to an applied crowding stressor., Results: Transcriptomic differences between wild and domesticated crosses were largely consistent between the control and stress conditions, and included down-regulation of environmental information processing, immune and nervous system pathways and up-regulation of genetic information processing, carbohydrate metabolism, lipid metabolism and digestive and endocrine system pathways in the domesticated fish relative to their wild counterparts, likely reflective of different selection pressures acting in wild and cultured populations. Many stress responsive functions were also shared between crosses and included down-regulation of cellular processes and genetic information processing and up-regulation of some metabolic pathways, lipid and energy in particular. The latter may be indicative of mobilization and reallocation of energy resources in response to stress. However, functional analysis indicated that a number of pathways behave differently between domesticated and wild salmon in response to stress. Reciprocal F1 hybrids permitted investigation of inheritance patterns that govern transcriptomic differences between these genetically divergent crosses. Additivity and maternal dominance accounted for approximately 42 and 25% of all differences under control conditions for both hybrids respectively. However, the inheritance of genes differentially expressed between crosses under stress was less consistent between reciprocal hybrids, potentially reflecting maternal environmental effects., Conclusion: We conclude that there are transcriptomic differences between the domesticated and wild salmon strains studied here, reflecting the different selection pressures operating on them. Our results indicate that stress may affect certain biological functions differently in wild, domesticated and hybrid crosses and these should be further investigated.