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After the initial opening of the Bering Strait 5.5–-5.0 My ago, there occurred several periods with exchange of marine species between the Pacific and Atlantic Oceans. The snow crab ( Chionoecetes opilio) was first reported in the Barents Sea (BAR) in 1996, presumably following introduction via Ballast water. Since then, the population has increased in size and distribution and has become self-reproducing and of economic importance. We implemented genetic analysis to identify the origin and pathway of introduction of BAR snow crab. Samples from BAR, Alaska, eastern Canada, and west Greenland were genotyped with 12 microsatellite loci. Pairwise FST between 15 samples showed three geographic clusters, each significantly different from one another. Unexpectedly, the largest genetic distance was between the BAR and Greenland clusters. This clustering may be the result of dispersals through Bering Strait from the North Pacific Ocean and passage through the Arctic Ocean. The BAR samples did not show signs of a bottleneck in population size, as would be expected after introduction of small numbers of individuals. Presence of snow crab in the BAR may thus be the result of recent natural range expansion from around Alaska.

Salmon farming in marine net pens is a major activity in many temperate regions. This industry may affect coastal ecosystems in several ways, such as with waste pollution and parasite spillover. Less is known about the extent to which salmon farming disrupts the use of inshore spawning grounds by wild fish, such as the Atlantic cod Gadus morhua. Acoustic telemetry was therefore used to explore cod space use during the spawning season in a coastal region in mid-Norway with multiple salmon farms. Acoustic receivers were placed in clusters at 5 known cod spawning grounds and 6 nearby salmon farms. Data from 481 adult cod caught at the spawning grounds during 2017-2019 and equipped with acoustic telemetry transmitters were analysed. Overall, fewer fish were detected at farms than spawning grounds, even when accounting for distance from release point. Individual cod residency (days detected / duration of spawning period) was generally higher at the spawning grounds close to farms but low at the farms themselves, with little apparent spawning at the farm localities. In contrast, spawning was clearly occurring at the nearby spawning grounds, with cod spending weeks (n = 316) or months (n = 158) there during the spawning period. Males had longer residence times at spawning grounds than females, likely linked to the cod mating system. Overall, we found little support for the assertion that salmon farms disrupt inshore spawning dynamics of cod using nearby spawning grounds presently, either by attracting spawners to farms or causing fish to leave these grounds.

1AbstractLumpfish (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) 4393 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 targeted 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 displays natal homing and potentially local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for lumpfish fishing stocks and in decisions related to sourcing and moving lumpfish for farming and cleaner fish use.

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., The genetics of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, was studied along the Scandinavian coastline and in Galicia, Spain. A distinct genetic break was detected in Scandinavia, dividing northwestern and southeastern clusters. Additionally, distinct genetic differences were observed between sympatric spotted and plain phenotypes in Galicia, but not in Scandinavia.

Sustainable fisheries management requires detailed knowledge of population genetic structure. The European sprat is an important commercial fish distributed from Morocco to the Arctic circle, Baltic, Mediterranean, and Black seas. Prior to 2018, annual catch advice on sprat from the International Council for the Exploration of the Sea (ICES) was based on five putative stocks: (a) North Sea, (b) Kattegat–Skagerrak and Norwegian fjords, (c) Baltic Sea, (d) West of Scotland—southern Celtic Seas, and (e) English Channel. However, there were concerns that the sprat advice on stock size estimates management plan inadequately reflected the underlying biological units. Here, we used ddRAD sequencing to develop 91 SNPs that were thereafter used to genotype approximately 2,500 fish from 40 locations. Three highly distinct and relatively homogenous genetic groups were identified: (a) Norwegian fjords; (b) Northeast Atlantic including the North Sea, Kattegat–Skagerrak, Celtic Sea, and Bay of Biscay; and (c) Baltic Sea. Evidence of genetic admixture and possibly physical mixing was detected in samples collected from the transition zone between the North and Baltic seas, but not between any of the other groups. These results have already been implemented by ICES with the decision to merge the North Sea and the Kattegat–Skagerrak sprat to be assessed as a single unit, thus demonstrating that genetic data can be rapidly absorbed to align harvest regimes and biological units. publishedVersion

The impacts of climate change on marine ecosystems can be seen in the changing distribution, migration, and abundance of species in the oceans. For some species this changing environment may be beneficial and can support population expansions. In the northeast Atlantic (NEA), the Atlantic mackerel (Scomber scombrus) is undergoing an increase in stock size accompanied by changing summer migration patterns, which have resulted in an expansion further north and north west than previously recorded. This study uses microsatellite loci to confirm the differentiation among NEA and northwest Atlantic (NWA) mackerel spawning populations and to assess the level of structuring within these populations. In addition, to enable population-specific exploitation rates to be factored into fisheries management, we identified the origin of individuals composing the expanding feeding aggregations in the central north Atlantic (Greenland, Iceland, Faroes), with all aggregations tested originating from spawning populations in the NEA. This study showed that microsatellite loci were useful to assess the contribution of NEA and NWA populations to mixed feeding aggregations across the north Atlantic for large pelagic fish stocks but were not powerful enough to evaluate the specific contribution of known stocks within NEA and NWA.

Blue ling is a deep-water species that has been severely fished upon into coastal and offshore fisheries since the early 1970s, thus causing the collapse of the populations in the last two decades. Genetic information is scarce in this species, and molecular markers are therefore needed to provide advice both for management and for rebuilding the stocks. A suite of 103 SNP markers was identified from ddRAD sequencing data. From those, 81 were organized in three multiplex reactions, and tested on 150 individuals from three different sampling locations. Good-quality amplification products were successfully obtained from 70 of the markers. All SNP loci were biallelic, with averaged He per locus ranging between 0.101 and 0.500.

Coastal Atlantic cod (Gadus morhua) in the Northeast Atlantic has seen a continuous decline since the industrialization of the coastal fishery, and management needs to address the spatial and temporal complexities of coexisting cod stocks. Toward that end, genetic analyses and oceanographic modelling of coastal and oceanic cod larval drift patterns were combined to elucidate the mechanisms responsible for an observed genetic cline over a >1500 km stretch along the coast of Norway. The results indicate that the north–south cline in coastal cod represents an extended contact zone between genetically divergent North Sea and Northeast Arctic cod and is maintained by two-way gene flow: by northward drift of pelagic eggs and larvae and by southward spawning migrations of Northeast Arctic cod. Computer simulations verify that the genetic cline can be established rapidly if gene flow into coastal populations is substantial. The shape of the cline, on the other hand, was found to be largely insensitive to the total amount of gene flow and therefore carries little information on extent of gene flow into and among coastal populations.

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.

Population connectivity is an increasingly important focal area for the understanding of how marine fish populations respond to anthropogenic pressures like climate change and fisheries. Our model species, the saithe Pollachius virens (Linnaeus, 1758), was chosen because genetic analyses have documented a mismatch between the assessed stocks and the biological populations. We combined laboratory experiments of saithe egg buoyancy and temperature-�modulated development time, genetic field data, and high-resolution oceanographic models to disentangle the mechanisms causing isolation and mixing between the management units and the biological populations. Saithe egg buoyancy and development data were included in an individual-based model to simulate transport from all known spawning grounds in the Northeast Atlantic. The results show that interannual variability in the transport of early life stages is strongly influenced by wider climate systems (e.g. the North Atlantic Oscillation). One sample (Rockall) showed genetic differences from the other samples, and this finding was supported by the model showing low mixing with other populations and strong local retention. Strong retention of early life stages around Iceland could indicate an isolated population; however, this possible isolation is counteracted by active migration of adults westward from the Norwegian coast, and no genetic differentiation from other populations was found. Overall, the dispersal modeling supports the genetic analysis, showing a large and well-connected Central Northeast Atlantic population distributed across several management units. This mismatch between population structure and management units can potentially increase the risk for overexploitation of saithe.

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. publishedVersion

Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in the herring is in conflict with the infinitesimal model for complex traits because of the large shifts in allele frequencies at hundreds of loci under selection.

BackgroundQuantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations.ResultsAfter rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets.DiscussionThe observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.

The advent of novel genetic methods has made it possible to investigate population structure and connectivity in mobile marine fish species: knowledge of which is essential to ensure a sustainable fishery. Haddock (Melanogrammus aeglefinus) is a highly exploited marine teleost distributed along the coast and continental shelf on both sides of the North Atlantic Ocean. However, little is known about its population structure. Here, we present the first study using single-nucleotide polymorphism (SNP) markers to assess the genetic population structure of haddock at multiple geographic scales, from the trans-Atlantic to the local (fjord) level. Genotyping 138 SNP loci in 1329 individuals from 19 locations across the North Atlantic revealed three main genetic clusters, consisting of a Northwest Atlantic cluster, a Northeast Arctic cluster, and a Northeast Atlantic cluster. We also observed a genetically distinct fjord population and a pattern of isolation by distance in the Northeast Atlantic. Our results contrast with the current management regime for this species in the Northeast Atlantic, as we found structure within some management areas. The study adds to the growing recognition of population structuring in marine organisms in general, and fishes in particular, and is of clear relevance for the management of haddock in the Northeast Atlantic.

The North Sea is an important spawning and nursery ground for many demersal and pelagic fishes whose spawning areas are largely overlapping in time and space. This makes ichthyoplankton visual identification from the various species particularly challenging. Despite historically intensive research in the area, detailed information on spawning sites and times for many taxa, are incomplete. To update and detail the mapping of fish spawning performance and distribution in the central and northern regions of the North Sea, the performance of a visual method and a molecular taxonomic approach used for taxonomic classification of ichthyoplankton was evaluated. Samples of fish eggs and larvae were collected regularly and in parallel at different latitudinal locations from the central to the northern North Sea, including a sample with 78 larvae used for direct comparison between both methods. A total of 5332 individuals were inspected and 36 different species were identified. The visual processing identified 89% of the collected larvae to species level, however, for the eggs the taxonomic resolution was lower with only 5% identified to species level. In comparison to visual identification, molecular barcoding gave higher precision of identification for larvae and especially for the eggs. For the larvae, 98% were assigned to species level, and for the eggs 94% were assigned to species level. We find that molecular barcoding is more effective and precise in taxonomic identification of both eggs and larvae to species level. However, visual identification is still needed to provide information on the developmental stages.

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 FST 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 (FST > 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 FST_173_loci = 0.065, FST_69_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.

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 km2 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. publishedVersion

Background Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which is the country with the largest remaining catch in the Atlantic, the population genetic structure of coastal cod (NCC) along the entire coastline has not yet been investigated. We sampled > 4000 cod from 55 spawning sites. All fish were genotyped with 6 microsatellite markers and Pan I (Dataset 1). A sub-set of the samples (1295 fish from 17 locations) were also genotyped with an additional 9 microsatellites (Dataset 2). Otoliths were read in order to exclude North East Arctic Cod (NEAC) from the analyses, as and where appropriate. Results We found no difference in genetic diversity, measured as number of alleles, allelic richness, heterozygosity nor effective population sizes, in the north-south gradient. In both data sets, weak but significant population genetic structure was revealed (Dataset 1: global FST = 0.008, P

Science-based management of marine fisheries and effective ecosystem monitoring both require the analysis of large amounts of often complex and difficult to collect information. Legislation also increasingly requires the attainment of good environmental status, which again demands collection of data to enable efficient monitoring and management of biodiversity. Such data is traditionally obtained as a result of research surveys through the capture and/or visual identification of organisms. Recent years have seen significant advances in the utilisation of environmental DNA (eDNA) in the marine environment in order to develop alternative cost-effective ways to gather relevant data. Such approaches attempt to identify and/or quantify the species present at a location through the detection of extra-organismal DNA in the environment. These new eDNA based approaches have the potential to revolutionise data collection in the marine environment using non-invasive sampling methods and providing snapshots of biodiversity beyond the capacity of traditional sampling. Here we present a non-technical summary of different approaches in the field of eDNA, and emphasise the broad application of this approach, with value for the governance and management of marine aquatic ecosystems. The review focuses on identifying those tools which are now readily applicable and those which show promise but are currently in development and require further validations. The aim is to provide an understanding of techniques and concepts that can be used by managers without genetic or genomic expertise when consulting with specialists to perform joint evaluations of the utility of the approaches. Spanish Ministry of Science, Innovation and Universities through the EDAMAME ("Environmental DNA based approaches for marine and aquatic monitoring and evaluation") project [CTM2017-89500-R]; Scientific Research Network "Eco-evolutionary dynamics in natural and anthropogenic communities" (Research Foundation - Flanders) [W 0.037.10N] info:eu-repo/semantics/publishedVersion

Wrasse (Labridae) species have been used as parasite cleaners in Atlantic salmon farming since the 1980s. However, their use has recently escalated, with millions now being introduced into salmon cages each year. Most fish are of wild origin, their exploitation potentially impacting native populations. Genetic information is urgently required to inform management decisions. We identified 174 microsatellite and 149 SNP markers from ddRAD sequence data. From these, 17 and 48 microsatellite and SNP markers, respectively, were validated by genotyping 150 goldsinny wrasse collected from five locations along the Norwegian and Swedish coasts. Two to 30 alleles were identified at the microsatellite loci, while gene diversity (H e ) ranged 0.101–0.907. All SNP loci were biallelic, with averaged H e per locus ranging between 0.063 and 0.495.

Fish stocks represent fundamental units in fisheries management, and their identification, especially in mixed-fisheries, represents one of the primary challenges to sustainable harvest. Here, we describe the first “real-time” genetic management program used to manage a mixed-stock fishery of a non-salmonid and commercially significant marine fish, the Atlantic cod (Gadus morhua L). Based upon the analysis of >18 000 fish sampled from the commercial catch in Lofoten (Norway), which represents the largest remaining cod fishery in the Atlantic, we estimated the fraction of North East Arctic cod (NEAC), and Norwegian Coastal cod (NCC), just 24 h post-landing. These estimates, based upon the analysis of the Pantophysin gene, were performed weekly in the winter and spring of each year in the period 2007–2017. The program has successfully permitted the Norwegian Directorate of Fisheries to actively manage the commercial exploitation of the highly abundant NEAC stock, while simultaneously limiting exploitation of the fragile NCC stock, both of which overlap at the spawning grounds. Data from this program have also revealed a distinct temporal increase in the fraction of NEAC on the spawning grounds in this region, which is consistent with the overall increased abundance of this stock as estimated by ICES. publishedVersion

The salmon industry is heavily dependent on wrasse for delousing infected fish. The goldsinny wrasse is numerically the most important, and each year, millions are harvested from the wild and transported large distances into fish farms. Population genetic knowledge is required to sustainably exploit this species. Here, 1051 goldsinny wrasses from 16 locations across Scandinavia, the British Isles, and Spain were genotyped with 14 microsatellite and 36 SNP markers. Within-population genetic diversity decreased towards north, and a genetic break was observed across the North Sea. Samples from Northern Norway differed from rest of the Scandinavian samples, and samples from the British Isles differed from the Spanish ones. Within Scandinavia, isolation-by-distance was detected. Observed genetic patterns fitted well with expectations derived from oceanographic drift simulations. A sample from mid-Norway deviated from these patterns however, and was genetically very similar to southern Scandinavian samples. We conclude that the population structure of this species is primarily determined by the opposing evolutionary forces of passive drift, limited adult migration and spawning-site fidelity, whereas the deviation in isolation-by-distance observed in mid-Norway is potentially caused by inadvertent translocations of wrasse from southern Scandinavia via current aquaculture practise. Inclusion of outlier loci gave greater resolution, suggesting that diversifying selection may also affect population structuring among goldsinny wrasses. publishedVersion

With the decline of many of the world’s fisheries, increased regulation, including marine protected areas (MPA), forms an increasingly important role in promoting sustainable resource use. Here, we present a novel “real-time” genetic monitoring programme used to protect the depleted Norwegian coastal cod stock (NCC) in an MPA during the spawning season, while a fishery targeted at the sustainable Northeast Arctic cod stock (NEAC) operates immediately outside. In the period 2009–2016, >6800 cod from the fishery were genotyped with the PanI locus that is discriminatory between these two stocks. The estimated fraction of NEAC increased during the study period until 2014; however, it did not exceed 70% for any sustained period. Therefore, the MPA remained closed for commercial harvest. Genetic analysis of eggs revealed a distinctly lower fraction of NEAC than in the catch from the adult stock, both immediately outside and within the MPA itself. We suggest that this discrepancy is likely to reflect differences in spawning areas used by NCC and NEAC. Estimated fractions of NEAC/NCC using PanI, otolith classification, and 39 single nucleotide polymorphisms were similar, thus validating the use of PanI to estimate NEAC/NCC composition.

Background Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions. Results In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of ~4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13–15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals. Conclusion Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2867-z) contains supplementary material, which is available to authorized users.

Otterå*, H., Agnalt, A-L., Thorsen, A., Kjesbu, O.S., Dahle, G., and Jørstad, K. 2012. Is spawning time of marine fish imprinted in the genes? A two-generation experiment on local Atlantic cod (Gadus morhua L.) populations from different geographical regions. – ICES Journal of Marine Science, 69: 1722–1728. Spawning time (onset of spawning) in Atlantic cod (Gadus morhua L.) was monitored in an experimental setup and combined with modelled spawning time estimates from the wild. The experiment broodstock were collected from several geographical areas and kept in a common environment. Their spawning times in 2004 were compared with the spawning times of their daughters in 2009 and 2010. Daughter spawning time was highly correlated with that of the mother, indicating genetic regulation of spawning time. However, large individual variation in spawning time was observed. The modelling data suggests a north-south gradient in onset of spawning along the Norwegian coast, driven by differences in temperature, i.e. later dates of spawning in the north.

Summary Gynogenesis is one of several chromosome-manipulating techniques used in fish. In gynogenesis the male does not contribute to the genetic material of the offspring, and the sperm cells act only as stimulators in order for the egg to start development. This technique has several applications, both in aquaculture and in biological research: gynogenetic fish may be used as a step in the production of all-female populations, the production of isogenetic- and inbred lines, revealing of the sex determination mechanism, construction of genetic maps, and testing of environmental vs genetic control of different traits. The aim of this study was to develop a simple protocol for production of gynogenetic cod (Gadus morhua L.) for further use in aquaculture research. Various milt dilutions and UV-irradiation doses were tested, in order to inactivate the sperm without destroying its ability to induce egg development. This was followed by pressure treatment of the eggs shortly after ‘fertilization’ to suppress the completion of meiosis II, and thereby restoring diploidy. A dose of 9000 erg mm−2, followed by a 5-min pressure treatment (58.6 MPa) 180 min-degrees after fertilization gave 100% gynogenetic larvae. Histologically, sexual differentiated fish were all females, possibly confirming female homogamety in Atlantic cod. No particular signs of reduced growth, survival or enhanced deformity rates were observed after the fish had reached the juvenile phase. Mortality was, however, high during the egg and larval stages. This protocol has made capable the production of gynogenetic cod juveniles in significant amounts using relatively simple means; the next step will be to elaborate on the technique in order to produce mitotic gynogenetic (double haploid) individuals, which are 100% homozygous.

Atlantic cod (Gadus morhua) encompasses many different populations or stocks, which in part are managed separately. In the northeast Atlantic cod is divided into two main management units; northeast Arctic cod and coastal cod. These two groups have traditionally been separated by otolith classification. In this study, the power of different classes of genetic markers in separating the two cod groups was investigated. The variation in thirteen genetic markers, including allozymes, haemoglobin, the scDNA locus Pantophysin (Pan I) and a number of microsatellites was investigated, and mixed stock analysis and individual assignment tests were performed on samples comprising a mixture of individuals of putative coastal and oceanic type cod. The genetic analyses showed a large genetic differentiation between outer stations and stations located closer to the mainland shore. Mixed stock analysis and individual assignment tests used for estimation of stock proportions gave results similar to those obtained by otolith classification.

Aquaculture production of cod has decreased from over 20,000 tonnes in 2009 to less than 2,000 tonnes in 2014 and the industry faces many challenges, one of which is high and unpredictably variable mortality rates in the early life stages. Hence, full-cycle farming with hatchery produced juveniles is still considered unprofitable compared to fisheries and on-growing of wild cod. In the present study, potential batch differences in progeny survival of wild-caught, hatchery-spawned Faroe Bank cod (Gadus morhua L.) were investigated at two defined periods during early life history; i) the embryo stage (60 day degrees post fertilisation) and ii) the fry stage (110 days post hatch), post metamorphosis. The fry stage experiment was conducted in three replicates (N = 300 per replicate), and a panel of three polymorphic microsatellite markers was used for parental analysis. Mean survival rate at the embryo stage was 69% (± 20% SD). Survival was positively associated with egg diameter (P < 0.01), explaining 90% of the variation in egg survival rates. The data were too scarce to conclude either way concerning a possible correlation between survival rates between the two periods (P < 0.10). Offspring from three batches (from a total of eight) dominated in the fry stage, contributing over 90% of the progeny, and results were consistent over all three replicate tanks. The skewed batch representation observed may be of relevance to the effective management of selective breeding programmes for cod.

Genetic variation among and within species of the genus Sebastes [ S. viviparus , S. fasciatus , S. mentella (including deep-sea and oceanic types) and S. marinus (both ordinary and giant types)] from the North Atlantic was investigated by polymerase chain reaction (PCR)-based random amplification of polymorphic DNA (RAPD). Initial analyses were based on 80 different 10 base pair primers applied to a small number of individuals of each of the four species. Four of the most variable primers were selected for analysis of the total samples from Norway, Iceland and Canada. Only one primer, OPA20, could be used to diagnostically distinguish among species. Statistical analysis clustered all samples in relation to known species structure. No genetic distance was found between ordinary and giant-type S. marinus and minor differences were observed between S. viviparus from Iceland and Norway. Sebastes mentella from the different locations clustered together, but some structuring was shown within this species. Twel...