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Targeted sequencing is an increasingly popular Next Generation Sequencing (NGS) approach for studying populations, through focusing sequencing efforts on specific parts of the genome of a species of interest. Methodologies and tools for designing targeted baits are scarce but in high demand. Here, we present specific guidelines and considerations for designing capture sequencing experiments for population genetics for both neutral genomic regions and regions subject to selection. We describe the bait design process for three diverse fish species: Atlantic salmon, Atlantic cod and tiger shark, which was carried out in our research group, and provide an evaluation of the performance of our approach across both historical and modern samples. The workflow used for designing these three bait sets has been implemented in the R-package supeRbaits, which encompass our considerations and guidelines for bait design to benefit researchers and practitioners. The supeRbaits R package is user‐friendly and versatile. It is written in C++ and implemented in R. supeRbaits and its manual are available from Github: https://github.com/BelenJM/supeRbaits

Many post-smolt tissues were collected and screened as part of the EU funded SALSEA-Merge (Project No. 212529) part of the Seventh Framework Programme and co-sponsored by the Atlantic Salmon Trust and the Total Foundation., Gilbey, J., Utne, K.R., Wennevik, V., Beck, A.C., Kausrud, K., Hindar, K., Garcia de Leaniz, C., Cherbonnel, C., Coughlan, J., Cross, T.F., Dillane, E., Ensing, D., García-Vázquez, E., Hole, L.R., Holm, M., Holst, J.C., Jacobsen, J.A., Jensen, A.J., Karlsson, S., Ó Maoiléidigh, N., Mork, K.A., Nielsen, E.E., Nøttestad, L., Primmer, C.R., Prodöhl, P., Prusov, S., Stevens, J.R., Thomas, K., Whelan, K., McGinnity, P., Verspoor, E.

Mixed-stock fisheries pose a challenge for fisheries management recommendations and management, as mixed stocks can lead to unintentional over- or under-exploitation of stocks, with both short- and long-term biological and economic consequences. This study demonstrates practical application and implementation of year-round high-resolution genetic stock monitoring in management of mixed Atlantic cod (Gadus morhua) stocks in western Greenland. Using a panel of 96 high resolution gene-associated SNPs, we identified the stock of origin for four cod stocks in the two major inshore mixed-stock fisheries. Contribution of individual stocks was quantified to identify if fjord sections, times of year, and fish size, would allow a “clean fishery” with a minimal contribution of the depleted West Greenland Offshore (WGO) population. High level of mixing was identified with 50% of inshore catches originating from the inshore stock, 20% from the East Greenland/Iceland offshore stock, and 30% from the WGO stock. Although some spatiotemporal variation of stock proportions was identified, a practice allowing exclusively fishing a specific stock was not possible. Accordingly, we demonstrate the need to allocate catches at the biological stock level and show that application of high-resolution genetics is a reliable and necessary tool.

This study provides the first standardized global microsatellite database for a shark species, the tiger shark (Galeocerdo cuvier). Genotyping of reference individuals was used to develop and apply a calibration key for data from eight microsatellite loci data produced by three different laboratories, thereby allowing merging of genotypes into a single dataset. The unified data helped to elucidate the global population structure of the species and provided improved statistical power, through allowing a higher number of samples per location compared to the original studies from which the samples were obtained. Pairwise FST estimates and PCA plots showed significant genetic differentiation between Atlantic and Indo-Pacific samples, confirming previous findings by identifying the presence of a strong genetic break between tiger sharks inhabiting the two ocean basins. In turn, the standardized database (n = 799) also allowed archived historical samples to be genotyped and assigned back to their population (ocean basin) of origin. We demonstrate how calibration tests in population structure studies using microsatellite data is important as it simply provides more data to single studies. Importance factors for successful assignment analysis is discussed, as well as how the possibility of assigning historical samples of unknown origin back to the population, increases sample value. Our results demonstrate that global calibration of microsatellite and other genetic datasets can improve the statistical power and resolution of population structure analysis; an approach applicable not only when working with highly mobile globally distributed species such as the tiger shark, but with any species for which multiple genetic datasets exist.

The Atlantic herring Clupea harengus L has a vast geographical distribution and a complex population structure with a few very large migratory units and many small local populations. Each population has its own spawning ground and/or time, thereby maintaining their genetic integrity. Several herring populations migrate between common feeding grounds and over-wintering areas resulting in frequent mixing of populations. Thus, many herring fisheries are based on mixed populations of different demographic status. In order to avoid overexploitation of weak populations and to conserve biodiversity, understanding the population structure and population mixing is important for maintaining biologically sustainable herring fisheries. The aim of this study was to investigate the genetic population structure of herring in the Faroese and surrounding waters, and to develop genetic markers for distinguishing between four herring management units (often called stocks), namely the Norwegian spring-spawning herring (NSSH), Icelandic summer-spawning herring (ISSH), North Sea autumn-spawning herring (NSAH), and Faroese autumn-spawning herring (FASH). Herring from the four stocks were sequenced at low coverage, and single nucleotide polymorphisms (SNPs) were called and used for population structure analysis and individual assignment. An ancestry-informative SNP panel with 118 SNPs was developed and tested on 240 individuals. The results showed that all four stocks appeared to be genetically differentiated populations, but at lower levels of differentiation between FASH and ISSH than the other two populations. Overall assignment rate with the SNP panel was 80.7%, and agreement between the genetic and traditional visual assignment was 75.5%. The NSAH and NSSH samples had the highest assignment rate (100% and 98.3%, respectively) and highest agreement between traditional and genetic assignment methods (96.6% and 94.9%, respectively). The FASH and ISSH samples had substantially lower assignment rates (72.9% and 51.7%, respectively) and agreement between traditional and genetic methods (39.5% and 48.4%, respectively)

Fisheries enforcement relies on visual catch identification and quantification at sea or when landed. Silage (fish dissolved in acid) and fish blocks (block frozen fish) are promising methods for on-board processing and storage of low-value catches. We examined the use of non-destructive sampling and two DNA-based methods, quantitative PCR (qPCR) and metabarcoding, to assess species composition and relative abundance in industrial grade experimental silage and fish blocks. We demonstrate the ability to identify and quantify DNA from fish species in both products. qPCR analysis of small silage samples collected over 21 days detected all target control species. DNA from one species (Atlantic wolffish) was consistently overrepresented while, for three species of gadoids (Atlantic cod, haddock and whiting), the DNA content matched input tissue proportions with high accuracy. qPCR and metabarcoding of fish blocks, sampled as run-off water and exterior swabs, provided consistent species detection, with the highest variance observed in quantification from swab samples. Our analysis shows that DNA-based methods have significant potential as a tool for species identification and quantification of complex on-board-processed seafood products and are readily applicable to taxonomically and morphologically similar fish. There is, however, a need for establishing DNA/weight calibration factors for primary fisheries species.

Environmental DNA (eDNA) is increasingly used for monitoring marine organisms; however, offshore sampling and time lag from sampling to results remain problematic. In order to overcome these challenges a robotic sampler, a 2nd generation Environmental Sample Processor (ESP), was tested for autonomous analysis of eDNA from four commercial fish species in a 4.5 million liter mesocosm. The ESP enabled in situ analysis, consisting of water collection, filtration, DNA extraction and qPCR analysis, which allowed for real-time remote reporting and archival sample collection, consisting of water collection, filtration and chemical preservation followed by post-deployment laboratory analysis. The results demonstrate that the 2G ESP was able to consistently detect and quantify target molecules from the most abundant species (Atlantic mackerel) both in real-time and from the archived samples. In contrast, detection of low abundant species was challenged by both biological and technical aspects coupled to the ecology of eDNA and the 2G ESP instrumentation. Comparison of the in situ analysis and archival samples demonstrated variance, which potentially was linked to diel migration patterns of the Atlantic mackerel. The study demonstrates strong potential for remote autonomous in situ monitoring which open new possibilities for the field of eDNA and marine monitoring.

Genetic data have great potential for improving fisheries management by identifying the fundamental management units—that is, the biological populations—and their mixing. However, so far, the number of practical cases of marine fisheries management using genetics has been limited. Here, we used Atlantic cod in the Baltic Sea to demonstrate the applicability of genetics to a complex management scenario involving mixing of two genetically divergent populations. Specifically, we addressed several assumptions used in the current assessment of the two populations. Through analysis of 483 single nucleotide polymorphisms (SNPs) distributed across the Atlantic cod genome, we confirmed that a model of mechanical mixing, rather than hybridization and introgression, best explained the pattern of genetic differentiation. Thus, the fishery is best monitored as a mixed‐stock fishery. Next, we developed a targeted panel of 39 SNPs with high statistical power for identifying population of origin and analyzed more than 2,000 tissue samples collected between 2011 and 2015 as well as 260 otoliths collected in 2003/2004. These data provided high spatial resolution and allowed us to investigate geographical trends in mixing, to compare patterns for different life stages and to investigate temporal trends in mixing. We found similar geographical trends for the two time points represented by tissue and otolith samples and that a recently implemented geographical management separation of the two populations provided a relatively close match to their distributions. In contrast to the current assumption, we found that patterns of mixing differed between juveniles and adults, a signal likely linked to the different reproductive dynamics of the two populations. Collectively, our data confirm that genetics is an operational tool for complex fisheries management applications. We recommend focussing on developing population assessment models and fisheries management frameworks to capitalize fully on the additional information offered by genetically assisted fisheries monitoring.

Over the last century, many populations of sharks have been reduced in numbers by overexploitation or attempts to mitigate human-shark interactions. Still, there is a general perception that populations of large ocean predators cover wide areas and therefore their diversity is less susceptible to local anthropogenic disturbance. Here we report retrospective genomic analyses of DNA using archived and contemporary samples of tiger shark (Galeocerdo cuvier) from eastern Australia. Using SNP loci, we documented a significant overall change in genetic composition of tiger sharks born over the last century. The change was most likely due to a shift over time in the relative contribution of two well differentiated, but hitherto cryptic populations. Our data strongly indicate a dramatic shift in relative contribution of the two populations to the overall tiger shark abundance of the east coast of Australia, possibly associated with differences in direct or indirect exploitation rates.

The identification of the genetic basis of domestication in fish species is of timely importance for the aquaculture industry in order to increase productivity, quality, and the welfare of farmed fish. The goal of this study is to investigate the largely unknown aquaculture-induced evolution in gilthead seabream, which is one of the most important farmed fish in the Mediterranean region. We used a panel of 1159 genome-wide SNPs, and genotyped 956 fish from 23 wild populations of Mediterranean-wide distribution and 362 farmed fish from five Greek hatcheries. We assessed the genetic diversity of the sampled populations and contrasted the results of four different approaches of outlier detection methods. We recognized one very strong candidate and two good candidate SNPs with evidence for aquaculture-induced evolution in gilthead seabream. The annotation of these SNPs revealed neighboring genes with biological roles from stress tolerance and disease resistance to sexual maturation that may explain our observations. In conclusion, we demonstrate that the genome of gilthead seabream, despite the fact that the species is often suggested to be in the early stages of the domestication process, shows evidence of aquaculture-induced evolution. We report on a list of genes that may explain our observations and that may be investigated further. We anticipate that our findings will stimulate additional research with the use of SNP panels of higher density that can elucidate the genomic architecture of domestication in this species of high aquacultural interest.

Based on collaboration with the Greenlandic fishing fleet, we document the presence of Atlantic bluefin tuna (Thunnus thynnus) in most years from 2012 to 2018 in the waters east of Greenland (northern Irminger Sea). In total, 84 individuals have been registered as bycatch in the commercial fisheries in Greenland waters, which indicates that the first catch of three individuals in 2012 was not a single extreme observation, but that East Greenland waters have become a new outer limit of an expanded tuna habitat. Genetic analyses indicate that specimens from this region are mostly of Mediterranean origin with a small proportion originating from the Gulf of Mexico stock. Stomach content analysis suggests that the main prey is Atlantic mackerel (Scomber scombrus). The tunas ranged in size from 140 to 270 cm, corresponding to an estimated age range of 5–16 years; most were probably mature. The wide size–age range suggests that many year classes are participating in the migration to this region. Sea temperatures during summer have been above the long-term average in recent years of interest. Summer residence of bluefin tuna in the region could be due to a combination of increasing temperatures and higher overall abundances of both bluefin tuna and a key prey species (Atlantic mackerel).

Seasonal prey bursts are important for the lifecycles and energy budgets of many predators. Here we document the diet and, especially, the importance of the ephemeral occurrence of capelin as prey for Atlantic cod (Gadus morhua) in Godthaabsfjord, west Greenland, over an annual cycle. The cod showed clear differences in diet composition on the eleven sampling dates resulting in a spring–summer, late summer‐autumn and winter cluster. Moreover, a single sampling date, May 12th, was defined by cod gorge feeding on spawning capelin, which led to average stomach contents 4.3 times higher than the average for the remaining sampling dates. Changes in nitrogen stable isotope values from April 22nd to July 7th in cod liver and muscle tissue was used to calculate the consumption of capelin. Based on this, the consumption of capelin varied between 538–658 g wet weight for a 1.3 kg cod. Using published consumption/biomass estimates and observed growth rates, the capelin intake corresponds to 10.1% – 33.3% of the annual food consumption and accounts for 28.1% – 34.5% of the annual growth of the cod. The present study documents the omnivorous feeding mode of Atlantic cod, but highlights the utilization and importance of ephemeral prey bursts for the annual energy budget of the cod. We hypothesize that access to capelin is critical for the post‐spawning recovery of Godthaabsfjord cod.

Monitoring, understanding, and communicating the impact of offshore oil and gas exploration and production (E&P) activities on marine mammal (MM) biodiversity can be challenging. Here, we share methods, results, and experiences accumulated during seven years of monitoring MM and underwater sound in a mature E&P activity area in the North-East Atlantic. We collected data on the distribution and behaviour of MM, their prey and changes associated with impulsive (e.g., seismic) and continuous (e.g., platform) sound generated by E&P operations. A program was created as an incentive for offshore staff to report systematically incidental MM sightings. Underwater acoustic recorders were placed around producing facilities and across a 3D seismic survey area before, during and after acquisition. A 2nd Generation Environmental Sample Processor (ESP) was deployed to collect and analyse environmental DNA (eDNA) from seawater to identify MM species and their potential prey. Monitoring data were shared with relevant stakeholders through publications in scientific journals, presentations at conferences and meetings, or through social media. Our data provided evidence of MM activity in the E&P activity area year-round. A total of eight species were sighted from platforms and vessels; harbour porpoise being the most common MM. Harbour porpoises were recorded as being within 800m of the platform three times more often than at stations further away. Near installations, acoustic data showed porpoises actively searched for prey whilst eDNA confirmed the presence of prey species - validating a strong reef-effect. Decrease in porpoise echolocation to 8-12 km from an active seismic vessel, is suggestive of a temporary displacement of animals in the corresponding area. There was no large scale or long-term displacement as harbour porpoises were detected again in the area few hours after airgun operations ended. The results indicate that despite elevated sound level in the E&P area, porpoise distribution appears to be linked to higher availability of prey around the artificial reef created by subsea O&G structures. The monitoring efforts generate valuable scientific knowledge, which form a sound basis to support management and regulation of E&P activities in Denmark. Additionally, several simultaneous tangible benefits resulted from the study such as staff awareness of biodiversity and increased stakeholder interactions. Results and methodologies may be used by HSE practitioners and O&G project managers to assess the potential impact of sound generated by O&G industry on marine mammals. Our success illustrates the value of long-term monitoring and should inspire and support HSE practitioners in their future environmental monitoring initiatives.

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 salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene–environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub-set of regions, suggesting that locus-specific variation was associated with local processes. A paired-population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub-sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.

Atlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large‐scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene–environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub‐set of regions, suggesting that locus‐specific variation was associated with local processes. A paired‐population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub‐sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.

Evidence from DNA‐analysis is commonplace in human criminal investigations, and while it is increasingly being used in wildlife crime, to date, its application to control and enforcement activities in fisheries and aquaculture has only been sporadic. Contemporary DNA‐analysis tools are capable of addressing a broad range of compliance issues, species identification, mislabelling of fish products, determining the origin of catches and the farm of origin of aquaculture escapees. Such applications have the potential to ensure traceability along the fish product supply chain and to combat consumer fraud and Illegal, Unreported and Unregulated fishing. Nevertheless, DNA‐analysis is not yet used routinely in investigations into compliance with fisheries and aquaculture legislation. One potential reason for this is that DNA‐analysis techniques may have been regarded as too expensive. However, costs have plummeted over the past decade prompting us to objectively assess whether the costs associated with routine use of DNA‐analysis techniques for fisheries and aquaculture control and enforcement activities do constitute an impediment. Based on a number of recent fisheries and aquaculture compliance investigations that incorporated DNA‐analysis, our results indicate that the use of genetic analysis was justified and worthwhile in all cases examined. We therefore conclude that the costs associated with DNA‐analysis do not represent a barrier to the routine adoption of DNA‐analysis techniques in fisheries and aquaculture compliance investigations. Thus, control and enforcement agencies should be encouraged to use such techniques routinely. publishedVersion

Biomass assesment of fish stocks is a difficult task that often involves costly fisheries trawl surveys. Trawl surveys rarely return replicate samples, as trawling attempts are expensive and difficult to reproduce. Furthermore, traditional benthic trawling is often detrimental to habitats and the organisms associated with the sea bottom. The rapidly developing field of environmental DNA (eDNA) analysis offers a new approach to non-invasive monitoring of fish. In the present study, we develop and test species-specific primers and probes for qPCR detection of eDNA from Atlantic herring (Clupea harengus ), Atlantic cod ( Gadus morhua ), European flounder ( Platichthys flesus ), European plaice ( Pleuronectes platessa), and Atlantic mackerel ( Scomber scombrus ) in the Baltic Sea. A recently published qPCR system was applied for European eel (Anguilla anguilla ). Filtered water samples were collected during a stratified benthic trawl survey, enabling parallel comparisons of eDNA concentrations with biomass caught by trawling. No significant correlation was found between eDNA concentrations and the biomass of fish caught by the trawl, although an association was observed between the measured concentrations of eDNA and the known distributions and main abundances of cod, herring, plaice and flounder. This indicates that while eDNA concentrations may not be directly comparable to results from existing methods – likely because aquatic eDNA concentrations are not controlled by the same combinations of factors as e.g. trawl biomass catch – eDNA analysis could prove a useful supplement for monitoring fish stocks in the future.

In this study, 11 microsatellite markers were used to determine the structure of West Greenlandic lumpfish Cyclopterus lumpus populations across six spawning locations spanning >1500 km and compared with neighbouring populations in Canada and Iceland. To evaluate whether data allow for identification of origin of C. lumpus in Greenlandic waters, genetic assignment analysis was performed for 86 C. lumpus sampled on a feeding migration. Significant structuring with isolation by distance was observed in the West Greenland samples and two major subpopulations, north and south, were suggested. Based on FST values, closer relationships were observed between Greenland and Canada, than Greenland and Iceland. Surprisingly, the North Greenland population showed more similarities with Canadian samples, than did the geographically closer south-west Greenland population. Origin could be assigned for a high proportion of non-spawning fish and demonstrated a marked east–west spatial separation of fish of Greenlandic and Icelandic genotypes.

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.

The rapid development of genetic science has improved the methods for fisheries stock assessments with increasing implications for management. One key accomplishment has been the identification of different sub-populations of Atlantic cod. Recognizing that local coastal fishers in the North Atlantic have often held a local knowledge about local cod populations, this study examines the extent to which genetic analysis corroborates this local knowledge and vice versa. In Nuuk, capital of Greenland situated by the Nuuk fiord system, local fishers say that they and generations before them have been observing both inshore and offshore cod in the Nuuk fiord system. Fisher interviews were conducted in order to understand the construction as well as the content of this specific local ecological knowledge. Furthermore, fishers were invited to assign cod from their catches into categories based on their knowledge of inshore and offshore cod. These cod were subsequently analyzed and assigned to population using genetic methodologies. The comparison between visual and genetic assignment was not able to confirm any convincing consensus between fishers' understanding of offshore and inshore cod and the corresponding genetic categories. However, an examination of existing inshore and off-shore catch surveys confirmed the relevance of the morphological characteristics (liver condition and shape) of ecologically defined inshore and off-shore cod that provided the basis for fishers' categorizations. This opens a discussion of the fishers' way of knowing about inshore and offshore cod respectively and if and how the content of their knowledge could be made relevant in relation to scientific advice procedures.

In the Western Baltic Sea two genetically distinct cod stocks “Eastern Baltic cod” and “Western Baltic cod” occur with considerable mixing of stocks. In this study we evaluated the applicability of otolith shape analysis for classification of individuals caught in the mixed stock cod fishery, using SNP (single nucleotide polymorphism) based genetic assignment of otolith shape baselines. We further developed a management aimed approach for mixed stock assignment by robust stochastic baseline selection and posterior bias correction by individual reassignment of the least likely classifications into the alternate stock. Classification criteria selected by Monte Carlo runs of Linear Discriminant Analysis were captured by otolith area and 20 Elliptic Fourier Descriptors of primarily low frequency harmonics. Classification success was considerably lower when using a baseline of spawning individuals only, compared to the better spatial coverage of a combined baseline also including genotyped individuals from the mixed stock area. Furthermore, the inclusion of genotyped individuals balanced the baseline size composition and to a large extent removed a strong size related bias in classification success. These results demonstrate the interplay of environmental, ontogenetic and genetic influences on otolith shape, which complicates the application of otolith shape for stock discrimination in mixed-stock scenarios. Rigours genetic validation and further studies on the temporal dynamics of shape formation are necessary.

Application of environmental DNA (eDNA) analysis has attracted the attention ofresearchers, advisors and managers of living marine resources and biodiversity. The apparent simplicity and cost-effectiveness of eDNA analysis make it highly attractive as species distributions can be revealed from water samples. Further, species-specific analyses indicate that eDNA concentrations correlate with biomass and abundance, suggesting the possibility for quantitative applications estimating abundance and biomass of specific organisms in marine ecosystems, such as for stock assessment. However, the path from detecting occurrence of an organism to quantitative estimates is long and indirect, not least as eDNA concentration depends on several physical, chemical and biological factors which influence its production, persistence and transport in marine ecosystems. Here, we provide an overview of basic principles in relation to eDNA analysis with potential for marine fisheries application. We describe fundamental processes governing eDNA generation, breakdown and transport andsummarize current uncertainties about these processes. We describe five major challenges in relation to application in fisheries assessment, where there is immediate need for knowledge building in marine systems, and point to apparent weaknesses of eDNA compared to established marine fisheries monitoring methods. We provide an overview of emerging applications of interest to fisheries management and point to recent technological advances, which could improve analysis efficiency. We advise precaution against exaggerating the present scope for application of eDNA analysis in fisheries monitoring, but also argue that with informed insights into strengths andlimitations, eDNA analysis can become an integrated tool in fisheries assessment and management

Regulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful, there are relatively few examples in marine fish displaying accurate origin assignment. We synthesize data for 156 single-nucleotide polymorphisms typed in 1039 herring, Clupea harengus L., spanning the Northeast Atlantic to develop a tool that allows assignment of individual herring to their regional origin. We show the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks, complicating management issues. We report novel genetic evidence that herring from the Baltic Sea contribute to catches in the North Sea, and find support that western Baltic feeding aggregations mainly constitute herring from the western Baltic with contributions from the Eastern Baltic. Our study describes a general approach and outlines a database allowing individual assignment and traceability of herring across a large part of its East Atlantic distribution.

Knowledge about mating patterns is essential for understanding and explaining rates of reproduction and genetic potential of copepods populations. The aim of this study was to examine (1) the occurrence of multiple paternity in Temora longicornis, (2) the effect of multiple paternity (if present) on the females reproductive output, and (3) whether mating is random or some individuals have a higher than average chance of fertilizing or being fertilized (super individuals). We show that multiple paternity is common in this copepod species, that females benefit from multiple matings by increased offspring production, and that a relatively small fraction of the males and females in a population account for most of the offspring production. In both males and females, mating is nonrandom. Superior individuals with a higher than average matings success were identified both among females and among males.

Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels, Mytilus spp. are ecosystem engineers in the coastal zone globally. In order to improve knowledge of distribution and genetic structure of the Mytilus edulis complex in the Arctic, we analyzed 81 SNPs in 534 Mytilus spp. individuals sampled at 13 sites to provide baseline data for distribution and genetic variation of Mytilus mussels in the European Arctic. Mytilus edulis was the most abundant species found with a clear genetic split between populations in Greenland and the Eastern Atlantic. Surprisingly, analyses revealed the presence of M. trossulus in high Arctic NW Greenland (77°N) and M. galloprovincialis or their hybrids in SW Greenland, Svalbard and the Pechora Sea. Furthermore, a high degree of hybridization and introgression between species was observed. Our study highlights the importance of distinguishing between congener species, which can display local adaptation and suggests that information on dispersal routes and barriers are essential for accurate predictions of regional susceptibility to range expansions or invasions of boreal species in the Arctic. Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels, Mytilus spp. are ecosystem engineers in the coastal zone globally. In order to improve knowledge of distribution and genetic structure of the Mytilus edulis complex in the Arctic, we analyzed 81 SNPs in 534 Mytilus spp. individuals sampled at 13 sites to provide baseline data for distribution and genetic variation of Mytilus mussels in the European Arctic. Mytilus edulis was the most abundant species found with a clear genetic split between populations in Greenland and the Eastern Atlantic. Surprisingly, analyses revealed the presence of M. trossulus in high Arctic NW Greenland (77°N) and M. galloprovincialis or their hybrids in SW Greenland, Svalbard and the Pechora Sea. Furthermore, a high degree of hybridization and introgression between species was observed. Our study highlights the importance of distinguishing between congener species, which can display local adaptation and suggests that information on dispersal routes and barriers are essential for accurate predictions of regional susceptibility to range expansions or invasions of boreal species in the Arctic.

Population genetic structure using nine polymorphic nuclear microsatellite loci was assessed for the tiger shark (Galeocerdo cuvier) at seven locations across the Indo-Pacific, and one location in the southern Atlantic. Genetic analyses revealed considerable genetic structuring (FST > 0.14,p G. cuvier.

Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the ‘shallow’ and ‘deep’ groups, beyond the Irminger Sea where they were described previously. A third group, ‘slope’, has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic Slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression. This article is protected by copyright. All rights reserved.

Recent technological developments have facilitated an increased focus on identifying genomic regions underlying adaptive trait variation in natural populations, and it has been advocated that this information should be important for designating population units for conservation. In marine fishes, phenotypic studies have suggested adaptation through divergence of life-history traits among natural populations, but the distribution of adaptive genetic variation in these species is still relatively poorly known. In this study, we extract information about the geographical distribution of genetic variation for 33 single nucleotide polymorphisms (SNPs) associated with life-history trait candidate genes, and compare this to variation in 70 putatively neutral SNPs in Atlantic cod (Gadus morhua). We analyse samples covering the major population complexes in the eastern Atlantic and find strong evidence for non-neutral levels and patterns of population structuring for several of the candidate gene-associated markers, including two SNPs in the growth hormone 1 gene. Thus, this study aligns with findings from phenotypic studies, providing molecular data strongly suggesting that these or closely linked genes are under selection in natural populations of Atlantic cod. Furthermore, we find that patterns of variation in outlier markers do not align with those observed at selectively neutral markers, and that outlier markers identify conservation units on finer geographical scales than those revealed when analysing only neutral markers. Accordingly, results also suggest that information about adaptive genetic variation will be useful for targeted conservation and management in this and other marine species.

Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.

Recent genetic analyses of candidate genes and gene expression in marine fishes have provided evidence of local adaptation in response to environmental differences, despite the lack of strong signals of population structure from conventional neutral genetic markers. In this study expression of the haemoglobin alpha and beta subunit genes was studied in reciprocally transplanted European flounder Platichthys flesus from the highly saline North Sea and the brackish Baltic Sea. Clear differences in expression patterns of haemoglobin alpha and beta subunit genes were found among different types of tissue in flounder. In gill tissue a plastic response to salinity treatments was observed with general up-regulation of these genes concomitant with higher salinity. For liver tissue a population specific expression differences was observed with lower expression at simulated non-native compared to native salinities. Finally, for kidney tissue a stress response was observed in one population, with gene up-regulation when North Sea flounders were transplanted to low salinity. This study underlines the importance of tissue specific gene expression and the significance of gene expression for evolution of local adaptation in high gene flow marine fishes.

Accurate prediction of species distribution shifts in the face of climate change requires a sound understanding of population diversity and local adaptations. Previous modeling has suggested that global warming will lead to increased abundance of Atlantic cod (Gadus morhua) in the ocean around Greenland, but the dynamics of earlier abundance fluctuations are not well understood. We applied a retrospective spatiotemporal population genomics approach to examine the temporal stability of cod population structure in this region and to search for signatures of divergent selection over a 78-year period spanning major demographic changes. Analyzing >900 gene-associated single nucleotide polymorphisms in 847 individuals, we identified four genetically distinct groups that exhibited varying spatial distributions with considerable overlap and mixture. The genetic composition had remained stable over decades at some spawning grounds, whereas complete population replacement was evident at others. Observations of elevated differentiation in certain genomic regions are consistent with adaptive divergence between the groups, indicating that they may respond differently to environmental variation. Significantly increased temporal changes at a subset of loci also suggest that adaptation may be ongoing. These findings illustrate the power of spatiotemporal population genomics for revealing biocomplexity in both space and time and for informing future fisheries management and conservation efforts.

Growing demands for marine fish products is leading to increased pressure on already depleted wild populations and a rise in the aquaculture production. Consequently, more captive bred fish are released into the wild through accidental escape or deliberate restocking, stock enhancement and sea ranching programs. The increased mixing of captive bred fish with wild conspecifics may affect the ecological and/or genetic integrity of wild fish populations. From a fisheries management perspective unambiguous identification tools for captive bred fish will be highly valuable to manage risks. Additionally there is great potential to use these tools in wildlife forensics (i.e. tracing back escapees to their origin and determining mislabelling of seafood products). Using SNP data from captive bred and wild populations of Atlantic cod (Gadus morhua L.) and sole (Solea solea L.), we explored the efficiency of population and parentage assignment techniques for the identification and tracing of captive bred fish. Simulated and empirical data were used to correct for stochastic genetic effects. Overall, parentage assignment performed well when a large effective population size characterizes the broodstock and escapees originate from early generations of captive breeding. Consequently, parentage assignments are particularly useful from a fisheries management perspective to monitor the effects of deliberate releases of captive bred fish on wild populations. Population assignment proved to be more efficient after several generations of captive breeding, which makes it a useful method in forensic applications for well-established aquaculture species. We suggest the implementation of a case by case strategy when choosing the best method.

Landscape genetics, which considers genetic population structure 1 in the context of spatially referenced parameters in the surrounding landscape, has been shown to be extremely useful for wildlife management. Unfortunately its widespread uptake beyond the research community is hampered due to a lack of effective communication of usable information in a suitable format for application by stakeholders such as wildlife regulators or managers. To improve the communication of suitable information, geovisualization of results should be facilitated in a comprehensible format for stakeholders without GIS or genetic expertise. While specialist applications exist, alternative accessible solutions do not provide adequate support for the visuali- zation of multi-attribute spatially referenced genetic population structure information. As a solution, we document our exploration for an appropriate symbology to communicate landscape genetic information through an accessible, web-based interface. A full problem description, review of available technologies, development rationale, and discussion of the symbology exploration are provided.

High gene flow is considered the norm for most marine organisms and is expected to limit their ability to adapt to local environments. Few studies have directly compared the patterns of differentiation at neutral and selected gene loci in marine organisms. We analysed a transcriptome-derived panel of 281 SNPs in Atlantic herring (Clupea harengus), a highly migratory small pelagic fish, for elucidating neutral and selected genetic variation among populations and to identify candidate genes for environmental adaptation. We analysed 607 individuals from 18 spawning locations in the northeast Atlantic, including two temperature clines (5‐12 � C) and two salinity clines (5‐35&). By combining genome scan and landscape genetic analyses, four genetically distinct groups of herring were identified: Baltic Sea, Baltic‐North Sea transition area, North Sea ⁄British Isles and North Atlantic; notably, samples exhibited divergent clustering patterns for neutral and selected loci. We found statistically strong evidence for divergent selection at 16 outlier loci on a global scale, and significant correlations with temperature and salinity at nine loci. On regional scales, we identified two outlier loci with parallel patterns across temperature clines and five loci associated with temperature in the North Sea ⁄North Atlantic. Likewise, we found seven replicated outliers, of which five were significantly associated with low salinity across both salinity clines. Our results reveal a complex pattern of varying spatial genetic variation among outlier loci, likely reflecting adaptations to local environments. In addition to disclosing the fine scale of local adaptation in a highly vagile species, our data emphasize the need to preserve functionally important biodiversity.

Widespread environmental changes including climate change, selective harvesting and landscape alterations now greatly affect selection regimes for most organisms. How animals and plants can adapt to these altered environments via contemporary evolution is thus of strong interest. We discuss how to use genetic monitoring to study adaptive responses via repeated analysis of the same populations over time, distinguishing between phenotypic and molecular genetics approaches. After describing monitoring designs, we develop explicit criteria for demonstrating adaptive responses, which include testing for selection and establishing clear links between genetic and environmental change. We then review a few exemplary studies that explore adaptive responses to climate change in Drosophila, selective responses to hunting and fishing, and contemporary evolution in Daphnia using resurrected resting eggs. We further review a broader set of 44 studies to assess how well they meet the proposed criteria, and conclude that only 23% fulfill all criteria. Approximately half (43%) of these studies failed to rule out the alternative hypothesis of replacement by a different, better-adapted population. Likewise, 34% of the studies based on phenotypic variation did not test for selection as opposed to drift. These shortcomings can be addressed via improved experimental designs and statistical testing. We foresee monitoring of adaptive responses as a future valuable tool in conservation biology, for identifying populations unable to evolve at sufficiently high rates and for identifying possible donor populations for genetic rescue. Technological advances will further augment the realization of this potential, especially next-generation sequencing technologies that allow for monitoring at the level of whole genomes.

Populations of marine fish, even from contrasting habitats, generally show low genetic differentiation at neutral genetic markers. Nevertheless, there is increasing evidence for differences in gene expression among populations that may be ascribed to adaptive divergence. Studying variation in salinity tolerance and gene expression among Atlantic cod (Gadus morhua) from two populations distributed across a steep salinity gradient, we observed high mortality (45% North Sea cod and 80% Baltic Sea cod) in a reciprocal common garden setup. Quantitative RT-PCR assays for expression of hsp70 and Na/K-ATPase α genes demonstrated significant differences in gene regulation within and between populations and treatment groups despite low sample sizes. Most interesting are the significant differences observed in expression of the Na/K-ATPase α gene in gill tissue between North Sea and Baltic cod. The findings strongly suggest that Atlantic cod are adapted to local saline conditions, despite relatively low levels of neutral genetic divergence between populations.