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A Standard Operating Procedure for validation of automatic louse counts
Get PDFAutomatisk telling av lus i på fisk i merder er under stadig utvikling. Men mangel på standardisering av prosedyrer for validering av teknologien hindrer fremdriften mot å erstatte manuell telling med automatisk. Basert på systematisk undersøkelse av variasjon og avvik mellom manuelle og automatiske lusetellinger, har dette dokumentet som mål å gi veiledning og anbefalinger for standardiserte manuelle lusetellinger. Veilederen er ment for å skape et robust datasett fra manuelt telling av infestasjonsnivåer og/eller validere et hvilket som helst automatisk tellesystem.Standard operasjonsprosedyre for manuell lusetelling til validering av automatisk tellingA Standard Operating Procedure for validation of automatic louse countspublishedVersio
Ecosystem damage by increasing tropical cyclones
Get PDFClimate change is driving an ongoing increase in tropical cyclone (TC) activity. While global economic losses are projected to double by 2100, there are no comparable predictions for TC impacts to coastal ecosystems that protect and sustain human lives and livelihoods. Here, rising North Atlantic TC (NATC) activity from 1970 to 2019, influenced by anthropogenic and natural climate forcing, is used to study the ecosystem impacts of intensifying TCs, potentially indicative of broader future climate change scenarios. Analysis of 97 NATC landfalls revealed 891 immediate post-storm impacts on ecosystems, with particularly detrimental effects on mangrove forests. Specifically, NATCs reduced the performance of individual species. Additionally, they altered community structure and processes through impacts on foundation species and their associated organisms. The severity of impacts was directly correlated with NATC landfall intensity (wind speed) for mangroves, whereas changes to waves, surge, sediments, and salinity caused most impacts on coral reefs, salt marshes, seagrass meadows, and oyster reefs (respectively), indicating complex intensity-damage interactions for many ecosystems. The analyses also revealed a positive correlation between very intense NATC activity and ecosystem damages. The research highlights a concerning trend of escalating impacts on coastal ecosystems under rising storm intensities, with the potential to challenge ecosystem resilience.publishedVersio
Poor performance of regime shift detection methods in marine ecosystems
Get PDFRegime shifts have been reported as ubiquitous features across the world’s oceans. Many regime shift detection methods are available, but their performance is rarely evaluated, and the supporting evidence for regime shifts may be thin because of the nature of marine ecological time series that are often short, autocorrelated, and uncertain. In the Norwegian Sea, a regime shift has been reported to have occurred in the mid-2000s, with simultaneous changes in oceanography, plankton, and fish. Here, we evaluate the evidence for this regime shift using four commonly used regime shift detection methods (Strucchange, STARS, EnvCpt, and Chronological Clustering) on 32 annual time series that describe the main components of the Norwegian Sea ecosystem, from hydrography and primary production up to fish population metrics. We quantify the performance of each method by measuring its false-positive rate, i.e. the proportion of times the method detects a regime shift that was not present in simulated control time series. Our results show that all methods have high to very high false-positive rates. This challenges the evidence for a regime shift in the Norwegian Sea and questions earlier reviews of regime shifts across the world’s oceans.publishedVersio
Genetic investigation of population structure in Atlantic chub mackerel, Scomber colias Gmelin, 1789 along the West African coast
Get PDFSustainable management of transboundary fish stocks hinges on accurate delineation of population structure. Genetic analysis offers a powerful tool to identify potential subpopulations within a seemingly homogenous stock, facilitating the development of effective, coordinated management strategies across international borders. Along the West African coast, the Atlantic chub mackerel (Scomber colias) is a commercially important and ecologically significant species, yet little is known about its genetic population structure and connectivity. Currently, the stock is managed as a single unit in West African waters despite new research suggesting morphological and adaptive differences. Here, eight microsatellite loci were genotyped on 1,169 individuals distributed across 33 sampling sites from Morocco (27.39°N) to Namibia (22.21°S). Bayesian clustering analysis depicts one homogeneous population across the studied area with null overall differentiation (FST = 0.0001ns), which suggests panmixia and aligns with the migratory potential of this species. This finding has significant implications for the effective conservation and management of S. colias within a wide scope of its distribution across West African waters from the South of Morocco to the North-Centre of Namibia and underscores the need for increased regional cooperation in fisheries management and conservation.publishedVersio
Standardisation of manual louse counts for validation of automatic camera systems - Final report (FHF project 901881)
Get PDFThe shift toward continuous and more precise monitoring of Atlantic salmon in aquaculture has been rapidly progressing, with new technologies being developed and ready for adoption before systematised validation has been made available. Automatic detection and estimation of salmon lice on fish is one such example, with multiple options now on the market. These systems could replace mandated manual counts, but the switch is hindered by the lack of a reference standard or a consensus in validation procedure. This project used small and large (commercial) scale experiments to quantify the variability and divergence of louse density estimates resulting from regular ‘farmer’ manual counts, standardised manual counts, and automatic systems. Factors affecting louse detection rates during manual counts were also investigated by scoring the same fish using rapid counts in air followed by standardised counts with the fish submerged in a shallow tub, as well as comparing detachment rates among louse stages in the anaesthetic bath. Standardised louse counts on salmon provides a higher number of lice than regular manual counts, and match better with automated counts. A high correlation coefficient between standardised and automated counts was found, and may be used as a simple proxy for evaluation and validation. From those results, and knowledge gathered from other sources, we developed a preliminary standard operating procedure for standardised manual louse counts that aims to reduce avoidable variation in manual counts, while improving repeatability and reproducibility of counts nationally. Considerations and recommendations for the validation of automated louse detection systems are also provided within the standard operating procedure (Rapport fra havforskningen 2024-56).Standardisation of manual louse counts for validation of automatic camera systems - Final report (FHF project 901881)publishedVersio
Field comparison of Antarctic krill (Euphausia superba) backscatter and aggregation types using NORTEK and SIMRAD echosounders
Get PDFTemporal distributions of Antarctic krill (Euphausia superba) density and aggregation types were characterized and compared using Nortek Signature100 and SIMRAD Wideband Autonomous Transceiver (WBAT) upward-looking echosounders. Noise varied between the two echosounders. With the Signature100, it was necessary to correct data for background, transient, and impulse noises, while the WBAT data needed to be corrected for background noise only. For selected regions with no visible backscatter, the signal-to-noise ratio of Sv values (i.e. the ratio between the signal and the background noise level) did not vary between the two echosounders. Surface echo backscatter was similar during similar time periods. Descriptive metrics were used to quantify spatial and temporal krill vertical distributions: volume backscatter, mean depth, center of mass, inertia, equivalent area, aggregation index, and proportion occupied. Krill backscatter density differed between the two instruments but was detected at similar mean depths. Krill aggregations were identified at each mooring location and classified in three types based on morphological characteristics. Each type of aggregation shape differed at the two spatially separated moorings, while the acoustic density of each aggregation type was similar. The Signature100 detected a lower number of krill aggregations (n = 133) compared to the WBAT (n = 707). Although both instruments can be used for autonomous deployment and sampling of krill over extended periods, there is a strong caveat for the use of the Signature100 due to significant differences in noise characteristics and krill detection.publishedVersio
Premises for a digital twin of the Atlantic salmon in its world: Agency, robustness, subjectivity and prediction
Get PDFAquaculture of Atlantic salmon Salmo salar is in transition to precision fish farming and digitalization. As it is easier, cheaper and safer to study a digital replica than the system itself, a model of the fish can potentially improve monitoring and prediction of facilities and operations and replace live fish in many what-if experiments. Regulators, consumers and voters also want insight into how it is like to be a salmon in aquaculture. However, such information is credible only if natural physiology and behaviour of the living fish is adequately represented. To be able to predict salmon behaviour in unfamiliar, confusing and stressful situations, the modeller must aim for a sufficiently realistic behavioural model based on the animal's proximate robustness mechanisms. We review the knowledge status and algorithms for how evolution has formed fish to control decisions and set priorities for behaviour and ontogeny. Teleost body control is through genes, hormones, nerves, muscles, sensing, cognition and behaviour, the latter being agentic, predictive and subjective, also in a man-made environment. These are the challenges when constructing the digital salmon. This perspective is also useful for modelling other domesticated and wild animals in Anthropocene environments.publishedVersio
Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins
Get PDFKrill are vital as food for many marine animals but also impacted by global warming. To learn how they and other zooplankton may adapt to a warmer world we studied local adaptation in the widespread Northern krill (Meganyctiphanes norvegica). We assemble and characterize its large genome and compare genome-scale variation among 74 specimens from the colder Atlantic Ocean and warmer Mediterranean Sea. The 19 Gb genome likely evolved through proliferation of retrotransposons, now targeted for inactivation by extensive DNA methylation, and contains many duplicated genes associated with molting and vision. Analysis of 760 million SNPs indicates extensive homogenizing gene-flow among populations. Nevertheless, we detect signatures of adaptive divergence across hundreds of genes, implicated in photoreception, circadian regulation, reproduction and thermal tolerance, indicating polygenic adaptation to light and temperature. The top gene candidate for ecological adaptation was nrf-6, a lipid transporter with a Mediterranean variant that may contribute to early spring reproduction. Such variation could become increasingly important for fitness in Atlantic stocks. Our study underscores the widespread but uneven distribution of adaptive variation, necessitating characterization of genetic variation among natural zooplankton populations to understand their adaptive potential, predict risks and support ocean conservation in the face of climate change.publishedVersio
European plaice (Pleuronectes platessa) in aquaculture – Nutritional, chemical, and physicochemical quality compared to wild stocks
Get PDFEuropean plaice (Pleuronectes platessa) is among Europe's top-consumed fish species, but wild stocks fluctuate and change their habitat due to drastic changes in climate. Their potential in aquaculture is under consideration, and therefore multiple quality aspects have been evaluated in this study. The chemical composition, nutritional profile, and physicochemical properties of European plaice (Pleuronectes platessa) from aquaculture and wild origin (Norwegian west-coast) and differences between female and male farmed individuals were studied. Differences between farmed and wild fish were found for the proximate composition, nutritional profile, and physicochemical attributes. Farmed fish generally had paler color (higher L*; 78.7 ± 4.2) but showed reduced water holding capacity (WHC; 80.3 ± 8.1%), but a firmer fillet texture compared to wild plaice. Farmed fish had significantly higher lipid and lower ash contents than wild individuals. Farmed fish's free amino acid (FAA) content (265.6 ± 59.0 mg/ 100 g) was significantly higher than in wild fish (89.72 ± 43.6 mg/ 100 g), especially the taste contributing FAA glutamate, glycine, alanine, and tyrosine. However, large individual varieties in FAA were observed within farmed and wild specimens. Farmed fish's fatty acid (FA) profile reflects the feed's composition. The overall quality of farmed European plaice was comparable to wild individuals with an excellent nutritional profile. Gender comparisons in farmed fish has shown that females were paler (higher L*) and showed higher hue (h) values, lower color saturation (Chroma, C), and yellowness (a*) compared to males. No apparent difference in texture was found, and no correlations between WHC and pH nor WHC and water content were detected between females and males. Farmed male individuals had higher lipid (2.35 ± 1.5%) and protein (16.97 ± 1.1%) concentrations compared to females (1.72 ± 1.1%; 15.52 ± 1.7%). The overall findings of this study are promising to further investigate this species for cultivation as a sustainable food resource.publishedVersio
Introgression affects Salmo trutta juvenile life-history traits generations after stocking with non-native strains
Get PDFIntrogression of non-native conspecifics changes the genetic composition of wildpopulations, potentially leading to loss of local adaptations and fitness declines.However, long-term data from wild populations are still relatively few. Here, westudied the effects of introgression in a Danish brown trout (Salmo trutta, L.) pop-ulation, subjected to intensive stocking with domesticated hatchery fish of non-native origin. We used wild-caught genetically wild and admixed trout as well asfish from the partly domesticated hatchery strain used for stocking the river upuntil ~15 years prior to this study, to produce 22 families varying in hatchery/wildadmixture. Following a replicated common-garden experiment conducted in fishtanks from first feeding through 23 weeks at 7, 12, and 16°C, we observed a signifi-cant positive relationship between family admixture and fish size upon termination,an effect observed through all levels of admixture. Furthermore, the admixtureeffect was most distinct at the higher rearing temperatures. Although the hatcherystrain used for stocking had been in culture for ~7 generations, it had not beendeliberately selected for increased growth. These data thus demonstrate: (i) thatgrowth had increased in the hatchery strain even in the absence of deliberate di-rectional selection for this trait, (ii) that the increasing effect of admixture by tem-perature could represent inadvertent selection for performance in the hatcherystrain at higher temperatures, and most significantly, (iii) that despite undergoingup to five generations of natural selection in the admixed wild population, the ge-netically increased growth potential was still detectable and thus persistent. Ourfindings suggest that altered growth patterns and potentially their cascading ef-fects are of importance to the severity of hatchery/wild introgression, especiallyunder changing-climate scenarios and are of general significance to conservationpractitioners seeking to evaluate long-term effects of intra-specific hybridizationincluding under recovery.publishedVersio