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Incorporation of observation uncertainty in stock assessment using spatio-temporal modeling of catch-at-length and age-at-length survey data
Get PDFSpatio-temporal models are essential tools for estimating abundance indices and quantifying the associated uncertainty. Time series of index uncertainties can be used to objectively determine the influence each index has on the assessment. This can involve reducing the influence of indices in years with limited data. However, incorporating uncertainty in age-length conversion into assessment models has remained a challenge. In this research, we propose an index estimation approach that combines an abundance-at-length model with a model for age-at-length to generate age-specific abundance indices. By jointly modeling abundance-at-length and age-at-length, we address uncertainties in both components of the index-at-age. Using North East Arctic haddock (Melanogrammus aeglefinus) as a case study, we validate the uncertainty of the indices by integrating them into the state space assessment model SAM. The results indicate that the uncertainty estimates are realistic, and we further demonstrate that incorporating uncertainty in age conversion has effects on the assessment results. Our case study demonstrates that incorporating the uncertainty in age-at-length data improves the characterization of uncertainty in stock assessment, and hence better accounts for risk in precautionary management.Incorporation of observation uncertainty in stock assessment using spatio-temporal modeling of catch-at-length and age-at-length survey datapublishedVersio
Bayesian estimation of spatially varying mortality risk using tagged animal data
Get PDFThe survival of animals is impacted by landscapes of spatially varying mortality factors including habitat type, predation risk or harvest risk, among others. Characterization of these spatial mortality processes is important for managing animal populations and their habitats, yet this information has proved challenging to capture. Advances in telemetry now make it possible to monitor tagged individuals' locations through time for a wide range of taxa, providing opportunity to assess movement and mortality simultaneously through spatial time-to-event data. Existing time-to-event modelling frameworks have largely ignored spatially varying mortality processes or have treated an animal's location as fixed at a regional level. Here we present a general spatial survival model for analysing time-to-event data arising from animal telemetry. Our model has a flexible Cox regression form and can estimate the effects of conventional non-spatial risk factors (size, seasonality, etc.), spatial covariates (e.g. habitat type) and spatial variation in risk not explained by covariates on mortality. We show how to fit our model using Bayesian methods and demonstrate applications of our model with several simulated examples and two animal telemetry case studies. Our model produced consistent and unbiased parameter estimates throughout simulations with a variety of spatial and non-spatial hazards. In the first case study, data from 147 tagged caribou in British Columbia, Canada, revealed a spatially heterogeneous mortality landscape with caribou survival varying by elevation, likely in response to space use by predators. Our second case study involved a dataset of 390 acoustically tagged Atlantic cod in a southern Norwegian fjord where a marine protected area (MPA) was established during the study. We found that the MPA led to a shift from mostly fishing mortality to mostly natural mortality within the fjord and that these risks had markedly different spatial hazard patterns. Our spatial time-to-event model can make use of data from a variety of widely used telemetry technologies to characterize landscapes of mortality risks for different taxa. Our work provides new opportunities to inform the spatial ecology and management of fish and wildlife populations.publishedVersio
A new method for regionalization of the vertebral column in salmonids based on radiographic hallmarks
Get PDFCurrent procedures to establish vertebral column regionalization (e.g., histology) in fish are time consuming and difficult to apply. The aim of this study was to develop a more rapid and accurate radiology-based method for Atlantic salmon (Salmo salar). A detailed analysis of 90 animals (4 kg) led to the establishment of region-specific radiographic hallmarks. To elucidate its transferability to other salmonid species, radiography was carried out in brown trout (Salmo trutta), Arctic char (Salvelinus alpinus), rainbow trout (Oncorhynchus mykiss), pink salmon (Oncorhynchus gorbuscha), and Chinook salmon (Oncorhynchus tshawytscha). This method was also evaluated for whole ungutted fish. The vertebral column of Atlantic salmon can be subdivided into five regions (R1–R5) based on anatomy: postcranial (R1, V1, and V2), abdominal (R2, V3–V26), transitional (R3, V27–V36), caudal (R4, V37–V53), and ural (R5, V54–V59). The following specific radiographic hallmarks allow the identification of regions: (i) lack of ribs in R1, (ii) modified parapophysis of the first vertebra of R3, (iii) prominent hemal spine of the first vertebra of R4, and (iv) the separated hemal spine of the most cranial pre-ural vertebra of R5. These hallmarks were all transferable to the other salmonid species assessed. The results include a further description of various region-specific characteristics in Atlantic salmon. The method was found applicable for sedated/whole ungutted fish, verifying it as quick and easy compared to other regionalization methods. The regions defined by radiology in this study agree with the vertebral column regions recently defined for Chinook salmon (O. tshawytscha). Thus, and considering the results of this study on various salmonid species, the currently developed regionalization protocol can be generally used for salmonids.publishedVersio
Mesopelagic Fish Traits: Functions and Trade-Offs
Get PDFFishes inhabiting the mesopelagic zone of the world's oceans are estimated to account for the majority of the world's fish biomass. They have recently attracted new attention because they are part of the biological carbon pump and have been reconsidered as a contribution to food security. Hence, there is an urgent need to understand how environmental conditions and species interactions shape their assemblages, and how they contribute to the functioning of marine ecosystems. Trait-based approaches are valuable for addressing these types of questions. However, the biology and ecology of mesopelagic fishes are understudied compared to fishes in shallow and epipelagic waters. Here, we synthesise existing knowledge of traits of mesopelagic fishes and relate them to their role in survival, feeding and growth and reproduction, the key functions that contribute to fitness. Vertical migrations, specialised vision and the use of bioluminescence are among the most striking adaptations to the conditions in the mesopelagic realm. Many traits are interrelated as a result of trade-offs, which may help to understand selection pressures. While morphological traits are straightforward to observe, major knowledge gaps exist for traits that require frequent sampling, assessment under experimental conditions or age determination. The unique adaptations of mesopelagic fishes need to be included in management strategies as well as fundamental research of the habitat.publishedVersio
Enriched local convenience foods with two different small pelagic fish species increases the nutritional value without compromising taste
Get PDFCereals and their derived products are important dietary sources for humans but are mostly deficient in protein and several micronutrients. To increase the nutrient content of rice and wheat flour-based recipes, nutrient-dense powders of the small pelagic fish species Anchovy (Engraulis encrasicolus) and Atlantic bumper (Chloroscombrus chrysurus) were used to enrich the high carbohydrate content mostly found in cereals. Sensory evaluation by 60 panelists showed that the enrichment of recipes with fish powder was acceptable. Recipes with dried anchovy showed higher sensory acceptance than recipes fortified with dried Atlantic bumper. Nutritional analyses showed that several of the tested recipes can be regarded as significant sources of micronutrients (vitamin A, D and B12, iodine and calcium) and the omega-3 fatty acids eicosapentaenoic acid and docosahexaenoic acid. The actual analysed nutrient content of the test diets differed from the estimated nutrient content of the recipes by using values from the West-African food composition table. For vitamin A, analysed values were generally higher than the estimated values, indicating that the values in the food composition table are not sufficient to estimate the nutritional fortification with powdered small fish. In conclusion, the fortified foods prepared according to the tested recipes were accepted by sensory panelists and can be regarded as significant source of several essential nutrients. Food composition tables should be revised to enable a better estimation of the nutritional value of fortified diets for the combat of malnutrition.publishedVersionpublishedVersio
Shifts in biodiversity and physical structure of seagrass beds across 5 decades at Carriacou, Grenadines
Get PDFCaribbean seagrass beds are facing increasing anthropogenic stress, yet comprehensive ground-level monitoring programs that capture the structure of seagrass communities before the 1980s are rare. We measured the distribution of seagrass beds and species composition and abundance of seagrass and associated macroalgae and macroinvertebrates in 3 years over a 47-year period (1969, 1994, 2016) at Carriacou, Granada, an area not heavily impacted by local human activity. Seagrass cover and physical parameters of fringing beds were measured in transects at high (HWE) and low wave energy (LWE) sites; frequency of occurrence of all species, and biomass and morphology of seagrasses, were measured at 100 m2 stations around the island. Losses in nearshore seagrass cover occurred at HWE but not LWE sites between 1969 and 2016 and were associated with increases in the seagrass-free inshore zone (SFI) and erosional scarps within beds. Total biomass did not vary across years although there were progressive changes in seagrass composition: a decline in the dominant Thalassia testudinum and concomitant increase in Syringodium filiforme, and establishment of invasive Halophila stipulacea in 2016 at LWE sites. Species richness and diversity of the seagrass community were highest in 1994, when 94% of macroalgae (excluding Caulerpa) were most abundant, and sea urchins were least abundant, compared to 1969 and 2016. Multivariate statistical analyses showed differences in community composition across the 3 years that were consistent with trends in urchin abundance. Increases in SFI and scarp number in seagrass beds at HWE sites occurred mainly after 1994 and likely were related to increased wave forcing following degradation of offshore coral reefs between 1994 and 2016. Our observations suggest that landward migration of seagrass beds with rapidly rising sea level in future will not be realized in reef-protected seagrass beds at Carriacou barring reversal in the processes that have caused reef flattening.publishedVersio
Joint Norwegian-Russian Fisheries Commission request to establish a management plan for capelin in the Barents Sea (subareas 1 and 2 excluding Division 2.a west of 5°W)
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Freshwater history influences farmed Atlantic salmon (Salmo salar) performance in seawater
Get PDFThe quality of smolts is one of the key factors for successful salmon production. We compared growth performance, physiological traits, and environmental adaptation in Atlantic salmon (Salmo salar) after transfer into a sea cages farm site from recirculating aquaculture system (RAS) to a similar sized group of the same genetic linage and produced in the same husbandry facility but under flow through system (FTS) conditions. Fish vertical distribution within the sea cages and water environment were continuously recorded, while biometry data and biological samples were collected monthly. No significant difference in size and smolt development between the FTS and RAS-produced fish were observed at the end of the freshwater phase. However, after transfer into seawater, the RAS fish showed an array of physiological and molecular differences that were maintained and resulted in significantly increased mortality and lower growth over the full production cycle. The RAS smolts were characterized by lower body weight, length, K factor, HSI (indicator of energy reserve), NKA activity, plasma levels of lactate, triacylglycerol, sodium, calcium, and phosphorus than FTS fish in seawater. This implicated osmoregulatory and allostatic maladaptation for the RAS fish during the first months in seawater. Both FTS and RAS fish showed physiological and behavioral adjustments during the seawater production linked with predictable (e.g., seasonal, diurnal) and short-term unpredictable variation in water temperature and oxygen. However, the RAS fish were characterized by lower physiological response to stressful effects of unpredictable environmental variability. Based on our data, the freshwater history sets the basis for the performance success of the FTS and RAS smolts in seawater. FTS fish showed faster adaptation to the seawater environment, with higher osmoregulatory capacity, and higher physiological robustness to seasonal changes than RAS fish, which reflected in their difference in growth and harvest size. We emphasize the crucial role of the freshwater rearing conditions as the foundation for successful physiological adaptation to seawater, growth, and the success of salmon farming production.publishedVersio
Classification of acoustic survey data: A comparison between seven teams of experts
Get PDFAcoustic surveys of mixed fish aggregations often rely on manual allocation of acoustic energy to target species, with auxiliary information such as trawl catches and target strength distributions aiding interpretation. However, different teams of experts may use the same auxiliary data differently. In this experiment, seven teams of experts interpreted the same acoustic data, and we compared their classification to target categories to quantify uncertainty in the manual classification process. The teams largely agreed on the total acoustic energy attributable to organisms, but there was significant variation in how the teams split this energy on different target categories. This was caused by differences in applied thresholds for separating plankton and fish, as well as disagreements in species classification. For all target categories, the variation due to teams was lower than the overall variability across acoustic segments, but when scaled up to the number of segments in a typical survey, the team effect either dominated or was of similar magnitude as the segment variability. These results imply a need for further standardisation and uncertainty estimation of expert evaluations in acoustic surveys involving manual interpretation of echo sounder data.publishedVersio
A gap analysis on modelling of sea lice infection pressure from salmonid farms. II. Identifying and ranking knowledge gaps: output of an international workshop
Get PDFSea lice are a major health hazard for farmed Atlantic salmon in Europe, and their impact is felt globally. Given the breadth of ongoing research in sea lice dispersal and population modelling, and focus on research-led adaptive management, we brought experts together to discuss research knowledge gaps. Gaps for salmon lice infection pressure from fish farms were identified and scored by experts in sea lice-aquaculture-environment interactions, at an international workshop in 2021. The contributors included experts based in Scotland, Norway, Ireland, Iceland, Canada, the Faroe Islands, England and Australia, employed by governments, industry, universities and non-government organisations. The workshop focused on knowledge gaps underpinning 5 key stages in salmon lice infection pressure from fish farms: larval production; larval transport and survival; exposure and infestation of new hosts; development and survival of the attached stages; and impact on host populations. A total of 47 research gaps were identified; 5 broad themes emerged with 13 priority research gaps highlighted as important across multiple sectors. The highest-ranking gap called for higher quality and frequency of on-farm lice count data, along with better sharing of information across sectors. We highlight the need for synergistic international collaboration to maximise transferable knowledge. Round table discussions through collaborative workshops provide an important forum for experts to discuss and agree research priorities.publishedVersio