ALBERT

Description: Fishermen are known to try to avoid fishing in stormy weather, as storms pose a physical threat to fishers, their vessels, and their gear. In this article, a dataset and methods are developed to investigate the degree to which fishers avoid storms, estimate storm aversion parameters, and explore how this response varies across vessel characteristics and across regions of the United States. The data consist of vessel-level trip-taking decisions from six federal fisheries across the United States combined with marine storm warning data from the National Weather Service. The estimates of storm aversion can be used to parameterize predictive models. Fishers’ aversion to storms decreases with increasing vessel size and increases with the severity of the storm warning. This information contributes to our understanding of the risk-to-revenue trade-off that fishers evaluate every time they consider going to sea, and of the propensity of fishers to take adaptive actions to avoid facing additional physical risk.

Description: Sardine Sardinops sagax is an ecologically and economically important Clupeid found off the entire South African coast that includes both coastal upwelling and western boundary current systems. Although the management of the sardine fisheries historically assumed a single, panmictic population, the existence of three, semi-discrete subpopulations has recently been hypothesized. We conducted otolith δ18O and microstructure analyses to investigate nursery habitat temperatures and early life growth rates, respectively, of sardine collected from three biogeographic regions around South Africa’s coast to test that hypothesis. Analyses indicated that for both summer- and winter-captured adults and summer-captured juveniles, fishes from the west coast grew significantly slower in water that was several degrees cooler than those from the south and east coasts. This suggests that mixing of sardines between regions, particularly the west and other coasts, is relatively limited and supports the hypothesis of semi-discrete subpopulations. However, the west-south differences disappeared in the results for winter-captured juveniles, suggesting that differences in early life conditions between regions may change seasonally, and/or that all or most winter-captured juveniles originated from the west coast. Further elucidating the interactions between South African sardine subpopulations and the mechanisms thereof is important for sustainable harvesting of this species.

Description: Progress towards ecosystem-based fisheries management calls for useful tools to prioritize actions. To select suitable methods for local circumstances, evaluating approaches used in other jurisdictions can be a cost-effective first step. We tested Productivity Susceptibility Analysis (PSA) to assess the potential vulnerability of the marine fish community in the Skagerrak–Kattegat (Eastern North Sea) to possible interactions with all Swedish fisheries operating in the area. This analysis combines attributes for a species productivity with attributes related to the susceptibility to capture to quantify a single score for vulnerability: high, medium, or low risk. Results indicate that demersal trawl and gillnet fisheries were associated with the highest risk levels if interaction occurs, i.e. having the highest prevalence of species with potentially high vulnerability to the fisheries. Mixed results were seen when comparing the assessment results with available data. The main benefit of utilizing PSA in the area is the comprehensiveness of the assessment, including data-deficient fisheries and species. Drawbacks include potential overestimation of actual risks. Overall, together with available data, PSA in the studied area provides a comprehensive map of potential risks for further actions and may progress a science-based, precautionary management of the area.

Description: While fisheries provide food and employment for hundreds of millions of people, they also can have significant impact on biodiversity. We explore the potential of area-based fisheries management to simultaneously maintain biodiversity and high levels of sustainable food production. We used two illustrative examples of fisheries that have different gear types, areas, and species to evaluate the trade-off between biodiversity and harvest. We calculate the optimal effort by gear and area that maximizes a weighted objective function of biodiversity and harvest, ranging from 100% of the weight on harvest to 100% on biodiversity. We found for both case studies that the trade-off was highly convex, with win–win solutions allowing for high levels of both fishery harvest and conservation. This is achieved by reducing or eliminating fishing effort that negatively impacts high conservation value species while maintaining fishing effort with gears and in areas where there is low conservation impact. We suggest that, in most fisheries, such situations can be found and that effective area-based management can provide for high levels of biodiversity protection and food production.

Description: Recent application of Fourier transform near infra-red spectroscopy (FT-NIRS) to predict age in fish otoliths has gained attention among fisheries managers as a potential alternative to costly production ageing of managed species. We assessed the age prediction capability of FT-NIRS scans in whole otoliths from red snapper, Lutjanus campechanus, collected from the US Gulf of Mexico and US Atlantic Ocean (South Atlantic). Otoliths were scanned with an FT-NIR spectrometer and resulting spectral signatures were regressed with traditionally estimated ages via partial least squares regression to produce calibration models, which were validated for predictive capability against test sets of otoliths. Calibration models successfully predicted age with R2 ranging 0.94–0.95, mean squared error ≤1.8 years, and bias 31 years were not well predicted, possibly due to light attenuation in the thickest otoliths. Our results suggest that FT-NIRS can improve efficiency in production ageing for fisheries management while maintaining data quality standards.

Description: This article investigates the diet of the snow crab (Chionoecetes opilio) and its feeding intensity in the Barents Sea. Data show that snow crab has a diverse diet that includes almost all types of benthic invertebrates living in the Barents Sea. There are differences between the diets of females and males and of juveniles and adults. Juveniles and females typically occupy shallow areas with communities of bivalve molluscs, while males typically live deeper on slopes and depressions where polychaetes and crustaceans are the most abundant groups. Stomach contents were analysed to determine the species composition and frequency of occurrence of various benthic taxa. Consumption of food was estimated and compared with data from the Russian seas of the Pacific region. The total annual consumption of macrozoobenthos by snow crab was calculated in accordance with its current distribution in the Barents Sea. Snow crab consumes at least 30 000 tonnes of benthos annually, which amounts to 0.1–0.2% of the total macrozoobenthic biomass in the investigated area. The population of snow crab causes the largest impact on the benthic communities in the northeastern part of the Barents Sea and near the south side of the Novaya Zemlya archipelago.

Description: Until the late 19th century, extensive beds of flat oyster Ostrea edulis populated the Central North Sea, which have vanished after intensive fisheries. At present, various initiatives are being carried out to investigate the potential to restore this former key species in the area. This historical ecological study contributes by delineating the former oyster bed area and through an assessment of its limits against known gradients in the North Sea. Extensive data from historical maps, texts, and ship-based surveys were used to synthesize our knowledge on the former beds. It was revealed that the area with oyster beds covered ∼6.2% of the total North Sea bottom, with a delineation that could partly be explained by hydrodynamic and temperature gradients. The position and extent of the area are notably different from the area that is used in recent feasibility studies on the restoration of North Sea oyster beds. The offshore oysters lived on muddy sand in relatively cold conditions, and there are several indications that their reproductive rate was low. The apparent disappearance of cold water adapted flat oysters will challenge restoration projects. This study provides indispensable information for the future restoration of flat oyster beds in the North Sea.

Description: Sialic acid acetyl esterase (SIAE) removes acetyl moieties from the hydroxyl groups in position 9 and 4 of sialic acid. Recently, a dispute has been opened on its association to autoimmunity. In order to get new insights on human SIAE biology and to clarify its seemingly contradictory molecular properties, we combined in silico characterization, phylogenetic analysis and homology modeling with cellular studies in COS7 cells. Genomic and phylogenetic analysis revealed that in most tissues only the "long" isoform, originally referred to lysosomal sialic acid esterase, is detected. Using the homology modeling approach, we predicted a model of SIAE 3D structure, which fulfills the topological features of SGNH-hydrolase family. In addition, the model and site-directed mutagenesis experiments allowed the definition of the residues involved in catalysis. SIAE transient expression revealed that the protein is glycosylated and is active in vitro as an esterase with a pH optimum corresponding to 8.4–8.5. Moreover, glycosylation influences the biological activity of the enzyme and is essential for release of SIAE into the culture medium. According to these findings, co-localization experiments demonstrated the presence of SIAE in membranous structures corresponding to endoplasmic reticulum and Golgi complex. Thus, at least in COS7 cells, SIAE behaves as a typical secreted enzyme, subjected to glycosylation and located along the classical secretory route or in the extracellular space. In these environments, the enzyme could act on 9- O -acetylated sialic acid residues, contributing to the fine-tuning of the various functions played by this acidic sugar.

Description: Vaccination against the ubiquitous parasite Toxoplasma gondii would provide the most efficient prevention against toxoplasmosis-related congenital, brain and eye diseases in humans. We investigated the immune response elicited by pathogen-specific glycosylphosphatidylinositol (GPI) glycoconjugates using carbohydrate microarrays in a BALB/c mouse model. We further examined the protective properties of the glycoconjugates in a lethal challenge model using the virulent T. gondii RH strain. Upon immunization, mice raised antibodies that bind to the respective GPIs on carbohydrate microarrays, but were mainly directed against an unspecific GPI epitope including the linker. The observed immune response, though robust, was unable to provide protection in mice when challenged with a lethal dose of viable tachyzoites. We demonstrate that anti-GPI antibodies raised against the here described semi-synthetic glycoconjugates do not confer protective immunity against T. gondii in BALB/c mice.

Description: Carbohydrate antigens are valuable as components of vaccines for bacterial infectious agents and human immunodeficiency virus (HIV), and for generating immunotherapeutics against cancer. The crystal structures of anti-carbohydrate antibodies in complex with antigen reveal the key features of antigen recognition and provide information that can guide the design of vaccines, particularly synthetic ones. This review summarizes structural features of anti-carbohydrate antibodies to over 20 antigens, based on six categories of glyco-antigen: (i) the glycan shield of HIV glycoproteins; (ii) tumor epitopes; (iii) glycolipids and blood group A antigen; (iv) internal epitopes of bacterial lipopolysaccharides; (v) terminal epitopes on polysaccharides and oligosaccharides, including a group of antibodies to Kdo-containing Chlamydia epitopes; and (vi) linear homopolysaccharides.

Description: Sialic acids (SAs) are widely expressed on immune cells and their levels and linkages named as sialylation status vary upon cellular environment changes related to both physiological and pathological processes. In this study, we performed a global profiling of the sialylation status of macrophages and their release of SAs in the cell culture medium by using flow cytometry, confocal microscopy and liquid chromatography tandem mass spectrometry (LC-MS/MS). Both flow cytometry and confocal microscopy results showed that cell surface α-2,3-linked SAs were predominant in the normal culture condition and changed slightly upon treatment with atorvastatin for 24 h, whereas α-2,6-linked SAs were negligible in the normal culture condition but significantly increased after treatment. Meanwhile, the amount of total cellular SAs increased about three times (from 369 ± 29 to 1080 ± 50 ng/mL) upon treatment as determined by the LC-MS/MS method. On the other hand, there was no significant change for secreted free SAs and conjugated SAs in the medium. These results indicated that the cell surface α-2,6 sialylation status of macrophages changes distinctly upon atorvastatin stimulation, which may reflect on the biological functions of the cells.

Description: Prion diseases are transmissible neurodegenerative disorders associated with the conversion of the cellular prion protein, PrP C , to a misfolded isoform called PrP Sc . Although PrP Sc is a necessary component of the infectious prion, additional factors, or cofactors, have been shown to contribute to the efficient formation of transmissible PrP Sc . Glycosaminoglycans (GAGs) are attractive cofactor candidates as they can be found associated with PrP Sc deposits, have been shown to enhance PrP misfolding in vitro, are found in the same cellular compartments as PrP C and have been shown to be disease modifying in vivo. Here we investigated the effects of the sulfated GAGs, heparin and heparan sulfate (HS), on disease associated misfolding of full-length recombinant PrP. More specifically, the degree of sulfation of these molecules was investigated for its role in modulating the disease-associated characteristics of PrP. Both heparin and HS induced a β-sheet conformation in recombinant PrP that was associated with the formation of aggregated species; however, the biochemical properties of the aggregates formed in the presence of heparin or HS varied in solubility and protease resistance. Furthermore, these properties could be modified by changes in GAG sulfation, indicating that subtle changes in the properties of prion disease cofactors could initiate disease associated misfolding.

Description: The display of cell-surface glycolipids and glycoproteins is essential for the motility, adhesion and colonization of pathogenic bacteria such as Campylobacter jejuni . Recently, the cell-surface display of C. jejuni glycoconjugates has been the focus of considerable attention; however, our understanding of the roles that glycosylation plays in bacteria still pales in comparison with our understanding of mammalian glycosylation. One of the reasons for this is that carbohydrate metabolic labeling, a powerful tool for studying mammalian glycans, is difficult to establish in bacterial systems and has a significantly more limited scope. Herein, we report the development of an alternative strategy that can be used to study bacterial cell-surface glycoconjugates. Galactose oxidase (GalO) is used to generate an aldehyde at C-6 of terminal GalNAc residues of C. jejuni glycans. This newly generated aldehyde can be conjugated with aminooxy-functionalized purification tags or fluorophores. The label can be targeted towards specific glycoconjugates using C. jejuni mutant strains with N -glycan or lipo-oligosaccharides (LOS) assembly defects. GalO-catalyzed labeling of cell-surface glycoproteins with biotin, allowed for the purification and identification of known extracellular N-linked glycoproteins as well as a recently identified O-linked glycan modifying PorA. To expand the scope of the GalO reaction, live-cell fluorescent labeling of C. jejuni was used to compare the levels of surface-exposed LOS to the levels of N-glycosylated, cell-surface proteins. While this study focuses on the GalO-catalyzed labeling of C. jejuni , it can in principle be used to evaluate glycosylation patterns and identify glycoproteins of interest in any bacteria.

Description: Human sialidases (NEUs) catalyze the removal of N -acetyl neuraminic acids from the glycome of the cell and regulate a diverse repertoire of nominal cellular functions, such as cell signaling and adhesion. A greater understanding of their substrate permissivity is of interest in order to discern their physiological functions in disease states and in the design of specific and effective small molecule inhibitors. Towards this, we have synthesized soluble fluorogenic reporters of mammalian sialidase activity bearing unnatural sialic acids commonly incorporated into the cellular glycocalyx via metabolic glycoengineering. We found cell-surface sialidases in Jurkat capable of cleaving unnatural sialic acids with differential activities toward a variety of R groups on neuraminic acid. In addition, we observed modulated structure–activity relationships when cell-surface sialidases were presented glycans with unnatural bulky, hydrophobic or fluorinated moieties incorporated directly via glycoengineering. Our results confirm the importance of cell-surface sialidases in glycoengineering incorporation data. We demonstrate the flexibility of human NEUs toward derivatized sugars and highlight the importance of native glycan presentation to sialidase binding and activity. These results stand to inform not only metabolic glycoengineering efforts but also inhibitor design.

Description: A defect in the assembly of the oligosaccharide donor (Dol-PP-GlcNAc 2 Man 9 Glc 3 ) for N-linked glycosylation causes hypoglycosylation of proteins by the oligosaccharyltransferase (OST). Mammalian cells express two OST complexes that have different catalytic subunits (STT3A or STT3B). We monitored glycosylation of proteins in asparagine-linked glycosylation 6 (ALG6) deficient cell lines that assemble Dol-PP-GlcNAc 2 Man 9 as the largest oligosaccharide donor. Based upon pulse labeling experiments, 30–40% of STT3A-dependent glycosylation sites and 20% of STT3B-dependent sites are skipped in ALG6-congenital disorders of glycosylation fibroblasts supporting previous evidence that the STT3B complex has a relaxed preference for the fully assembled oligosaccharide donor. Glycosylation of STT3B-dependent sites was more severely reduced in the ALG6 deficient MI8-5 cell line. Protein immunoblot analysis and RT–PCR revealed that MI8-5 cells express 2-fold lower levels of STT3B than the parental Chinese hamster ovary cells. The combination of reduced expression of STT3B and the lack of the optimal Dol-PP-GlcNAc 2 Man 9 Glc 3 donor synergize to cause very severe hypoglycosylation of proteins in MI8-5 cells. Thus, differences in OST subunit expression can modify the severity of hypoglycosylation displayed by cells with a primary defect in the dolichol oligosaccharide assembly pathway.

Description: Xenopus laevis (African clawed frog) has two types of proto-type galectins that are similar to mammalian galectin-1 in amino acid sequence. One type, comprising xgalectin-Ia and -Ib, is regarded as being equivalent to galectin-1, and the other type, comprising xgalectin-Va and -Vb, is expected to be a unique galectin subgroup. The latter is considerably abundant in frog skin; however, its biological function remains unclear. We determined the crystal structures of two proto-type galectins, xgalectin-Ib and -Va. The structures showed that both galectins formed a mammalian galectin-1-like homodimer, and furthermore, xgalectin-Va formed a homotetramer. This tetramer structure has not been reported for other galectins. Gel filtration and other experiments indicated that xgalectin-Va was in a dimer–tetramer equilibrium in solution, and lactose binding enhanced the tetramer formation. The residues involved in the dimer–dimer association were conserved in xgalectin-Va and -Vb, and one of the Xenopus (Silurana) tropicalis proto-type galectins, but not in xgalectin-Ia and -Ib, and other galectin-1-equivalent proteins. Xgalectin-Va preferred Galβ1-3GalNAc and not Galβ1-4GlcNAc, while xgalectin-Ib preferred Galβ1-4GlcNAc as well as human galectin-1. Xgalectin-Va/Vb would have diverged from the galectin-1 group with accompanying acquisition of the higher oligomer formation and altered ligand selectivity.

Description: Legionaminic acids (Leg) are bacterial analogs of neuraminic acid, with the same stereochemistry but different substituents at C5, C7 and C9. Hence they may be incorporated into useful analogs of sialoglycoconjugates, and we previously reported two sialyltransferases that could utilize cytidine monophosphate (CMP)-Leg5Ac7Ac for preparation of Leg glycoconjugates, which were resistant to sialidases [Watson DC, Leclerc S, Wakarchuk WW, Young NM. 2011. Enzymatic synthesis and properties of glycoconjugates with legionaminic acid as a replacement for neuraminic acid. Glycobiology . 21:99–108.]. These were the porcine ST3Gal1 and Pasteurella multocida sialyltransferases. We now report two additional sialyltransferases with superior Leg-transferase properties to the previous two. These are (i) a truncated form of a Photobacterium α2,6-sialyltransferase with an Ala-Met mutation in its active site, and (ii) an α2,3-sialyltransferase from Neisseria meningitidis MC58 with a higher transferase activity than the P. multocida enzyme, with either CMP-Neu5Ac or CMP-Leg5Ac7Ac as the donor. These enzymes will enable the production of useful Leg5Ac7Ac glycoconjugate derivatives with either α2,6 or α2,3 linkages and unique biological properties.

Description: The rare N-unsubstituted glucosamine ( $$\hbox{ GlcN }{{\hbox{ H }}_{3}}^{+}$$ ) residues in heparan sulfate (HS) have important biological and pathophysiological roles. Because of their low natural abundance, the use of chemically generated, structurally defined, N-unsubstituted heparin/HS oligosaccharides can greatly contribute to the investigation of their natural role in HS. However, the sequencing of mixtures of chemically generated oligosaccharides presents major challenges due to the difficulties in separating isomers and the available detection methods. In this study, we developed and validated a simple and sensitive method for the sequence analysis of N-unsubstituted heparin/HS oligosaccharides. This protocol involves pH 4 nitrous acid (HNO 2 ) degradation, size-exclusion HPLC and ion-pair reversed-phase liquid chromatography-ion trap/time-of-flight mass spectrometry (IPRP-LC-ITTOF MS). We unexpectedly found that absorbance at 232 nm (normally used for specific detection of C4–C5 unsaturated oligosaccharides) was, in most cases, still sufficiently sensitive to also simultaneously detect saturated oligosaccharides during HPLC, thus simplifying the positional analysis of $$\hbox{ GlcN }{{\hbox{ H }}_{3}}^{+}$$ residues. The IPRP-LC-ITTOF MS system can supply further structural information leading to full sequence determination of the original oligosaccharide. This new methodology has been used to separate and sequence a variety of chemically generated, N-unsubstituted dp6 species containing between 1 and 3 $$\hbox{ GlcN }{{\hbox{ H }}_{3}}^{+}$$ residues per oligosaccharide in different positional combinations. This strategy offers possibilities for the sequencing of natural N-unsubstituted oligosaccharides from HS and should also be applicable, with minor modification, for sequencing at N-sulfated residues using alternative pH 1.5 HNO 2 scission.

Description: A major aspect of carbohydrate-dependent galectin functionality is their cross-linking capacity. Using a cell surface as biorelevant platform for galectin binding and a panel of 40 glycans as sensor part of a fluorescent polyacrylamide neoglycopolymer for profiling galectin reactivity, properties of related proteins can be comparatively analyzed. The group of the chicken galectins (CGs) is an especially suited system toward this end due to its relatively small size, compared with mammalian galectins. The experiments reveal particularly strong reactivity toward N -acetyllactosamine repeats for all tested CGs and shared reactivity of CG-1A and CG-2 to histo-blood group ABH determinants. In cross-species comparison, CG-1B's properties closely resembled those of human galectin-1, as was the case for the galectin-2 (but not galectin-3) ortholog pair. Although binding-site architectures are rather similar, reactivity patterns can well differ.

Description: Successful implementation of Ecosystem-Based Fisheries Management (EBFM) requires appropriate action as informed by reference points in an ecosystem context. Thresholds in the response of ecological indicators to system drivers have been suggested as reference points for EBFM, though the management performance of these indicators and possible values for their reference points have not been widely evaluated. We used Management Strategy Evaluation to test the performance of control rules that used ecological indicators to adjust the advice from single-species stock assessments, using the Georges Bank finfish fishery as a case study. We compare the performance of control rules that used ecological indicators to that of single-species F MSY control rules when the system dynamics were governed by the same multispecies population model. Control rules that used indicator-based reference points were able to perform better against catch and biodiversity objectives than when harvests were based on single-species advice alone. Indicators and values for reference points associated with good performance varied depending on the management objective. We quantified tradeoffs between total catch, biodiversity, and interannual variability in catch, noting that it was possible in some instances to achieve higher than average biodiversity while maintaining high catches using indicator-based control rules. While improved performance was noted using ecological indicators, outcomes were variable, and the gains in performance obtained may be similar to alternative methods of implementing precaution in single-species fishery control rules.

Description: Climate change and fishing can have major impacts on the distribution of natural marine resources. Climate change alters the distribution of suitable habitat, forcing organisms to shift their range or attempt to survive under suboptimal conditions. Fishing reduces the abundance of marine populations and truncates their age structure leading to range contractions or shifts. Along the east coast of the United States, there have been major changes in fish populations due to the impacts of fishing and subsequent regulations, as well as changes in the climate. Black sea bass, scup, summer flounder, and winter flounder are important commercial and recreational species, which utilize inshore and offshore waters on the northeast shelf. We examined the distributions of the four species with the Northeast Fisheries Science Center trawl surveys to determine if the along-shelf centres of biomass had changed over time and if the changes were attributed to changes in temperature or fishing pressure through changes in abundance and length structure. Black sea bass, scup, and summer flounder exhibited significant poleward shifts in distributions in at least one season while the Southern New England/Mid-Atlantic Bight stock of winter flounder did not shift. Generalized additive modelling indicated that the changes in the centres of biomass for black sea bass and scup in spring were related to climate, while the change in the distribution of summer flounder was largely attributed to a decrease in fishing pressure and an expansion of the length–age structure. While the changes in ocean temperatures will have major impacts on the distribution of marine taxa, the effects of fishing can be of equivalent magnitude and on a more immediate time scale. It is important for management to take all factors into consideration when developing regulations for natural marine resources.

Description: Many snow crab fisheries have fluctuated widely over time in a quasi-cyclic way due to highly variable recruitment. The causes of this variability are still debated. Bottom-up processes related to climate variability may strongly affect growth and survival during early life, whereas top-down predator effects may be a major source of juvenile mortality. Moreover, intrinsic density-dependent processes, which have received much less attention, are hypothetically responsible for the cycles in recruitment. This study explored how climate, larval production, intercohort cannibalism and groundfish predation may have affected recruitment of early juvenile snow crab in the northwest Gulf of St Lawrence (eastern Canada) over a period of 23 years. Abundance of early juvenile snow crabs (2.5–22.9 mm in carapace width), representing the first 3 years of benthic life, came from an annual trawl survey and was used to determine cohort strength. Analyses revealed a cyclic pattern in abundance of 0 + crabs that may arise from cohort resonant effects. This pattern consisted of three recruitment pulses but was reduced to two pulses by age 2 + , while the interannual variability of cohort strength was dampened. This reconfiguration of the earliest recruitment pattern was dictated primarily by bottom water temperature and cannibalism, which progressively overruled the pre-settlement factors of larval production and surface water temperature that best explained abundance of 0 + crabs. The results strongly suggest that bottom-up and density-dependent processes prevail over top-down control in setting the long-term trends and higher-frequency oscillations of snow crab early recruitment patterns.

Description: Fisheries biology encompasses a tremendous diversity of research questions, methods, and models. Many sub-fields use observational or experimental data to make inference about biological characteristics that are not directly observed (called "latent states"), such as heritability of phenotypic traits, habitat suitability, and population densities to name a few. Latent states will generally cause model residuals to be correlated, violating the assumption of statistical independence made in many statistical modelling approaches. In this exposition, we argue that mixed-effect modelling (i) is an important and generic solution to non-independence caused by latent states; (ii) provides a unifying framework for disparate statistical methods such as time-series, spatial, and individual-based models; and (iii) is increasingly practical to implement and customize for problem-specific models. We proceed by summarizing the distinctions between fixed and random effects, reviewing a generic approach for parameter estimation, and distinguishing general categories of non-linear mixed-effect models. We then provide four worked examples, including state-space, spatial, individual-level variability, and quantitative genetics applications (with working code for each), while providing comparison with conventional fixed-effect implementations. We conclude by summarizing directions for future research in this important framework for modelling and statistical analysis in fisheries biology.

Description: While the impact of environmental forcing on recruitment variability in marine populations remains largely elusive, studies spanning large spatial areas and many stocks are able to identify patterns common to different regions and species. In this study, we investigate the effects of the environment on the residuals of a Ricker stock–recruitment (SR) model, used as a proxy of prerecruits' survival, of 18 assessed stocks in the Baltic and North Seas. A probabilistic principal components (PCs) analysis permits the identification of groups of stocks with shared variability in the prerecruits' survival, most notably a group of pelagics in the Baltic Sea and a group composed of gadoids and herring in the North Sea. The first two PCs generally grouped the stocks according to their localizations: the North Sea, the Kattegat–Western Baltic, and the Baltic Sea. This suggests the importance of the local environmental variability on the recruitment strength. Hence, the prerecruits' survival variability is studied according to geographically disaggregated and potentially impacting abiotic or biotic variables. Time series (1990–2009) of nine environmental variables consistent with the spawning locations and season for each stock were extracted from a physical–biogeochemical model to evaluate their ability to explain the survival of prerecruits. Environmental variables explained 〉70% of the survival variability for eight stocks. The variables water current, salinity, temperature, and biomass of other fish stocks are regularly significant in the models. This study shows the importance of the local environment on the dynamics of SR. The results provide evidence of the necessity of including environmental variables in stock assessment for a realistic and efficient management of fisheries.

Description: Ecosystem-based fisheries management seeks to consider trade-offs among management objectives for interacting species, such as those that arise through predator–prey linkages. In particular, fisheries-targeting forage fish (small and abundant pelagic fish) might have a detrimental effect on fisheries-targeting predators that consume them. However, complexities in ecological interactions might dampen, negate, or even reverse this trade-off, because small pelagic fish can be important predators on egg stages of piscivorous fish. Further, the strength of this trade-off might depend on the extent to which piscivorous fish targeted by fisheries regulate forage species productivity. Here, we developed a novel delay-differential bioeconomic model of predator–prey and fishing dynamics to quantify how much egg predation or weak top-town control affects the strength of trade-off between forage and piscivore fisheries, and to measure how ecological interactions dictate policies that maximize steady-state profits. We parameterized the model based on ecological and economic data from the North Sea Atlantic cod ( Gadus morhua ) and Atlantic herring ( Clupea harengus ). The optimal policy was very sensitive to the ecological interactions (either egg predation or weak top-down control of forage by predators) at relatively low forage prices but was less sensitive at high forage fish prices. However, the optimal equilibrium harvest rates on forage and piscivores were not substantially different from what might be derived through analyses that did not consider species interactions. Applying the optimal multispecies policy would produce substantial losses (〉25%) in profits in the piscivore fishery, and the extent of loss was sensitive to ecological scenarios. While our equilibrium analysis is informative, a dynamic analysis under similar ecological scenarios is necessary to reveal the full economic and ecological benefits of applying ecosystem-based fishery management policies to predator–prey fishery systems.

Description: Leptocephali, the larvae of eels, grow to large sizes and are widely distributed in tropical and subtropical oceans. Their role in oceanic food webs is poorly known because they are rarely reported as food items in fish stomach content studies. Data from 13 years of research on the trophic dynamics of Pacific Ocean predatory fish indicate that among 8746 fish of 76 species/taxa (33 families) that had been feeding, only 16 fish of 6 species had remains of 34 leptocephali in their stomachs. Only 0.013% of the 256 308 total prey items were leptocephalus larvae, and 0.03% of the total prey items were juvenile or adult eels (mostly snipe eels: Nemichthyidae). There were 10 fish of 2 species of lancetfish ( Alepisaurus spp., n = 152), 2 rainbow runners ( Elagatis bipinnulata , n = 222), and 2 yellowfin tuna ( Thunnus albacares , n = 3103) that had leptocephali in their stomach contents, but all except one T. albacares (contained 15 leptocephali) had each eaten ≤3 leptocephali. A swallower, Pseudoscopelus sp., and a frigate tuna, Auxis thazard , had eaten single leptocephali. Twenty-eight bigeye tuna, Thunnus obesus , had eaten 76 juvenile/adult nemichthyid or serrivomerid eels. A literature survey found that only 15 out of 75 examined publications listed leptocephali in the stomach contents of a total of 6 species out of ~ 42 300 predatory fish of 40 species. The transparency of leptocephali and their apparent mimicry of gelatinous zooplankton could contribute to lower rates of predation. Their soft bodies likely digest rapidly, so although this study and existing literature indicate that leptocephali sometimes contribute to predatory fish diets, particularly for fish that do not exclude gelatinous prey types, and fish with low digestion rates in their stomachs such as lancetfish, their levels of contribution to fish diets and the impacts of predators on eel recruitment remain uncertain.

Description: Effective individual transferable quotas (ITQ) systems rebuild stocks and allow transfer of quotas to more efficient operators. This process requires functional markets for both quota sales and temporary quota leases. These markets are expected to respond to changes in economic rent from the fishery, which is influenced by stock abundance and the international rock lobster price. This research used multistate Markov modelling and Granger causality test to examine changes in the permanent and temporary quota trade in the Tasmanian rock lobster fishery quota market, during periods of both increasing and decreasing stock abundance. The permanent quota trade market was more active during the period of stock growth, while the quota lease market was active in both periods of stock growth and decline. In contrast to theoretical trends in ITQ fisheries, trades in both markets were not linked to the technical efficiency (i.e. catching capability) of operators, but were more driven by the quota owners' financial capacity (i.e. number of owned quotas). Prolonged and unexpected stock decline affected the quota market so that it deviated from the theoretical pattern of ITQ fisheries. Operators previously active in the market reduced their activity, while smaller operators and firms that previously had not traded became more active, so the fleet expanded with smaller operators entering.

Description: Jellyfish disruption of fisheries has been described in some coastal systems, but few thorough investigations have been conducted. To ascertain the economic impact and trend of jellyfish blooms in the Northern California Current (NCC), we mailed surveys to resident commercial shrimpers, salmon trollers, rockfish (blue, black), and groundfish fishers ( n = 872). We asked fishers to estimate the damages caused by jellyfish—including costs of relocating to avoid blooms, lost fishing time, time lost to bycatch sorting, fish depreciation, and gear damage. Of the total respondents ( n = 111), 67% reported that jellyfish reduce their seasonal revenue, but the degree of impact ranged considerably by fishery and location. Highest jellyfish nuisance corresponded to regions with the most salmon trolling effort. Using the mean revenue losses provided by respondents, we estimate that the combined economic impact of jellyfish on Oregon's salmon and pink shrimp fishers was over $650 000 in peak jellyfish season (June–September) in 2012. Fishers reported that jellyfish biomass varies annually, but most respondents (51%) reported observing no appreciable change in jellyfish populations in the last 5 years. Since economic impact analyses have been conducted primarily in areas with anomalous, high-density blooms, data from the NCC, which is not known to be experiencing increases in jellyfish abundance, provides baseline information on the socio-economic impact of jellyfish blooms in this region. In addition, the finding that jellyfish impact hook and line fisheries—not solely net fisheries—has implications for many other regions where fishers employ this gear type.

Description: Odontocete depredation on longlines involves socioeconomic and conservation issues with significant losses for fisheries and potential impacts on wild populations of depredating species. As technical solutions to this conflict are limited and difficult to implement, this study aimed to identify fishing practices that could reduce odontocete depredation, with a focus on killer whales (Orcinus orca) interacting with Patagonian toothfish (Dissostichus eleginoides) longliners off the Crozet islands. Data collected by fishery observers from 6013 longline sets between 2003 and 2013 allowed us to statistically detect the significant influence of five operational variables using GLMMs. The probability of interactions between vessels and killer whales was decreased by (i) the number of vessels operating simultaneously in the area: the limited number of depredating killer whales may induce a dilution effect with increased fleet size, and (ii) depth of longline sets: vessels operating in shallow waters may be more accessible to whales that are initially distributed on peri-insular shelves. The cpue was negatively influenced by (iii) length of longlines: longer sets may provide killer whales access to a greater proportion of hooked fish per set, and positively influenced by (iv) hauling speed: increased speed may shorten the time during which toothfish are accessible to whales during hauling. The time it takes for killer whales to reach vessels was positively correlated to (v) the distance travelled between longline sets with an estimated threshold of 100 km beyond which whales seem to temporarily lose track of vessels. These findings provide insightful guidelines about what fishing strategy to adopt given these variables to reduce killer whale depredation here and in similar situations elsewhere. To a greater extent, this study is illustrative of how collaborative work with fishermen in a fully controlled fishery framework may lead to the definition of cost-limited and easy-to-implement mitigation solutions when facing such human-wildlife conflict.

Description: In Alaskan waters, depredation on sablefish longline gear by sperm whales increases harvesting cost, negatively biases stock assessments, and presents a risk of entanglement for whales. The Southeast Alaska Sperm Whale Avoidance Project (SEASWAP), a collaborative effort involving industry, scientists, and managers, since 2003 has undertaken research to evaluate depredation with a goal of recommending measures to reduce interactions. Prior to 2003, little was known about sperm whale distribution and behaviour in the Gulf of Alaska (GOA). Although fishers were reporting increasing interactions, the level of depredation varied with no apparent predictor of occurrence across vessels. Between 2003 and 2007, fishers were provided with fishery logbooks and recorded information on whale behaviour, whale presence and absence, during the set, soak, and haul for 319 sets in the GOA. Data were evaluated for a vessel, area, and seasonal (month) effect in the presence and absence of sperm whales. Using catch per unit effort ( cpue ) as a metric, in kg/100 hooks, results indicated that depredation depended on both the vessel and the area. More whales associated with vessels from April to August. Sperm whales were also likely to be present when cpue was high, revealing that whales and fishers both knew the most productive fishing areas, but confounding the use of cpue as a metric for depredation. Using a Bayesian mark-recapture analysis and the sightings histories of photo-identified whales, an estimated $$\hat{N}=135$$ (95% CI 124, 153) sperm whales were associating with vessels in 2014. A spatial model was fitted to 319 longline sets and quantified a 3% loss in cpue , comparable to other global studies on sperm whale depredation. Through all phases of SEASWAP, our understanding of depredation has gained significantly. This successful collaboration should be considered as a model to create partnerships and build collaborations between researchers and fisherpeople encountering marine mammal interactions with fishing gear.

Description: This paper provides a synthesis of results obtained as part of a long-term collaborative study involving biologists, fishers, and resource managers—centring on the occurrence of killer whales in the Crozet Archipelago before and after the implementation of a demersal longline fishery for Patagonian toothfish. Depredation behaviour was reported as soon as the fishery was initiated, with dramatic effects on both the demographic trajectories of the killer whales and on the amount of fish lost by the fishers. Killer whales interacting with the fishery exhibited very high mortality rates when illegal fishing took place, while killer whales not interacting were unaffected. However, after illegal fishing ended, killer whales interacting with the fishery exhibited both higher fecundity and survival rates compared with killer whales not interacting. Since whales typically removed fish entirely from the hooks, an adapted methodology that did not rely on determining the number of damaged fish was developed to estimate depredation rates. In the Crozet EEZ over a 10-year period, 33.9% of the total amount of Patagonian toothfish caught, representing a total of 28 million , was estimated to be lost due to the combined effects of killer whale and sperm whale depredation. In an effort to reduce depredation losses, modifications to fishing methods, such as changing the fishing season, changing fishing areas when exposed to depredation and changing longline length and hauling speed were successfully tested. Acoustic deterrent devices were ineffective in deterring killer whales from depredating longlines. Alternative fishing gears, such as fish pots, were also tested. However, while providing encouraging results regarding the suppression of depredation and seabird bycatch, fish pots were not efficient enough to sustain an economically viable fishery. In conclusion, we discuss how the findings of this comprehensive study can be used elsewhere in fisheries confronted with depredation.

Description: Glycosaminoglycans (GAG) play a ubiquitous role in tissues and cells. In eukaryotic cells, heparan sulfate (HS) is initially degraded by an endo-β-glucuronidase called heparanase-1 (HPSE). HS oligosaccharides generated by the action of HPSE intensify the activity of signaling molecules, activating inflammatory response, tumor metastasis, and angiogenesis. The aim of the present study was to understand if sulfated GAG could modulate HPSE, since the mechanisms that regulate HPSE have not been completely defined. CHO-K1 cells were treated with 4-methylumbelliferone (4-MU) and sodium chlorate, to promote total inhibition of GAG synthesis, and reduce the sulfation pattern, respectively. The GAG profile of the wild CHO-K1 cells and CHO-745, deficient in xylosyltransferase, was determined after [ 35 S]-sulfate labeling. HPSE expression was determined via real-time quantitative polymerase chain reaction. Total ablation of GAG with 4-MU in CHO-K1 inhibited HPSE expression, while the lack of sulfation had no effect. Interestingly, 4-MU had no effect in CHO-745 cells for these assays. In addition, a different enzyme location was observed in CHO-K1 wild-type cells, which presents HPSE mainly in the extracellular matrix, in comparison with the CHO-745 mutant cells, which is found in the cytoplasm. In view of our results, we can conclude that GAG are essential modulators of HPSE expression and location. Therefore, GAG profile could impact cell behavior mediated by the regulation of HPSE.

Description: Glycomics may assist in uncovering the structure–function relationships of protein glycosylation and identify glycoprotein markers in colorectal cancer (CRC) research. Herein, we performed label-free quantitative glycomics on a carbon-liquid chromatography–tandem mass spectrometry-based analytical platform to accurately profile the N-glycosylation changes associated with CRC malignancy. N -Glycome profiling was performed on isolated membrane proteomes of paired tumorigenic and adjacent non-tumorigenic colon tissues from a cohort of five males (62.6 ± 13.1 y.o.) suffering from colorectal adenocarcinoma. The CRC tissues were typed according to their epidermal growth factor receptor (EGFR) status by western blotting and immunohistochemistry. Detailed N -glycan characterization and relative quantitation identified an extensive structural heterogeneity with a total of 91 N -glycans. CRC-specific N-glycosylation phenotypes were observed including an overrepresentation of high mannose, hybrid and paucimannosidic type N -glycans and an under-representation of complex N -glycans ( P 〈 0.05). Sialylation, in particular α2,6-sialylation, was significantly higher in CRC tumors relative to non-tumorigenic tissues, whereas α2,3-sialylation was down-regulated ( P 〈 0.05). CRC stage-specific N-glycosylation was detected by high α2,3-sialylation and low bisecting β1,4-GlcNAcylation and Lewis-type fucosylation in mid-late relative to early stage CRC. Interestingly, a novel link between the EGFR status and the N-glycosylation was identified using hierarchical clustering of the N -glycome profiles. EGFR-specific N -glycan signatures included high bisecting β1,4-GlcNAcylation and low α2,3-sialylation (both P 〈 0.05) relative to EGFR-negative CRC tissues. This is the first study to correlate CRC stage and EGFR status with specific N -glycan features, thus advancing our understanding of the mechanisms causing the biomolecular deregulation associated with CRC.

Description: Fucosylated chondroitin sulfate (FCS) is a glycosaminoglycan found in sea cucumbers. It has a backbone like that of mammalian chondroitin sulfate (4-β- d -GlcA-1-〉3-β- d -GalNAc-1) n but substituted at the 3rd position of the β- d -glururonic acid residues with α-fucose branches. The structure of these branches varies among FCSs extracted from different species of sea cucumbers, as revealed by solution NMR spectroscopy. Some species ( Isostichopus badionotus and Patalus mollis ) contain branches formed by single α-fucose residues but with variable sulfation patterns (2,4-, 3,4- and 4-sulfation). FCS from Ludwigothurea grisea is distinguished because it contains preponderant branches formed by disaccharide units containing non-sulfated and 3-sulfated α-fucose units at the reducing and non-reducing ends, respectively. Despite the structural variability on their α-fucose branches, these FCSs have similar anticoagulant action on assays using purified reagents. They have serpin-dependent and serpin-independent effects. Pharmacological assays using experimental animals showed that the three types of FCSs have similar antithrombotic effect and bleeding tendency. They also activate factor XII on the same range of concentration. Based on these observations, we proposed that only few sulfated α-fucose branches along the FCS chain are enough to assure the binding of this glycosaminoglycan to proteins of the coagulation system. Substitution with additional sulfated α-fucose does not increase further the activity. Overall, the use of FCSs with marked variability on their branches of α-fucose allowed us to establish correlations between structures vs biological effects of these glycosaminoglycans on a more refined basis. It opens new avenues for therapeutic intervention using FCSs.

Description: Enzymes that affect glycoproteins of the human immune system, and thereby modulate defense responses, are abundant among bacterial pathogens. Two endoglycosidases from the human pathogen Streptococcus pyogenes , EndoS and EndoS2, have recently been shown to hydrolyze N-linked glycans of human immunoglobulin G. However, detailed characterization and comparison of the hydrolyzing activities have not been performed. In the present study, we set out to characterize the enzymes by comparing the activities of EndoS and EndoS2 on a selection of therapeutic monoclonal antibodies (mAbs), cetuximab, adalimumab, panitumumab and denosumab. By analyzing the glycans hydrolyzed by EndoS and EndoS2 from the antibodies using matrix-assisted laser desorption ionization time of flight, we found that both the enzymes cleaved complex glycans and that EndoS2 hydrolyzed hybrid and oligomannose structures to a greater extent compared with EndoS. A comparison of ultra-high-performance liquid chromatography (LC) profiles of the glycan pool of cetuximab hydrolyzed with EndoS and EndoS2 showed that EndoS2 hydrolyzed hybrid and oligomannose glycans, whereas these peaks were missing in the EndoS chromatogram. We utilized this difference in glycoform selectivity, in combination with the IdeS protease, and developed a LC separation method to quantify high mannose content in the Fc fragments of the selected mAbs. We conclude that EndoS and EndoS2 hydrolyze different glycoforms from the Fc-glycosylation site on therapeutic mAbs and that this can be used for rapid quantification of high mannose content.

Description: Calnexin (CNX), known as a lectin chaperone located in the endoplasmic reticulum (ER), specifically recognizes G 1 M 9 GN 2 -proteins and facilitates their proper folding with the assistance of ERp57 in mammalian cells. However, it has been left unidentified how CNX works in Aspergillus oryzae , which is a filamentous fungus widely exploited in biotechnology. In this study, we found that a protein disulfide isomerase homolog TigA can bind with A. oryzae CNX (AoCNX), which was revealed to specifically recognize monoglucosylated glycans, similarly to CNX derived from other species, and accelerate the folding of G 1 M 9 GN 2 -ribonuclease (RNase) in vitro. For refolding experiments, a homogeneous monoglucosylated high-mannose-type glycoprotein G 1 M 9 GN 2 -RNase was chemoenzymatically synthesized from G 1 M 9 GN-oxazoline and GN-RNase. Denatured G 1 M 9 GN 2 -RNase was refolded with highest efficiency in the presence of both soluble form of AoCNX and TigA. TigA contains two thioredoxin domains with CGHC motif, mutation analysis of which revealed that the one in N-terminal regions is involved in binding to AoCNX, while the other in catalyzing protein refolding. The results suggested that in glycoprotein folding process of A. oryzae , TigA plays a similar role as ERp57 in mammalian cells, as a partner protein of AoCNX.

Description: Polysialic acid (polySia) is a linear polymer of sialic acid that modifies neural cell adhesion molecule (NCAM) in the vertebrate brain. PolySia is a large and exclusive molecule that functions as a negative regulator of cell–cell interactions. Recently, we demonstrated that polySia can specifically bind fibroblast growth factor 2 (FGF2) and BDNF; however, the protective effects of polySia on the proteolytic cleavage of these proteins remain unknown, although heparin/heparan sulfate has been shown to impair the cleavage of FGF2 by trypsin. Here, we analyzed the protective effects of polySia on the proteolytic cleavage of FGF2 and proBDNF/BDNF. We found that polySia protected intact FGF2 from tryptic activity via the specific binding of extended polySia chains on NCAM to FGF2. Oligo/polySia also functioned to impair the processing of proBDNF by plasmin via binding of oligo/polySia chains on NCAM. In addition, the polySia structure synthesized by mutated polysialyltransferase, ST8SIA2/STX(SNP7), which was previously identified from a schizophrenia patient, was impaired for these functions compared with polySia produced by normal ST8SIA2. Taken together, these data suggest that the protective effects of polySia toward FGF2 and proBDNF may be involved in the regulation of the concentrations of these neurologically active molecules.

Description: A model combining qualitative and historical quantitative data in an innovative rule-based fuzzy cognitive map framework is used to assess and compare the long-term bioeconomic impact of adopting gear modifications aimed at reducing bycatch in the Portuguese crustacean trawl fishery. The impact of codend-related changes (mesh size and shape) and the introduction of a sorting device (sorting grid system) on the main target crustacean species (deepwater rose shrimp Parapenaeus longirostris and Norway lobster Nephrops norvegicus ) and the main fish bycatch species (blue whiting Micromesistius poutassou , horse mackerel Trachurus trachurus , and European hake Merluccius merluccius ) were evaluated. Horse mackerel was the only fish species for which changing codends negatively affected landings per unit of effort by large percentages. The use of a sorting grid system, only evaluated for blue whiting and Norway lobster, led to a strong decrease in landings per unit of effort, especially for the former species. The impact of gear alterations was negligible on fish spawning-stock biomass, but was significant for crustaceans, particularly rose shrimp. A straightforward evaluation of the economic impact (fishers' revenues) of the three bycatch reduction options showed these to be negligible or small.

Description: The difficulty of ensuring adequate statistical coverage of whole fleets is a challenge for the implementation of observer programmes and may reduce the usefulness of the data they obtain for management purposes. This makes it necessary to find cost-effective alternatives. Electronic monitoring (EM) systems are being used in some fisheries as an alternative or a complement to human observers. The objective of this study was to test the use and reliability of EM on the tropical tuna purse-seine fishery. To achieve this objective, seven trips of tuna purse seiners operating in the three Oceans were closely monitored to compare the information provided by EM and on-board observers to determine if EM can reliably document fishing effort, set type, tuna catch, and bycatch. Total tuna catch per set was not significantly different between EM and observer datasets; however, regarding species composition, only main species matched between EM and observers. Success on set-type identification using EM varied between 98.3 and 56.3%, depending on the camera placement. Overall, bycatch species were underestimated by EM, but large bodied species, such as billfishes, were well documented. The analyses in this study showed that EM can be used to determine the fishing effort (number of sets) and total tuna catch as reliably as observers can. Set-type identification also had very promising results, but indicated that refinement of the methods is still needed. To be fully comparable with observer data, improvements for accurately estimating the bycatch will need to be developed in the application and use of the EM system. Operational aspects that need to be improved for an EM programme to be implemented include standardizing installation and on-board catch handling methodology as well as improvements in video technology deployment.

Description: In this paper, we synthesize information presented at the 2nd Fishery Dependent Information (FDI) Conference, held in Rome, Italy, from 2 to 6 March 2014. We review current issues and advances in the collection, interpretation and application of fishery-dependent data, and highlight emergent findings in the field. Key issues include (i) the design and collection of data associated with commercial and recreational fisheries and the use of these data to support conventional and novel approaches to fisheries science and management and (ii) the role of fishers in co-management and policy setting. We noted that since the 2010 FDI conference a paradigm shift towards full engagement of key stakeholders started to take place. It also became evident that trust between stakeholders, managers, and scientists is necessary to develop efficient fishery monitoring programmes. While building such trust among key players often begins in informal settings, eventually one must evolve structured, formalized, and agreed processes for such interactions. We also conclude that because of the diversity of fisheries any determination of "best practices" may be difficult. Instead, we provide a list of "best principles" emerged from the conference.

Description: The walleye pollock ( Gadus chalcogrammus ) fishery in the Bering Sea is one of the largest fisheries in the world. The North Pacific Fishery Management Council (NPFMC) provides management advice for this fishery, including the development of measures to minimize salmon bycatch to the extent practicable, one of the stated objectives of the US Magnuson–Stevens Fishery Conservation and Management Act National Standard Guidelines. Salmon have a unique cultural and nutritional importance in the State of Alaska and are the subject of fully allocated mixed commercial, recreational, and subsistence fisheries. Chinook salmon ( Oncorhynchus tshawytscha ) stocks in Alaska have been declining for the last decade, and all sources of mortality are being considered to help in rebuilding stocks. Given the extensive scientific National Marine Fisheries Service observer data collection programme, the NPFMC has developed bycatch management measures that place limits by fishery sector on the allowable catch of Chinook salmon. Part of this programme includes industry-proposed incentive programmes designed to encourage lower bycatch. Evaluating the efficacy of the new measures poses a number of challenges, particularly in light of changing ocean conditions (perhaps affecting the degree of overlap between pollock and salmon). In this study, data on pre- and post-programme implementation were evaluated to determine if the programme is meeting stated goals and objectives or if modifications are needed. These evaluations included consideration of fleet-level bycatch numbers and rates, seasonality of bycatch by sector, and individual vessel bycatch rates. Results suggest that revised management regulations appear to have resulted in reduced bycatch of salmon overall. Also, lower bycatch rates seem to reflect changing behaviour in response to new management measures. However, the extent to which the programme is effective at the vessel level remains difficult to ascertain without explicit vessel-specific benchmarks developed for evaluating programme efficacy.

Description: Part of the European Union (EU) Common Fisheries Policy revision of 2013 is a commitment to implement a land-all policy, under which the practice of discarding caught fish back into the sea will be forbidden. This measure will be applied first to the pelagic fleet in 2015, with a phased implementation for the demersal fleet between 2016 and 2019. As part of trials to determine the efficacy of a land-all policy for North Sea cod ( Gadus morhua L.), Remote Electronic Monitoring (REM) systems were installed on seven Scottish demersal vessels in 2008. Vessels were permitted additional days-at-sea and cod quota, and were obliged to land all cod caught in the North Sea. This arrangement has been renewed each year as part of the Scottish Cod Conservation Credits scheme, and while the list of vessels involved has not remained constant, the scheme remains attractive to skippers (27 vessels in 2014), has always been oversubscribed, and is likely to remain a key part of the Scottish Government's approach to land-all enforcement. Marine Scotland Science is granted access to all REM data collected from Scottish vessels. This paper summarizes the scientific analyses carried out using these data from 2008 onwards, including the installation and operation of REM systems for scientific purposes; the programme developed to train REM analysts; systems for combining length measurements with fish counts; the potential use of REM data in management advice; and studies on such aspects as discard-rate estimation, activity mapping, estimating the relative costs of on-board and REM observation, morphometric length inference, and automated image analysis. We conclude that, while further development work is certainly needed, REM provides a rich source of fisheries information for science as well as for compliance and management. However, care will need to be taken to ensure that science monitoring and analysis resources do not become overwhelmed.

Description: Chinook salmon ( Oncorhynchus tshawytscha ) are taken as bycatch in the Bering Sea pollock ( Gadus chalcogrammus ) fishery, with recently revised management measures in place to limit the overall Chinook salmon catch. Historical impact of the bycatch on regional salmon stocks is made difficult because, until recently, sampling for the stock composition of the bycatch was patchy and diverse in approaches. In this study, extensive observer data on the biological attributes (size and age composition) of the bycatch were used to estimate the impact on specific regional stock groups (RSGs), as defined given available genetic stock identification estimates. Our model provides estimates of the impact on Chinook salmon RSGs, given seasonal and spatial variability in the bycatch, and accounts for observed in-river age compositions, uncertainty in age-specific oceanic natural mortality of Chinook salmon, and between-year variability in genetic information. The upper Yukon River stock is transboundary and subject to heightened management interest and international management agreements on escapement goals. Our study updates results from an earlier analysis used to develop the management regulations that went into place in 2011. It shows that the new data result in slight changes in previous estimates, and that the lower overall Chinook salmon bycatch since 2008 has resulted in lower impacts to the main western Alaskan RSGs.

Description: Change is an important feature of commercial fisheries; yet the fishing industry, including fishers, fishery management authorities, and other stakeholders, is, in many respects, highly resistant to change. Examples of this include the application of conservation engineering solutions to bycatch problems and transitions towards ecosystem-based fishery management. A key reason for this resistance may be conditioning, cultural conservatism, and uncertainty. Change is often considered uncontrollable and unpredictable and a threat to established processes and systems that forces individuals to face an unknown future. In the business world, many models of change management have been applied to assist individuals and corporations in responding to an ever-changing environment. While fragments of these models have been applied in a fisheries context, the deliberate application of entire models has not. The application of these models could help to improve many aspects of fishery-dependent data collection such as using fishery-dependent information in stock assessment, implementing technologies such as vessel monitoring systems and electronic logbooks, and sharing information that is traditionally not shared. We present a well-known model for change management and describe how its application in a fisheries context can guide change initiatives and produce enhanced outcomes. We also explore how competing commitments and big assumptions influence a fisher's resistance to change, including conservation engineering initiatives, and posit how this can influence their involvement in the collection of fishery-dependent data.

Description: During the last centuries, populations of marine megafauna—such as seabirds, turtles, and mammals—were intensively exploited. At present, other threats such as bycatch and pollution affect these species, which play key ecological roles in marine ecosystems as apex consumers and/or nutrient transporters. This study analyses the distribution of six megafaunal species ( Chelonia mydas , Caretta caretta , Dermochelys coriacea , Thalassarche melanophris , Otaria flavescens , and Arctocephalus australis ) coexisting in the Southwestern Atlantic to discuss their protection in terms of current management strategies in the region. Through the prediction of the species potential distributions and their relation to bathymetry, sea temperature and oceanographic fronts, key ecological areas are defined from a multi-taxa perspective. Information on the distribution of 70 individuals (18 sea turtles, 19 albatrosses, and 33 otariids) was obtained through satellite tracking conducted during 2007–2013 and analysed using a Geographic Information System and maximum entropy models. During the autumn–winter period, megafaunal species were distributed over the continental shelves of Argentina, Uruguay, and Brazil, mainly over the Argentine Exclusive Economic Zone and the Argentina-Uruguay Common Fishing Zone. Despite some differences, all megafaunal species seems to have similar environmental requirements during the autumn–winter period. Mostly waters shallower than 50 m were identified as key ecological areas, with the Río de la Plata as the habitat with the highest suitability for all the species. This area is highly productive and sustains the main coastal fisheries of Uruguay and Argentina, yet its role as a key ecological area for megafaunal species has been underestimated until now. This approach provides a basis to analyse the effect of anthropic activities on megafaunal species through risk maps and, ultimately, to generate knowledge to improve national and bi-national management plans between Argentina and Uruguay.

Description: In the North Sea flatfish fishery, electric pulse trawls have been introduced to replace the conventional mechanical method. Pulse trawls reduce the fuel consumption, reduce adverse impact on the ecosystem but cause injuries in gadoids. We describe the design and electrical properties of pulse trawls currently in use and study the behavioural response and injuries in cod exposed to electrical pulses under controlled conditions. Pulse trawls operate at an average power of 0.7 kW m –1 beam length and a duty cycle of ~2%. The electric field is heterogeneous with highest field strength occurring close to the conductors. Cod were exposed to three different pulse types for a range of field strengths, frequencies, and duty cycles. Two size classes were tested representing cod that escape through the meshes (11–17 cm) and market-sized cod that are retained in the net (34–56 cm). Cod exposed to a field strength of ≥37 V m –1 responded by moderate-to-strong muscular contractions. Some of the large cod ( n = 260) developed haemorrhages and fractures in the spine, and haemal and neural arches in the tail part of the body. The probability of injuries increased with field strength and decreased when frequency was increased from 100 to 180 Hz. None of the small cod ( n = 132) were injured and all survived. The field strength at the lateral boundaries of the trawl was too low to inflict injuries in cod.

Description: A coupled biophysical model is used to explore the physical controls involved in the timing of the spring phytoplankton bloom in fjords. Observations from Rivers Inlet, British Columbia, are used to force and evaluate the model. It is found that the interannual variation in timing is due primarily to variations in retention, in particular, to variations in horizontal advection out of the fjord. The two dominant processes are (i) strong outflow winds rapidly advecting the surface layer and thus the phytoplankton population out of the fjord and (ii) losses due to high river flux increasing the estuarine circulation. Both processes delay the timing of spring bloom. Smaller effects on the interannual variation are due to increased wind mixing which deepens the mixing layer and reduces light to phytoplankton, and increased river flow which increases the stratification and decreases the mixing layer depth. Observed interannual variations in cloudiness were small. Strong outflow winds are common in winter along the British Columbia coast, but generally cease after the spring wind transition. Thus, observed interdecadal variations in the spring transition date probably imply strong variations in the timing of spring phytoplankton blooms in British Columbia fjords.

Description: Since "balanced harvest" was proposed in 2010 as a possible tool in the operationalization of the ecosystem approach to fisheries (EAF), the concept gained extensive international attention. Because maintaining ecosystem structure and achieving maximum sustainable yields have become two of the key international legal obligations in fisheries management, balanced harvest is as topical as ever. An international workshop on balanced harvest, organized by the IUCN Fisheries Expert Group at FAO headquarters in 2014, reviewed the progress in the field and discussed its prospects and challenges. Several articles in this theme set, mostly based on presentations from the workshop, discuss ecological, economical, legal, social, and operational issues surrounding the key management goals. Progress is being made on understanding of the theoretical underpinnings of balanced harvest and its practical feasibility. Yet, a basic debate on the concept of balanced harvest continues. To move the EAF forward, we anticipate and encourage further research and discussion on balanced harvest and similar ideas.

Description: Sampling of euphausiids is difficult because of their intermediate size between macrozooplankton and micronekton. The Barents Sea is one of the few marine areas where there have been long-term studies of euphausiids. We have examined three monitoring datasets on euphausiids and consider likely sources of errors associated with the sampling. Results indicated a high degree of patchiness in the distribution of euphausiids, even at the largest scale of sampling with a pelagic trawl. This indicates that euphausiids may occur in large, but infrequent, swarms that have a low probability of being sampled by small nets. The mean biomass of euphausiids sampled with MOCNESS was 2 g wet weight m –2 integrated over the water column, which is an underestimate due to avoidance of large individuals. The mean biomass obtained with pelagic trawl in the upper 60 m of water at night during an autumn survey was 10 g wet weight m –2 . The plankton net on bottom trawl collected mean and median density of euphausiids (0.1–0.2 g wet weight m –3 ) near bottom during a winter survey similar to the values found with pelagic trawl in the upper layer during autumn. The mean density for the autumn survey showed an increase from 2000 to 2011, while the winter survey showed generally a decrease from 2000–2007 to 2011. The increase in the autumn series coincided with a general warming trend presumably with a larger influx of euphausiids with Atlantic water, notably of Meganyctiphanes norvegica . In contrast, the decline during winter may reflect a decrease, particularly of Thysanoessa raschii in the southeastern Barents Sea in the most recent years. Improvements in sampling gears combined with more and better use of acoustical and optical technologies offer great promise for improved monitoring and quantification of the roles of euphausiids in the Barents Sea ecosystem.

Description: Balanced fishing proposes a considerable change to current fisheries management to increase overall biomass harvested while reducing the ecosystem impacts of large-scale fisheries. However, to date, the work to a large degree has focused on simplified models, which exclude much of the variability in real ecosystems, as well as basing harvesting rates on a perfect, but unrealistic, knowledge on stock productivity. Furthermore, the published studies have avoided examining the practicalities of implementing balanced fishing in a real world. This has resulted in a gap that remains to be overcome before balanced fishing can be considered a viable management strategy for large marine ecosystems. We discuss variability in recruitment, in biology and life history characteristics, in data quality, and in fishing practice and management, and their implications for implementation of balanced fishing, using examples from the Barents Sea. We try to outline the complexities that need to be investigated as a precursor to moving balanced fishing from an academic exercise to a practical management scheme. Given the difficulties in moving to "full" balanced fishing, we highlight the importance of investigating to what extent benefits can be gained by implementing only the most achievable parts of a balanced fishing regime.

Description: European eel ( Anguilla anguilla ) is considered as critical endangered and even under the best circumstances it may take decades before the stock recovers. Estimation of eel escapement biomass, B escapement , is of critical importance to evaluate management schemes and to predict the recovery potential for the eel stock. Westerberg and Wickström (2015. Stock assessment of eels in the Baltic: reconciling survey estimates to achieve quantitative analysis. ICES Journal of Marine Science, 73: 75–83) attempt to estimate potential B escapement based on the assumptions that all elvers at the entrance of the Baltic also migrate into the Baltic Sea and that natural mortality is low under the whole growth stage (close to 0.02 at the age of 10 years and older). As a consequence, Westerberg and Wickström estimated the present potential B escapement at ~10–20 000 tonnes and fishing mortality close to 0.05–0.10, while it was also suggested that other sources of anthropogenic mortality may reduce the actual escapement to unknown levels. Here we argue that these conclusions are entirely speculative and contradicted by tagging experiment and fishery data, which instead indicate a much higher fishing mortality (mortality induced by legal professional fishery) rates and a considerably smaller eel biomass.

Description: Discard bans have been proposed as part of management policies aimed at balanced harvest (BH). Nationwide discard bans exist in several countries, including Chile, the European Union, Norway, and New Zealand. We analysed experiences from these countries to determine whether or not discard bans are in contradiction with BH, based on six aspects: policy objectives, species/sizes applicability, accompanying technical measures, at-sea monitoring and control, and possible impacts. When discard bans are fully implemented, fishing operations change to more selective fishing, typically targeting bigger individuals of main commercial species. This is consistent with the primary objective of many discard policies, i.e. to reduce unwanted catch. In contrast, proponents of BH argue that broader catch diversity, a product of a widespread harvest strategy, should be sought to avoid major impacts on the ecosystem. Our analysis demonstrates that the scope of discard bans is often limited to main commercial species, although usually they can be extended to include more ecosystem components. Some of the policies examined also prohibit the use of unwanted catches for human consumption, thus limiting their effective use. However, the implementation of discard bans requires high levels of at-sea monitoring and effective control, and/or strong incentives to fish more selectively, neither of which applied in most cases examined. We conclude that if discard bans were set differently, they could contribute to fishery management policies aiming at BH. Their goals should be in line with BH, i.e. to reach a wider global harvest pattern, or at least be established within management regimes that promote high compliance. Finally, the extent to which a discard ban contributes to achieve BH depends also on the relative importance of the ecosystem benthic and megafauna components.

Description: Energy allocation models have proved useful for clarifying the ecological mechanisms which influence growth and reproduction schemes in species with indeterminate growth and for understanding how traits correlate with generate the life history of specific species. In view of the need to understand how exploitation affects species for which few data on key population parameters such as reproductive potential and population growth rate are available, it would be helpful if simple energy allocation schemes parametrized by easily obtainable data could be used to estimate parameters such as reproductive effort and output. Testing the predictions of three such models on fecundity data from a range of species, we show how the simplifications required in a generalized energy allocation scheme are reflected in the deviations between model predictions and empirical data, and discuss the validity of the assumptions underlying these models. We caution against over-reliance on generalized and simplified models to predict reproductive effort.

Description: Since 2007, the biomass of sardine and anchovy in the NW Mediterranean has remained persistently low, whereas the biomass of the commercially low-valued sprat has exploded. Also, simultaneous decreases in condition, size, and/or age of these populations were observed. Altogether, this resulted in a drop in landings of small pelagics. To understand the amplitude of these events and to provide a baseline scenario against which current changes can be compared, we compiled exceptionally long landing series (1865–2013) of sardine, anchovy, and mackerel for different subregions of the southern French coast. We characterized the fluctuations of these landings and compared these with environmental drivers (sea surface temperature, Rhône river discharge, North Atlantic Oscillation, Western Mediterranean Oscillation—WeMO, and Atlantic Multidecadal Oscillation—AMO), using different time-series analyses. We also collated historical data to infer qualitative changes in fishing effort over time. A fishing effort related increase in landings was observed around 1962 for all three species, although current sardine landings have dropped below levels observed before this period. Sardine and anchovy landings were, respectively, positively and negatively related to the AMO index and anchovy landings were also positively related to the WeMO. We finished by discussing the potential role of the environmental variables and fishing on long-term fishery landings trends.

Description: We examine whether the landing rates of Belgian beam trawlers in the Southern Bight of the North Sea were affected through competitive interactions with the Dutch beam trawler fleet and whether the development of a pulse trawler fleet has altered competitive interactions between both fleets. Effects of competition were investigated through a natural experiment based on the different weekly exploitation patterns of both fleets. Logbook data were used to fit a generalized additive mixed model for the daily landing rates of the target species sole ( Solea solea ) and plaice ( Pleuronectes platessa ). Results showed that landing rates of sole by the Belgian beam trawlers (〉221 kW) from 2006 to 2013 were lower during weekdays than during weekends when the Dutch trawler fleet is in harbour, while no such an effect was found for plaice. After the development of a pulse trawler fleet in 2011, the negative weekday effect in the sole landing rates was much more pronounced in 2012 and 2013. This increased loss of efficiency during weekdays, as a result of increased competition with the Dutch trawler fleet, coincided with a reallocation of fishing effort by the Belgian beam trawler fleet.

Description: Fishers' knowledge research (FKR) aims to enhance the use of experiential knowledge of fish harvesters in fisheries research, assessment, and management. Fishery participants are able to provide unique knowledge, and that knowledge forms an important part of "best available information" for fisheries science and management. Fishers' knowledge includes, but is much greater than, basic biological fishery information. It includes ecological, economic, social, and institutional knowledge, as well as experience and critical analysis of experiential knowledge. We suggest that FKR, which may in the past have been defined quite narrowly, be defined more broadly to include both fishery observations and fishers "experiential knowledge" provided across a spectrum of arrangements of fisher participation. FKR is part of the new and different information required in evolving "ecosystem-based" and "integrated" management approaches. FKR is a necessary element in the integration of ecological, economic, social, and institutional considerations of future management. Fishers' knowledge may be added to traditional assessment with appropriate analysis and explicit recognition of the intended use of the information, but fishers' knowledge is best implemented in a participatory process designed to receive and use it. Co-generation of knowledge in appropriately designed processes facilitates development and use of fishers' knowledge and facilitates the participation of fishers in assessment and management, and is suggested as best practice in improved fisheries governance.

Description: The origin and life history of 186 Atlantic salmon caught at sea within Icelandic waters were investigated using microsatellites to assess the origin and scales and otoliths to assess freshwater and sea age. A total of 184 samples were aged using scales or otolithes or both. Most of the samples were from individuals in their first year at sea (72.8%). The freshwater age varied from 1 to 5 years with an average of 2.6 years. The most common freshwater age was 2 years (42%), with a further substantial proportion of 3-year-old fish (28%). Genetic assignment of individual fish to their most likely population of origin was performed using Bayesian genetic individual assignments with a baseline consisting of 284 Eastern Atlantic rivers and 466 sample sites genotyped at the 14 microsatellite. A total of 186 samples of salmon caught at sea were assigned to their origin. Eight samples, from post-smolts and caught close to land, were assigned as having come from Iceland. Of the remaining 178 samples, 121 individuals (68%) were from the Southern Group, i.e. from mainland Europe, the UK, and Ireland, 53 individuals (30%) were from the Northern Group, i.e. Scandinavia and Northern Russia, and 4 individuals were from Iceland (2%). Stock mixture proportions were estimated for four periods using ONCOR and cBAYES. Stock mixture analysis generally supported the individual assignments, but did not suggest a seasonal component to the distribution of salmon stocks. These results indicate that the sea south and east of Iceland are important as feeding areas for migrating Atlantic salmon, particularly for salmon originating in the UK, Ireland, and southern Europe. Furthermore, the lack of adult Icelandic fish so close to Iceland is remarkable and suggests that Atlantic salmon from Icelandic stocks are using different feeding grounds.

Description: Demands for management advice on mixed and multispecies fisheries pose many challenges, further complicated by corresponding requests for advice on the environmental impacts of alternate management options. Here, we develop, and apply to North Sea fisheries, a method for collectively assessing the effects of, and interplay between, technical interactions, multispecies interactions, and the environmental effects of fishing. Ecological interactions involving 21 species are characterized with an ensemble of 188 plausible parameterizations of size-based multispecies models, and four fleets (beam trawl, otter trawl, industrial, and pelagic) characterized with catch composition data. We use the method to evaluate biomass and economic yields, alongside the risk of stock depletion and changes in the value of community indicators, for 10 000 alternate fishing scenarios (combinations of rates of fishing mortality F and fleet configuration) and present the risk vs. reward trade-offs. Technical and multispecies interactions linked to the beam and otter trawl fleets were predicted to have the strongest effects on fisheries yield and value, risk of stock collapse and fish community indicators. Increasing beam trawl effort led to greater increases in beam trawl yield when otter trawl effort was low. If otter trawl effort was high, increases in beam trawl effort led to reduced overall yield. Given the high value of demersal species, permutations of fleet effort leading to high total yield (generated primarily by pelagic species) were not the same as permutations leading to high catch values. A transition from F for 1990 to 2010 to F MSY , but without changes in fleet configuration, reduced risk of stock collapse without affecting long-term weight or value of yield. Our approach directly addresses the need for assessment methods that treat mixed and multispecies issues collectively, address uncertainty, and take account of trade-offs between weight and value of yield, state of stocks and state of the environment.

Description: Underwater video recordings in the mouth of a squid trawl were used to evaluate the effectiveness of a trawl configured with drop-chain groundgear to catch longfin inshore squid ( Doryteuthis pealeii ) and reduce bycatch of finfish in the Nantucket Sound squid fishery off Cape Cod, Massachusetts, USA. Entrance through the trawl mouth or escape underneath the fishing line and between drop chains was quantified for targeted squid, and two major bycatch species, summer flounder ( Paralichthys dentatus ) and skates (family Rajidae). Additionally, contact and impingement between animals and groundgear were also quantified. Fish and squid swimming behaviours, positions, orientations, and time in the trawl mouth were quantified and related to capture or escape at the trawl mouth. Squid entered the trawl singly and in schools, and no squid were observed escaping under the fishing line. Most squid entered the trawl in the upper portion of the trawl mouth; mantle orientated away from the trawl and swimming in the same direction, and were gradually overtaken, not actively attempting to escape. Summer flounder and skates were observed to remain on or near the seabed, orientated, and swimming in the same direction as the approaching trawl. The majority (60.5%) of summer flounder entered the trawl above the fishing line. Summer flounder that changed their orientation and turned 180° were significantly more likely to enter the trawl ( p 〈 0.05). Most skates (89.7%) avoided trawl entrance and escaped under the fishing line. Neither squid nor summer flounder were observed to make contact or become impinged to the groundgear; however, 35.4% of skates had substantial contact with groundgear, with 12.3% becoming impinged. Video analysis results showed that the drop-chain trawl is effective at retaining targeted squid while allowing skates to escape. However, it is ineffective at avoiding the capture of summer flounder.

Description: Species-transformation provisions allow fishers to convert quota of one species to that of another species at prescribed conversion rates. These provisions, along with other catch-quota balancing mechanisms, are meant to aid fishers in matching available quota to actual catch so that incentives to discard are reduced. In this paper, we use a bioeconomic model to examine how species-transformation provisions affect sustainability and profitability of a multispecies fishery. We base parameterization of the model loosely on management of the Icelandic demersal fishery, which currently employs one of the broadest implementations of species transformations. To represent fisher behaviour in each year, effort is allocated among two or three métiers, such that total profit for that year is maximized. Each métier represents a combination of three species’ catchability rates that define which species are targeted by each métier and how independent a species’ catch rate is from that of other species. Assumptions regarding the degree to which fishers can target specific species by shifting effort between métiers, as well as how relative profitability among métiers varies, are paramount to understanding more generally how fishing regulations such as species transformations can be expected to change fishing patterns. This constraint depends not only on how strongly associated species catches are within a métier but also on relative species abundance and what alternate métiers are available.

Description: Based on previous work, dome-shaped fishery selectivity patterns are expected in place of asymptotic patterns when one-way fish movements among areas are considered. It is less clear if this occurs when the "round-trip" seasonal movements are considered. A simulation of a long-distance migrating fish stock (Atlantic menhaden) was used to study the influence of life history and fishery processes on selectivity, under an "areas as fleet" stock assessment context. When age-constant two-way migration was assumed to occur at a low rate, a domed selectivity pattern in the area experiencing the highest fishing mortality was produced, consistent with previous work. However, as the two-way migration rate increased, the domed selectivity pattern diminished and eventually disappeared. When age-varying migration was introduced, with a higher movement probability for older fish, domed selectivity prevailed in the source (i.e. spawning) area. If movement away from the spawning area occurs at younger ages than are selected by the fishing gear, the extent of the dome in this area is reduced. When movement away from the spawning area occurs at ages that are already available to the fishing gear, the dome in the spawning area is exaggerated. The area in which domed selectivity occurred was primarily determined by whether the probability of movement increased or decreased with age. In contrast to previous work that considered one-way or diffusive movement, the temporal or spatial distribution of recruitment and overall fishing mortality did not have a significant influence on selectivity. Building simulations that reflect the life history of the stock can guide assessment efforts by placing priors and constraints on model fits to selectivity patterns and be used to explore trade-offs between model complexity and the ability to produce reasonable management advice. Their development is encouraged as a standard feature in the assessment of migratory fish stocks.

Description: Fish stock assessment models often rely on size- or age-specific observations that are assumed to be statistically independent of each other. In reality, these observations are not raw observations, but rather they are estimates from a catch-standardization model or similar summary statistics based on observations from many fishing hauls and subsamples of the size and age composition of the data. Although aggregation mitigates the strong intra-haul correlation between sizes/ages that is usually found in haul-by-haul data, violations of the independence assumption can have a large impact on the results and specifically on reported confidence bounds. A state-space assessment model that allows for correlations between age groups within years in the observation model for catches and surveys is presented and applied to data on several North Sea fish stocks using various correlation structures. In all cases the independence assumption is rejected. Less fluctuating estimates of the fishing mortality is obtained due to a reduced process error. The improved model does not suffer from correlated residuals unlike the independent model, and the variance of forecasts is decreased.

Description: The northern shrimp ( Pandalus borealis L.) stock in the Skagerrak is shared by Sweden, Norway, and Denmark. Although the fishery is regulated by an annual agreement between the EU and Norway, there are also national regulations as well as differences in fleet composition and shrimp markets. In early 2014, the World Wildlife Fund gave all Skagerrak shrimp a red light in their seafood consumer guide, which led to an extensive debate, especially in Sweden, about the sustainability of this fishery. The aim of this study was to quantify a set of indicators that together give a broad picture of the sustainability of the three fisheries to provide an objective basis for a discussion on needed measures. The different indicators concerned environmental, economic or social aspects of sustainability and were quantified per tonne of shrimp landed by each country in 2012. The Danish fishery was most efficient in terms of environmental and economic indicators, while the Swedish fishery provided most employment per tonne of shrimp landed. Fuel use in all fisheries was high, also when compared with other shrimp fisheries. Interesting patterns emerged, with smaller vessels being more fuel efficient than larger ones in Sweden and Norway, with the opposite trend in Denmark. The study also demonstrated major data gaps and differences between the countries in how data are collected and made available. Various improvement options in the areas data collection and publication, allocation of quotas and enforcement of regulations resulted. Product-oriented studies could be useful to follow-up performance of fisheries over time and to identify how to best utilize the Skagerrak shrimp stock. This could involve evaluating novel solutions in terms of technology and management, based on current and future scenarios aiming to maximize societal benefits generated from this limited resource, at minimized environmental impacts.

Description: The capacity to observe, retrieve, and model the physiographical and hydrographical features of the sea (i.e. seascapes) has surpassed our ability to integrate this information into the assessment and stewardship of marine ecosystems. However, current marine policy that mandates integrated ecosystem assessments demands temporally intensive and spatially extensive predictions of key populations and ecosystem processes and services, particularly those related to habitat use and distribution. In this sense, seascape ecology represents an operational linkage between basic oceanography and applied ecology and management that embraces spatially explicit models of the dynamic distributions of populations, communities and foodwebs through a joint consideration of observational data and ecological processes. For these reasons, the ICES Journal of Marine Science solicited contributions to the article theme set, " Frontiers in seascape ecology ". In this introduction, we present current concepts and developments in seascape ecology, briefly summarize the 10 articles that appear herein, and discuss the most relevant challenges to this nascent discipline. The contributions included in this theme set illustrate the growing relevance of seascape ecology in the multidisciplinary management of marine ecosystems.

Description: A shift towards ecosystem-based management in recent decades has led to new analytical tools such as end-to-end marine ecosystem models. End-to-end models are complex and typically simulate full ecosystems from oceanography to foodwebs and fisheries, operate on a spatial framework, and link to physical oceanographic models. Most end-to-end approaches allow multiple ways to implement human behaviours involving fishery catch, fleet movement, or other impacts such as nutrient loading or climate change effects. Though end-to-end ecosystem models were designed specifically for marine management, their novelty makes them unfamiliar to most decision makers. Before such models can be applied within the context of marine management decisions, additional levels of vetting will be required, and a dialogue with decision makers must be initiated. Here we summarize a review of an Atlantis end-to-end model, which involved a multi-day, expert review panel with local and international experts, convened to challenge models and data used in the management context. We propose nine credibility and quality control standards for end-to-end models intended to inform management, and suggest two best practice guidelines for any end-to-end modelling application. We offer our perspectives (as recent test subjects or "guinea pigs") on how a review could be motivated and structured and on the evaluation criteria that should be used, in the most specific terms possible.

Description: Accounting for connectivity is essential in marine spatial planning and the proper design and management of marine protected areas, given that their effectiveness depends on the patterns of dispersal and colonization between protected and non-protected areas. The genetic structure of populations is commonly used to infer connectivity among distant populations. Here, we explore how population genetic structure is affected by pre- and settlement limitations with a spatially explicit coupled metapopulation-gene flow model that simulates the effect of demographic fluctuations on the allele frequencies of a set of populations. We show that in closed populations, regardless of population growth rate, the maintenance of genetic diversity at saturating initial population density increases with species life expectancy as a result of density-dependent recruitment control. Correlatively, at low initial population density, the time at which a population begins to lose its genetic diversity is driven larval and post-settlement mortality (comprised in the recruitment success parameter)—the larger the recruitment success, the stronger the genetic drift. Different spatial structures of connectivity established for soft bottom benthic invertebrates in the Gulf of Lions (NW Mediterranean, France) lead to very different results in the spatial patterns of genetic structuration of the metapopulation, with high genetic drift in sites where the local retention rate was larger than 2%. The effect of recruitment failure and the loss of key source populations on heterozygosity confirm that transient demographic fluctuations help maintain genetic diversity in a metapopulation. This study highlights the role of intraspecific settlement limitations due to lack of space when the effective number of breeders approaches saturating capacity, causing a strong reduction in effective reproduction. The present model allows to: (i) disentangle the relative contribution of local demography and environmental connectivity in shaping seascape genetics, and (ii) perform in silico evaluations of different scenarios for marine spatial planning.

Description: The potential influence of climate change on the future distribution and abundance of fish (and therefore commercial fisheries and food security) is increasingly recognized in the fishery management community. A changing climate will likely have differing effects on different species; some will flourish, some will flounder. Management targets for fishing mortality and spawning biomass are often calculated by assuming stationary population processes, but under climate change, this assumption may be violated. Non-stationary population processes can introduce bias into estimates of biomass from stock assessments and calculations of target fishing mortalities and biomasses. However, few accepted frameworks exist for incorporating the changing influence of the environment on exploited populations into management strategies. Identifying changes in population processes due to environmental influences is important in order to enable climate-enhanced management strategy evaluations to elucidate the potential benefits and costs of changing management targets. Cost/benefit analyses will also be useful when coincidentally caught species respond differently to environmental change.

Description: For decades, many Australian coastal communities have been changing, in varying degrees, from traditional "fishing towns" to "mining", "tourism", or "retirement" towns. However, environmental changes, such as climate change, have increased the vulnerability of these communities and their capacity to continue to successfully adapt is unknown. A framework for the assessment of socio-ecological vulnerability is used to provide information on the response to change in Geraldton, Western Australia. Geraldton has traditionally been a port and fishing town and has recently become a hub for the expanding mining industry. An innovative historical assessment of adaptive capacity using sustainable livelihoods analysis with indicators of social, economic, human, financial, physical, and natural capital is used to calculate socio-ecological vulnerability over time. The framework integrates adaptive capacity with environmental change, resource dependence, and the socio-economic importance of the fished species during four census years: 1921, 1954, 1981, and 2011. The earlier years are characterized by high adaptive capacity and low socio-ecological vulnerability in keeping with strong economic growth and low unemployment rates following the First and Second World Wars. The years 1981 and 2011 showed markedly higher socio-ecological vulnerability and lower adaptive capacities. This result was due to progressively greater exposure to climate change and the high socio-economic importance of fished species, as well as relatively poor physical, social, and natural capital. With continuing environmental and economic change, the fishing industry and the broader Geraldton population is likely to become increasingly vulnerable. Proactive rather than passive adaptation may speed the recovery and reduce a decline in the fishing industry and local economies. The paper briefly discusses potential adaptation in Geraldton which may be useful as a guideline for other coastal communities.

Description: As a discipline, marine historical ecology (MHE) has contributed significantly to our understanding of the past state of the marine environment when levels of human impact were often very different from those today. What is less widely known is that insights from MHE have made headway into being applied within the context of present-day and long-term management and policy. This study draws attention to the applied value of MHE. We demonstrate that a broad knowledge base exists with potential for management application and advice, including the development of baselines and reference levels. Using a number of case studies from around the world, we showcase the value of historical ecology in understanding change and emphasize how it either has already informed management or has the potential to do so soon. We discuss these case studies in a context of the science–policy interface around six themes that are frequently targeted by current marine and maritime policies: climate change, biodiversity conservation, ecosystem structure, habitat integrity, food security, and human governance. We encourage science–policy bodies to actively engage with contributions from MHE, as well-informed policy decisions need to be framed within the context of historical reference points and past resource or ecosystem changes.

Description: The collapse of the Northwest Atlantic cod ( Gadus morhua ) stocks in the early 1990s led to widespread ecological changes offshore. Changes in coastal fish communities are less known, largely due to the lack of historical records and long-term, standardized research surveys in coastal ecosystems. We aimed to overcome this with a unique dataset known as the Fleming survey. From 1959 to 1964, a systematic beach-seine survey was conducted to examine juvenile cod abundance in 84 bays (42 of which were consistently sampled and therefore analysed) along the east coast of Newfoundland. In addition to cod, all other fish collected in the seines were recorded. These surveys were repeated from 1992 to 1996 after the cod collapse, and document a substantial reduction in a dominant inshore species—juvenile Atlantic cod. We show that total fish abundance declined significantly with the decrease of cod, whereas Shannon diversity and species evenness significantly increased. Species richness increased in some regions but decreased in others. We also found significant changes in the composition of the fish community likely due to a combination of release from predation from fewer large cod feeding in inshore areas as well as a release from competition from fewer juvenile cod occupying the coastal habitat. Region and the presence of vegetated habitats also significantly influenced the fish community. This study shows a strong reorganization of coastal fish communities after a large-scale fisheries collapse with implications for ecosystem-based and cross-ecosystem management.

Description: The southwestern Norwegian Sea is characterized by an inflow of warm and saline Atlantic water from the southwest and cold and less saline East Icelandic Water (EIW), of Arctic origin, from the northwest. These two water masses meet and form the Iceland-Faroe Front (IFF). In this region, the copepod Calanus finmarchicus plays a key role in the pelagic ecosystem. Time-series of C. finmarchicus and Calanus hyperboreus in May and September, extending back to the early 1990s, were studied in relation to phytoplankton bloom dynamics and hydrography. The main reproductive period of C. finmarchicus started consistently earlier south of the IFF, resulting in different life cycles and stage compositions in the two water masses. In 2003, a sudden shift occurred north of the IFF, resulting in a similar phenology pattern to south of the IFF. Before this, only one generation of C. finmarchicus was produced in the Arctic water, but the earlier reproduction enabled the species to produce two generations after 2003. Simultaneously, C. hyperboreus , an expatriate in the EIW, largely disappeared. Food availability is unlikely the reason for the phenological differences observed across the front, as the typical pattern of the phytoplankton spring bloom showed an earlier onset north of the IFF. Temperature and salinity peaked at record high values in 2003 and 2004, and therefore possible links to oceanography are discussed. The dominant role of Calanus spp. and the potential linkages to water mass exchanges may herald strong effects on the ecosystem and pelagic fish in this subpolar Atlantic region under expected climate change.

Description: Marine historical research has made progress in bridging the gap between science and policy, but examples in which it has been effectively applied remain few. In particular, its application to aquaculture remains unexplored. Using actual examples of natural resource management in the state of South Australia, we illustrate how historical data of varying resolution can be incorporated into aquaculture planning. Historical fisheries records were reviewed to identify data on the now extinct native oyster Ostrea angasi fishery throughout the 1800 and early-1900s. Records of catch, number of boats fishing, and catch per unit effort (cpue) were used to test fishing rates and estimate the total quantity of oysters taken from select locations across periods of time. Catch quantities enabled calculation of the minimum number of oysters per hectare for two locations. These data were presented to government scientists, managers, and industry. As a result, interest in growing O. angasi increased and new areas for oyster aquaculture were included in regulatory zoning (spatial planning). Records of introductions of the non-native oyster Saccostrea glomerata , Sydney rock oysters, from 1866 through 1959, were also identified and used to evaluate the biosecurity risk of aquaculture for this species through semi-quantitative risk assessment. Although applications to culture S. glomerata in South Australia had previously been declined, the inclusion of historical data in risk assessment led to the conclusion that applications to culture this species would be accepted. The examples presented here have been effectively incorporated into management processes and represent an important opportunity for the aquaculture industry in South Australia to diversify. This demonstrates that historical data can be used to inform planning and support industry, government, and societies in addressing challenges associated with aquaculture, as well as natural resource management more broadly.

Description: The changing geographical distribution of species, or range shift, is one of the better documented fingerprints of climate change in the marine environment. Range shifts may also lead to dramatic changes in the distribution of economic, social, and cultural opportunities. These challenge marine resource users' capacity to adapt to a changing climate and managers' ability to implement adaptation plans. In particular, a reluctance to attribute marine range shift to climate change can undermine the effectiveness of climate change communications and pose a potential barrier to successful adaptation. Attribution is a known powerful predictor of behavioural intention. Understanding the cognitive processes that underpin the formation of marine resource users' beliefs about the cause of observed marine range shift phenomena is therefore an important topic for research. An examination of the attribution by marine resource users of three types of range shifts experienced in a marine climate change hotspot in southeast Australia to various climate and non-climate drivers indicates the existence of at least three contributing cognitions. These are: (i) engrained mental representations of environmental phenomena, (ii) scientific complexity in the attribution pathway, and (iii) dissonance from the positive or negative nature of the impact. All three play a part in explaining the complex pattern of attribution of marine climate change range shifts, and should be considered when planning for engagement with stakeholders and managers around adaptation to climate change.

Description: Arrowtooth flounder ( Atheresthes stomias ) are an important predator of juvenile walleye pollock ( Gadus chalcogramus ) in the eastern Bering Sea (EBS) shelf and have increased 3-fold in biomass from 1977 to 2014. Arrowtooth flounder avoid the summer "cold pool" (bottom water ≤2°C) and variability in cold pool size and location has affected their spatial overlap with juvenile walleye pollock. Developing a method to account for the relationship between climate change and pollock mortality can highlight ecosystem dynamics and contribute to better assessments for fisheries management. Consequently, spatially resolved predation mortality rates were estimated within an age-structured walleye pollock stock assessment population model (based on spatial information on diet and abundance from trawl surveys), along with the effect of sea surface temperature (SST) on pollock recruitment. Projections of SST and cold pool area to 2050 were obtained (or statistically downscaled) from nine global climate models and used within an age-structure population model to project pollock abundance given estimated relationships between environmental variables and predator and prey spatial distributions, pollock recruitment, and maximum rate of arrowtooth flounder consumption. The climate projections show a wide range of variability but an overall trend of increasing SST and decreasing cold pool area. Projected pollock biomass decreased largely due to the negative effect of increased SST on pollock recruitment. A sensitivity analysis indicated that the decline in projected pollock biomass would be exacerbated if arrowtooth flounder increased their relative distribution in the EBS northwest middle shelf (an area of relatively high density of juvenile pollock) in warm years.

Description: Climate-driven changes in the marine ecosystem largely influence the distribution, abundance, and the consequent availability of marine resources to the fishery. In this study, we examined the potential habitat distributions of the neon flying squid ( Ommastrephes bartramii ) under the projected impacts of ocean warming. We used the sea surface temperature (SST) from the three CMIP5 climate scenarios (RCP4.5, RCP6.0, and RCP8.5) with the low to high future emissions. Based on the squid habitat models, SST showed the highest effect on the present potential squid habitat distribution that accounted for at least 60% of the predicted spatial patterns from May to July 2000–2010. This result underpinned the species' high sensitivity to the temperature changes in its feeding environments. Moreover, the projected future potential squid habitats revealed pronounced differences in the spatial and temporal patterns relative to the present habitat distributions across the different regions of the western and central North Pacific. The future squid habitat predictions revealed a net reduction in the suitable squid habitat coupled with the corresponding northward habitat retreat. Moreover, the magnitude of the predicted habitat changes was proportional to the levels of warming for the representative periods from May to July 2025, 2050, and 2100. The highest decrease in the spatial extent and poleward retreat of the potential squid habitat were observed from May to July 2100 under the RCP 8.5 scenario. These trends could translate to shorter squid fishing periods and offshore shifts of the squid fishing grounds. Thus, insights into the future spatio-temporal patterns and trajectories of the potential squid habitats could lend important implications on the availability of squid resources to the fishery and subsequent evaluation of squid fishery management options under climate change.

Description: The fisheries sector is crucial to the Bangladeshi economy and wellbeing, accounting for 4.4% of national gross domestic product and 22.8% of agriculture sector production, and supplying ca. 60% of the national animal protein intake. Fish is vital to the 16 million Bangladeshis living near the coast, a number that has doubled since the 1980s. Here, we develop and apply tools to project the long-term productive capacity of Bangladesh marine fisheries under climate and fisheries management scenarios, based on downscaling a global climate model, using associated river flow and nutrient loading estimates, projecting high-resolution changes in physical and biochemical ocean properties, and eventually projecting fish production and catch potential under different fishing mortality targets. We place particular interest on Hilsa shad ( Tenualosa ilisha ), which accounts for ca. 11% of total catches, and Bombay duck ( Harpadon nehereus ), a low price fish that is the second highest catch in Bangladesh and is highly consumed by low-income communities. It is concluded that the impacts of climate change, under greenhouse emissions scenario A1B, are likely to reduce the potential fish production in the Bangladesh exclusive economic zone by 〈10%. However, these impacts are larger for the two target species. Under sustainable management practices, we expect Hilsa shad catches to show a minor decline in potential catch by 2030 but a significant (25%) decline by 2060. However, if overexploitation is allowed, catches are projected to fall much further, by almost 95% by 2060, compared with the Business as Usual scenario for the start of the 21st century. For Bombay duck, potential catches by 2060 under sustainable scenarios will produce a decline of 〈20% compared with current catches. The results demonstrate that management can mitigate or exacerbate the effects of climate change on ecosystem productivity.

Description: During the last 15 years, northern European hake ( Merluccius merluccius ) has increased in abundance, and its spatial distribution has expanded in the North Sea region in correlation with temperature. In a context of global warming, this spatial shift could impact local trophic interactions: direct impacts may affect forage fish through modified predator–prey interactions, and indirect impacts may materialize through competition with other resident predators. For instance, North Sea saithe ( Pollachius virens ) spatial overlap with hake has increased while saithe spawning-stock biomass has decreased recently notwithstanding a sustainable exploitation. In this context, we investigated the range of potential impacts resulting from most recent hake emergence in the North Sea, with a particular focus on saithe. We carried out a multispecies assessment of North Sea saithe, using the Stochastic MultiSpecies (SMS) model. In addition to top-down processes already implemented in SMS, we built in the model bottom-up processes, relating Norway pout ( Trisopterus esmarkii ) abundance and saithe weight-at-age. We simulated the effects, on all North Sea species being considered but focusing on Norway pout and saithe, of combining different hake abundance trends scenarios with the inclusion of bottom-up processes in SMS. North Sea saithe F MSY was then evaluated in a multispecies context and contrasted with single-species value. The different scenarios tested revealed a negative impact of hake emergence on saithe biomass, resulting from an increase of predation pressure on Norway pout. These results confirm the competition assumption between saithe and hake in the North Sea and might partially explain the most recent decrease of saithe biomass. This study also highlighted that taking into account bottom-up processes in the stock assessment had a limited effect on the estimation of saithe F MSY which was consistent with single-species value.

Description: There is an essentially circular interaction between the human social system and the marine ecosystem. The Oceans Past V Conference "Multidisciplinary perspectives on the history of human interactions with life in the ocean" held in Tallinn, Estonia, in May 2015 was an opportunity for the presentation and discussion of papers on a diverse array of topics that examined this socio-ecological system from a historical perspective. Here we provide background to the disciplines participating in the conference and to the conference itself. We summarize the conference papers that appear in this special volume of the ICES JMS and highlight issues which arose during general discussion. We make two conclusions. First, to have greater impact and ensure more efficient use of knowledge gained from marine historical ecology (MHE) and marine environmental history (MEH) in ecosystem-based management and related policy development, practitioners need to work more routinely with population and ecological modellers and statisticians. This will allow greater processing of the available historical data to derive ecologically meaningful properties that can then be used to assess the ecological impact of long-term changes of affected species and define appropriate and realistic management targets. Second, increased multi- and trans-disciplinary effort is required to better understand the relative importance of different human demographic, technological, economic, and cultural drivers on the patterns, intensities and trajectories of human activities affecting marine ecosystems.

Description: The 3rd International Symposium on the Effects of Climate Change on the World's Oceans was held in Santos, Brazil, in March 2015, convened by the International Council for the Exploration of the Sea (ICES), the North Pacific Marine Science Organization (PICES), and the Intergovernmental Oceanographic Commission of UNESCO (IOC), and organized locally by the Oceanographic Institute, University of Sao Paulo (IO-USP). The symposium was designed to do two things. First, to get updates on new scientific developments that would address recognized uncertainties that remained from Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report and to contribute to building bridges between research in the natural and social sciences in respect to the human dimensions of climate change, with a focus on coastal communities, management objectives, governance and adaptation measures. The choice of the venue in Santos, Brazil, was aimed to stimulate and widen this thematic discussion in Latin America and southern Atlantic regions, where there still are important knowledge gaps and scientific, politic and societal challenges to be overcome. The meeting was attended by 280 participants from 38 countries, contributing 336 oral and poster presentations. This paper summarizes the main outcomes of the symposium and introduces a number of papers submitted to this special issue.

Description: In recent years, historical ecologists have turned their attention to the long-term impact of fishing on coastal marine ecosystems in the North Atlantic. Through the examination of non-traditional sources, scientists and scholars are beginning to piece together a clearer picture of ecosystem change over centuries of anthropogenic influence. One aspect of this long-term approach is that data are being recovered from some surprising sources, and, when placed alongside other evidence, are being used to create models of change through time where previously none would have been thought possible. Taking its lead from this work, our research takes a mixed approach to the history of Scotland's regional fisheries in the 19th century, combining the anecdotal evidence of fishers to parliamentary commissions of enquiry with data relating to landings and fishing effort which were gathered by the United Kingdom Fishery Board from 1809 onwards. As a result, it has been possible to calculate catch per unit effort (cpue) for the period between 1845 and the mid-1880s which, when placed alongside the direct evidence of fishers, lead to some unexpected conclusions. In particular, we demonstrate that inshore stocks of commercial whitefish appear to have been in decline by the mid-1850s in some areas, many years before the widespread adoption of beam trawling in Scotland; and we conclude that the most likely reason for this decline is the rapid intensification of fishing from open boats using the traditional techniques of handlines and longlines.

Description: The Fifth Assessment Report of the Intergovernmental Panel on Climate Change highlights that climate change and ocean acidification are challenging the sustainable management of living marine resources (LMRs). Formal and systematic treatment of uncertainty in existing LMR projections, however, is lacking. We synthesize knowledge of how to address different sources of uncertainty by drawing from climate model intercomparison efforts. We suggest an ensemble of available models and projections, informed by observations, as a starting point to quantify uncertainties. Such an ensemble must be paired with analysis of the dominant uncertainties over different spatial scales, time horizons, and metrics. We use two examples: (i) global and regional projections of Sea Surface Temperature and (ii) projection of changes in potential catch of sablefish ( Anoplopoma fimbria ) in the 21st century, to illustrate this ensemble model approach to explore different types of uncertainties. Further effort should prioritize understanding dominant, undersampled dimensions of uncertainty, as well as the strategic collection of observations to quantify, and ultimately reduce, uncertainties. Our proposed framework will improve our understanding of future changes in LMR and the resulting risk of impacts to ecosystems and the societies under changing ocean conditions.

Description: Marine zoological stations played an important role in the history of biology and the study of marine life. From the 1870s onward, a large number of biological stations were founded across Europe from Naples to Bergen. In the light of the new theory of evolution and the emerging discipline of ecology, it becomes increasingly necessary for biologists to study nature in the field. Beginning in the second half of the 19th century, much of the research on aquatic organisms was conducted at such stations. The aquatic environment appeared to be particularly suitable for research on the theory of evolution, on embryology, physiology, anatomy, and organism–environment interactions. Marine stations also served as sites for the study of fishery management and fish farming and aquaculture. The hydrobiological station located in the town of Chioggia on the Venetian Lagoon represents one of the less well-known examples of such research centres. It was set up in 1940 by the Italian zoologist Umberto D'Ancona of the University of Padua (1896–1964), who modelled it on already existing zoology, hydrobiology, and fish farming stations in Italy and abroad. Their research was conducted on the ecosystems of the Venetian Lagoon and the northern part of the Adriatic Sea, the natural stocks of valuable commercial fish species, and the reproductive biology of various teleosts. This essay will review the history of the Hydrobiological Station in Chioggia during the period 1940–1964 when it was directed by D'Ancona, its work in the fields of marine biology and fishery, and its ties with other marine stations in Italy and abroad.

Description: Projections of the impacts of climate change on marine ecosystems are a key prerequisite for the planning of adaptation strategies, yet they are inevitably associated with uncertainty. Identifying, quantifying, and communicating this uncertainty is key to both evaluating the risk associated with a projection and building confidence in its robustness. We review how uncertainties in such projections are handled in marine science. We employ an approach developed in climate modelling by breaking uncertainty down into (i) structural (model) uncertainty, (ii) initialization and internal variability uncertainty, (iii) parametric uncertainty, and (iv) scenario uncertainty. For each uncertainty type, we then examine the current state-of-the-art in assessing and quantifying its relative importance. We consider whether the marine scientific community has addressed these types of uncertainty sufficiently and highlight the opportunities and challenges associated with doing a better job. We find that even within a relatively small field such as marine science, there are substantial differences between subdisciplines in the degree of attention given to each type of uncertainty. We find that initialization uncertainty is rarely treated explicitly and reducing this type of uncertainty may deliver gains on the seasonal-to-decadal time-scale. We conclude that all parts of marine science could benefit from a greater exchange of ideas, particularly concerning such a universal problem such as the treatment of uncertainty. Finally, marine science should strive to reach the point where scenario uncertainty is the dominant uncertainty in our projections.

Description: Balanced harvesting has been proposed as a way for fisheries management to achieve the requirements of both the Law of the Sea Convention (LOSC)—to maintain stocks at the level at which they could produce MSY—and the Convention on Biological Diversity (CBD)—to maintain ecosystem structure and functioning. This paper examines these requirements and briefly presents four system-level relationships (spectra), representing ecosystem structures that might guide management decision-making aiming to meet both requirements. These spectra would fit in the widely accepted frameworks of the Ecosystem Approach enshrined in the CBD and adopted by FAO for Fisheries. A size spectrum, relating biomass to body length, is used as an example to illustrate its potential to support management decision-making—much like present stock-based harvest control rules—in more ecosystem-compliant fishing strategies at a sector or ecosystem level, as a complement to those currently used at a stock/population level.

Description: This paper explores economic aspects of a recent proposal to shift fisheries to a "Balanced Harvesting" (BH) strategy, as a means to achieve the goal, set by the Convention on Biological Diversity and related to the Ecosystem Approach to Fisheries, of "conservation of ecosystem structure and functioning" within fishery ecosystems. Studies indicate that a BH strategy—broadening the range of species and sizes caught in the aquatic ecosystem, and lowering exploitation rates for some conventionally targeted species—may provide improved ecological performance relative to conventional harvesting strategies. However, the potential economic implications have received little attention to date. This paper provides a preliminary economic assessment of BH, focusing on six main themes: (i) assessing benefits and costs, (ii) factors affecting the economics of BH, (iii) economic issues in implementing the ingredients of BH, (iv) effects of incremental and/or partial implementation of BH, (v) transition options within the harvesting sector of the fishery, and (vi) distributional impacts arising across fisheries, fleet sectors, and fishing gears, and between the present and the future.

Description: A global assessment of fishing patterns and fishing pressure from 110 different Ecopath models, representing marine ecosystems throughout the world and covering the period 1970–2007, show that human exploitation across trophic levels ( TLs ) is highly unbalanced and skewed towards low productive species at high TLs , which are around two TLs higher than the animal protein we get from terrestrial farming. Overall, exploitation levels from low trophic species were 〈15% of production, and only 18% of the total number of exploited groups and species were harvested 〉40% of their production. Generally, well-managed fisheries from temperate ecosystems were more selectively harvested at higher exploitation rates than tropical and upwelling (tropical and temperate) fisheries, resulting in potentially larger long-term changes to the ecosystem structure and functioning. The results indicate a very inefficient utilization of the food energy value of marine production. Rebuilding overfished components of the ecosystem and changing focus to balancing exploitation across a wider range of TLs , i.e. balanced harvesting, has the potential to significantly increase overall catches from global marine fisheries.

Description: Balanced harvesting (BH) has been proposed as an alternative to the paradigm of more selective fishing as practiced in most European and North American fisheries management. We examine options for the implementation of BH and evaluate the issues raised in such an implementation. Implementation is considered at the whole ecosystem level, in terms of the patterns of removal for all species, both commercial and bycatch. We suggest that a "laissez-faire" approach analogous to the African lakes where BH was first observed is inappropriate in managed developed world fisheries. We consider two further approaches: focusing on either the species caught or on the sizes of animal alone. We find that aiming to harvest all species with an exploitation rate appropriate to their productivity would require a degree of micro-management that is probably unachievable, with all captured species "choking" the fishery in sequence. The size-based approach works with an exploitation rate appropriate to the productivity at size, with no consideration of the species involved. This might superficially be easier to implement, as management would involve a limited number of size classes only. However, problems may arise due to the likely faster capture of the more easily catchable fish, and also likely targeting of the more valuable species within a size class. We identify a possible third option of "broad brush" métier-based management that may resolve some of these problems. Other issues include the management of protected, endangered, and threatened species (including mammals, reptiles, and birds), the management of already severely depleted stocks, and the capture of benthic invertebrates.

Description: Balanced harvest (BH) proposes to distribute a moderate mortality from fishing across the widest possible range of species, stocks, and sizes in an ecosystem, in proportion to their natural productivity so that the relative size and species composition are maintained, in line with the CBD requirement for sustainable use. This proposal has many and not always intuitive implications for fisheries management, e.g. in relation to selectivity, protection of juveniles and spawning sites, models of harvesting strategies, a focus on size and species, the impacts of discarding, aspects of emblematic species and ecosystem services, operational complexity, partial implementation, ecosystem rebuilding, and relations with broader management frameworks. The paper closes with a discussion of BH implementation, concluding that a logical step would be to integrate several separate initiatives to move fisheries into a more ecosystem-conscious context. Implementation challenges will be encountered, but there are lessons to be drawn from fishery ecosystems already close to BH, as in some tropical multispecies fisheries, and further, the implementation challenges are already being taken on in many well-managed fisheries and areas as management begins to address the realities of what ecosystem-based fishery management actually entails.

Description: Several factors influence catches and the sustainability of fisheries, and such factors might be different depending on the scale on which fisheries work. We investigated the existence of possible subdivisions within small-scale fisheries (SSF) themselves, regarding their economic performance and relative social and environmental impacts to understand which categories of these two types of fleets are best positioned to support sustainability. By doing so, we investigated if it is a good strategy for SSF to aim to grow towards larger scales. We obtained economic and ecological data from landing samplings and information on technological efficiency of this fleet, using a northeastern Brazilian state as a case study. We defined a cut-off point to separate the SSF into two categories of boats, according to their size and gear. We compared their cpue and the factors affecting it within each category; we also compared economic (number of boats, number of landings, jobs, gears, catch, travel time and total time of the fishery, revenues, costs, profits, revenue per unit of effort, and profit per unit of effort) and ecological factors (vulnerability of species caught) between the two categories. We found that small boats spent less time fishing and employed comparatively more people per landed value and catch. The cpue and profits of small boats were also higher. Both large and small boats exploit species with the same overall vulnerability. Therefore, being smaller, even within the SSF category, seems to be a more advantageous social and economic strategy for guaranteeing higher catches and more employment opportunities per catch. These findings need to be taken into account when defining new policies, such as the distribution of subsidies that support or not the sustainable use of fishery resources.

Description: Following advice from the International Council for the Exploration of the Seas and North Atlantic Salmon Conservation Organization, Irish salmon stocks have been managed on a river-by-river basis since 2007 with biological reference points (BRPs) based on maximum sustainable yield (MSY). A method for estimating BRPs at the river scale and the associated variability arising from observed variability in population structures and fecundities is presented here. Calculations of BRPs (referred to as conservation limits, CLs) were updated and their natural variability was included. Angling logbooks provided new river-specific weight data to give sea age and fecundity ranges, and improved estimates of river-wetted areas, to account for available nursery habitat for juveniles and river-specific carrying capacities, were introduced. To transport BRPs, Bayesian stock–recruitment analysis was re-run with an updated list of monitored rivers and smolt ages. Results were converted to salmon numbers per river in Monte Carlo simulations incorporating the variability in sea ages and fecundities. Minimum sample size rules were implemented to reduce sampling error effects. Results showed that average total CL increased by 7%, average one sea-winter (1SW) CL decreased by 5% and average multi-sea-winter (MSW) CL increased by 157%. Differences were attributed to increases in wetted areas, MSW proportions, and changes in both 1SW and MSW fecundities. While some changes were large, we believe that these updated CLs provide more accurate estimates and with associated confidence limits they are more robust, river-specific, and readily incorporated into stock assessments. As a significant improvement on their predecessors, they represent a major development for the conservation and management of salmon stocks. Additionally, the approach described is portable across stocks and has the potential to be implemented in other jurisdictions to improve the management of Atlantic salmon. Finally, this method of incorporating variation has application for the development of BRPs and management of other species.

Description: The approach to fisheries termed "balanced harvesting" (BH) calls for fishing across the widest possible range of species, stocks, and sizes in an ecosystem, in proportion to their natural productivity, so that the relative size and species composition is maintained. Such fishing is proposed to result in higher catches with less negative impact on exploited populations and ecosystems. This study examines the models and the empirical evidence put forward in support of BH. It finds that the models used unrealistic settings with regard to life history (peak of cohort biomass at small sizes), response to fishing (strong compensation of fishing mortality by reduced natural mortality), and economics (uniform high cost of fishing and same ex-vessel price for all species and sizes), and that empirical evidence of BH is scarce and questionable. It concludes that evolutionary theory, population dynamics theory, ecosystem models with realistic assumptions and settings, and widespread empirical evidence do not support the BH proposal. Rather, this body of evidence suggests that BH will not help but will hinder the policy changes needed for the rebuilding of ecosystems, healthy fish populations, and sustainable fisheries.

Description: Landscape components can affect all the important biological processes of invertebrate populations, including their harvest quality, yet they are rarely considered in fisheries management frameworks. Here, we explore landscape, economic and ecologic variables to demonstrate that landscape metrics can be a valuable component in the management of sessile invertebrate fisheries. We developed a map-derived model that links landscape variables with the quality of a fishing resource, using five topographical variables—coastal convexity, orientation, complexity, exposure, and distance from the coast—all but the latter were tested at 23 different spatial scales. The model was ground-truthed using the case study of the gooseneck barnacle fishery in Asturias (N. Spain). Distance from the coast, coastal convexity on a scale of 25 km and exposure on a scale of 1 km appear to be driving the quality of the resource. Our model can predict high-quality gooseneck barnacle fishing zones with 72% accuracy. Moreover, we used a 10-year time-series of gooseneck barnacle landings and sales to analyse the impact of quality on the fishery. Fishers have a bias towards harvesting high-quality gooseneck barnacles, which are sold at higher market values. Thus, quality directly affects landings and sales. Our results highlight the interest of incorporating landscape metrics in fisheries management to generate and support spatially explicit conservation and exploitation policies.

Description: In a recent publication (Froese et al. , ICES Journal of Marine Science ; 73: 1640–1650), we presented a critique of the balanced harvesting (BH) approach to fishing. A short section dealt with the size-spectrum models used to justify BH, wherein we pointed out the lack of realism of these models, which mostly represented ecosystems as consisting of a single cannibalistic species. Andersen et al. ( ICES Journal of Marine Science ; 73: 1651–1655) commented on our paper and suggested that we criticized size-spectrum models in general and that we supposedly made several erroneous statements. We stress that we only referred to the size-spectrum models that we cited, and we respond to each supposedly erroneous statement. We still believe that the size-spectrum models used to justify BH were highly unrealistic and not suitable for evaluating real-world fishing strategies. We agree with Andersen et al. that BH is unlikely to be a useful guiding principle for ecosystem-based fisheries management, for many reasons. The use of unrealistic models is one of them.

Description: A recent publication about balanced harvesting (Froese et al ., ICES Journal of Marine Science ; 73: 1640–1650) contains several erroneous statements about size-spectrum models. We refute the statements by showing that the assumptions pertaining to size-spectrum models discussed by Froese et al. are realistic and consistent. We further show that the assumption about density-dependence being described by a stock recruitment relationship is responsible for determining whether a peak in the cohort biomass of a population occurs late or early in life. Finally, we argue that there is indeed a constructive role for a wide suite of ecosystem models to evaluate fishing strategies in an ecosystem context.

Description: In this study, we modelled fishery observer data to compare methods of identifying community structure using cluster analyses to determine stratifications and probabilistic models for examining species co-occurrence in the Gulf of Mexico deepwater reef fish fishery. Comparing cluster analysis methods, the correlation measure of dissimilarity in combination with average agglomerative linkage was the most efficient method for determining species relationships using simulated random species as a comparison tool. Cluster analysis revealed distinct species stratifications and in combination with multiscale bootstrapping generated probabilities indicating the strength of stratifications in the fishery. A more parsimonious approach with probabilistic models was also developed to quantify pairwise species co-occurrence as random, positive, or negative based on the observed vs. expected fishing sets with co-occurrence. For the most common species captured, the probabilistic models predicted positive or negative co-occurrence between 84.2% of the pairwise combinations examined. These methods provide fishery managers tools for determining multispecies quota allocations and offer insights into other bycatch species of interest.

Description: Climate change, eutrophication, and fishing are main pressures associated with changes in the abiotic and biotic environment in several sub-basins of the Baltic Sea. Identifying the nature of such changes is of relative importance for fisheries and environmental management. The Bothnian Bay is the northernmost sub-basin in the Baltic Sea and the responses of the foodweb to long-term changes in combined pressures have not been investigated. In this study, we explore long-term changes in the Bothnian Bay foodweb, represented by key species across all trophic levels over the past 34 years, and identify potential environmental and anthropogenic drivers. The results indicate that salinity is the most important driver to explain changes in the composition of the offshore biota in the Bothnian Bay. These changes are probably driven by indirect effects of salinity rather than bottom-up effects. A decline in the herring spawning-stock biomass was most plausibly attributed to an increased competition for food due to a parallel increase in vendace, which uses the same food resources (zooplankton and zoobenthos) and may benefit from declining salinity due to its limnic origin. A strong increase in the abundance of grey seal and ringed seal populations was seen in the late 2000s but was not related to any of the pressure variables analysed. Temperature and nutrients were not identified as important drivers of changes in the overall biota. Our study explores correlative relationships between variables and identifies potential interactions in the foodweb to generate hypotheses for further studies.

Description: Applied seascape ecology rests on paradigms of terrestrial landscape ecology. Patches defined by persistent seabed features are the basic units of analysis. Persistent oceanographic features provide context while dynamic features are usually ignored. Should seascape ecology rest on terrestrial paradigms? I use Reimann’s rules of analysis to identify differences between seascapes and landscapes. Reimann’s method uses hypotheses about system function to guide the development of models of system components based upon fundamental "laws". The method forced me to avoid using terrestrial analogies in understanding of organism-habitat relationships. The fundamental laws applying to all organisms were the conservative metabolic requirements underlying individual performance and population growth. Physical properties of the environment; specifically those dictating strategies available to organisms meeting metabolic requirements, were the "laws" applying to the external environment. Organisms living in the ocean’s liquid meet most metabolic requirements using strong habitat selection for properties of the liquid that are controlled by "fast", often episodic, atmospheric and tidal forces. Seascapes are therefor primarily driven by dynamic hydrography including mixing processes. In contrast, most terrestrial organisms are decoupled by gravity and physiological regulation from an atmospheric fluid that is metabolically more challenging. They show strong habitat selection for many essential metabolic materials concentrated on the land surface where slower biogeochemical processes including soil development drive ecological dynamics. Living in a liquid is different from living in a gas and resource use management in the oceans needs to be tuned to seascapes dynamics that is driven primarily by hydrodynamics and secondarily by seabed processes. Advances in ocean observing and data assimilative circulation models now permit the rapid development of applied seascape ecology. This development is essential now that changes in global climate are being rapidly translated into changes in the dynamics of the ocean hydrosphere that structures and controls ecological dynamics within seascapes.