SEAwise report on the bycatch mortality risk of potentially endangered and threatened species of fish, seabirds, reptiles and mammals

The SEAwise project works to deliver a fully operational tool that will allow fishers, managers, and policy makers to easily apply Ecosystem Based Fisheries Management (EBFM) in their fisheries and bycatch of protected, endangered and threatened (PET) species is a major concern in EBFM implementation. This SEAwise report evaluates the effects of fishing on bycatch of PET species by applying a hierarchical framework that moves from qualitative to quantitative methodologies depending on species vulnerability to bycatch and data availability. By these means, this work identifies current areas of highest bycatch risk across the case studies and assesses the sustainability of bycatch levels on PET populations.The first step of this report consisted of the application of the semi-quantitative Productivity-Susceptibility Analysis (PSA) to a wide range of sensitive species across European waters, including cetaceans, bony and cartilaginous fishes and a single seabird species. PSA measures the risk of a species to over-exploitation by a fishery based on two properties; productivity, defined by the life history characteristics determining the intrinsic rate of population increase, and susceptibility, based on the interactions between population and fishing dynamics. This analysis scores species’ productivity and susceptibility attributes from 1 (low risk) to 3 (high risk) for each fishery or gear of interest, allowing a rapid screening of the species most likely affected by bycatch.Cetaceans were assessed in the Bay of Biscay and Irish waters, and in both cases, gillnets were identified as the gears with the highest bycatch risk, especially for common dolphin (Delphinus delphis) and harbour porpoise (Phocoena phocoena). Cartilaginous fishes were assessed in the Mediterranean Sea, including pelagic species such as the blue shark (Prionace glauca) and demersal species such as the longnose spurgod (Squalus blainville), the bull ray (Aetomylaeus bovinus) and the common smooth-hound (Mustelus mustelus). The blue shark, which is Critically Endangered in the Mediterranean, showed a high risk of being bycaught by pelagic longline, while demersal species were all highly threatened by bottom trawlers. A combination of elasmobranchs and teleost fishes was assessed along the North Sea, Bay of Biscay, and Celtic Seas, including common skate complex (Dipturus spp.), blonde ray (Raja brachyura), spurdog (Squalus acanthias), tope (Galeorhinus galeus), spotted ray (Raja montagui), undulate ray (Raja undulata), starry ray (Amblyraja radiata), John dory (Zeus faber), Atlantic wolffish (Anarhichas lupus) and Atlantic halibut (Hippoglossus hippoglossus). Highest bycatch risk was found for the common skate complex, spurdog and tope, showing highest bycatch risk for both beam- and otter trawls, as well as gillnets. The only seabird species analysed was the critically endangered Balearic shearwater (Puffinus mauretanicus), which showed a high risk to longlines in the Bay of Biscay.Where quantitative data were available for populations size and bycatch in e.g, ICES reports, the impact of fisheries bycatch was estimated quantitively by estimating reference points and by comparing them to total bycatch mortalities. This quantitative assessment was completed for two cetaceans and two elasmobranch species that were also included in the previous step. Bycatch impact for the common dolphin in the Northeast Atlantic and for harbour porpoise in Irish waters was found to be unsustainable, as current bycatch mortalities are above the “allowable” capture limits in both cases. For spurdog and undulate ray in the Northeast Atlantic and English Channel, respectively, the fishing pressure on the stock was sustainable, as it is below the harvest rate of Maximum Sustainable Yield (MSY). Reference points for seabirds were also estimated, but no comparison with bycatch mortality could be done due to lack of data. Additionally, quantitative assessments were produced for grey seal in the North Sea and loggerhead turtle in the Mediterranean (despite not being included in the previous step), where current bycatch rates were evaluated to be sustainable.Specific analyses were conducted for the Baltic Sea harbour porpoise with previously unused bycatch data from gillnets. Bycatch was modelled to estimate total bycatch mortality, addressing several objectives at once. On one hand, estimated total bycatch was compared with reference points, which showed that the current bycatch level was unsustainable for the population. Secondly, estimated total bycatch was compared with the results provided by previous simpler extrapolations, demonstrating that the later should not be applied when the fishery is heterogeneous due to the potential to provide biased estimates.Overall, the qualitative approaches are commonly used as a tool to identify species that are minimally affected, so the more intensive analysed are limited to high-risk species. Here, most species analysed showed-medium-high risk and therefore, all of them should have been analysed in further steps. However, many of those species lack the necessary information to conduct a quantitative assessment, and as result, the impact of bycatch at population level could only be evaluated, as seen above, for a few of them. This highlights the need for more exhaustive data collection and further research that could answer to the requirements of the EBFM.More information about the SEAwise project can be found at https://seawiseproject.org/</p

Haplotype parsimony networks of <i>Raja miraletus</i>, <i>Raja asterias</i>, <i>Raja polystigma</i>, <i>Raja radula</i> and <i>Torpedo marmorata</i> reconstructed using ELASMOMED COI barcode sequences.

<p>Each circle represents one haplotype and its size is proportional to frequency. Colours indicate the origin of samples according to FAO fishing divisions. Mutations and positions characterizing each haplotype, as well as the size (bp), and the number of the sequences included in each species network, are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170244#pone.0170244.s004" target="_blank">S4 Table</a>.</p

Cases of specimens’ misidentification by FAO fishing division.

<p>The number of misidentified individuals over the total number of barcoded individuals is given in parenthesis.</p

Mean and maximum intraspecific distances and Nearest-Neighbour distance (p-distance values) of the 41 chondrichthyan species barcoded for the ELASMOMED library.

<p>The <i>Dasyatis pastinaca</i> cluster is not separated.</p

Neighbour-Joining tree based on genetic p-distances of COI barcode sequences of 17 shark species.

<p>Numbers near nodes indicate bootstrap values (>50%). The distance scale bar is given. Each species' sample size and geographic origin are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170244#pone.0170244.s002" target="_blank">S2 Table</a>.</p

Neighbour-Joining tree based on genetic p-distances of COI barcode sequences of 23 skate species.

<p>Numbers near nodes indicate bootstrap values (>50%). The distance scale bar is given. Each species' sample size and geographic origin are detailed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170244#pone.0170244.s002" target="_blank">S2 Table</a>.</p

Species with discordant BINs found by the ‘BIN Discordance Report’ sequence analysis tool on BOLD.

<p>Taxonomic ranks of conflict are reported including species of the same genus up to taxa belonging to different orders. The column BIN Taxon Variation shows the number of records for each taxon in parenthesis.</p

SEAwise Report on the key species and habitats impacted by fishing

The implementation of ecosystem-based fisheries management requires knowledge on the ecological impact of fishing activities on species and their habitats – those both targeted and not targeted by fisheries. To identify which ecological impacts are key and what is known about them, SEAwise consulted stakeholders through European Advisory Councils and conducted a systematic review of the scientific literature to map the available knowledge and evidence. Specific reference was given to the bycatch of Protected, Endangered and Threatened (PET) species, benthic habitats, food webs and biodiversity, and impact from fisheries-related litter and ghost nets.  At the stakeholder consultations, sharks and/or elasmobranchs, turtles, species interactions, and seals or marine mammals were identified as top ranked in at least three out of the five regions. Other terms identified by at least two Case Study regions were: seabirds, sensitive species, benthic habitats, litter, PET species, invasive species and species interactions.  Relevant data were extracted from 549 retained papers. The majority of studies were conducted in the Mediterranean Sea, whereas only few papers reported on fishing impacts in the Baltic Sea (see figure below). Bony fish (teleosts) and benthos were the most studied ecosystem components in all Case Study regions, whereas marine mammals and cartilaginous fish were often studied in relation to bycatch of PET species.  Out of the 549 papers, most of them were related to fishing impacts on food webs and biodiversity and benthic habitats, followed by bycatch of PET species and other fishing impact studies (not related to any task). Fewest studies were related to the impact of fisheries-related litter and ghost nets. Demersal trawls were by far the most studied gear in studies on commercial fishing impacts. For recreational fisheries, hooks and lines, in particular angling, was the most studied fishing activity.  Among the items identified by the stakeholders, marine mammals, seabirds and reptiles were all covered in at least 25 papers each, indicating that there is a considerable body of knowledge even though not all areas may have information for all species. Litter was the key item that was least frequently reported on in the literature, especially outside the Mediterranean, where scientific papers were rare. As a consequence, areas outside the Mediterranean may lack information for further analysis unless a dedicated effort is made in SEAwise to remedy this. The regional differences in topics identified by stakeholder scoping did not reflect the regional amount of papers available.  This report describes results of the SEAwise project. More information about the project can be found at https://seawiseproject.org/</p

SEAwise Report on improved predictive models of growth, production and stock quality.

The SEAwise project works to deliver a fully operational tool that will allow fishers, managers, and policy makers to easily apply Ecosystem Based Fisheries Management (EBFM) in their fisheries and understanding how ecological drivers impact stock productivity through growth, condition and maturity is essential to this proces. In this SEAwise report, we present the predictive models of fish growth, condition and maturity obtained so far in each of the four regional case studies.The biological processes (fish growth, condition and maturity) were studied in terms of body size (weight-at-age, length-at-age), condition factor, otolith increments and size at first maturity. Underlying data were available at different levels, ranging from individual fish, to sampling haul or stock level. Accordingly, the methods employed varied across case studies to adapt to the specific features of the process under study and the available data.The methodology encompassed statistical models (linear models, generalised additive models, mixed models, Bayesian nested hierarchical models, changepoint models), otolith growth increment analyses and mechanistic models (DEB-IBM model coupled to the environment and mizer model). Some of these models were focused on detecting overall trends, including potential changepoints along the time series or identification of the main intrinsic factors. Other models explored the impact of ecological drivers such as temperature, salinity, food availability or density dependence.In the Baltic Sea, two regimes were identified in the weight-at-age time series of herring in the Gulf of Riga (1961-1988 and 1989-2020). During the first period the main driver of the individual annual growth of the fish was the abundance of the copepod L. macrurus macrurus, while the abundance of the adult stages of E. affinis affinis was the dominating explanatory variable affecting herring growth during the second period. Neither SSB nor summer temperature during the main feeding period were significant drivers of the individual growth in the two distinct ecosystem regimes.In the Mediterranean Sea, the analysis of the impact of the environmental variables on biological parameters like size at first maturity, condition factor and growth in South Adriatic Sea and North-West Ionian Sea showed some significant effects in relation to the different species/area. In most of the cases, the environmental driver was bottom temperature, although some relationships with bottom salinity and primary production were also found. The model outcomes suggested that temperatures prevailing in deeper waters were the most significant factor affecting gonad maturity of hakes, while those in the shallow zone had the main impact on the L50 of red mullets. Condition factor of hake and red mullet in the Eastern Ionian Sea were affected not only by temperature, but also by zooplankton abundance.In the North Sea, mediated length-based growth models, linear mixed models and state-space linear mixed models were applied to four gadoids, two flatfishes and one pelagic stock and their performances were assessed in terms of model fit and predictive capability. For the mediated length-based growth model approach, the best model differed across stocks, but density dependent mediation effects were significant for five out of the seven stocks. Regarding the linear mixed models, the two types of models and the different penalisation procedures led to different models across stocks. Among the additional ecological variables, surface temperature was the most frequently included in the final model, closely followed closely by SSB and to a lesser extent by NAO. Detailed otolith increment analysis was used in the development of multidecadal biochronologies of average annual growth of sole in the North Sea and in the Irish Sea. In the North Sea, the best extrinsic model of sole growth included sea bottom temperature, fishing mortality at age, and stock biomass at maturity stage, and their interactions with age and maturity stage, while in the Irish Sea, the best extrinsic model included sea bottom temperature and fishing mortality at maturity stage and its interaction with maturity stage. These results confirmed the expected positive effect of temperature on adult growth. However, in the North Sea, temperature showed unexpected negative effect on juvenile growth, which might be linked to changes in food availability and/or intraspecific competition and need to be further studied. The mizer model (package for size-spectrum ecological modelling) with environmental forcing was used to study whether warming in the North Sea is responsible for the failure of the cod stock. The simulated fish community response when recruitment and carrying capacity depended on surface temperature fitted better with the assessment data than when the environment was fixed. However, the qualitative differences remain, suggesting that temperature effects were not the main cause of the model-assessment disparity.In the Western Waters, the mediated length-based growth models developed for the North Sea case study were applied to 14 stocks in the Celtic Sea. The best model differed across stocks, but again SSB mediation was significant for most of the stocks. From visual inspection of the plots, however, it was noted that the raw data from certain stock objects showed a reduced growth compared to the model fits, requiring further analyses. The analysis on biological measurements of individuals collected at fish markets, observers at sea or during scientific cruises allowed to study temporal variations in body size and condition factor of benthic, pelagic and demersal species in the Celtic Sea and the Bay of Biscay. The linear models indicated a significant negative monotonic relationship of sizes at all ages for anchovy and pilchard, but variations in size at age were less clear and significant for benthic and demersal species. In contrast, the results of the body condition indices showed a moderate but significant decrease for all the studied 19 species over time. The in-depth analysis for anchovy in the Bay of Biscay based on research surveys confirmed the decline in the length and weight of anchovy in the Bay of Biscay and pointed to a decline in body condition toward slender body shapes. Detected associations between temperature and size became more apparent for adult age classes than for juveniles, whereas the association between anchovy size and the biomass of spawners was more important for juvenile than for adult age classes. Associations between anchovy size and chlorophyll-a concentration were in general weak. Finally, the DEB-IBM model coupled to the environment that is under development for the two main seabass stocks of the North East Atlantic will provide further insights on how growth, condition and maturation can affect the future dynamics and productivity of these stocks.Read more about the project at www.seawiseproject.org</p