Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods

Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently

Cryptic Biodiversity and Phylogeographic Patterns of Seychellois \u3cem\u3eLigia\u3c/em\u3e Isopods

Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently

Cryptic Biodiversity and Phylogeographic Patterns of Seychellois \u3cem\u3eLigia\u3c/em\u3e Isopods

Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently

Mesoscale productivity fronts and local fishing opportunities in the European Seas

This study evaluates the relationship between both commercial and scientific spatial fisheries data and a new satellite-based estimate of potential fish production (Ocean Productivity available to Fish, OPFish) in the European Seas. To construct OPFish, we used productivity frontal features derived from chlorophyll-a horizontal gradients, which characterize 10%–20% of the global phytoplankton production that effectively fuels higher trophic levels. OPFish is relatively consistent with the spatial distribution of both pelagic and demersal fish landings and catches per unit of effort (LPUEs and CPUEs, respectively). An index of harvest relative to ocean productivity (HP index) is calculated by dividing these LPUEs or CPUEs with OPFish. The HP index reflects the intensity of fishing by gear type with regard to local fish production. Low HP levels indicate lower LPUEs or CPUEs than expected from oceanic production, suggesting over-exploitation, while high HP levels imply more sustainable fishing. HP allows comparing the production-dependent suitability of local fishing intensities. Our results from bottom trawl data highlight that over-exploitation of demersal species from the shelves is twice as high in the Mediterranean Sea than in the North-East Atlantic. The estimate of HP index by dominant pelagic and demersal gears suggests that midwater and bottom otter trawls are associated with the lowest and highest overfishing, respectively. The contrasts of fishing intensity at local scales captured by the HP index suggest that accounting for the local potential fish production can promote fisheries sustainability in the context of ecosystem-based fisheries management as required by international marine policies

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 whichecological 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 bybycatch 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

SEAwise report on historic and future spatial distribution of fished stocks

This SEAwise report assesses the distribution of fish species across European seas. To this end, an ICES workshop, WKFISHDISH2, was co-organised to reach out to the broader scientific community and acquire as much knowledge as possible on scientific surveys and species distribution models. A large amount of historical scientific survey data, stored in the DATRAS and MEDITS databases, served as basis for the development of guidelines on how to appropriately pre-process such data, analyse them with state-of-the-art species distribution models (SDMs), and define metrics on how to compare species distributions. Distribution maps were generated separately for the Mediterranean Sea and the Northeast Atlantic spanning the Baltic Sea, North Sea, Celtic Seas, Bay of Biscay and Iberian Coast.  In general, there was good agreement between the distributions generated by different models that were applied to four different reference species with different characteristics in terms of spatial distribution. Differences between models were mainly related to the configuration of spatiotemporal processes, and the extrapolation, mainly in areas with few observations, or where correlates extend to values outside the observed range.  Trends in species distribution were species specific. Some species have shifted in a northward direction, while the distribution of other species was static, or characterized by a southward trend. It is difficult to have a mechanistic understanding, e.g. migration due to climate change, local outbursts, and/or local depletion of fish stocks, of these changes based on survey data that does not allow tracking of individual fish. Potential climate related shifts were instead investigated by linking the survey data with oceanographic variables generated through coupled hydrodynamic-biochemical models. This allowed us to explore how species distributions may change under different scenarios of climate change.  More information about the SEAwise project can be found at www.seawiseproject.org</p

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

SEAwise Report on consistency of existing targets and limits for indicators in an ecosystem context

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. This SEAwise report investigates the consistency of existing targets and limits from the Common Fisheries Policy (CFP) and the Marine Strategy Framework Directive (MSFD). Trade-offs between different objectives (ecological, economic, social), targets and limits are highlighted. A wide range of model types (from bio-economic to full ecosystem models) has been applied to various case study areas accross the North East Atlantic and Mediterranean. Although model predictions are by nature uncertain, this study provides important information on likely inconsistencies between existing targets and limits and trade-offs expected under ecosystem- based fisheries management (EBFM). The scenarios investigated include the current range of management applied in terms of the Maximum Sustainable Yield (MSY) concept (i.e. strict MSY approach vs. Pretty Good Yield (PGY) approach allowing sustainable deviations from single species point estimates). The landing obligation is a key aspect of current fisheries management and was fully considered, in particular for mixed demersal fisheries.Maintaining current fishing effort without further management measures was the least sustainable option in nearly all cases studies. This approach led to increased risk of stocks falling below critical biomass limits. Although the fishing effort adaptions needed is highly case specific, this indicates that further management measures are likely to be needed to ensure a sustainable exploitation of all stocks.Scenarios applying a strict MSY approach in combination with the landing obligation as upper limit with fisheries ending when the first stock reaches in most case studies led to the lowest fishing effort. This had positive effects on MSFD related indicators such as bycatch of Protected, Endangered and Threatened (PET) species, benthic impact and the Large Fish Indicator as well as global indicators such as CO emission or ecosystem-based indicators like catch per . However, this scenario often led to the lowest catches from mixed demersal fisheries due to strong choke effects because fleets had to stop when their first quota was exhausted. This reduces social indicators such as food security, employment and wages. In terms of economic performance, the gains and loses were highly case specific. Scenarios applying the Pretty Good Yield concept and allowing sustainable deviations from the point estimate when stocks are in a healthy state often outperformed the scenarios applying as strict upper limit. Such scenarios, applying a more flexible interpretation of the MSY concept, led to reduced fishing effort compared to the status quo effort, but relaxed choke situations in mixed demersal fisheries to some extent leading to higher gross profits and in some case studies also to higher catches. Hence, they may constitute a compromise between the need to attain social as well as ecological objectives. Whether the associated effort levels lead to conflicts with MSFD objectives must be analysed when more internationally agreed thresholds become available for e.g., bycatch of PET species or benthic impact.The majority of case studies exceeded suggested thresholds for the global ecosystem indicators catch per km or primary production even under scenarios with high effort reductions. This can be explained to some extent by the fact that these indices are mainly driven by pelagic and industrial fisheries not always part of the models applied. Nevertheless, it indicates potential conflicts with such more holistic ecosystem indicators in their current form.Additional trade-offs in terms of yield were identified within the food web if e.g., demersal piscivorous predators feed on small pelagic fish and both groups are fished. Further, in case studies where small-scale fisheries (SSF) play an important role (e.g., Eastern Ionian Sea) additional trade-offs became apparent as different scenarios led to different ratios between revenues from small scale fisheries and revenues from large-scale fisheries. This adds another level of complexity when such aspects need to be taken more into account in future fisheries management under EBFM.The modelling assumed current selectivities and catchabilities will be maintained in the future. Especially trade-offs arising from fleets having to stop fishing when their first quota is exhausted or when e.g., a threshold for bycatch of PET species is reached may be resolved by improving selectivities via technical measures (e.g., closed areas or innovative gears) in the future. Deliverable 6.8 in month 36 will test such scenarios. Furthermore, the list of indicators and their targets and limits will be updated based on research within and outside SEAwise. Predictive capability of models will be enhanced by incorporating improved biological and economic sub-models in relation to environmental change. Climate change scenarios will be run and new harvest control rules (HCRs), proposed by SEAwise, will be tested. Finally, consistent targets and limits will be proposed for implementing EBFM