STRING: known and predicted protein–protein associations, integrated and transferred across organisms

A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, ‘association’ can mean direct physical binding, but can also mean indirect interaction such as participation in the same metabolic pathway or cellular process. Currently, information about protein association is scattered over a wide variety of resources and model organisms. STRING aims to simplify access to this information by providing a comprehensive, yet quality-controlled collection of protein–protein associations for a large number of organisms. The associations are derived from high-throughput experimental data, from the mining of databases and literature, and from predictions based on genomic context analysis. STRING integrates and ranks these associations by benchmarking them against a common reference set, and presents evidence in a consistent and intuitive web interface. Importantly, the associations are extended beyond the organism in which they were originally described, by automatic transfer to orthologous protein pairs in other organisms, where applicable. STRING currently holds 730 000 proteins in 180 fully sequenced organisms, and is available at http://string.embl.de/

The demersal fisheries of Mauritaniua in 2003: description of the fleets and assessment of resources: First report of a joint IMROP/RIVO project

Demersal fisheries in the Mauritanian Exclusive Economic Zone (EEZ) are described, with a review of the state of the stocks that are exploited by these fisheries. The assessment of the various stocks is based primarily on the results of the “Groupe de Travail” (GT), held in December 2002 at the Mauritanian fisheries research institute IMROP, Nouadhibou. The conclusions of these assessments are that the octopus stock in the Mauritanian EEZ is overexploited and that fishing effort is about 30% above the optimum level. Shrimps appear to be exploited near their maximum level. Fishing mortality on hake should be reduced, and the fishing effort in the roundfish fleet should not be further increased

Scientific Advice on the estimation of surplus for Sustainable Fisheries Partnership Agreements.

Scientific advice on the concept of surplus, as defined by the UNCLOS, was provided for three types of Sustainable Fisheries Partnership Agreements (SFPAs): i) Mixed SFPAs in West Africa, ii) Tuna SFPAs and iii) SFPA with Greenland. For Mixed SFPAs in West Africa, methods for surplus computation were defined, including alternatives for cases of data limited stocks. These methods may use as input five parameters that could be obtained from those recent stocks assessments that are representative of the current stock status. Surplus estimates would need to be regularly updated (ideally, yearly), according to every new stock assessments and following the enforcement of a management plan (or, by default, according to a transition scheme towards reaching Fmsy in 2020). In the case of West African transboundary stocks, a theoretical share of the surplus could be calculated using a standard rule based on historical catches within EEZs. The Surplus concept is not applicable for Tuna SFPAs, due to the high migratory character of tuna or tuna-like species, the fact that these stocks are mostly found in areas beyond national jurisdictions, the lack of direct estimates of local abundance and impossibility to calculate the capacity of the coastal States. For the SFPA with Greenland, Surplus is considered as any TAC allocated to Greenland and not utilised by this coastal State

Strong fisheries management and governance positively impact ecosystem status

Bundy, Alida ... et al.-- 28 pages, 6 figures, 8 tables, supporting information https://dx.doi.org/10.1111/faf.12184Fisheries have had major negative impacts on marine ecosystems, and effective fisheries management and governance are needed to achieve sustainable fisheries, biodiversity conservation goals and thus good ecosystem status. To date, the IndiSeas programme (Indicators for the Seas) has focussed on assessing the ecological impacts of fishing at the ecosystem scale using ecological indicators. Here, we explore fisheries ‘Management Effectiveness’ and ‘Governance Quality’ and relate this to ecosystem health and status. We developed a dedicated expert survey, focused at the ecosystem level, with a series of questions addressing aspects of management and governance, from an ecosystem-based perspective, using objective and evidence-based criteria. The survey was completed by ecosystem experts (managers and scientists) and results analysed using ranking and multivariate methods. Results were further examined for selected ecosystems, using expert knowledge, to explore the overall findings in greater depth. Higher scores for ‘Management Effectiveness’ and ‘Governance Quality’ were significantly and positively related to ecosystems with better ecological status. Key factors that point to success in delivering fisheries and conservation objectives were as follows: the use of reference points for management, frequent review of stock assessments, whether Illegal, Unreported and Unregulated (IUU) catches were being accounted for and addressed, and the inclusion of stakeholders. Additionally, we found that the implementation of a long-term management plan, including economic and social dimensions of fisheries in exploited ecosystems, was a key factor in successful, sustainable fisheries management. Our results support the thesis that good ecosystem-based management and governance, sustainable fisheries and healthy ecosystems go togetherThis is a contribution to the IndiSeas Working Group, which, by the time of the study, was cofunded by IOC-UNESCO (www.ioc-unesco.org), EuroMarine (http://www.euromarinenetwork.eu), the European FP7 MEECE research project, the European Network of Excellence Eur-Oceans and the FRB EMIBIOS project (contract n°212085)Peer Reviewe

Ecological indicators to capture the effects of fishing on biodiversityand conservation status of marine ecosystems

IndiSeas (“Indicators for the Seas”) is a collaborative international working group that was established in2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data avail-ability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii)mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species,and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011–2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our under-standing of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses,and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems

Ecological indicators to capture the effects of fishing on biodiversityand conservation status of marine ecosystems

IndiSeas (“Indicators for the Seas”) is a collaborative international working group that was established in2005 to evaluate the status of exploited marine ecosystems using a suite of indicators in a comparative framework. An initial shortlist of seven ecological indicators was selected to quantify the effects of fishing on the broader ecosystem using several criteria (i.e., ecological meaning, sensitivity to fishing, data avail-ability, management objectives and public awareness). The suite comprised: (i) the inverse coefficient of variation of total biomass of surveyed species, (ii) mean fish length in the surveyed community, (iii)mean maximum life span of surveyed fish species, (iv) proportion of predatory fish in the surveyed community, (v) proportion of under and moderately exploited stocks, (vi) total biomass of surveyed species,and (vii) mean trophic level of the landed catch. In line with the Nagoya Strategic Plan of the Convention on Biological Diversity (2011–2020), we extended this suite to emphasize the broader biodiversity and conservation risks in exploited marine ecosystems. We selected a subset of indicators from a list of empirically based candidate biodiversity indicators initially established based on ecological significance to complement the original IndiSeas indicators. The additional selected indicators were: (viii) mean intrinsic vulnerability index of the fish landed catch, (ix) proportion of non-declining exploited species in the surveyed community, (x) catch-based marine trophic index, and (xi) mean trophic level of the surveyed community. Despite the lack of data in some ecosystems, we also selected (xii) mean trophic level of the modelled community, and (xiii) proportion of discards in the fishery as extra indicators. These additional indicators were examined, along with the initial set of IndiSeas ecological indicators, to evaluate whether adding new biodiversity indicators provided useful additional information to refine our under-standing of the status evaluation of 29 exploited marine ecosystems. We used state and trend analyses,and we performed correlation, redundancy and multivariate tests. Existing developments in ecosystem-based fisheries management have largely focused on exploited species. Our study, using mostly fisheries independent survey-based indicators, highlights that biodiversity and conservation-based indicators are complementary to ecological indicators of fishing pressure. Thus, they should be used to provide additional information to evaluate the overall impact of fishing on exploited marine ecosystems

Are we ready to track climate-driven shifts in marine species across international boundaries? - A global survey of scientific bottom trawl data

Marine biota are redistributing at a rapid pace in response to climate change and shifting seascapes. While changes in fish populations and community structure threaten the sustainability of fisheries, our capacity to adapt by tracking and projecting marine species remains a challenge due to data discontinuities in biological observations, lack of data availability, and mismatch between data and real species distributions. To assess the extent of this challenge, we review the global status and accessibility of ongoing scientific bottom trawl surveys. In total, we gathered metadata for 283,925 samples from 95 surveys conducted regularly from 2001 to 2019. We identified that 59% of the metadata collected are not publicly available, highlighting that the availability of data is the most important challenge to assess species redistributions under global climate change. Given that the primary purpose of surveys is to provide independent data to inform stock assessment of commercially important populations, we further highlight that single surveys do not cover the full range of the main commercial demersal fish species. An average of 18 surveys is needed to cover at least 50% of species ranges, demonstrating the importance of combining multiple surveys to evaluate species range shifts. We assess the potential for combining surveys to track transboundary species redistributions and show that differences in sampling schemes and inconsistency in sampling can be overcome with spatio-temporal modeling to follow species density redistributions. In light of our global assessment, we establish a framework for improving the management and conservation of transboundary and migrating marine demersal species. We provide directions to improve data availability and encourage countries to share survey data, to assess species vulnerabilities, and to support management adaptation in a time of climate-driven ocean changes.En prensa6,86