Publish wisely or perish? an open archive for MarBEF

While scientists are publishing around two million papers annually (Odlyzko, 1998), it is surprising to notice that this growing resource of information is seldom easily accessible, even to those scientists. Basically, it is the community at large that funds almost all research, so all information resulting from this research should in principle be publicly available. However, in reality, too many barriers (mostly installed by the publisher) are blocking free and open access to scientific information

MarBEF publishing revisited

Networking and integration served within a partnership approach and covered with a delicious sauce of free and open access to data and information is MarBEF’s main dish, and it is this recipe that has helped MarBEF to successfully bring marine biodiversity research to a European level. Numerous meetings, workshops, training courses and Responsive Mode Projects (RMPs) have brought together many scientists. This integration has created endless new possibilities for new initiatives – the MarBEF Publication Series and the MarBEF Open Archive, to mention just two. So, is this having any effect on the way we publish as a network today

BioTIME: A Database of Biodiversity Time Series for the Anthropocene

Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene. Main types of variables included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record. Spatial location and grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km(2) (158 cm(2)) to 100 km(2) (1,000,000,000,000 cm(2)). Time period and grainBio: TIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year. Major taxa and level of measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates

Data Management Strategy to Improve Global Use of Ocean Acidification Data and Information

International audienceOcean acidification (OA) refers to the general decrease in pH of the global ocean as a result of absorbing anthropogenic CO2 emitted in the atmosphere since preindustrial times (Sabine et al., 2004). There is, however, considerable variability in ocean acidification, and many careful measurements need to be made and compared in order to obtain scientifically valid information for the assessment of patterns, trends, and impacts over a range of spatial and temporal scales, and to understand the processes involved. A single country or institution cannot undertake measurements of worldwide coastal and open ocean OA changes; therefore, international cooperation is needed to achieve that goal. The OA data that have been, and are being, collected represent a significant public investment. To this end, it is critically important that researchers (and others) around the world are easily able to find and use reliable OA information that range from observing data (from time-series moorings, process studies, and research cruises), to biological response experiments (e.g., mesocosm), data products, and model output. [...

The marine fish food web is globally connected

The productivity of marine ecosystems and the services they provide to humans are largely dependent on complex interactions between prey and predators. These are embedded in a diverse network of trophic interactions, resulting in a cascade of events following perturbations such as species extinction. The sheer scale of oceans, however, precludes the characterization of marine feeding networks through de novo sampling. This effort ought instead to rely on a combination of extensive data and inference. Here we investigate how the distribution of trophic interactions at the global scale shapes the marine fish food web structure. We hypothesize that the heterogeneous distribution of species ranges in biogeographic regions should concentrate interactions in the warmest areas and within species groups. We find that the inferred global metaweb of marine fish—that is, all possible potential feeding links between co-occurring species—is highly connected geographically with a low degree of spatial modularity. Metrics of network structure correlate with sea surface temperature and tend to peak towards the tropics. In contrast to open-water communities, coastal food webs have greater interaction redundancy, which may confer robustness to species extinction. Our results suggest that marine ecosystems are connected yet display some resistance to perturbations because of high robustness at most locations.Using a global interaction dataset, the authors quantify the distribution of trophic interactions among marine fish, finding a high degree of geographic connectivity but low spatial modularity.C.A. was supported by a MELS-FQRNT Postdoctoral Fellowship and a Ressources Aquatique Québec (RAQ) fellowship during the conception and writing of this manuscript. T.P., D.G. and D.B.S. acknowledge financial support by the CIEE through their working group programme. M.B.A. is funded through FCT project No. PTDC/AAG-MAA/3764/2014. A.R.C. is funded by a Natural Sciences and Engineering Research Council of Canada (NSERC) PGS-D scholarship. D.G., T.P., M.-J.F., P.A. and S.J.L. are supported by NSERC Discovery Grants. T.P. also acknowledges a FRQNT New Investigator award and a Université de Montréal starting grant. D.B.S. acknowledges support from the Royal Society of New Zealand (via Marsden Fast-Start No. UOC-1101 and a Rutherford Discovery Fellowship)

Toward a new data standard for combined marine biological and environmental datasets - expanding OBIS beyond species occurrences

The Ocean Biogeographic Information System (OBIS) is the world's most comprehensive online, open-access database of marine species distributions. OBIS grows with millions of new species observations every year. Contributions come from a network of hundreds of institutions, projects and individuals with common goals: to build a scientific knowledge base that is open to the public for scientific discovery and exploration and to detect trends and changes that inform society as essential elements in conservation management and sustainable development. Until now, OBIS has focused solely on the collection of biogeographic data (the presence of marine species in space and time) and operated with optimized data flows, quality control procedures and data standards specifically targeted to these data. Based on requirements from the growing OBIS community to manage datasets that combine biological, physical and chemical measurements, the OBIS-ENV-DATA pilot project was launched to develop a proposed standard and guidelines to make sure these combined datasets can stay together and are not, as is often the case, split and sent to different repositories. The proposal in this paper allows for the management of sampling methodology, animal tracking and telemetry data, biological measurements (e.g., body length, percent live cover, ...) as well as environmental measurements such as nutrient concentrations, sediment characteristics or other abiotic parameters measured during sampling to characterize the environment from which biogeographic data was collected. The recommended practice builds on the Darwin Core Archive (DwC-A) standard and on practices adopted by the Global Biodiversity Information Facility (GBIF). It consists of a DwC Event Core in combination with a DwC Occurrence Extension and a proposed enhancement to the DwC MeasurementOrFact Extension. This new structure enables the linkage of measurements or facts - quantitative and qualitative properties - to both sampling events and species occurrences, and includes additional fields for property standardization. We also embrace the use of the new parentEventID DwC term, which enables the creation of a sampling event hierarchy. We believe that the adoption of this recommended practice as a new data standard for managing and sharing biological and associated environmental datasets by IODE and the wider international scientific community would be key to improving the effectiveness of the knowledge base, and will enhance integration and management of critical data needed to understand ecological and biological processes in the ocean, and on land.Fil: De Pooter, Daphnis. Flanders Marine Institute; BélgicaFil: Appeltans, Ward. UNESCO-IOC; BélgicaFil: Bailly, Nicolas. Hellenic Centre for Marine Research, MedOBIS; GreciaFil: Bristol, Sky. United States Geological Survey; Estados UnidosFil: Deneudt, Klaas. Flanders Marine Institute; BélgicaFil: Eliezer, Menashè. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Fujioka, Ei. University Of Duke. Nicholas School Of Environment. Duke Marine Lab; Estados UnidosFil: Giorgetti, Alessandra. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Goldstein, Philip. University of Colorado Museum of Natural History, OBIS; Estados UnidosFil: Lewis, Mirtha Noemi. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; ArgentinaFil: Lipizer, Marina. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Mackay, Kevin. National Institute of Water and Atmospheric Research; Nueva ZelandaFil: Marin, Maria Rosa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Moncoiffé, Gwenaëlle. British Oceanographic Data Center; Reino UnidoFil: Nikolopoulou, Stamatina. Hellenic Centre for Marine Research, MedOBIS; GreciaFil: Provoost, Pieter. UNESCO-IOC; BélgicaFil: Rauch, Shannon. Woods Hole Oceanographic Institution; Estados UnidosFil: Roubicek, Andres. CSIRO Oceans and Atmosphere; AustraliaFil: Torres, Carlos. Universidad Autonoma de Baja California Sur; MéxicoFil: van de Putte, Anton. Royal Belgian Institute for Natural Sciences; BélgicaFil: Vandepitte, Leen. Flanders Marine Institute; BélgicaFil: Vanhoorne, Bart. Flanders Marine Institute; BélgicaFil: Vinci, Mateo. Istituto Nazionale di Oceanografia e di Geofisica Sperimentale; ItaliaFil: Wambiji, Nina. Kenya Marine and Fisheries Research Institute; KeniaFil: Watts, David. CSIRO Oceans and Atmosphere; AustraliaFil: Klein Salas, Eduardo. Universidad Simon Bolivar; VenezuelaFil: Hernandez, Francisco. Flanders Marine Institute; Bélgic

Critical Habitats and Biodiversity: Inventory, Thresholds and Governance

The High Level Panel for Sustainable Ocean Economy (https://oceanpanel.org/) has commissioned a series of “Blue Papers” to explore pressing challenges at the nexus of the ocean and the economy. This paper is part of a series of 16 papers to be published between November 2019 and October 2020. It addresses how multiple human impacts will impact biodiversity underpinning ecosystem services such as marine fisheries, aquaculture, coastal protection and tourism. The paper examines the distribution of marine species and critical marine habitats around the world; analyses trends in drivers, pressures, impacts and response; and establishes thresholds for protecting biodiversity hot spots, and indicators to monitor change. From this scientific base, it assesses the current legal framework and available tools for biodiversity protection, current gaps in ocean governance and management and the implications for achieving a sustainable ocean economy tailored to individual coastal states grouped by social indicators

Integrating ocean observations across body‐size classes to deliver benthic invertebrate abundance and distribution information

Invertebrate animals living at the seafloor make up a prominent component of life globally, spanning 10 orders of magnitude in body size over 71% of Earth's surface. However, integrating information across sizes and sampling methodologies has limited our understanding of the influence of natural variation, climate change and human activity. Here, we outline maturing practices that can underpin both the feasibility and impact of establishing Benthic Invertebrate Abundance and Distribution as a Global Ocean Observing System—Essential Ocean Variable, including: (1) quantifying individual body size, (2) identifying the well-quantified portions of sampled body-size spectra, (3) taking advantage of (semi-)automated information processing, (4) application of metadata standards such as Darwin Core, and (5) making data available through internationally recognized access points. These practices enable broader-scale analysis supporting research and sustainable development, such as assessments of indicator taxa, biodiversity, biomass, and the modeling of carbon stocks and flows that are contiguous over time and space

Recommendations for the standardisation of open taxonomic nomenclature for image-based identifications

This paper recommends best practice for the use of open nomenclature (ON) signs applicable to image-based faunal analyses. It is one of numerous initiatives to improve biodiversity data input to improve the reliability of biological datasets and their utility in informing policy and management. Image-based faunal analyses are increasingly common but have limitations in the level of taxonomic precision that can be achieved, which varies among groups and imaging methods. This is particularly critical for deep-sea studies owing to the difficulties in reaching confident species-level identifications of unknown taxa. ON signs indicate a standard level of identification and improve clarity, precision and comparability of biodiversity data. Here we provide examples of recommended usage of these terms for input to online databases and preparation of morphospecies catalogues. Because the processes of identification differ when working with physical specimens and with images of the taxa, we build upon previously provided recommendations for specific use with image-based identifications