Bio-ORACLE v2.0 : extending marine data layers for bioclimatic modelling

Motivation: The availability of user-friendly, high-resolution global environmental datasets is crucial for bioclimatic modelling. For terrestrial environments, WorldClim has served this purpose since 2005, but equivalent marine data only became available in 2012, with pioneer initiatives like Bio-ORACLE providing data layers for several ecologically relevant variables. Currently, the available marine data packages have not yet been updated to the most recent Intergovernmental Panel on Climate Change (IPCC) predictions nor to present times, and are mostly restricted to the top surface layer of the oceans, precluding the modelling of a large fraction of the benthic diversity that inhabits deeper habitats. To address this gap, we present a significant update of Bio-ORACLE for new future climate scenarios, present-day conditions and benthic layers (near sea bottom). The reliability of data layers was assessed using a cross-validation framework against in situ quality-controlled data. This test showed a generally good agreement between our data layers and the global climatic patterns. We also provide a package of functions in the R software environment (sdmpredictors) to facilitate listing, extraction and management of data layers and allow easy integration with the available pipelines for bioclimatic modelling. Main types of variable contained: Surface and benthic layers for water temperature, salinity, nutrients, chlorophyll, sea ice, current velocity, phytoplankton, primary productivity, iron and light at bottom. Spatial location and grain: Global at 5 arcmin (c.0.08 degrees or 9.2 km at the equator). Time period and grain: Present (2000-2014) and future (2040-2050 and 2090-2100) environmental conditions based on monthly averages. Major taxa and level of measurement: Marine biodiversity associated with sea surface and epibenthic habitats. Software format: ASCII and TIFF grid formats for geographical information systems and a package of functions developed for R software

Fishing for data and sorting the catch : assessing the data quality, completeness and fitness for use of data in marine biogeographic databases

Being able to assess the quality and level of completeness of data has become indispensable in marine biodiversity research, especially when dealing with large databases that typically compile data from a variety of sources. Very few integrated databases offer quality flags on the level of the individual record, making it hard for users to easily extract the data that are fit for their specific purposes. This article describes the different steps that were developed to analyse the quality and completeness of the distribution records within the European and international Ocean Biogeographic Information Systems (EurOBIS and OBIS). Records are checked on data format, completeness and validity of information, quality and detail of the used taxonomy and geographic indications and whether or not the record is a putative outlier. The corresponding quality control (QC) flags will not only help users with their data selection, they will also help the data management team and the data custodians to identify possible gaps and errors in the submitted data, providing scope to improve data quality. The results of these quality control procedures are as of now available on both the EurOBIS and OBIS databases. Through the Biology portal of the European Marine Observation and Data Network (EMODnet Biology), a subset of EurOBIS records-passing a specific combination of these QC steps-is offered to the users. In the future, EMODnet Biology will offer a wide range of filter options through its portal, allowing users to make specific selections themselves. Through LifeWatch, users can already upload their own data and check them against a selection of the here described quality control procedures

Dataset of ocean vessel traffic in the North Sea

DATA AVAILABILITY : OpenAIS:vessel_density (Original data) (VLIZ Geoserver)Automatic Identification System (AIS) is a technology that allows ships to broadcast their position, course, speed, and other information to other vessels or shore-based stations. By collecting and analysing this data, it is possible to create a heatmap of ship activity in a particular region, such as the North Sea. This heatmap acts as a representation of vessel activity per class. A heatmap in a standard geoinformatics format may be preferable to scientific researchers as it would quickly allow users to overlay their own data onto the vessel density layer thus providing spatial context and an ability to compare their dataset to the distribution and intensity of ship activity in a particular region. This dataset represents ocean vessel activity in the North Sea for 2022 and was created using AIS data collected using multiple coastal receivers. The dataset was created from reported vessel positions aggregated both spatially and temporally. The end goal of this data processing is to provide a publicly available spatial layer that can be queried to provide monthly vessel traffic statistics for a region in the North Sea. The data was spatially filtered to only include AIS messages for Latitudes between 49.5 and 53.8 degrees North, and 0.2 and 7 degrees East. The bounding box was chosen as it includes Belgium canals and the Belgium part of the North Sea.http://www.elsevier.com/locate/dibam2024Electrical, Electronic and Computer EngineeringNon

Marine phytoplankton community composition data from the Belgian part of the North Sea, 1968-2010

The Belgian Phytoplankton Database (BPD) is a comprehensive data collection comprising quantitative phytoplankton cell counts from multiple research projects conducted since 1968. The collection is focused on the Belgian part of the North Sea, but also includes data from the French and the Dutch part of the North Sea. The database includes almost 300 unique sampling locations and more than 3,000 sampling events resulting in more than 86,000 phytoplankton cell count records. The dataset covers two periods: 1968 to 1978 and 1994 to 2010. The BPD can be accessed online and provides high quality phytoplankton count data. The species taxonomy is updated, and the count values are quality checked and standardized. Important metadata like sampling date, sampling location, sampling depth and methodology is provided and standardized. Additionally, associated abiotic data and biovolume values are available. The dataset allows to conduct analyses of long-term temporal and spatial trends in phytoplankton community structure in the southern part of the North Sea, including changes in phytoplankton phenology and seasonality

Contrasting Geographical Distributions as a Result of Thermal Tolerance and Long-Distance Dispersal in Two Allegedly Widespread Tropical Brown Algae

BackgroundMany tropical marine macroalgae are reported from all three ocean basins, though these very wide distributions may simply be an artifact resulting from inadequate taxonomy that fails to take into account cryptic diversity. Alternatively, pantropical distributions challenge the belief of limited intrinsic dispersal capacity of marine seaweeds and the effectiveness of the north-south oriented continents as dispersal barriers. We aimed to re-assess the distribution of two allegedly circumtropical brown algae, Dictyota ciliolata and D. crenulata, and interpret the realized geographical range of the respective species in relation to their thermal tolerance and major tectonic and climatic events during the Cenozoic.Methodology/Principal FindingsSpecies delimitation was based on 184 chloroplast encoded psbA sequences, using a Generalized Mixed Yule Coalescent method. Phylogenetic relationships were inferred by analyzing a six-gene dataset. Divergence times were estimated using relaxed molecular clock methods and published calibration data. Distribution ranges of the species were inferred from DNA-confirmed records, complemented with credible literature data and herbarium vouchers. Temperature tolerances of the species were determined by correlating distribution records with local SST values. We found considerable conflict between traditional and DNA-based species definitions. Dictyota crenulata consists of several pseudocryptic species, which have restricted distributions in the Atlantic Ocean and Pacific Central America. In contrast, the pantropical distribution of D. ciliolata is confirmed and linked to its significantly wider temperature tolerance.Conclusions/SignificanceTectonically driven rearrangements of physical barriers left an unequivocal imprint on the current diversity patterns of marine macroalgae, as witnessed by the D. crenulata–complex. The nearly circumglobal tropical distribution of D. ciliolata, however, demonstrates that the north-south oriented continents do not present absolute dispersal barriers for species characterized by wide temperature tolerances

Atypical development of Chaetomorpha antennina in culture (Cladophorales, Chlorophyta)

The green seaweed genus Chaetomorpha is characterized by unbranched filaments. Molecular phylogenetic data indicate that Chaetomorpha forms a clade that is nested in a paraphyletic assemblage of branched species (Cladophora). It follows that the unbranched condition is evolutionarily conserved and likely evolved early in the evolution of this clade. In this study we show that under laboratory culture conditions, the filaments of C. antennina frequently produce lateral branches, similar to Cladophora. Our results thus indicate that the unbranched thallus architecture is not entirely genetically constrained, but at least in part subject to morphological plasticity. Additionally, culture observations of C. antennina allowed a detailed study of rhizoidal development, which seems unique among Cladophorales

Linked Data Publishing of the World Register of Marine Species (WoRMS) as a Basis for Uniformly Linking-up Resources to Accepted Taxon Names

The World Register of Marine Species (WoRMS) is an authoritative classification and catalogue of marine names. The WoRMS portal and available web-services are a gateway to access a treasure-chest of information, not only on taxon names themselves, but also on their mutual relations (e.g., original names, accepted versus unaccepted names, taxonomic classification), and related information such as ecological traits, distributions and linked literature.Over its fifteen years of existence, WoRMS has not only been growing in content and quality, thanks to the voluntary efforts of more than 300 experts worldwide, it has also kept a technical trajectory that involves adapting to new standards and technologies. Although WoRMS has always been relatively easily accessible through its portal and web services, and applied the basic data-sharing principles of FAIR (Findable, Accessible, Interoperable, and Reusable), there is still room for improvement. The recently growing call for globally uniform identifiers coming from the application of the FAIR data sharing principles, and the growing investment into globally open and interlinked "digital twin" representations of our oceans and the organisms found in them, have introduced the fundamentals for growing a marine knowledge graph, and as a consequence, has directed some technical attention towards applying semantic web technologies.WoRMS plays a key role in the field of (marine) biodiversity, as this research field strongly relies on the correct usage of species names, and understanding the taxonomic relationships between taxon names. As WoRMS is regarded as the authoritative resource for marine names, it is also heavily used as a quality-control tool for the correct usage of taxon names within various European and global initiatives. WoRMS provides support to global databases and infrastructures that use (or are in need of) a marine taxonomic backbone, such as the LifeWatch Species Information Backbone, the Ocean Biodiversity Information System (OBIS) and the Global Ocean Observing System (GOOS), as well as improves the content and strengthens relationships with environment-independent initiatives and infrastructures such as the Catalogue of Life (COL), the Barcode of Life Data System (BoLD) & GenBank. In addition to the taxonomic value of WoRMS, it is also highly valued for its available information on species traits, which form a critical component in ecological marine research.In its role as a marine taxonomic backbone, along with being linked to numerous other environment-independent initiatives and infrastructures, WoRMS has always required an adaptability towards the challenging new ways specific applications and concrete research have been choosing to apply the identifiers affixed by WoRMS. It is in this tradition we now announce and describe our approach to publish the content of the register as fully linked open data, using semantic web technologies.We describe in some detail the choices madeto select and apply specific vocabularies that already exist for the description and interconnected linking of taxon names,to address the tension between hanging on to an historic (URN) persistent identifier and providing a dereferenceable URI that supports the appreciated "follow your nose" property,to link to other relevant registries,to design meaningful predicates for inbound links to the register and, more technicallyto divide the available content into meaningful sub-sections for retrieval of optional detail, andto provide a roadmap for meaningful fragmentations of the full register to allow for an effective consumption of the relevant (e.g., newly updated) parts into specific data-consumption scenarios.We believe this work to be an important step towards achieving some future goals. It should further facilitate the production of automated, managed or hybrid crosswalks between various taxonomic registers and classifications. To be especially considered here, is helping to make omics taxonomic references more meaningfully comparable with WoRMS. In the process of others linking their digital objects (e.g., services, datasets, publications, experts) to taxon IDs in WoRMS, they are effectively also linking to each other, which opens the doors between apparently unconnected bodies. Its continuing use as a global standard and trustworthy reference of community-accepted names for biological taxa becomes the essential glue connecting all sorts of services, initiatives, communities