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News

In Memoriam - J. Frederick Grassle

We are very sad to learn about the loss of Dr J. Frederick (Fred) Grassle. Fred is one of the Godfathers of OBIS. We are extremely thankful for all his support and great wisdom and hope with OBIS we can keep his dreams and vision alive.

July 09, 2018 - OBISIn Memoriam Fred Grassle

IODE/OBIS-Event-Data workshop on animal tagging and tracking, 23-26 April 2018, Oostende, Belgium

Several major marine animal telemetry networks met at the OBIS project office and agreed to use the OBIS-ENV-DATA Darwin Core standard for the exchange and publication of detection data through OBIS (both acoustic and satellite) and work with OBIS and the scientific community to calculate species home ranges, migration pathways and movement patterns.

May 18, 2018 - OBISOBIS animal tracking OBIS-ENV-DATA Darwin Core Event Core

FishNet2 and FishBase together are the new global thematic Fish OBIS node

Quantitative Aquatics (Philippines) and the Tulane University Biodiversity Research Institute (USA), which host Fishbase and FishNet2 respectively, joined the IODE network as Associate Data Units (ADUs) and jointly will operate the global thematic Fish OBIS node.

May 08, 2018 - OBISOBIS network Fish

IOC invests in OBIS2.0, a major re-engineering of the OBIS platform

Through extra-budgetary funding, the IOC of UNESCO invests US$170,000 to further modernise the OBIS infrastructure and technology stack which will support real-time data integration, quality control, and analysis of rich marine data streams. The release of OBIS2.0 is expected around the end of 2018.

April 17, 2018 - OBISOBIS2.0 Infrastructure

Vacancy Senior computer scientist

The Flanders Marine Institute (VLIZ) is looking for a senior computer scientist (m/f/x, 100% employment, permanent contract) for immediate employment to support us at the UNESCO/IOC Project Office for IODE in Oostende (Belgium).

March 20, 2018 - OBISvacancy

The First U.S. IOOS Biological Data Training Workshop, 8-9 February 2018

The US Integrated Ocean Observing System (IOOS) and the Ocean Biogeographic Information System (OBIS) organized a training workshop to develop a community of practice around the management and analysis of biological ocean observing data. Outcomes from the workshop include a collection of software and scripts available on a GitHub repository to aid in the curation of biological data and an expanded network of IOOS, Canadian and OBIS collaborators that are all motivated to expand the global repository of marine biodiversity information. The training materials are also available on the OceanTeacher website.

March 20, 2018 - Jennifer BoschOBIS training USA

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Use cases

More losers than winners for Southern Ocean marine life in a warmer future.

biodiversity loss species composition Southern Ocean

A study of the marine invertebrates living in the seas around Antarctica reveals there will be more ‘losers’ than ‘winners’ over the next century as the Antarctic seafloor warms. The results are published in the journal Nature Climate Change.

A team at British Antarctic Survey (BAS) examined the potential distribution of over 900 species of shelf-dwelling marine invertebrates under a warming scenario produced by computer models. The authors used the known distributions of 963 benthic species with ≥20 records, from <1,000 m depth, from south of 40 °S. The records came from the SCAR Biogeographic Atlas of the Southern Ocean & OBIS. The climate models used were an ensemble of 19 different models from the CMIP5 database of mean seafloor temperatures for 2099 under the IPCC RCP8.5 scenario (the most extreme of all the scenarios where emissions continue to rise throughout the 21st century).

Southern Ocean seafloor water temperatures are projected to warm by an average of 0.4 °C over this century with some areas possibly increasing by as much as 2°C. The team conclude that, while some species in some areas will benefit, within the current century, warming temperatures alone are unlikely to result in wholesale extinction or invasion affecting Antarctic seafloor life. However, 79% of Antarctica’s endemic species do face a significant reduction in suitable temperature habitat (an average 12% reduction). Their findings highlight the species and regions most likely to respond significantly (negatively and positively) to warming and have important implications for future management of the region.

Reference: Griffiths, Huw J., Andrew JS Meijers, and Thomas J. Bracegirdle. "More losers than winners in a century of future Southern Ocean seafloor warming." https://www.nature.com/articles/nclimate3377.

Counting seals with drones and thermal imagery

species population UAV OBIS data

Marine megafauna populations are challenging to assess, thanks to their cryptic nature and patchy availability to many forms of remote sensing. The Duke University Marine Robotics and Remote Sensing lab (MaRRS) strives to advance marine wildlife assessment methodology by fusing unoccupied aerial vehicles (UAV), advanced sensor packages and computer vision algorithms. This combination promises to improve the efficiency, economy and safety for surveys that are often tedious and dangerous for those that conduct them in remote parts of the world.

In the spring of 2015, the MaRRS lab conducted surveys over two grey seal breeding colonies in Nova Scotia using a small fixed-wing UAV called an “ebee”, taking pictures of the colonies with standard RGB and thermal cameras mounted in the belly of the aircraft. In the thermal images, seal pups and adults showed up as hot “blips” on a frigid background of ice and frozen earth, presenting an ideal opportunity to compare how humans and automated machine learning approaches detect and count animals in remotely-sensed data. The MaRRS lab computer vision algorithm proved extremely accurate, yielding total seal counts only 2% different than manual counts by humans, even tackling a long-time hurdle in automated detection by consistently discriminating seals within closely packed “piles”.

The above case study is widely applicable to species that seasonally aggregate on land, particularly pinnipeds and colonial seabirds. UAVs, by their very nature, are capable of rapid deployment and can take advantage of temporal windows where weather is good and animals are visible on land. The MaRRS computer vision algorithm operates in the common program ArcMap (ESRI), and is designed for quick modification to apply to other pinnipeds and even entirely different genera. This type of flexible and easily-modifiable model design is critical for practical applications in wildlife management. Algorithm development is time consuming and if time must be taken to extensively retrain a model for each new dataset, many advantages in efficiency are lost over traditional, manual-counting methods.

As UAVs proliferate and more data is collected, analysis becomes a bottleneck for getting relevant information to resource managers and decision makers. Combining UAVs with computer vision is a way to stay ahead of the curve and ensure that big data is an advantage and not a stumbling-block for wildlife management.

In total, 3,355 grey seals were counted in this case study led by Alexander Seymour and his team at the Duke University Marine Laboratory, North Carolina, USA and Fisheries and Oceans Canada. The locations of the identified grey seals are available through the OBIS web site titled “Atlantic grey seal breeding colonies in Hay and Saddle Islands, Nova Scotia” at http://iobis.org/explore/#/dataset/4534. The more detailed information, georeferenced RGB pictures and thermal images are available through the OBIS-SEAMAP web site at http://seamap.env.duke.edu/dataset/1462.

Reference: Seymour, A., Dale, J., Hammill, M., Halpin, P and Johnston, D. 2017. Automated detection and enumeration of marine wildlife using unmanned aircraft systems (UAS) and thermal imagery. Scientific Reports. 7: 45127. https://www.nature.com/articles/srep45127.

Identifying relevant predictors for marine species distribution modelling with MarineSPEED

species distribution modelling predictor selection OBIS data

Climatological conditions are currently changing at an unprecedented rate and anthropogenic activities displace species out of their native area across the globe. Both processes have the potential to alter biological communities and reduce ecosystem services. Knowing under which environmental conditions species may maintain or establish viable populations therefore is more critical than ever. Species distributions are increasingly modelled for conservation and ecological purposes. A better understanding of mechanisms shap- ing species distributions allows for more accurate predictions of future distributions of species in a rapidly changing world.

Thanks to the availability of an increasing number of online distribution records (e.g., OBIS, GBIF), pre-processed environmental data layers (e.g., WorldClim, Climond, Bio-ORACLE, MARSPEC) and modelling algorithms accessible through various statistical packages, SDM has become a widely applied technique in ecology and conservation biology.

Altough the importance for SDM of selecting biologically relevant predictors, and its impact on model uncertainty and transferability has been highlighted by several studies, to date no comprehensive study on the relevance of the predictors of marine species distributions across taxa has been performed.

In this study, Bosch et al. (2017) created the Marine SPEcies with Environmental Data (MarineSPEED) dataset and used it to: (1) identify the most relevant predictors of marine species distributions and (2) identify which parts of the SDM process impact the relevance of predictors the most.

For MarineSPEED, we selected well-studied and identifiable species from all major marine taxonomic groups. Distribution records were compiled from public sources (e.g., OBIS, GBIF, Reef Life Survey) and linked to environmental data from Bio-ORACLE and MARSPEC. Using this dataset, predictor relevance was analysed under different variations of modelling algorithms, numbers of predictor variables, cross-validation strategies, sampling bias mitigation methods, evaluation methods and ranking methods. SDMs for all combinations of predictors from eight correlation groups were fitted and ranked, from which the top five predictors were selected as the most relevant.

We collected two million distribution records from 514 species across 18 phyla. Mean sea surface temperature and calcite are, respectively, the most relevant and irrelevant predictors. A less clear pattern was derived from the other predictors. The biggest differences in predictor relevance were induced by varying the number of predictors, the modelling algorithm and the sample selection bias correction. The distribution data and associated environmental data are made available through the R package marinespeed and at http://marinespeed.org.

Full reference:

  • Bosch S., Tyberghein L., Deneudt K., Hernandez F., & De Clerck O. (2018) In search of relevant predictors for marine species distribution modelling using the MarineSPEED benchmark dataset. Diversity and Distributions, 24. http://dx.doi.org/10.1111/ddi.12668

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