Coastal and marine biodiversity has been declining at an alarming rate in recent years due to anthropogenic activity, climate change, ocean acidification and other factors.
To help protect and preserve these precious ecosystems, the new research project under the name of ANERIS (operAtional seNsing lifE technologies for maRIne ecosystemS) and coordinated by the Institute of Marine Sciences (ICM-CSIC) was launched under the Horizon Europe program.
ANERIS aims to contribute to improving the understanding, monitoring and protection of these ecosystems through technological, scientific and methodological innovation in the fields of marine life-sensing and monitoring.
Pensoft is joining the ANERIS consortium as a leader of WP6 Exploitation, Communication and Networking. The Pensoft team is to develop and implement sustainable communication and dissemination strategies, which will ensure the impactful knowledge exchange between partners and external stakeholders.
In addition, Pensoft is responsible for the development of a long-lasting brand identity of the project, which shall be reached by establishing and maintaining a user-friendly and eye-appealing public website. The overall visual identity of ANERIS will be supported by a set of innovatively-designed promotional materials.
The project
ANERIS project’s intro video: Towards a network of Operational Marine Biology
ANERIS launched in January 2023 and will be running until December 2026 with the support of EUR 10 million of funding provided by the European Union’s Horizon Europe program and the work on the project officially kicked off with the project’s first consortium meeting, which took place on the 8th and 9th of March 2023 in Barcelona, Spain.
The joint mission of the ANERIS partners for the next four years is to build the next generation of marine-sensing instruments and infrastructure for systematic routine measurements and monitoring of oceanic and coastal life, and their rapid interpretation and dissemination to all interested stakeholders.
In total, ANERIS aims to pioneer 11 novel technologies rerelated to marine ecosystem monitoring, data processing and dissemination:
NANOMICS – NAnopore sequeNcing for Operational Marine genomICS
MARGENODAT – workflows for the MARine GENOmics DAta managemenT
SLIM-2.0 – A Virtual Environment for genomic data analysis (ANERIS extended version)
EMUAS – Expandable Multi-imaging Underwater Acquisition System
AIES-ZOO – Automatic Information Extraction System for ZOOplankton images
AIES-PHY – Automatic Information Extraction System for PHYtoplankton images
ATIRES – Automatic underwaTer Image REstoration System
AIES-MAC – Automatic Information Extraction System for MACroorganisms
AMAMER – Advanced Multiplatform App for Marine lifE Reporting
AMOVALIH – Advanced Marine Observations VALidation-Identification system based on Hybrid intelligence
AWIMAR – Adaptive Web Interfaces for MARine life reporting, sharing and consulting
These technologies will be validated across four ANERIS case studies which aim to bridge the gaps between existing technologies and incorporate them into a functional technological framework:
High-temporal resolution marine life monitoring in research infrastructure observatories;
Improved spatial and temporal resolution of marine life monitoring based on genomics;
Large scale marine participatory actions;
Merging imaging and genomic information in different monitoring scenarios.
The final goal of the project through the creation and validation of these novel technologies and involving academia, industry, governments and civil society, is to build up the concept of Operational Marine Biology (OMB) to provide faster, higher quality, reliable, and accessible marine and coastal life data. OMB opens the door for near-real-time marine observations, data interpretation and decision making based on that data.
International Consortium
The interdisciplinary ANERIS consortium consists of 25 partnering organisations from 13 countries around Europe, the Mediterranean basin and Israel, bringing diverse expertise spanning from robotics, biooptics, marine biology and genomics, to programming and sustainability.
Many partners represent acclaimed scientific institutions with rich experience in collaboration in EU projects, specifically in the fields of marine research.
The Southern Flying Squirrel (Glaucomys volans) was spotted in an area where forestry and silvicultural activities are carried out for the sustainable exploitation of pine logging and timber.
The presence of The Southern Flying Squirrel (Glaucomys volans) was documented in Honduras for the first time after 43 years. The record is from a site of the forest management plan called “Las Lechuzas”, municipality of Concordia, department of Olancho.
Apart from this newly confirmed location, the species has also been recorded in Zambrano, department of Francisco Morazán in 1935, in Gracias, department of Lempira, and finally in the Department of paradise in 1979. Based on these records, Honduras is considered the southernmost distribution known for this species.
G.volans before it started to glide to the oaks. Photograph by MATC.
The discovery was possible thanks to a project of El Aserradero Sansone, a company focused on sustainable forestry activities in Honduras, and is published in a research article in the peer-reviewed journal Check List.
This finding confirmed that there is at least one population of G. volans in the country, at the Las Lechuzas site, which is currently also the southernmost locality known in its global distribution.
The species has been assessed as Least Concern by the IUCN (meaning it has stable populations), but is considered Data Deficient on the Red List of Honduran species. Considering the low number of records and the high rate of destruction of pine forests in Honduras, G. volans is a priority for conservation in the country.
Part of the team that helped to encounter the squirrel. Photograph by MATC.
In support of the conservation of the biodiversity of Las Lechuzas, the company Sansone is now committed to giving priority to the conservation of G. volans in the area. The use of artificial shelters for G. volans is also being studied, as the animal is at greater risk when its nests are disturbed.
Based on recommendations suggested in the study, Sansone will work to increase the quantity and quality of tree seedlings that will grow in the canopy and educate people in the community about the need to protect pine ecosystems and rare animals. Additionally, within the 3,139.62 ha of the management plan of Las Lechuzas, there are 836.63 ha that have been declared as hydrological protection zones. Currently, there is no record of G. volans in any protected area of Honduras.
“As a professional with an experience of 43 years, I capitalize on the detection of the Flying Squirrel as an event that opens the doors to the true dimension posed by the Honduran forest law in the proper administrative management. That includes biodiversity conservation and protection and rationality of the protection of natural resources. The latter turns out to be of greater importance in view of the strong social pressures in favor of the conversion of the use of forest land destined for extensive agriculture and livestock, as well as the environmental impacts caused by climate change that is being sustained by the mismanagement of our resources,”
says José Muñoz, one of the authors in the study.
About El Aserradero Sansone:
El Aserradero Sansone was founded in 1957, characterized by compliance with the laws of Honduras, especially those related to forest management. It has developed an evolutionary and progressive process of achievements in the implementation of management plans, including such related to the evaluation of environmental impacts.
In this sense, the environmental importance in the management of natural resources has continued to promote evolution, defining the need to venture into aspects related to the conservation of flora and fauna as well as the incidence of climatic and environmental factors in the administration of natural resources. Within this responsibility, the last challenge that the company Sansone is welcoming with great optimism lies in adhering to the international criteria and indicators of the forest certification process through the principles of FSC (Forest Stewardship Council) and through the GFA company of Hamburg, Germany.
Research article:
Turcios-Casco MA, Hernández GS, Mancía FE, Molinero CF, Muñoz J, López CM, Ordóñez-Garza N (2023) Unseen for 43 years! A new occurrence of Glaucomys volans (Linnaeus, 1758) (Rodentia, Sciuridae) in Honduras. Check List 19(1): 133-139. https://doi.org/10.15560/19.1.133
Spectacular subtropical montane forest scenery in Yushan National Park. Credit: Ms. Wen-Ling Tsai
Montane forests, known as biodiversity hotspots, are among the ecosystems facing threats from climate change. To comprehend potential impacts of climate change on birds in these forests, researchers set up automatic recorders in Yushan National Park, Taiwan, and developed an AI tool for species identification using bird sounds. Their goal is to analyze status and trends in animal activity through acoustic data.
Compared to traditional observation-based methods, passive acoustic monitoring using automatic recorders to capture wildlife sounds provides cost-effective, long-term, and systematic alternative for long-term biodiversity monitoring.
The authors deployed six recorders in Yushan National Park, Taiwan, a subtropical montane forest habitat with elevations ranging from 1,200 to 2,800 meters. From 2020 to 2021, they recorded nearly 30,000 hours of audio files with abundant biological information.
An automatic recorder was installed on a tree to capture the surrounding soundscape. Credit: Ph.D. Candidate Shih-Hung Wu
However, analyzing this vast dataset is challenging and requires more than human effort alone.
To tackle this challenge, the authors utilized deep learning technology to develop an AI tool called SILIC that can identify species by sound.
SILIC can quickly pinpoint the precise timing of each animal call within the audio files. After several optimizations, the tool is now capable of recognizing 169 species of wildlife native to Taiwan, including 137 bird species, as well as frogs, mammals, and reptiles.
In this study, authors used SILIC to extract 6,243,820 vocalizations from seven montane forest bird species with a high precision of 95%, creating the first open-access AI-analyzed species occurrence dataset available on the Global Biodiversity Information Facility. This is the first open-access dataset with species occurrence data extracted from sounds in soundscape recordings by artificial intelligence.
The Gray-chinned Minivet (left) displays a secondary non-breeding season peak (right) which is possibly related to flocking behavior. Credit: Shih-Hung Wu, Ph.D. Candidate
The dataset unveils detailed acoustic activity patterns of wildlife across both short and long temporal scales. For instance, in diel patterns, the authors identify a morning vocalization peak for all species. On an annual basis, most species exhibit a single breeding season peak; however, some, like the Gray-chinned Minivet, display a secondary non-breeding season peak, possibly related to flocking behavior.
As the monitoring projects continue, the acoustic data may help to understand changes and trends in animal behavior and population across years in a cost-effective and automated manner.
The sound of Gray-chinned Minivet. Credit: Ph.D. Candidate Shih-Hung Wu
The authors anticipate that this extensive wildlife vocalization dataset will not be valuable only for the National Park’s headquarters in decision-making.
“We expect our dataset will be able to help fill the data gaps of fine-scale avian temporal activity patterns in montane forests and contribute to studies concerning the impacts of climate change on montane forest ecosystems,”
they say.
Original source:
Wu S-H, Ko JC-J, Lin R-S, Tsai W-L, Chang H-W (2023) An acoustic detection dataset of birds (Aves) in montane forests using a deep learning approach. Biodiversity Data Journal 11: e97811. https://doi.org/10.3897/BDJ.11.e97811
You can also follow Biodiversity Data Journal on Twitter and Facebook.
The Cinereous Vulture (Aegypius monachus) – also known as Black Vulture, Monk Vulture or Eurasian Black Vulture – is the largest bird of prey in Europe.
Globally classified as Near Threatened, its populations in southern Europe, once abundant, have been experiencing a dramatic decline since the late 1800s. So dramatic, in fact, that by the mid-1900s, these birds had already been nowhere to be seen throughout most of their distributional range across the Old Continent. In Bulgaria, the species has been considered locally extinct since 1985.
Thanks to the re-introduction initiative that was started in 2015 by three Bulgarian non-governmental organisations: the leading and oldest environmental protection NGO in Bulgaria: Green Balkans, the Fund for Wild Flora and Fauna and the Birds of Prey Protection Society, the species is now back in the country.
By mid-2022, the team imported a total of 72 individuals from Spain and European zoos, before releasing them in strategically-chosen sites in the Eastern Balkan Mountains and the Vrachanski Balkan Nature Park in Northwestern Bulgaria.
The team brought 63 immatures from Spain, where the birds had been found in distress and rehabilitated in aviaries. The other nine juveniles were captive-bred in zoos, and then released by means of hacking, which involves an artificial nest, from where the fledglings can gradually ‘’take off” to a life in the wild.
The re-introduction campaign to date is presented in a research article, published in the open-access Biodiversity Data Journal. There, the scientists led by Ivelin Ivanov (Green Balkans), report on and discuss the effectiveness and challenges of the different release methods and offer tips on the conservation and re-introduction.
For example, hacking proved to be inefficient for establishing an entirely new core (or nucleus) population of Cinereous Vultures in the Balkan Mountains in Bulgaria. It did not work for supplementing a small settled group of individuals either.
Instead, the team recommend the aviary method and delayed release, where captive-bred birds are introduced to the new locality after a period of acclimatisation, where the birds can gain life experience to the local environment.
“The Cinereous Vulture re-introduction establishment phase in Bulgaria in the two first release sites is running according to the plan, and the first results are satisfactory,”
the scientists comment.
“Two distinct nuclei are now created, and the species started breeding, which might be a reason to up-list it in the Red Data Book of Bulgaria from ’Extinct’ to ‘Critically Endangered.’”
These two newly created breeding nuclei of the Cinereous Vulture in Bulgaria are the second and third of their kind in the Balkan Peninsula.
“Following a dramatic decline throughout the 20th century for decades, the species had remained in only one breeding colony in Dadia-Lefkimi-Soufli Forest National Park in north-eastern Greece. Now, exchange between the three colonies will facilitate the exchange of individuals, ensure long-term stability, and give rise to the regional population,”
the authors of the study say.
However, the team points out that further monitoring and modelling and adaptive management are indispensable for the long-term persistence of the new national population. Now that there is already evidence that the imported vultures have been successfully breeding in Bulgaria, there is one step left before it can be officially confirmed that the Cinereous Vulture species has successfully re-established in the country. This conclusion can only be made after the core breeding populations begin to produce about ten chicks every year and after the locally fledged individuals begin to reproduce on their own. Such results are expected by 2030.
The re-introduction of the Cinereous Vulture is the latest in a series of conservation projects focused on birds of prey in Bulgaria.
First, in a programme that started in 2009, the Griffon Vulture was successfully re-introduced in Bulgaria after about 50 years of “extinction”. In fact, the team took a lot of the know-how and methods used in that project to apply in the present project. The success story was published in a research paper in the Biodiversity Data Journal in 2021.
In fact, the very same day in 2021 saw two publications in the Biodiversity Data Journal that reported on re-introduction successes involving birds of prey in Bulgaria, which had gone missing for decades. The second instance was the discovery of the first nesting Saker Falcons in twenty years
Both scientific publications are part of a dynamic ‘living’ collection, titled “Restoration of species of conservation importance”, whose aim is to collate publicly available research studies reporting on the reintroduction and/or restocking of animal and plant species of conservation importance around the world. The collection was inspired by the “International Scientific Conference on Restoration of Conservation-Reliant Species and Habitats” held in Sofia, Bulgaria, in 2020.
“The restoration of species is one of the most important conservation tools in the context of constantly intensified human-driven global biodiversity loss. The reintroduction/restocking activities are related to significant research and data gathering before and during the work process, which ensures their sustainable success,”
explain the collection editors.
Research article:
Ivanov I, Stoynov E, Stoyanov G, Kmetova–Biro E, Andevski J, Peshev H, Marin S, Terraube J, Bonchev L, Stoev IP, Tavares J, Loercher F, Huyghe M, Nikolova Z, Vangelova N, Stanchev S, Mitrevichin E, Tilova E, Grozdanov A (2023) First results from the releases of Cinereous Vultures (Aegypius monachus) aiming at re-introducing the species in Bulgaria – the start of the establishment phase 2018–2022. Biodiversity Data Journal 11: e100521. https://doi.org/10.3897/BDJ.11.e100521
You can also follow Biodiversity Data Journal on Twitter and Facebook.
Apart from communication, dissemination and data management tasks, within SOLO, Pensoft is also responsible for the development of the key project output: the SOLO platform
As the foundation of our food systems, healthy soils are essential for life on Earth. They provide clean water and habitats for biodiversity while contributing to climate resilience and support our cultural heritage and landscapes and are the basis of our economy and prosperity.
Soils are under multiple pressures, including climate change, urbanisation, pollution, overexploitation, nutrient mining and biodiversity loss with the European Commission estimating that under current management practices, it’s between 60% and 70% of our soils that are unhealthy.
funding an ambitious research and innovation programme with a strong social science component;
putting in place an effective network of 100 living labs and lighthouses to co-create knowledge, test solutions and demonstrate their value in real-life conditions;
developing a harmonised framework for soil monitoring in Europe;
raising people’s awareness on the vital importance of soils.
Achieving those objectives requires a direct involvement of a wide range of stakeholders, bringing together multiple perspectives in ecological, environmental, economic and social contexts.
The project
SOLO launched in December 2022 and will be running until November 2027 with the support of 5 million euros provided by the European Union’s Horizon Europe program.
SOLO will identify current knowledge gaps, drivers, bottlenecks, and novel research and innovation approaches to be considered in the European Soil Mission research and innovation roadmap.
The project aims to create a knowledge hub for soil health research and innovation that will last beyond the project’s lifespan by establishing strategic partnerships and by implementing a participatory and transparent process.
The project will implement Think Tanks, one for each Mission objective, with the aim of co-creating knowledge and identifying the knowledge gaps, drivers, bottlenecks, and novel approaches in terms of research and innovation.
The Think Tanks will consist of groups of experts who will together tackle the issues regarding soil health, set out in the EU Mission ‘A Soil Deal for Europe’. Together with an open digital platform, based on Pensoft’s ARPHA Writing Tool, the Think Tanks will function as an operational tool for implementing a participatory process that will last beyond SOLO’s lifespan.
The project will engage users at regional, national and European level to support the co-design of comprehensive research and innovation roadmaps for the Soil Mission and identify knowledge gaps and novel avenues for European soil research and innovation in the context of the Soil Mission objectives.
Furthermore, SOLO will identify, describe and assess the drivers and barriers to soil health in Europe, develop dynamic roadmapsas effective research and innovation agendas for the Soil Mission with a particular focus on the integration and synthesis across sectors.
The 3rd Global Soil Biodiversity Conference (March 2023; Dublin, Ireland) saw several talks by researchers involved in the SOLO project, while communication materials provided additional information to the delegates who stopped by the Pensoft exhibition stand.
You can find out more about the project on the Soils for Europe (SOLO) website: soils4europe.eu. Stay up to date with the project’s progress on Twitter (@soils4europe) and LinkedIn (/Soils-for-Europe).
The innovative open-access digital publishing platform provides a forum for open review and co-creation of the European Mission Soil research and innovation roadmaps in support of more integrative and encompassing policies aiming to achieve improvements in soil health and a thriving environment for soil-related research in Europe.
The consortium
SOLO’s consortium comprises a European network of established professionals from the academic and non-academic fields from various backgrounds, who have agreed to work collaboratively to fulfil the objectives set by the EU Mission “A Soil Deal for Europe” which aims to create a shared research and innovation vision that will accelerate Europe’s trajectory towards sustainable soil management and restoration as part of a wider, green transition in rural and urban areas.
Ambitious goals have been set by the European Union, in order to tackle the biodiversity conservation challenges over the coming decade. No less ambitious are the goals of the Horizon Europe project SELINA, which is one of the current major initiatives looking in the same direction.
SELINA (Science for Evidence-based and Sustainable Decisions about Natural Capital) is a transdisciplinary project aimed at promoting the conservation of biodiversity, enhancing ecosystem conditions, and supporting the sustainable use of the environment through evidence-based decision-making.
As an experienced science communicator and open-science publisher, Pensoft will be leading the project’s communication and dissemination activities.
“Ecosystem services is one of the topics that Pensoft has been involved in for more than 10 years, so it was only natural for us to continue our work as a communicator of scientific information in the ambitious SELINA project as well,”
says Prof Pavel Stoev, COO at Pensoft.
“We have already collaborated with many of the partners within the earlier EC Horizon 2020 project ESMERALDA, which concluded with the launch of a pan-European network of scientific institutions engaged with biodiversity conservation and ecosystem services.
In addition, Pensoft has been strongly connected to the community through the scholarly journal One Ecosystem, which is supported by Ecosystem Services Partnership, and offers an opportunity for scientists in the field to publish their results in a new and innovative way.”
he adds.
The project
SELINA was launched in July 2022 and will run for 5 years. Having received EUR 13 million in funding, the project is seen as an unprecedented opportunity for smart, cost-effective, and nature-based solutions to historic societal challenges such as climate change, biodiversity loss, and food security.
One of the project’s main objectives is to identify biodiversity, ecosystem condition, and ecosystem service factors that can be successfully integrated into decision-making processes in both the public and private sectors.
To achieve this objective, SELINA will develop, test, and integrate new and existing knowledge, including methodological approaches to improve biodiversity, ecosystem condition, and ecosystem service information uptake by decision-makers.
In addition, the project will utilise EU-wide workshops and multi-disciplinary Communities of Practice involving a wide range of stakeholders, including scientists, policymakers, business leaders, and civil society organisations.
The project will also organise Demonstration Projects on biodiversity, ecosystem condition, and ecosystem service integration in decision-making and co-create a Compendium of Guidance that will allow stakeholders to make full use of the project’s results and fit-for-purpose recommendations with real-world applications in policy-making and business decisions.
International consortium
SELINA project brings together experts from 50 partnering organisations across all European Union member states, Norway, Switzerland, Israel, and the United Kingdom.
The project comprises a Pan-European and transdisciplinary network of professionals from the academic and non-academic sectors with various (inter)disciplinary backgrounds – including ecologists, economists, social scientists – who have agreed to work collaboratively to support transformative change based on evidence-based decision-making related to the management of natural resources.
Find out more about the project on the SELINA website: project-selina.eu/.
Apart from science communication, Pensoft is also tasked with the development and maintenance of the CANOPY platform, whose aim is to support policymakers and national and regional authorities
Dedicated to bridging the gap between science, policy, industry and society, Pensoft is striving to maximise ForestPaths’ impact in meeting Europe’s climate and biodiversity targets
The backdrop
The European Union (EU) has set ambitious targets to reduce greenhouse gas emissions by at least 55% in 2030 and to become climate neutral by 2050, which require urgent and major societal and economic reforms.
In the meantime, the EU also aims to protect biodiversity and reverse the degradation of ecosystems, while using natural resources to mitigate climate change.
ForestPaths – a recently started Horizon Europe project will help meet Europe’s climate and biodiversity targets by providing clear policy options that enable European forests and the forest-based sector to contribute to climate change mitigation, while conserving their biodiversity and sustaining the services they provide to people.
As an experienced science communicator, Pensoft is dedicated to maximising ForestPaths’ impact. The team will do so by means of tailored communication, dissemination and exploitation strategies aimed at sharing the project’s results with relevant stakeholder groups.
Furthermore, Pensoft is tasked with the development and long-term maintenance of the CANOPY platform, whose aim is to support policymakers and national and regional authorities by granting them access to the knowledge and scientific evidence acquired within ForestPaths long after the project is finalised.
Building on these options, the project will collaborate with policymakers and key authorities through a series of Policy labs, where the partners will co-design policy pathways, which will then be analysed with next-generation integrated assessment techniques.
Lastly, ForestPaths will apply this framework for an all-round assessment of the climate mitigation potential of European forests and the forest-based sector.
Aerial view of a forest road.
The ForestPaths legacy
ForestPaths’ policy pathways – as well as their supporting information and evidence – will be made openly available through the project’s policy-support platform CANOPY, hosted on the ForestPaths website.
The platform, whose launch is scheduled for 2026, will feature an interactive policy analysis tool explaining the policy pathways and showcasing their implications, as well as providing detailed assessment results and policy recommendations in an easily accessible manner. Its long-term mission is to become the go-to place for easily accessible assessment results and policy recommendations.
“We are excited to be doing our part for Europe’s fight for climate neutrality by extending ForestPaths reach to policy, industry and society at large! As an open-access scientific publisher engaged in about 50 environmental research projects, Pensoft echoes ForestPaths’ aim to support the EU’s climate neutrality transition through what we are sure will be a prolific international research collaboration,” says ForestPaths’ WP7 leader Anna Sapundzhieva.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.
In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.
“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.
“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”
he adds.
At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.
Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL.
As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions.
Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.
Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.
On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.
“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”
Guest blog post by Daniela N. López, Eduardo Fuentes-Contreras, Cecilia Ruiz, Sandra Ide, Sergio A. Estay
Understanding the history of non-native species arrivals to a country can shed light on the origins, pathways of introduction, and the current and future impacts of these species in a new territory. In this sense, collecting this information is important, and sometimes essential, for researchers and decision makers. However, in most cases, reconstructing this history takes a lot of work. Finding antique references is hard work. To add more complexities, changes in the taxonomy of species or groups could be frustrating as we try to track the moment when a species was referenced in the country for the first time, sometimes centuries ago. Of course, we only learned about these issues when, almost seven years ago, we thought that compiling a database for the exotic insects established in Chile would be interesting to people working on invasive species in the country.
Tremex fuscicornis caught in Chile. Photo by Sergio Estay
First, we collected information from physical and electronic books and journals available in our institutional libraries, but soon we noticed that we needed a more significant effort. In Chile, the National Library and The National Congress library allowed us to review and collect information from texts, in many cases, over a hundred years old. We also had to request information from foreign specialized libraries and bookstores. Sometimes, we had to negotiate with private collectors to buy antique books or documents. When we figured the first version of the database was ready, we began a second step for detecting errors, correcting the taxonomy, and completing the information about the reported species.
Ctenarytaina eucalypti individuals and damage in Chile. Photo by Sergio Estay
The analysis began when we finally completed the database. What types of questions could we answer using this data? Was the database complete enough to detect historical, biogeographic, and ecological patterns? Two competing hypotheses were the starting point for the study at this stage. On the one hand, the species that dominated the non-native insect assemblage could have come from original environmental conditions that matched Chile’s. Or, the pool of non-native insects arrived using pathways associated with the country’s economic activities, regardless of their origin.
We found records of almost 600 non-native insect species established in continental Chile. Most species corresponded to Hemiptera (true bugs and scales, among others) from Palaearctic origin and were linked to agriculture and forestry, as we initially hypothesized. These characteristics point to the central role of intercontinental human-mediated transport in structuring non-native insect assemblages in Chile. Non-native insect introductions began immediately after the arrival of Europeans to the central valley of Chile and have shown an enormous acceleration since 1950. Using data on the economic history of Chile, we can preliminary link this acceleration with the strong development in agriculture and forestry in Chile after World War II and the increase in intercontinental air traffic.
Exotic aphids in garden in Chile. Photo by Sergio Estay
The development and analysis of this database gave us some preliminary answers about the ecology of invasive insect species and opened the door to new questions. Also, this is a work in progress. We need the scientific community’s support to improve and correct the records, provide new reports and collect further references to support the database. Our data and analysis may be representative of other countries in South America. Similarities between our countries can facilitate using this information to manage recent introductions and prevent significant economic, social, or environmental damage.
Reference
López DN, Fuentes-Contreras E, Ruiz C, Ide S, Estay SA (2023) A bug’s tale: revealing the history, biogeography and ecological patterns of 500 years of insect invasions. NeoBiota 81: 183-197. https://doi.org/10.3897/neobiota.81.87362
EIVE 1.0 is the most comprehensive system of ecological indicator values of vascular plants in Europe to date. It can be used as an important tool for continental-scale analyses of vegetation and floristic data.
Geographic coverage of the 31 ecological indicator value systems that entered the calculation of the consensus system of EIVE 1.0 (image from the original article).
It took seven years and hundreds of hours of work by an international team of 34 authors to develop and publish the most comprehensive system of ecological indicator values (EIVs) of vascular plants in Europe to date.
EIVE 1.0 provides the five most-used ecological indicators, M – moisture, N – nitrogen, R – reaction, L – light and T – temperature, for a total of 14,835 vascular plant taxa in Europe, or between 13,748 and 14,714 for the individual indicators. For each of these taxa, EIVE contains three values: the EIVE niche position indicator, the EIVE niche width indicator and the number of regional EIV systems on which the assessment was based. Both niche position and niche width are given on a continuous scale from 0 to 10, not as categorical ordinal values as in the source systems.
Evidently, EIVE can be an important tool for continental-scale analyses of vegetation and floristic data in Europe.
It will allow to analyse the nearly 2 million vegetation plots currently contained in the European Vegetation Archive (EVA; Chytrý et al. 2016) in new ways.
Since EVA apart from elevation, slope inclination and aspect hardly contains any in situ measured environmental variables, the numerous macroecological studies up to date had to rely on coarse modelled environmental data (e.g. climate) instead. This is particularly problematic for soil variables such as pH, moisture or nutrients, which can change dramatically within a few metres.
Here, the approximation of site conditions by mean ecological indicator values can improve the predictive power substantially (Scherrer and Guisan 2019). Likewise, in broad-scale vegetation classification studies, mean EIVE values per plot would allow a better characterisation of the distinguished vegetation units. Lastly, one should not forget that most countries in Europe do not have a national EIV system, and here EIVE could fill the gap.
Violin plots showing largely continuous value distributions of the niche position and niche width values of the five indicators in EIVE 1.0 (image from the original article).
Almost on the same day as EIVE 1.0 another supranational system of ecological indicator values in Europe has been published by Tichý et al. (2023) with a similar approach.
Thus, it will be important for vegetation scientists in Europe to understand the pros and cons of both systems to allow the wise selection of the most appropriate tool:
EIVE 1.0 is based on 31 regional EIV systems, while Tichý et al. (2023) uses 12.
Both systems provide indicator values for moisture, nitrogen/nutrients, reaction, light and temperature, while Tichý et al. (2023) additionally has a salinity indicator.
Tichý et al. (2023) aimed at using the same scales as Ellenberg et al. (1991), which means that the scales vary between indicators (1–9, 0–9, 1–12), while EIVE has a uniform interval scale of 0–10 for all indicators.
Only EIVE provides niche width in addition to niche position. Niche width is an important aspect of the niche and might be used to improve the calculation of mean indicator values per plot (e.g. by weighting with inverse niche width).
The taxonomic coverage is larger in EIVE than in Tichý et al. (2023): 14,835 vs. 8,908 accepted taxa and 11,148 vs. 8,679 species.
EIVE provides indicator values for accepted subspecies, while Tichý et al. (2023) is restricted to species and aggregates. Separate indicator values for subspecies might be important for two reasons: (a) subspecies often strongly differ in at least one niche dimension; (b) many of the taxa now considered as subspecies have been treated at species level in the regional EIV systems.
Tichý et al. (2023) added 431 species not contained in any of the source systems based on vegetation-plot data from the European Vegetation Archive (EVA; Chytrý et al. 2016) while EIVE calculated the European indicator values only for taxa occurring at least in one source system.
While both systems present maps that suggest a good coverage across Europe, Tichý et al. (2023)’s source systems largely were from Central Europe, NW Europe and Italy, but, unlike EIVE, these authors did not use source systems from the more “distal” parts of Europe, such as Sweden, Faroe Islands, Russia, Georgia, Romania, Poland and Spain, and they used only a small subset of indicators of the EIV systems of Ukraine, Greece and the Alps.
In a validation with GBIF-derived data on temperature niches, Dengler et al. (2023) showed that EIVE has a slightly stronger correlation than Tichý et al. (2023)’s indicators (r = 0.886 vs. 0.852).
The correlation of EIVE-T values of species with GBIF-derived temperature niche data was high and even higher when restricting the calculation to those species whose consensus value was based on at least four sources (image from the original article).
How did EIVE manage to integrate all EIV systems in Europe that contained at least one of the selected indicators for vascular plants, while Tichý et al. (2023) used only a small subset?
This difference is mainly due to a more complex workflow in EIVE (which also was one of the reasons why the preparation took so long). First, Tichý et al. (2023) restricted their search to EIV systems and indicators that had the same number of categories as the “original” Ellenberg system.
Second, from these they discarded those that showed a too low correlation with Ellenberg. By contrast, EIVE’s workflow allowed the use of any system with an ordinal (or even metric) scale, irrespective of the number of categories or the initial match with Ellenberg et al. (1991).
EIVE also did not treat one system (Ellenberg) as the master to assess all others but considered each of them equally valid. While indeed the individual EIV systems are often quite inconsistent, i.e. even if they refer to Ellenberg, the same value of an indicator in one system might mean something different in another system, our iterative linear optimisation enabled us to adjust all 31 systems for the five indicators to a common basis.
This in turn allowed deriving EIVE as the consensus system of all the source systems. The fact that in our validation of the temperature indicator, EIVE performed better than Tichý et al. (2023) and much better than most of the regional EIV systems might be attributable to the so-called “wisdom of the crowd”, going back to the statistician Francis Galton who found that averaging numerous independent assessments (even by laymen) of a continuous quantity can leads to very good estimates of the true value.
Apart from the indicator values themselves, EIVE has a second main feature that might not be so obvious at first glance, but which actually took the EIVE team, including several taxonomists, more time than the workflow to generate the indicator values themselves: the taxonomic backbone. EIVE for vascular plants is fully based on the taxonomic concept (including the synonymic relationships) of the Euro+Med Plantbase.
However, since Euro+Med lacks an important part of taxa that are frequently recorded in vegetation plots, to make our backbone fully usable to vegetation science, we expanded it beyond Euro+Med to something called “Euro+Med augmented”. We particularly added hybrids, neophytes and aggregates, three groups of plants hitherto only very marginally covered in Euro+Med. All additions were done by experts consistently with the taxonomic concept of Euro+Med and are fully documented. Likewise, many additional synonym relationships had to be added that were missing in Euro+Med.
Finally, we implemented the so-called “concept synonymy” (see Jansen and Dengler 2010), which allows the assignment of the same name from different sources to different accepted names (“taxonomic concepts”). This applies mainly to nested taxa that are treated at different levels in different sources, e.g. once as species with several subspecies, once as aggregate with several species. However, there are also some cases of misapplied names (i.e. names that were not used in agreement with their nomenclatural type in certain EIV systems). Such cases generally cannot be solved by the various tools for automatic taxonomic cleaning, but require experts who make a case-by-case decision.
The whole taxonomic workflow of EIVE is fully transparent with an R code that “digests”:
(a) the names as they are in the source systems,
(b) the official Euro+Med database and
(c) tables that document our additions and modifications (with reasons and references).
This comprehensive documentation will allow continuous and efficient improvement in the future, be it because of taxonomic novelties adopted in Euro+Med or because EIVE’s experts decide to change certain interpretations. That way, “Euro+Med augmented” and the accompanying R-based workflow can also be a valuable tool for other projects that wish to harmonise plant taxonomic information from various sources at a continental scale, e.g. in vegetation-plot databases such as GrassPlot (Dengler et al. 2018) and EVA (Chytrý et al. 2016).
The publication of EIVE 1.0 is not the endpoint, but rather a starting point for future developments in a community-based approach.
Together with interested colleagues from outside, the EIVE core team plans to prepare better and more comprehensive releases of EIVE in the future, including updates to its taxonomic backbone.
Future releases of EIVE will be published in fixed versions, typically together with a paper that describes the changes in the content.
As steps for the next two years, we anticipate that we will first add further taxa (bryophytes, lichens, macroalgae) and some additional indicators, both of which are relatively easy with our established R-based workflow. Then we plan EIVE 2.0 that will use the approx. 2 million vegetation plots in EVA (Chytrý et al. 2016) to re-calibrate EIVE for all taxa (see https://euroveg.org/requests/EVA-data-request-form-2022-02-10-Dengleretal.pdf).
We invite you to get into contact with us if you have:
(a) a new or overlooked indicator value system for any taxonomic group in Europe and adjacent areas (including comprehensive datasets of measured environmental data in vegetation plots);
(b) suggestions for improvements of our taxonomic backbone;
(c) a paper idea in the EIVE context that you would like to realise together with the EIVE core team (since everything is OA, you can, of course, use EIVE 1.0 for any possible purpose without notifying us as long as you cite EIVE properly).
Last but not least, any test of the validity and performance of EIVE, alone or in comparison with Tichý et al. (2023), with in situ measured environmental variables, locally or even continentally, would be most welcome.
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This Behind the paper post refers to the article Ecological Indicator Values for Europe (EIVE) 1.0 by Jürgen Dengler, Florian Jansen, Olha Chusova, Elisabeth Hüllbusch, Michael P. Nobis, Koenraad Van Meerbeek, Irena Axmanová, Hans Henrik Bruun, Milan Chytrý, Riccardo Guarino, Gerhard Karrer, Karlien Moeys, Thomas Raus, Manuel J. Steinbauer, Lubomir Tichý, Torbjörn Tyler, Ketevan Batsatsashvili, Claudia Bita-Nicolae, Yakiv Didukh, Martin Diekmann, Thorsten Englisch, Eduardo Fernandez Pascual, Dieter Frank, Ulrich Graf, Michal Hájek, Sven D. Jelaska, Borja Jiménez-Alfaro, Philippe Julve, George Nakhutsrishvili, Wim A. Ozinga, Eszter-Karolina Ruprecht, Urban Šilc, Jean-Paul Theurillat, and François Gillet published in Vegetation Classification and Survey (https://doi.org/10.3897/VCS.98324).
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Brief personal summaries:
Jürgen Dengler is a Professor of Vegetation Ecology at the Zurich University of Applied Science (ZHAW) in Wädenswil, Switzerland. Among others, he cofounded the European Vegetation Database (EVA), the global vegetation-plot database “sPlot” and the “GrassPlot” database of the Eurasian Dry Grassland Group. His major research interests are grassland ecology, grassland conservation, biodiversity patterns, macroecology, vegetation change, broad-scale vegetation classification, methodological developments in vegetation ecology and ecoinformatics.
Florian Jansen is a Professor of Landscape Ecology at the University of Rostock, Germany. His research interests are vegetation ecology and dynamics, mire ecology including greenhouse gas emissions, and numerical ecology with R. He (co-)founded the German Vegetation Database vegetweb.de, the European Vegetation Database (EVA), and the global vegetation-plot database “sPlot”. He wrote the R package eHOF for modelling species response curves along one-dimensional ecological gradients.
François Gillet is an Emeritus Professor of Community Ecology at the University of Franche-Comté in Besançon, France. His major research interests are vegetation diversity, ecology and dynamics, grassland and forest ecology, integrated synusial phytosociology, numerical ecology with R, dynamic modelling of social-ecological systems.
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References:
Chytrý, M., Hennekens, S.M., Jiménez-Alfaro, B., Knollová, I., Dengler, J., Jansen, F., Landucci, F., Schaminée, J.H.J., Aćić, S., (…) & Yamalov, S. 2016. European Vegetation Archive (EVA): an integrated database of European vegetation plots. Applied Vegetation Science 19: 173–180.
Dengler J, Wagner V, Dembicz I, García-Mijangos I, Naqinezhad A, Boch S, Chiarucci A, Conradi T, Filibeck G, … Biurrun I (2018) GrassPlot – a database of multi-scale plant diversity in Palaearctic grasslands. Phytocoenologia 48: 331–347.
Dengler, J., Jansen, F., Chusova, O., Hüllbusch, E., Nobis, M.P., Van Meerbeek, K., Axmanová, I., Bruun, H.H., Chytrý, M., (…) & Gillet, F. 2023. Ecological Indicator Values for Europe (EIVE) 1.0. Vegetation Classification and Survey 4: 7–29.
Ellenberg H, Weber HE, Düll R, Wirth V, Werner W, Paulißen D (1991) Zeigerwerte von Pflanzen in Mitteleuropa. Scripta Geobotanica 18: 1–248.
Jansen F, Dengler J (2010) Plant names in vegetation databases – a neglected source of bias. Journal of Vegetation Science 21: 1179–1186.
Midolo, G., Herben, T., Axmanová, I., Marcenò, C., Pätsch, R., Bruelheide, H., Karger, D.N., Acic, S., Bergamini, A., Bergmeier, E., Biurrun, I., Bonari, G., Carni, A., Chiarucci. A., De Sanctis, M., Demina, O., (…), Dengler, J., (…) & Chytrý, M. 2023. Disturbance indicator values for European plants. Global Ecology and Biogeography 32: 24–34.
Scherrer D, Guisan A (2019) Ecological indicator values reveal missing predictors of species distributions. Scientific Reports 9: Article 3061.
Tichý, L, Axmanová, I., Dengler, J., Guarino, R., Jansen, F., Midolo, G., Nobis, M.P., Van Meerbeek, K., Aćić, S., (…) & Chytrý, M. 2023. Ellenberg-type indicator values for European vascular plant species. Journal of Vegetation Science 34: e13168.
