Unraveling nature’s chorus: AI detects bird sounds in Taiwan’s montane forests

Researchers developed an AI tool which identifies 169 species native to Taiwan from the sound of their calls.

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.

Prof. Hsueh-Wen Chang and Ph.D. Candidate Shih-Hung Wu from National Sun Yat-Sen University, Taiwan, Dr. Ruey-Shing Lin, Assistant Researcher Jerome Chie-Jen Ko from the Endemic Species Research Institute, and Ms. Wen-Ling Tsai from Yushan National Park Headquarters have published a paper in the open access journal Biodiversity Data Journal, detailing their use of AI to detect 6 million bird songs.

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.

Endangered vulture returns to Bulgaria after being extinct for 36 years

Preliminary results from the releases of Cinereous Vultures (Aegypius monachus) were published in the Biodiversity Data Journal.

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.

The project, aptly named  “Vultures Back to LIFE“, where the Vulture Conservation Foundation (Switzerland), EuroNatur (Germany) and Junta de Extremadura (Spain) are also partners, has been co-financed by the LIFE+ financial instrument of the European Commission.

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.

A Cinereous Vulture on a hacking platform.
Photo by Hristo Peshev, Fund for Wild Flora and Fauna.

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.

Pensoft joins EU-funded project SOLO, supporting the EU Mission “A Soil Deal for Europe”

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

The issue at hand

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.

The ‘deal’ with soils

The EU Mission “A Soil Deal for Europe” aims to address these issues by:

  • 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 roadmaps as 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 (SOLOwebsitesoils4europe.eu. Stay up to date with the project’s progress on Twitter (@soils4europe) and LinkedIn (/Soils-for-Europe).

UPDATE: The Soils for Europe journal is NOW LIVE at: https://journal.soils4europe.eu/.


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.

Full list of partners:
  1. National Resources Institute Finland
  2. University of Leipzig
  3. Pesticide Action Network
  4. Agroecology Europe
  5. Leitat Technological Centre
  6. Netherlands Institute of Ecology
  7. Leibniz Centre for Agricultural Landscape Research
  8. Lund University
  9. Pensoft Publishers
  10. University of Évora
  11. Institute of Advanced Studies Kőszeg
  12. National Observatory of Athens
  13. Norwegian University of Life Sciences
  14. University of Antwerp
  15. University of Trento
  16. Fraunhofer Society
  17. ICLEI European Secretariat GMBH

Comprehensive review of Burmese python science released

A USGS-led publication offers a new look at the constrictor that has invaded southern Florida.

The U.S. Geological Survey has released a comprehensive synthesis of Burmese python science, showcasing results from decades of USGS-funded research on python biology and potential control tools. The giant constrictor now represents one of the most challenging invasive species management issues worldwide.

Occurrence records were obtained from a large geospatial database of invasive species reports (Early Detection & Distribution Mapping System) submitted by both researchers and the public. The map illustrates the chronology of python removals across southern Florida and represents the best professional estimate of the invasion front, which is not exact and will change over time.

“For the first time, all the science on python ecology and potential control tools has been consolidated into one document, allowing us to identify knowledge gaps and important research areas to help inform future python management strategies. This synthesis is a major milestone for Burmese python research; six years in the making, it represents the consensus of the scientific community on the python invasion,” said USGS Ecologist Jacquelyn Guzy, lead author for the publication.

Burmese pythons were confirmed to have an established breeding population in Everglades National Park in 2000. The population has since expanded and now occupies much of southern Florida. They consume a wide range of animals and have altered the food web and ecosystems across the Greater Everglades.

The synthesis, which pulled together the expertise of scientists and managers nationwide, provides a breakdown of 76 prey species found in python digestive tracts, which primarily included mammals and birds, as well as two reptile species, American alligator and Green iguana. However, as the scientists noted, the number of animals may increase as the python population expands to new areas.

It also reports new findings including a summary of body sizes of pythons measured by state and federal agencies between 1995 and 2022, as well as descriptions of length-mass relationships, the estimated geographic spread of pythons over time, and a comprehensive assessment of all control tools explored to date.

Illustration by Natalie Claunch demonstrates typical features of the Burmese python.

One of the hallmark issues of the Burmese python invasion has been the difficulty of visually detecting or trapping pythons in an immense natural landscape, Guzy said. Pythons do not readily enter any type of trap, occupy vast stretches of inaccessible habitat, and camouflage extremely well within the subtropical Florida environment.

“Extremely low individual python detection rates hamper our ability to both estimate python abundance and expand control tools across the extensive natural landscape” says USGS Research Ecologist Kristen Hart, an author of the publication.

Because the Burmese python has spread throughout southern Florida, eradication of the population across the landscape is not possible with existing tools, the publication states. However, researchers at USGS and partner institutions are exploring potential novel techniques such as genetic biocontrol, that may one day provide an avenue towards larger-scale population suppression.

In the meantime, important areas of research according to the publication include reproductive life history and estimation of demographic vital rates such as survival, to help managers evaluate and refine existing control tools. With improved control tools managers may be able to reduce population expansion and minimize the future impact of pythons on the environment.

The USGS python research over the past decades has been largely supported by the USGS Greater Everglades Priority Ecosystem Sciences (GEPES) Program with additional support from the USGS Biothreats and Invasive Species program.

Research article:

Guzy JC, Falk BG, Smith BJ, Willson JD, Reed RN, Aumen NG, Avery ML, Bartoszek IA, Campbell E, Cherkiss MS, Claunch NM, Currylow AF, Dean T, Dixon J, Engeman R, Funck S, Gibble R, Hengstebeck KC, Humphrey JS, Hunter ME, Josimovich JM, Ketterlin J, Kirkland M, Mazzotti FJ, McCleery R, Miller MA, McCollister M, Parker MR, Pittman SE, Rochford M, Romagosa C, Roybal A, Snow RW, Spencer MM, Waddle JH, Yackel Adams AA, Hart KM (2023) Burmese pythons in Florida: A synthesis of biology, impacts, and management tools. NeoBiota 80: 1-119. https://doi.org/10.3897/neobiota.80.90439

Story originally published by the USGS. Republished with permission.

Redefining nature-based decision-making: Pensoft joins EU project SELINA

“Ecosystem services is one of the topics that Pensoft has been involved in for over 10 years,” points out COO Prof Pavel Stoev.

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/.

Stay up to date with the project’s progress on Twitter, Facebook, Linkedin and YouTube.

BiCIKL Project supports article collection in Biodiversity Data Journal about use of linked data

Welcomed are taxonomic and other biodiversity-related research articles, which demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data

The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) will support free of charge publications* submitted to the dedicated topical collection: “Linking FAIR biodiversity data through publications: The BiCIKL approach” in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data, so that they can be easily harvested, distributed and re-used to generate new knowledge. 

BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc. to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles.

Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem.


The new article collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

To be eligible for the collection, a manuscript must comply with at least two of the conditions listed below. In the submission form, the author needs to specify the condition(s) applicable to the manuscript. The author should provide the explanation in a cover letter, using the Notes to the editor field.

All submissions must abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics. 

The data used in the articles must comply with the Data Quality Checklist and Fair Data Checklist available in the Authors’ instructions of the journal.


Conditions for publication in the article collection:

  • The authors are expected to use explicit Globally Unique Persistent and Resolvable Identifiers (GUPRI) or other persistent identifiers (PIDs), where such are available, for the different types of data they use and/or cite in the manuscripts (specimens IDs, sequence accession numbers, taxon name and taxon treatment IDs, image IDs, etc.)

  • Global taxon reviews in the form of “cyber-catalogues” are welcome if they contain links of the key data elements (specimens, sequences, taxon treatments, images, literature references, etc.) to their respective records in external repositories. Taxon names in the text should not be hyperlinked. Instead, under each taxon name in the catalogue, the authors should add external links to, for example, Catalogue of Life, nomenclators (e.g. IPNI, MycoBank, Index Fungorum, ZooBank), taxon treatments in Plazi’s TreatmentBank or other relevant trusted resources.

  • Taxonomic papers (e.g. descriptions of new species or revisions) must contain persistent identifiers for the holotype, paratypes and at least most of the specimens used in the study.

  • Specimen records that are used for new taxon descriptions or taxonomic revisions and are associated with a particular Barcode Identification Number (BIN) or Species Hypothesis (SH) should be imported directly from BOLD or PlutoF, respectively, via the ARPHA Writing Tool data-import plugin.

  • More generally, individual specimen records used for various purposes in taxonomic descriptions and inventories should be imported directly into the manuscript from GBIF, iDigBio, or BOLD via the ARPHA Writing Tool data-import plugin. 

  • In-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome in any taxonomic revision or catalogue. The in-text citations should be hyperlinked to the original treatment data at TreatmentBank.

  • Hyperlinking other terms of importance in the article text to their original external data sources or external vocabularies is encouraged.

  • Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s linked data tables guidelines.

  • Theoretical or methodological papers on linking FAIR biodiversity data are eligible for the BiCIKL collection if they provide real examples and use cases.

  • Data papers or software descriptions are eligible if they use linked data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.

  • Articles that contain nanopublications created or added during the authoring process in Biodiversity Data Journal. A nanopublication is a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, for example biotic relationship between taxa, or habitat preference of a taxon. The in-built workflow ensures the linkage and its persistence, while the information is simultaneously human-readable and machine-interpretable.
  • Manuscripts that contain or describe any other novel idea or feature related to linked or semantically enhanced biodiversity data will be considered too.

We recommend authors to get acquainted with these two papers before they decide to submit a manuscript to the collection: 


Here are several examples of research questions that might be explored using semantically enriched and linked biodiversity data: 

(1) How does linking taxon names or Operational Taxonomic Units (OTUs) to related external data (e.g. specimen records, sequences, distributions, ecological & bionomic traits, images) contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?

(2) How could the production and publication of taxon descriptions and inventories – including those based mostly on genomic and barcoding data – be streamlined? 

(3) How could general conclusions, assertions and citations in biodiversity articles be expressed in formal, machine-actionable language, either to update prior work or express new facts (e.g. via nanopublications)? 

(4) How could research data and narratives be re-used to support more extensive and data-rich studies? 

(5) Are there other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR biodiversity data?


All manuscripts submitted to the Biodiversity Data Journal have their data audited by data scientists prior to the peer review stage.

Once published, specimen records data are being exported in Darwin Core Archive to GBIF.

The data and taxon treatments are also exported to several additional data aggregators, such as TreatmentBank, the Biodiversity Literature Repository, and SiBILS amongst others. The full-text articles are also converted to Linked Open Data indexed in the OpenBiodiv Knowledge Graph.


All articles will need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section.

* The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at € 650. Authors of larger manuscripts will need to cover the surplus charge (€10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net.

Follow the BiCIKL Project on Twitter and Facebook. Join the conservation on via #BiCIKL_H2020.

You can also follow Biodiversity Data Journal on Twitter and Facebook.

Japanese scientists use a novel research approach to study populations of deep-sea brittle stars

Researchers designed two new sets of PCR primers for the detection of brittle stars through eDNA metabarcoding.

For the first time, researchers developed a metabarcoding technology for brittle stars.

Japanese scientists, led by Dr Masanori Okanishi of the Hiroshima Shudo University and the University of Tokyo, analyzed environmental DNA (eDNA) released from marine invertebrates in the water, and successfully identified the species they were looking for. The study is published in the open-access journal Metabarcoding and Metagenomics.

Metabarcoding allows researchers to easily and quickly identify species and determine their number in a given location on the basis of environmental DNA (that is DNA released into, for example, the water in a particular lake). 

In Japan, this method has been used successfully to detect the number of species in specific locations in the sea by sampling as little as a bucket of water. Monitoring species is part of the effort for conservation of biological resources and maintenance of their economic value, and metabarcoding can be utilized as a less labor-intensive and more cost-effective tool for marine surveys of biodiversity.

The new study reports on the research team’s development of the first DNA primers for metabarcoding of brittle stars. 

Brittle stars are the most abundant species in the phylum Echinodermata (approximately 2,100 species), making them promising indicator organisms for environmental DNA metabarcoding. These marine invertebrates are thought to release abundant environmental DNA due to their size, large populations, and habitats in a variety of seafloor environments.

 Brittle stars collected from Sagami Sea, Japan (credit: Hisanori Kohtsuka, The University of Tokyo)

To determine the origin of DNA sequences obtained from samples and used for metabarcoding, Okanishi’s team constructed a database of reference DNA sequences based on specimens identified to 60 brittle star species from Sagami Bay. 

Up until now, metabarcoding had not been used for organisms with little mobility such as brittle stars, because many reference DNA sequences had been misidentified or unidentified. The new database will aid further research and application of the technology.

“If metabarcoding becomes possible through the development of additional primers and richer databases of reference DNA sequences, it will be possible to monitor the marine environment with a precision never before thought possible,”

say the authors in conclusion.

Original source: Okanishi M, Kohtsuka H, Wu Q, Shinji J, Shibata N, Tamada T, Nakano T, Minamoto T (2023) Development of two new sets of PCR primers for eDNA metabarcoding of brittle stars (Echinodermata, Ophiuroidea). Metabarcoding and Metagenomics 7: e94298. https://doi.org/10.3897/mbmg.7.94298

Expert Contact: Masanori Okanishi: Hiroshima Shudo University Assistant Professor. E-mail: okahoku@gmail.com


Follow Metabarcoding & Metagenomics on Facebook and Twitter.

New spider genus named after pop band ABBA

Two ABBA-mad arachnologists from Murdoch University in Perth, Australia, have described a new genus dedicated to the famous band.

Spiders of the family Araneidae are known for building vertical orbicular webs to catch upon prey. They can be easily identified by their eye pattern, the abdomen normally overlapping the carapace, and complex genitalia. The family currently has 188 genera and 3,119 species worldwide.

Two scientists from Murdoch University in Perth (Australia), Dr Pedro Castanheira and Dr Volker Framenau, described a new spider genus of Araneids following a comprehensive study of orb-weaving spiders found in Australian zoological collections. They named it after one of their favourites bands, the Swedish pop group ABBA, paying tribute to the band members Agnetha Fältskog, Björn Ulvaeus, Benny Andersson, and Anni-Frid Lyngstad.

The band’s “songs and subsequent musicals Mamma Mia! (2008) and Mamma Mia – Here We Go again! (2018), provided hours of entertainment for the authors,” they explain in their study, which was published in the journal Evolutionary Systematics.

Abba transversa. Photo by Volker Framenau

The new genus is composed of a relatively small single species (ca. 3-4 mm), Abba transversa (Rainbow, 1912), whose specimens are currently known from the coastal area of New South Wales and Queensland. It is differentiated from other species within the family by the presence of two dark spots in the middle of abdomen and by the thick macrosetae on the first pair of legs of the males.

The description comes after 15 years of scientific work, with the researchers looking at 12,000 records in Australian museums and overseas collections.

“Describing new taxa is vital for conservation management plans to assess biodiversity and protect forests areas across Australia,” says study author Dr Pedro Castanheira. “Currently, 80% of Australian spider species are unknown, and many of the described ones are misplaced in different genera, like Abba transversa used to be.”

Original source:

Castanheira PS, Framenau VW (2023) Abba, a new monotypic genus of orb-weaving spiders (Araneae, Araneidae) from Australia. Evolutionary Systematics 7(1): 73-81. https://doi.org/10.3897/evolsyst.7.98015

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BiCIKL keeps on adding project outcomes in own collection in RIO Journal

The publications so far include the grant proposal; conference abstracts, a workshop report, guidelines papers and deliverables submitted to the Commission.

The dynamic open-science project collection of BiCIKL, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” (doi: 10.3897/rio.coll.105), continues to grow, as the project progresses into its third year and its results accumulate ever so exponentially. 

Following the publication of three important BiCIKL deliverables: the project’s Data Management Plan, its Visual identity package and a report, describing the newly built workflow and tools for data extraction, conversion and indexing and the user applications from OpenBiodiv, there are currently 30 research outcomes in the BiCIKL collection that have been shared publicly to the world, rather than merely submitted to the European Commission.

Shortly after the BiCIKL project started in 2021, a project-branded collection was launched in the open-science scholarly journal Research Ideas and Outcomes (RIO). There, the partners have been publishing – and thus preserving – conclusive research papers, as well as early and interim scientific outputs.

The publications so far also include the BiCIKL grant proposal, which earned the support of the European Commission in 2021; conference abstracts, submitted by the partners to two consecutive TDWG conferences; a project report that summarises recommendations on interoperability among infrastructures, as concluded from a hackathon organised by BiCIKL; and two Guidelines papers, aiming to trigger a culture change in the way data is shared, used and reused in the biodiversity field. 

In fact, one of the Guidelines papers, where representatives of the Consortium of European Taxonomic Facilities (CETAF), the Society for the Preservation of Natural History Collections (SPNHC) and the Biodiversity Heritage Library (BHL) came together to publish their joint statement on best practices for the citation of authorities of scientific names, has so far generated about 4,000 views by nearly 3,000 unique readers.

At the time of writing, the top three of the most read papers in the BiCIKL collection is completed by the grant proposal and the second Guidelines paper, where the partners – based on their extensive and versatile experience – present recommendations about the use of annotations and persistent identifiers in taxonomy and biodiversity publishing. 

Access to data and services along the entire data and research life cycle in biodiversity science.
The figure was featured in the BiCIKL grant proposal, now made available from the BiCIKL project collection in RIO Journal.

What one might find quite odd when browsing the BiCIKL collection is that each publication is marked with its own publication source, even though all contributions are clearly already accessible from RIO Journal

So, we can see many project outputs marked as RIO publications, but also others that have been published in the likes of F1000Research, the official journal of TDWG: Biodiversity Information Science and Standards, and even preprints servers, such as BiohackrXiv

This is because one of the unique features of RIO allows for consortia to use their project collection as a one-stop access point for all scientific results, regardless of their publication venue, by means of linking to the original source via metadata. Additionally, projects may also upload their documents in their original format and layout, thanks to the integration between RIO and ARPHA Preprints. This is in fact how BiCIKL chose to share their latest deliverables using the very same files they submitted to the Commission.

“In line with the mission of BiCIKL and our consortium’s dedication to FAIRness in science, we wanted to keep our project’s progress and results fully transparent and easily accessible and reusable to anyone, anywhere,” 

explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft. 

“This is why we opted to collate the outcomes of BiCIKL in one place – starting from the grant proposal itself, and then progressively adding workshop reports, recommendations, research papers and what not. By the time BiCIKL concludes, not only will we be ready to refer back to any step along the way that we have just walked together, but also rest assured that what we have achieved and learnt remains at the fingertips of those we have done it for and those who come after them,” he adds.

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You can keep tabs on the BiCIKL project collection in RIO Journal by subscribing to the journal newsletter or following @RIOJournal on Twitter and Facebook.

Towards a climate-neutral society: Pensoft takes part in the Horizon project ForestPaths

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.

The ForestPaths approach

ForestPaths will work with practitioners through four demo cases to determine climate- and biodiversity-smart forest management options

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.

You can find out more about the project on the ForestPath website: forestpaths.eu. Stay up to date with the project’s progress on Twitter (@forestpaths_eu) and LinkedIn (/forestpaths-project).

Full list of project partners:
  1. European Forest Institute
  2. Lund University
  3. Technical University of Munich
  4. Karlsruhe Institute of Technology
  5. Natural Resources Institute Finland
  6. Wageningen Research
  7. Flemish Institute for Technological Research
  8. PBL Netherlands Environmental Assessment Agency
  9. Oeko-Institut
  10. Euro-Mediterranean Center on Climate Change
  11. Prospex Institute
  12. Transilvania University of Brasov
  13. Pensoft Publishers
  14. Joint Research Centre – European Commission
  15. University of Edinburgh
  16. Teesside University