Category: Biodiversity Data Journal

Cyber catalogue and revision of the nematode genus Enchodelus 

All available information on Enchodelus species is brought together. This will contribute to a more complete assessment of species diversity and distribution.

Guest blog post by Milka Elshishka and Vlada Peneva

The order Dorylaimida is the most diverse nematode group, with over 2640 valid species and more than 260 valid genera, with new taxa being described each year. They are the richest nematode order in number of species in natural soils. Dorylaims are often regarded as good environmental bio-indicators since the number of species/specimens drastically decreases following any significant disturbance in their habitat.

In our study, published in the Biodiversity Data Journal, we examined one intriguing free-living dorylaimid nematode taxon: the genus Enchodelus which is considered to have conservation value. The genus currently includes 28 species, which display a distinct distributional pattern, being spread mainly in high altitudinal enclaves of the Northern Hemisphere (with the exception of E. brasiliensis, only known to occur in Brazil). Its representatives are often associated with mosses and cliff vegetation. Although their feeding habits have not been studied with experimental protocols, it is traditionally assumed that they are omnivorous.

Distribution of Enchodelus species

The genus Enchodelus has not been recently revised; the descriptions of many ‘old species’ (that have been described long ago and have not been reported since their original discovery) are of poor quality, hardly discoverable, and do not conform to today’s taxonomical standards.

An Enchodelus species.

Actually, information available from databases often is limited to some of the species and usually incomplete as relevant data are missing. Consequently, a comprehensive compilation and analysis of literature data is indispensable to reach new insights into the taxonomy of the genus and to elucidate its evolutionary relationships.

Our work provides a cyber catalogue of Enchodelus species, where all available data for the species are accessible and collected in one place, which will greatly facilitate future research. It compiles available information from key European Research Infrastructures, such as TreatmentBank, the Swiss Institute of Bioinformatics Literature Services (SIBiLS), the Catalogue of Life (CoL), the Global Biodiversity Information Facility (GBIF), the European Nucleotide Archive (ENA) and the Biodiversity Literature Repository (BLR). Data about their distribution (geographical records and habitats) are incorporated too and all brought together. It is completed with discussion and notes for some species, along with information on species distributions and microhabitats.

Here, all available information on Enchodelus species is brought together. This will contribute to a more complete assessment of species diversity and distribution and support further biogeographical and ecological research.

The type species Enchodelus macrodorus is the most widely spread and reported Enchodelus species. It is a typical member of Palearctic nematode fauna, recorded in a myriad of countries and habitats and very sporadically recorded in Nearctic and Indomalayan enclaves. In our study we add new morphological and molecular data for this species collected from Spain.

Enchodelus macrodorus from Spain.

Additionally, type material of Enchodelus vestibulifer, belonging to Edmond Altherr’s collection, deposited at the Museo Cantonale di Storia Naturale di Lugano (Switzerland), is re-examined.

Enchodelus vestibulifer

This species was described by the Swiss nematologist Edmond Altherr in 1952 on the basis of a single female from Switzerland and no later record of it exists. The re-examination of this material revealed that several relevant traits are not compatible with those characterising the genus Enchodelus and we considered it as incertae sedis.

In our study we also present one new species, Enchodelus enguriensis. It was collected from moss on stone (Tortellasquarrosa) in Caucasus, Georgia (Samegrelo-Zemo Svaneti Region, Bogreshi, Enguri River, Tower of Love). The description of the new species was supported by a comprehensive phylogenetic analysis based on D2-D3 of 28S rRNA. When naming the new taxon, we selected the name of the place from which the material was collected, namely the River Enguri; it was recovered from the stone next to the Tower of Love on the bank of the river.

Enchodelus enguriensis

We are grateful for the support the BiCIKL project, Grant No 101007492.

Research article:

Elshishka M, Mladenov A, Altash S, Álvarez-Ortega S, Peña-Santiago R, Peneva V (2024) Cyber catalogue and revision of the nematode genus Enchodelus (Dorylaimida, Nordiidae). Biodiversity Data Journal 12: e126315. https://doi.org/10.3897/BDJ.12.e126315

Better data practices advance biodiversity knowledge

A framework to retrieve, refine and align secondary biodiversity data with FAIR standards.

Guest blog post by Nubia Marques et al.

In a world increasingly defined by data-driven decisions, biodiversity research stands to benefit from standardized and accessible data. Despite their importance for research, biodiversity datasets often fail to meet FAIR (Findable, Accessible, Interoperable, Reusable) standards, leading to concerns about data quality, reliability, and accessibility.

How to ensure biodiversity data are FAIR, linked, open and future-proof?

To address this, we propose a framework to retrieve, refine and align secondary biodiversity data with FAIR standards, utilizing the Darwin Core model. We followed four steps:

  1. data localization (systematic review)
  2. quality validation
  3. standardization using the Darwin Core standard
  4. sharing and archive in the appropriate repository.

Our approach integrates data validation and quality control steps to ensure that secondary data sets can be trusted.

Our study in Biodiversity Data Journal focused on ecotonal estuarine ecosystems near the easternmost Amazon, where we recovered data from 46,000 individuals representing 3,871 taxa across eight biotic groups (birds, amphibians, reptiles, mammals, fish, phytoplankton, benthos, and plants) from 1985 to 2022. These data were used to illustrate how our strategy improves validation, making the data more reliable for macroecological modeling and conservation management. As data becomes more standardized, researchers around the world will be better equipped to collaborate, identify trends, protect ecosystems, and advance sustainability efforts.

Relationships between numbers of taxa and occurrences gathered through an extensive review of secondary biodiversity data from the Golfão Maranhense area, in the estuarine regions of eastern Amazonia.

Accessible biodiversity data empowers stakeholders and provides critical insights into ecosystem health and species conservation. However, without standardized formats, this data is often fragmented, incomplete, or difficult to compare. By creating a consistent framework for collecting, storing, and sharing data, we are opening the door to more informed decision-making and innovation in biodiversity conservation.

The key to conserving biodiversity is collaboration and transparency. By prioritizing accessible and standardized data, we ensure that vital information reaches those who need it most – whether it’s for scientific study, habitat management or policymaking.

Let’s continue to make biodiversity data a tool for global change!

Research article:

Marques N, Soares CDdeM, Casali DdeM, Guimarães E, Fava F, Abreu JMdaS, Moras L, Silva LGda, Matias R, Assis RLde, Fraga R, Almeida S, Lopes V, Oliveira V, Missagia R, Carvalho E, Carneiro N, Alves R, Souza-Filho P, Oliveira G, Miranda M, Tavares VdaC (2024) Retrieving biodiversity data from multiple sources: making secondary data standardised and accessible. Biodiversity Data Journal 12: e133775. https://doi.org/10.3897/BDJ.12.e133775

First scientific publication using digital specimen DOIs is out

Now, scientists will be in a much better position to really exchange and link data across institutions.

“The genera Chrysilla and Phintelloides revisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications” is the first scientific publication that uses digital specimen DOIs.

Linking data across collections

It is nothing new that our planet is facing a number of serious threats: climate change, biodiversity loss, pandemics… If you have been watching the news, all this is probably familiar to you. The wealth of data hosted in Natural history collections can contribute to finding a response to these challenges.Alas, today’s practices of working with collected bio- and geodiversity specimens lack some efficiency, thus limiting what our scientists can achieve.

In particular, there is a rather serious absence of linkages between specimen data. Sure, each specimen in a collection usually has its own catalogue ID that is unique within that collection, but the moment collections attempt to work with other collections -as they should in the face of planetary threats- problems start to arise because usually, each collection has its own way of identifying their data, thus leading to confusion.

Persistent identifiers: the DOIs

To avoid this problem, several initiatives have been launched in recent years to establish a globally accepted system of persistent identifiers (PIDs) that guarantee the “uniqueness” of collection specimens—physical or digital—over time. 

Digital specimen DOIs can point to individual specimens in a collections.

You can think of a PID as a marker, an identifier that points at a single individual object and only one, differentiating it from any other in the world. You must have heard of acronyms such as ISBN or ORCID. Those are PIDs for books and individual scholars, respectively. For digital research content, the most widely used PID is the DOI (Digital Object Identifier), proposed by the DOI Foundation. 

A DOI is an alphanumeric code that looks like this: 10.prefix/sufix 

For example, if you type https://doi.org/10.15468/w6ubjx in your browser, you will reach the Royal Belgian Institute of Natural Sciences’s mollusk collection database, accessed through GBIF. This specific DOI will never point at anything else, and the identifier will remain the same in the future, even if changes occur in the content of this particular database.

DiSSCo and the DOIs

The Distributed System of Scientific Collections (DiSSCo) aims to provide a DOI for all individual digital specimens in European natural history collections. The point is not only to accurately identify specimens. That is, of course, crucial, but the DOI of a digital specimen provides a number of other advantages that are extremely interesting for DiSSCo and natural history collections in general. Among them, two are simply revolutionary. 

The digital specimen DOI stores quick-access, basic metadata about the specimen.

Firstly, using DOIs allows linking the digital specimen to all other relevant information about the same specimen that might be hosted in other repositories (e.g. ecological data, genomic data, etc.). In creating this extended digital specimen that links different data types, digital specimen DOIs make a huge contribution to inter-institutional scientific work, filling the gap that is described at the beginning of this piece. Now scientists will be in a much better position to really exchange and link data across institutions.

Second, in contrast to most other persistent identifiers, the DOI of a digital specimen stores additional metadata (e.g. name, catalogue number) beyond the URL to which it redirects. This allows access to some information about the specimen without having to retrieve the full data object, i.e. without having to be redirected to the specimen HTML page. This metadata  facilitates AI systems to quickly navigate billions of digital specimens and perform different automated work on them, saving us (humans) precious time.

Use of DOIs in publications

With all this in mind, it is easier to understand why being able to cite digital specimens in scholarly publications using DOIs is an important step. So far, the only DOIs that we could use in publications were those at the dataset level, not at the individual specimen level. In the example above, if a scientist were to publish an article about a specific type of bivalve in the Belgian collection, the only DOI that she or he would have available for citation in the article would be that of the entire mollusk database -containing hundreds or thousands of specimens- not the one of the specific oyster or scallop that might be the focus of the publication. 

Main page of DiSSCo’s sandbox, the future DiSSCover service.

The publication in Biodiversity Data Journal about the Chrysilla and Phintelloides genera is the first of its kind and opens the door to citing not only dataset-level objects but also individual specimens in publications using DOIs. You can try it yourself: Hover over the DOIs that are cited in the publication and you will get some basic information that might save you the time of visiting the page of the institution where the specimen is. Click on it and you will be taken to DiSSCo’s sandbox -the future DiSSCover service- where you will find all the information about the digital specimen. There you will also be able to comment, annotate the specimen, and more, thus making science in a more dynamic and efficient way than until now.

A note about Christa Deeleman-Reinhold

At 94 years old, the Dutch arachnologist Christa Deeleman-Reinhold is not only one of the authors of the Chrysilla and Phintelloides article but also one of the most important arachnologists in the world. Born in 1930 on the island of Java -then part of the Dutch East Indies- Christa gained her PhD from Leiden University in 1978. Since then, she has developed a one-of-a-kind scientific career, mainly focused on spider species from South Asia. In her Forest Spiders of South East Asia (2001), Dr. Deeleman-Reinhold revised six spider families, describing 18 new genera and 115 new species. The Naturalis Biodiversity Center hosts the Christa Laetitia Deeleman-Reinhold collection, with more than 20,000 specimens.

Text and images provided by DiSSCo RI.

Research article:

Deeleman-Reinhold CL, Addink W, Miller JA (2024) The genera Chrysilla and Phintelloides revisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications. Biodiversity Data Journal 12: e129438. https://doi.org/10.3897/BDJ.12.e129438

Orthoptera and origami: Pensoft at the International Congress of Entomology

Meeting our authors in person was a chance for us to gather valuable feedback and make sure we are doing our best.

The International Congress of Entomology 2024 (ICE2024), which took place on August 25-30 2024 in Kyoto, Japan, was arguably the biggest entomology event of the year. For the Pensoft team, it was an excellent chance to catch up with our authors and editors and discuss new partnerships.

At the Kyoto International Conference Center, entomologists visited lectures, symposia, and poster presentations, but they also enjoyed insect-themed haikus, origami, and artworks, and got to sample some edible insects.

Meeting our authors in person was a chance for us to gather valuable feedback and make sure we are doing our best to provide entomologists with a frictionless process that makes their published research shine.

  • Robin Kundrata, author in ZooKeys
  • Deepa Pureswaran, author and editor in NeoBiota
  • Alain Roques, author and editor in NeoBiota
  • Jessica Gillung, author in ZooKeys
  • Ranjith AP, editor in Check List and author in ZooKeys and Journal of Hymenoptera Research
  • Minoo Heidari Latibari, author in ZooKeys
  • Elisabeth Geiser, author in ZooKeys
  • Sven Bradler, author and editor in ZooKeys
  • Showtaro Kakizoe, author in ZooKeys
  • Antonio Carapelli, author and reviewer in ZooKeys

At Stand 25, congress participants browsed the company’s open-access entomological journals, including ZooKeys, Biodiversity Data Journal, and Deutsche Entomologische Zeitschrift, as well as its wide range of books on insect diversity, systematics, and ecology.

Scientific illustrator Denitsa Peneva’s beautiful works adorned Pensoft’s stand; Mostafa Ghafouri Moghaddam, subject editor at ZooKeys and Biodiversity Data Journal and author at a number of Pensoft-published journals even got to take one of her prints home after winning a raffle that Pensoft organised. He won a beautiful illustration of Bombus fragrans on Trifolium pratense.

Pensoft’s founder and CEO and one of the founding editors of the company’s flagship journal ZooKeys, Prof. Lyubomir Penev, was there representing the company and meeting with fellow entomologists.

  • Prof. Penev with Evgeny Zakharov of the Centre for Biodiversity Genomics
  • Prof. Penev with researchers Jadranka Rota, Niklas Wahlberg, Alexander Konstantinov, and Michael Schmidt
  • Prof. Penev with researcher Caroline S. Chaboo

They also got the chance to learn about the ARPHA Platform, a next-generation publishing solution that offers a streamlined and efficient workflow for authors, reviewers, and editors.

ARPHA Platform’s 15 top features enjoyed by client journals and publishers

At ICE2024, Pensoft also presented its newest open-access jorunal, Natural History Collections and Museomics. A peer-reviewed journal for research, discussion and innovation of natural history collections, NHCM will publish under a diamond open access model, allowing free access to published content without any fees for authors or readers.

New Diamond OA journal Natural History Collections and Museomics launches on ARPHA Platform

In addition to its publishing endeavors, Pensoft also presented some of the EU-funded pollinator projects that it takes part in such as Safeguard, PollinERA, and WildPosh.

ICE2024 was a chance to advance entomological science and foster collaboration within the global scientific community. For those who missed the chance to connect with Pensoft in Kyoto, the company’s journals and platforms remain accessible online, offering opportunities to read and produce groundbreaking research in insect diversity and ecology.

Truffles and tulips: Pensoft and the 12th International Mycological Congress

Over 1,000 fungi enthusiasts gathered in Maastricht for the biggest mycology event of the year.

The Pensoft team had a fantastic time at the 12th International Mycological Congress in Maastricht, the Netherlands.

Organised by the International Mycological Association, together with the Dutch Mycological Society and the Westerdijk Fungal Biodiversity Institute, the four-day meeting saw around 1,400 fungi fanatics gather for the biggest mycology event of the year.

It all began with an opening ceremony complete with live music and stunning visuals, which set the stage for five days of research exchange and collaboration.

Pensoft welcomed faces new and old at a decorated stand featuring numerous illustrated materials designed by scientific illustrator Denitsa Peneva. Manning the stand were Prof Dr Lyubomir Penev (MycoKeys Founding Editor & Pensoft Founder and CEO) and Slavena Peneva (Pensoft Head of Graphic Design).

MycoKeys materials esigned by Denitsa Peneva.
Urmas Kõljalg and Lyubomir Penev.
Lyubomir Penev, Dmitry Schigel and Slavena Peneva.

The booth hosted a special gathering for MycoKeys editors, including Editor-in-Chief Prof Dr Thorsten Lumbsch, who were shown a video looking back on the history of the journal. Many long-time collaborators of Pensoft, such as Prof Dr Urmas Kõljalg of Pluto F and Dr Dmitry Schigel of Pluto F, also dropped by to say hello.

The congress provided the perfect opportunity to announce Pensoft’s new, exciting partnership with the International Mycological Association. This collaboration will see the IMAFungus journal move to the ARPHA platform, where it will benefit from cutting-edge publishing technology and workflows.

Several MycoKeys contributors presented and hosted keynote lectures, bridging sessions, and workshops across the seven major topics of the conference:

  • Cell biology, biochemistry and physiology
  • Environment, ecology and interactions
  • Evolution, biodiversity and systematics
  • Fungal pathogenesis and disease control
  • Genomics, genetics and molecular biology
  • Applied Mycology
  • Nomenclature

The full program can be found on the congress website.

The next International Mycology Congress will be held in Incheon, South Korea, in 2027. IMC13 already has an active website and the Pensoft team look forward to another exciting installment!

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Plants, prizes and paella: Pensoft at the International Botanical Congress 2024

Held every six years, the world’s largest botany event hosted thousands of researchers and enthusiasts in Madrid, Spain.

Towards the end of July 2024, members of the Pensoft team travelled to Madrid for the XX International Botanical Congress, where an estimated 3,000 botanists gathered for the biggest event of the year.

Held once every six years, the congress has enlarged its scope over more than a century to become an integrated forum for knowledge on the plant and mycological world.

Proceedings kicked off with a fantastic lecture from PhytoKeys Editor-in-Chief Sandy Knapp titled, “Why botany? Why now?” The following day, Thorsten Lumbsch, Editor-in-Chief of MycoKeys, gave a keynote lecture titled, “Unravelling diversity and evolution of lichens in the genomic era.”

In fact, many authors, editors and readers of Pensoft’s journals were in attendance. And several gave presentations, including a plenary talk by renowned PhytoKeys editor, Pamela S. Soltis, on the changing face of herbarium collections.

Pensoft and PhytoKeys stand at the International Botany Congress.
Denitsa Peneva greeting researchers at the Pensoft stand.
A man giving a presentation at the Pensoft and PhytoKeys stand at the International Botany Congress.
Lyubomir Penev giving a presentation to PhytoKeys editor.

The Pensoft team welcomed attendees with a bespoke stand, complete with print copies, illustrations and various promotional materials depicting beautiful species featured in PhytoKeys.

Lyubomir Penev, founder of Pensoft and founding editor of PhytoKeys, hosted a gathering of PhytoKeys editors at the stand, where he presented the story, latest results and highlights of the journal.

A woman posing with a PhytoKeys journal at the Pensoft and PhytoKeys stand at the International Botany Congress.
Two men posing at the Pensoft and PhytoKeys stand at the International Botany Congress.
A man and a woman posing at the Pensoft and PhytoKeys stand at the International Botany Congress.
Researchers who found their publications on display at the Pensoft stand.

The congress included numerous lectures, symposia sessions, workshops and meetings across a variety of subject matters, all of which can be found on the IBC 2024 website. The major topics of the event were:

  • Systematics, phylogenetics, biogeography and evolution
  • Ecology, environment and global change, including invasive species and plant-animal interactions
  • Biodiversity and conservation
  • Structure, physiology and development, including Evo-Devo
  • Genetics, genomics and bioinformatics
  • Plants and Society

At the closing ceremony, multiple awards were presented, including Pensoft’s Early Career Researcher Talk Award. Sandy Knapp presented the award to Sonia Molino for her talk on a global study of the genus Parablechnum, a lineage of ferns of the family Blechnaceae. The award grants her a free publication in PhytoKeys. 

Describing her study, Sofia Molino said: “To date there has been no study that takes into account all the centres of diversity of the genus at the same time, and what we have found is that it has a very complex evolutionary history, with several cases of cryptic diversity, hybridisation and rapid radiation.”

On her plans to use her free publication for a pending study on a series of novelties within Parablechnum in Bolivia, she added: “Although this is probably the country in South America where Parablechnum has been studied the most, after one expedition we have still found a lot of new things, such as several undescribed species, hybrids and new localities of some species that were only known from type material.”

The next International Botanical Congress is in 2029 and will take place in South Africa, where the Pensoft team looks forward to seeing plenty of new faces and old friends!

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The race to discover biodiversity: 11 new marine species and a new platform for rapid species description

The initiative boasts the discovery of eleven new marine species from all over the globe, occurring at depths from 5.2 to 7081 meters.

Accelerating global change continues to threaten Earth’s vast biodiversity, including in the oceans, which remain largely unexplored. To date, only a small fraction of an estimated two million total living marine species have been named and described. A major challenge is the time it takes to scientifically describe and publish a new species, which is a crucial step in studying and protecting these species. The current scientific and publishing landscape often results in decade-long delays (20-40 years) from the discovery of a new species to its official description. As an alternative to this, the Ocean Species Discoveries initiative was launched, offering a new platform for rapid but thorough taxonomic description of marine invertebrate species.

Lepechinella naces, a newly described amphipod, on a black background.
One of the newly described species, Lepechinella naces.

Ocean Species Discoveries is coordinated by the Senckenberg Ocean Species Alliance (SOSA), a project of the Senckenberg Research Institute and Natural History Museum Frankfurt. SOSA’s goal is to facilitate the discovery, protection, and awareness of marine invertebrate species before they become extinct.

The project coordinated 25 different researchers and produced data on thirteen marine invertebrate taxa, including one new genus, eleven new species, and one redescription and reinstatement. The species, which originate from all over the globe and at depths from 5.2 to 7081 meters, are brought together in an open-access publication in the Biodiversity Data Journal.

Only by leveraging the collective strengths of global progress, expertise, and technological advancements, will we be able to describe the estimated 1.8 million unknown species living in our oceans.

Prof. Dr. Julia Sigwart

This is the first of a series of publications related to SOSA’s initiative, in collaboration with Biodiversity Data Journal, presenting a revolutionary approach in new species descriptions, thanks to which the publication of new species takes years, sometimes even decades, less. The ARPHA publishing platform, which powers the Biodiversity Data Journal, further expedites species descriptions and their use in studies and conservation programs by employing a streamlined data publishing workflow. ARPHA automatically exports all species data, complete with images and descriptions, to GBIF—the Global Biodiversity Information Facility and the Biodiversity Literature Repository at Zenodo, from where other researchers can easily find and use them.

Dorsal, ventral, and lateral images of a newly described hydrothermal vent limpet, Lepetodrilus marianae, on a black background.

One of the new OSD species – a hydrothermal vent limpet, Lepetodrilus marianae. Photo credit: Chong Chen, Hiromi Kayama Watanabe, and Miwako Tsuda

One of the new species described in the Ocean Species Discoveries is Cunicolomaera grata, a curious amphipod whose burrows along the seafloor perplexed scientists. Another is a wrinkly-shelled limpet called Lepetodrilus marianae that lives on hydrothermal vents, underwater volcanoes in the deep-sea where temperatures can reach 400 degrees C. Normally, the descriptions for these two very different species wouldn’t be in the same publication, but this new publication format allows for species descriptions from different marine invertebrate taxa to be published together in one ‘mega-publication,’ offering a huge incentive for researchers to make their discoveries public.

Top: a newly described hole-making amphipod, Cunicolomaera grata, on a black background. Bottom: A photo of burrows on the ocean floor where the amphipod is presumed to live.
One of the new OSD species – a hole-making amphipod, Cunicolomaera grata. Photo credit: Anne Helene S. Tandberg and Anna M. Jażdżewska

“Currently, there’s a notable delay in naming and describing new animals, often because journals expect additional ecological or phylogenetic insights. This means many marine species go undescribed due to lack of data. OSD addresses this by offering concise, complete taxonomic descriptions without requiring a specific theme, refocusing attention on taxonomy’s importance,” says Dr. Torben Riehl, who is one of the researchers featured in Ocean Species Discoveries.

Top: Psychropotes buglossa, a newly described sea cucumber species. Bottom: Psychropotes buglossa grabbed by the mechanic arm of a remote-operated vehicle.

The reinstated OSD species – a purple long-tailed sea cucumber, Psychropotes buglossa. Photo credit: Amanda Serpell-Stevens, Tammy Horton, and Julia Sigwart

Reducing the time it takes to get from discovering a new animal to a public species description is crucial in our era of increasing biodiversity loss. The wrinkly-shelled limpet and two other species described in the Ocean Species Discoveries live in hydrothermal vent zones – an environment threatened by deep-sea mining. Another OSD species, Psychropotes buglossa, a purple sea cucumber (sometimes also called a gummy squirrel), lives in the North Atlantic, but similar species live in areas of high economic interest, where polymetallic-nodule extraction could soon endanger sea life. Threats like these risk driving species to extinction before we even get the chance to know and study them. Through efforts like SOSA’s Ocean Species Discoveries, we can get closer to understanding the biodiversity of our oceans and protecting it before it’s too late.

Dorsal and ventral views of a newly described species of deep-sea chiton, Placiphorella methanophila.

One of the new OSD species – a deep-sea chiton, Placiphorella methanophila. Photo credit: Katarzyna Vončina

“Only by leveraging the collective strengths of global progress, expertise, and technological advancements, will we be able to describe the estimated 1.8 million unknown species living in our oceans. Every taxonomist specialized on some group of marine invertebrates is invited to contribute to the Ocean Species Discoveries,” says Prof. Dr. Julia Sigwart in conclusion.

Research article:

(SOSA) SOSA, Brandt A, Chen C, Engel L, Esquete P, Horton T, Jażdżewska AM, Johannsen N, Kaiser 5, Kihara TC, Knauber H, Kniesz K, LandschoffJ, Lörz A-N, Machado FM, Martínez-Muñoz CA, Riehl T, Serpell-Stevens A, Sigwart JD, Tandberg AHS, Tato R, Tsuda M, Vončina K, Watanabe HK, Went C, Williams JD (2024) Ocean Species Discoveries 1-12 — A primer for accelerating marine invertebrate taxonomy. Biodiversity Data Journal 12: e128431. https://doi.org/10.3897/BDJ.12.e128431

Monster Hunter in real life: eyeless spider named after video game monstrosity

Discovered in China, the cave-dwelling arachnid was assigned a rather unflattering species name.

Deep within a cave in the Du’an Yao Autonomous County of Guangxi, China, researchers discovered a pale, eyeless spider unknown to science.

This discovery, detailed in the open-access Biodiversity Data Journal adds a remarkable member to the Otacilia genus. And, as is often the case, the scientist behind the revelation turned to popular culture to name the new species.

They settled on Otacilia khezu.

A close-up shot of the face Khezu from Monster Hunter at night. It is a wwyvern with no eyes and many teeth.
Khezu in Monster Hunter.

The Khezu wyvern features in the popular video game series Monster Hunter. It is known for its blindness and unsettling appearance, just like newly discovered species. By naming the spider Otacilia khezu, the researchers highlight its troglobitic – or cave-dwelling – nature, particularly the complete absence of its eyes.

“Its long, elastic neck stretching out while it clings to a wall or the ceiling is a sight straight out of a nightmare. Make sure you do not get overwhelmed by its horrific appearance.”

Khezu description, Monster Hunter Wiki.

Otacilia khezu, like many troglobitic creatures, lacks eyes and pigmentation, has elongated appendages, and has developed heightened sensory adaptations to navigate and thrive in its dark environment.

A pale eyeless spider on a cave floor.
Otacilia khezu juvenile, in life. Photo: Shanmi Zheng.

The research team led by Yejie Li,  Langfang Normal University, note the significance of the discovery, as it marks the first recorded troglobitic Otacilia species in China. Prior to this, only two troglobitic Otacilia species had been identified, both in Laos. 

The species is one of many spiders named after influential fictional characters. In fact, one spider was named after a character and the actor playing him.

The Venom Spider: new genus named after Tom Hardy’s Marvel character

The documentation and publication of this new species set the stage for further studies on the ecological roles of troglobitic spiders and their evolutionary adaptations.

Chinese civillians can rest assured that Otacilia khezu is considerably less dangerous than its namesake when they keep an eye out for the eyeless arachnid.

Original source:

Lin Y, Chen H, Wang X, Li S (2024) Otacilia khezu sp. nov., a new troglobitic spider (Araneae, Phrurolithidae) from Guangxi, China. Biodiversity Data Journal 12: e126716. https://doi.org/10.3897/BDJ.12.e126716

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Pensoft at the 7th European Congress of Conservation Biology as a publisher and Horizon project partner

At the Pensoft’s stand, delegates learned about the scientific publisher’s versatile open-access journal portfolio, as well as related publishing services and the Horizon project where Pensoft is a partner.

Between 17th and 22nd June 2024, Pensoft’s scholarly publishing and project teams joined the European Congress of Conservation Biology (ECCB), organised by the Society for Conservation Biology and hosted by the University of Bologna.

Here’s a fun fact: the University of Bologna is the oldest one still in operation in the world. It is also etched in history for being the first institution to award degrees of higher learning.  

This year, the annual event themed “Biodiversity positive by 2030” took place in the stunning Italian city of Bologna famous for its historical and cultural heritage, in a way building a bridge between the past of European civilisation and the future, which is now in our hands.

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At the Pensoft’s stand, delegates learned about the scientific publisher’s versatile open-access journal portfolio of over 30 journals covering the fields of ecology and biodiversity, as well as other related services and products offered by Pensoft, including the end-to-end full-featured scholarly publishing platform ARPHA, which hosts and powers all Pensoft journals, in addition to dozens other academic outlets owned by learned societies, natural history museums and other academic institutions.

In addition to its convenient collaborative online environment, user interface and automated export/import workflows, what ARPHA’s clients enjoy perhaps the most, are the various human-provided services that come with the platform, including graphic and web design, assistance in journal indexing, typesetting, copyediting and science communication.

Visitors at the stand could also be heard chatting with Pensoft’s Head of Journal development, Marketing and PR: Iva Boyadzhieva about the publisher’s innovative solutions for permanent preservation and far-reaching dissemination and communication of academic outputs that do not match the traditional research article format.

For example, the Research Ideas and Outcomes (RIO) journal was launched in 2015 by Pensoft as an open-science journal that would publish ‘unconventional’ research outputs, such as Grant proposals, Policy briefs, Project reports, Data management plans, Research ideas etc. Its project-branded open-science collections are in fact one of the Pensoft’s products that enjoys particular attention to participants in scientific projects funded by the likes of the European Commission’s Horizon programme.

Another innovation by Pensoft that easily becomes a talking point at forums like ECCB, is the ARPHA Conference Abstract (ACA) platform, which is basically a journal for conference abstracts, where abstracts are treated and published much like regular journal articles (a.k.a. ‘mini papers’) to enable permanent preservation, but also accessibility, discoverability and citability. Furthermore, ACA has been designed to act as an abstracts submission portal, where the abstracts undergo review and receive feedback before being published and indexed at dozens of relevant scientific databases.

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At ECCB 2024, our team was also happy to meet in person many authors and editors, whose work has frequented the pages of journals like Nature Conservation, Biodiversity Data Journal, ZooKeys and NeoBiota, to name a few.

On Wednesday, delegates also got a chance to hear the talk by renowned vegetation ecologist at the ZHAW Zurich University of Applied Sciences and Editor-in-Chief at the Vegetation Classification and Survey journal: Prof. Dr. Jürgen Dengler. He presented findings and conclusions concerning neophytes in Switzerland, while drawing comparisons with other European countries and regions.

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At this year’s ECCB, Pensoft took a stand as an active Horizon project participant too. At the publisher’s booth, the delegates could explore various project outputs produced within REST-COAST, SpongeBoost and BioAgora. Each of these initiatives has been selected by the European Commission to work on the mitigation of biodiversity decline, while aiming for sustainable ecosystems throughout the Old continent.

In all three projects, Pensoft is a consortium member, who contributes with expertise in science communication, dissemination, stakeholder engagement and technological development.

Coordinated by the Catalonia University of Technology UPC-BarcelonaTech and involving over 30 European institutions, REST-COAST has been working on developing tools to address key challenges to coastal ecosystems – all consequences of a long history of environmental degradation of our rivers and coasts.

Having started earlier this year, SpongeBoost is to build upon existing solutions and their large-scale implementation by implementing innovative approaches to improve the functional capacity of sponge landscapes. The project is coordinated by the Helmholtz Centre for Environmental Research (UFZ) and will be developed with the active participation of 10 partnering institutions from seven countries across Europe. 

In the meantime, since 2022, the five-year BioAgora project has been working towards setting up the Science Service for Biodiversity platform, which will turn into an efficient forum for dialogue between scientists, policy actors and other knowledge holders. BioAgora is a joint initiative, which brings together 22 partners from 13 European countries led by the Finnish Environment Institute (SYKE).

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Still, REST-COAST, SpongeBoost and BioAgora were not the only Horizon projects involving Pensoft that made an appearance at ECCB this year thanks to the Pensoft team. 

On behalf of OBSGESSION – another Horizon-funded project, Nikola Ganchev, Communications officer at Pensoft, presented a poster about the recently started project. Until the end of 2027, the OBSGESSION project, also led by the Finnish Environment Institute (SYKE) and involving a total of 12 partnering organisations, will be tasked with the integration of different biodiversity data sources, including Earth Observation, in-situ research, and ecological models. Eventually, these will all be made into a comprehensive product for biodiversity management in both terrestrial and freshwater ecosystems. 

On Tuesday evening, the CO-OP4CBD (abbreviation for Co-operation for the Convention on Biological Diversity) team: another Horizon Europe project, where Pensoft contributes with expertise in science communication and dissemination, held a workshop dedicated to what needs to be done to promote CBD activities in Central and Eastern Europe.

On the next day, scientists from the EuropaBON consortium: another project involving Pensoft that had concluded only about a month ago, held a session to report on the final conclusions from the project concerning the state and progress in biodiversity monitoring.

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You can find the detailed scientific programme of this year’s ECCB on the congress’ website. 

Use the #ECCB2024 hashtag on X (formerly Twitter) to relive highlights from the ECCB congress. 

Brand new computer language describes organismal traits to create computable species descriptions

Describing traits with Phenoscript is like programming a computer code for how an organism looks.

The beetle species Grebennikovius basilewskyi. Numbers next to arrows indicate patterns of phenotype statements explained in the section “Phenoscript: main patterns of phenotype statements”. Arrow numbers from T1 to T5 illustrate individual body parts. See more in the research study.

One of the most beautiful aspects of Nature is the endless variety of shapes, colours and behaviours exhibited by organisms. These traits help organisms survive and find mates, like how a male peacock’s colourful tail attracts females or his wings allow him to fly away from danger. Understanding traits is crucial for biologists, who study them to learn how organisms evolve and adapt to different environments.

To do this, scientists first need to describe these traits in words, like saying a peacock’s tail is “vibrant, iridescent, and ornate”. This approach works for small studies, but when looking at hundreds or even millions of different animals or plants, it’s impossible for the human brain to keep track of everything.

Computers could help, but not even the latest AI technology is able to grasp human language to the extent needed by biologists. This hampers research significantly because, although scientists can handle large volumes of DNA data, linking this information to physical traits is still very difficult.

To solve this problem, researchers from the Finnish Museum of Natural History, Giulio Montanaro and Sergei Tarasov, along with collaborators, have created a special language called Phenoscript. This language is designed to describe traits in a way that both humans and computers can understand. Describing traits with Phenoscript is like programming a computer code for how an organism looks.

Phenoscript uses something called semantic technology, which helps computers understand the meaning behind words, much like how modern search engines know the difference between the fruit “apple” and the tech company “Apple” based on the context of your search.

“This language is still being tested, but it shows a lot of promise. As more scientists start using Phenoscript, it will revolutionise biology by making vast amounts of trait data available for large-scale studies, boosting the emerging field of phenomics,”

explains Montanaro.

In their research article, newly published in the open-access, peer-reviewed Biodiversity Data Journal, the researchers make use of the new language for the first time, as they create semantic phenotypes for four species of dung beetles from the genus Grebennikovius. Then, to demonstrate the power of the semantic approach, they apply simple semantic queries to the generated phenotypic descriptions. 

Finally, the team takes a look yet further ahead into modernising the way scientists work with species information. Their next aim is to integrate semantic species descriptions with the concept of nanopublications, “which encapsulates discrete pieces of information into a comprehensive knowledge graph”. As a result, data that has become part of this graph can be queried directly, thereby ensuring that it remains Findable, Accessible, Interoperable and Reusable (FAIR) through a variety of semantic resources.

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Research paper:

Montanaro G, Balhoff JP, Girón JC, Söderholm M, Tarasov S (2024) Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae). Biodiversity Data Journal 12: e121562. https://doi.org/10.3897/BDJ.12.e121562

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The hereby study is the latest addition to the special topical collection: “Linking FAIR biodiversity data through publications: The BiCIKL approach”, launched and supported by the recently concluded Horizon 2020 project: Biodiversity Community Integrated Knowledge Library (BiCIKL). The collection aims to bring together scientific publications that demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

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What expert recommendations did the BiCIKL consortium give to policy makers and research funders to ensure that biodiversity data is FAIR, linked, open and, indeed, future-proof? Find out in the blog post summarising key lessons learnt from the Horizon 2020 project.

How to ensure biodiversity data are FAIR, linked, open and future-proof?

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