Category: Nature Conservation

Nanopublications tailored to biodiversity data

Novel nanopublication workflows and templates for associations between organisms, taxa and their environment are the latest outcome of the collaboration between Knowledge Pixels and Pensoft.

First off, why nanopublications?

Nanopublications complement human-created narratives of scientific knowledge with elementary, machine-actionable, simple and straightforward scientific statements that prompt sharing, finding, accessibility, citability and interoperability.

By making it easier to trace individual findings back to their origin and/or follow-up updates, nanopublications also help to better understand the provenance of scientific data.

With the nanopublication format and workflow, authors make sure that key scientific statements – the ones underpinning their research work – are efficiently communicated in both human-readable and machine-actionable manner in line with FAIR principles. Thus, their contributions to science are better prepared for a reality driven by AI technology.

The machine-actionability of nanopublications is a standard due to each assertion comprising a subject, an object and a predicate (type of relation between the subject and the object), complemented by provenance, authorship and publication information. A unique feature here is that each of the elements is linked to an online resource, such as a controlled vocabulary, ontology or standards.

Now, what’s new?

As a result of the partnership between high-tech startup Knowledge Pixels and open-access scholarly publisher and technology provider Pensoft, authors in Biodiversity Data Journal (BDJ) can make use of three types of nanopublications:

Nanopublications associated with a manuscript submitted to BDJ. This workflow lets authors add a Nanopublications section within their manuscript while preparing their submission in the ARPHA Writing Tool (AWT). Basically, authors ‘highlight’ and ‘export’ key points from their papers as nanopublications to further ensure the FAIRness of the most important findings from their publications.

Standalone nanopublication related to any scientific publication, regardless of its author or source. This can be done via the Nanopublications page accessible from the BDJ website. The main advantage of standalone nanopublication is that straightforward scientific statements become available and FAIR early on, and remain ready to be added to a future scholarly paper.

Nanopublications as annotations to existing scientific publications. This feature is available from several journals published on the ARPHA Platform, including BDJ. By attaching an annotation to the entire paper (via the Nanopublication tab) or a text selection (by first adding an inline comment, then exporting it as a nanopublication), a reader can evaluate and record an opinion about any article using a simple template based on the Citation Typing Ontology (CiTO).

Nanopublications for biodiversity data?

At Biodiversity Data Journal (BDJ), authors can now incorporate nanopublications within their manuscripts to future-proof the most important assertions on biological taxa and organisms or statements about associations of taxa or organisms and their environments.

On top of being shared and archived by means of a traditional research publication in an open-access peer-reviewed journal, scientific statements using the nanopublication format will also remain ‘at the fingertips’ of automated tools that may be the next to come looking for this information, while mining the Web.

Using the nanopublication workflows and templates available at BDJ, biodiversity researchers can share assertions, such as:

So far, the available biodiversity nanopublication templates cover a range of associations, including those between taxa and individual organisms, as well as between those and their environments and nucleotide sequences.

Nanopublication template customised for biodiversity research publications available from Nanodash.

As a result, those easy-to-digest ‘pixels of knowledge’ can capture and disseminate information about single observations, as well as higher taxonomic ranks.

The novel domain-specific publication format was launched as part of the collaboration between Knowledge Pixels – an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing and the open-access scholarly publisher Pensoft.

… so, what exactly is a nanopublication?

General structure of a nanopublication:

“the smallest unit of publishable information”,

as explained on nanopub.net.

Basically, a nanopublication – unlike a research article – is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists as a reusable and cite-able pieces of a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.

These semantic statements expressed in community-agreed terms, openly available through links to controlled vocabularies, ontologies and standards, are not only freely accessible to everyone in both human-readable and machine-actionable formats, but also easy-to-digest for computer algorithms and AI-powered assistants.

In short, nanopublications allow us to browse and aggregate such findings as part of a complex scientific knowledge graph. Therefore, nanopublications bring us one step closer to the next revolution in scientific publishing, which started with the emergence and increasing adoption of knowledge graphs.

“As pioneers in the semantic open access scientific publishing field for over a decade now, we at Pensoft are deeply engaged with making research work actually available at anyone’s fingertips. What once started as breaking down paywalls to research articles and adding the right hyperlinks in the right places, is time to be built upon,”

said Prof. Lyubomir Penev, founder and CEO at Pensoft, which had published the very first semantically enhanced research article in the biodiversity domain back in 2010 in the ZooKeys journal.

Why are nanopublications necessary?

By letting computer algorithms access published research findings in a structured format, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each of those fragments of scientific information is interconnected and traceable back to its author(s) and scientific evidence.

A nanopublication is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists within a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels.

By building on shared knowledge representation models, these data become Interoperable (as in the I in FAIR), so that they can be delivered to the right user, at the right time, in the right place , ready to be reused (as per the R in FAIR) in new contexts.

Another issue nanopublications are designed to address is research scrutiny. Today, scientific publications are produced at an unprecedented rate that is unlikely to cease in the years to come, as scholarship embraces the dissemination of early research outputs, including preprints, accepted manuscripts and non-conventional papers.

A network of interlinked nanopublications could also provide a valuable forum for scientists to test, compare, complement and build on each other’s results and approaches to a common scientific problem, while retaining the record of their cooperation each step along the way.

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We encourage you to try the nanopublications workflow yourself when submitting your next biodiversity paper to Biodiversity Data Journal.

Community feedback on this pilot project and suggestions for additional biodiversity-related nanopublication templates are very welcome!

This Nanopublications for biodiversity workflow was created with a partial support of the European Union’s Horizon 2020 BiCIKL project under grant agreement No 101007492 and in collaboration with Knowledge Pixels AG.The tool uses data and API services of ChecklistBank, Catalogue of Life, GBIF, GenBank/ENA, BOLD, Darwin Core, Environmental Ontology (ENVO), Relation Ontology (RO), NOMEN, ZooBank, Index Fungorum, MycoBank, IPNI, TreatmentBank, and other resources.

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On the journal website: https://bdj.pensoft.net/, you can find more about the unique features and workflows provided by the Biodiversity Data Journal (BDJ), including innovative research paper formats (e.g. Data Paper, OMICS Data Paper, Software Description, R Package, Species Conservation Profiles, Alien Species Profile), expert-provided data audit for each data paper submission, automated data export and more.

Don’t forget to also sign up for the BDJ newsletter via the Email alert form on the journal’s homepage and follow it on Twitter and Facebook.

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How it works: Nanopublications linked to articles in RIO Journal

Earlier this year, Knowledge Pixels and Pensoft presented several routes for readers and researchers to contribute to research outputs – either produced by themselves or by others – through nanopublications generated through and visualised in Pensoft’s cross-disciplinary Research Ideas and Outcomes (RIO) journal, which uses the same nanopublication workflows.

Psychedelic rock gecko among dozens of species in need of further conservation protection in Vietnam

Researchers recommend IUCN CPSG’s One Plan Approach to Conservation measures, which include both habitat conservation and increasing the number of threatened species in breeding stations and zoos.

Endangered psychedelic rock gecko (*Cnemaspis psychedelica*)
Photo by Thomas Ziegler. Licence: CC-BY.

Further conservation measures are required to protect Vietnamese reptiles, such as the psychedelic rock gecko (Cnemaspis psychedelica), from habitat loss and overharvesting, concludes a new report, published in the open-access scientific journal Nature Conservation.

Having identified areas of high reptile diversity and large numbers of endangered species, the study provides a list of the 50 most threatened species as a guide for further research and conservation action in Vietnam.

The study, based on the bachelor thesis of Lilli Stenger (University of Cologne, Germany), recommends IUCN CPSG’s One Plan Approach to Conservation measures, which, next to improved habitat conservation, also involves increasing the number of threatened species in breeding stations and zoos to maintain populations suitable for restocking.

Co-authors of the report are Anke Große Hovest (University of Cologne, Germany), Truong Quang Nguyen (Vietnam Academy of Science and Technology), Cuong The Pham, (Vietnam Academy of Science and Technology), Anna Rauhaus (Cologne Zoo, Germany), Minh Duc Le (Vietnam National University), Dennis Rödder (Leibniz Institute for the Analysis of Biodiversity Change, Germany) and Thomas Ziegler (University of Cologne and Cologne Zoo, Germany).

“Modern zoos, as well as local facilities, can play a crucial role in not only conducting or financially supporting in situ conservation projects, that is to say in nature, but also by protecting species from extinction through maintaining ex situ assurance colonies to reinforce in situ conservation programs,”
said Prof. Dr. Thomas Ziegler, Vietnam conservation team member and coordinator from Cologne Zoo, Germany.

Endangered Truong Son pit viper or Quang Binh pit viper (*Trimeresurus truongsonensis*).
Photo by Thomas Ziegler. Licence: CC-BY.

The scientists identified 484 reptile species known to Vietnam, aiming to provide a baseline to authorities, conservationists, rescue centers, and zoos, so they can follow up with appropriate conservation measures for endangered species. They note that the number is likely to go up, as the country is regarded as a top biodiversity hotspot, and the rate of new reptile species discoveries remains high.

According to the IUCN Red List, 74 of the identified species are considered threatened with extinction, including 34 endemic species. For more than half of Vietnam’s endemic reptiles (85 of 159), the IUCN Red List status is either missing or outdated, and further research is imperative for these species, the researchers say.

Vietnam has a high level of reptile diversity and an outstanding number of endemic species. The species richness maps in the study revealed the Central Annamites in central Vietnam to harbor the highest endemic species diversity (32 species), which highlights it as a site of particular importance for reptile conservation. Alarmingly, a protected area analysis showed that 53 of the 159 endemic species (33.2%) including 17 threatened species, have been recorded exclusively from unprotected areas, such as the Psychedelic Rock Gecko.

The Critically Endangered Annam pond turtle (*Mauremys annamensis*) is one of the most endangered turtle species in Vietnam and in the world. It is not known from any protected area. Despite likely being extinct in the wild, ex situ conservation programs have been implemented in time with a high number of individuals being kept and bred in zoos and stations and now ready for restocking actions.
Photo by Thomas Ziegler. Licence: CC-BY.

In General, Vietnam is considered a country with high conservation priority due to habitat loss and overharvesting for trade, traditional medicine and food.

Globally, reptiles are considered a group of special conservation concern, as they play an important role in almost all ecosystems and often have relatively small distribution ranges, making them especially vulnerable to human threats.

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Original source:

Stenger L, Große Hovest A, Nguyen TQ, Pham CT, Rauhaus A, Le MD, Rödder D, Ziegler T (2023) Assessment of the threat status of reptile species from Vietnam – Implementation of the One Plan Approach to Conservation. Nature Conservation 53: 183 221. https://doi.org/10.3897/natureconservation.53.106923

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Genetic study reveals that a captive-bred population could save endangered crocodile from extinction

Since this species is almost extinct in the wild, the news brings hope for the recovery of populations.

The Orinoco crocodile (Crocodylus intermedius) is a critically endangered species native to the Orinoco River basin in Colombia and Venezuela. It is one of the largest crocodilian species in the world, reaching lengths of up to seven meters. Despite its impressive size, it is also the most endangered and least-studied of the New World crocodilians.

Female Orinoco crocodile from the Roberto Franco Tropical Biological Station´s ex-situ population.

The species has faced a severe population decline due to commercial overexploitation of its skin, which was highly sought after by the fashion industry of Europe, the USA and Japan in the 20^th century. As a result, the current estimated global population stands at less than 250 adult individuals.

Recognizing the critical status of the species, herpetologist Federico Medem established a captive breeding program for the Orinoco crocodile in 1971 at the Roberto Franco Tropical Biological Station (RFTBS) in Villavicencio. Currently, the RFTBS houses over 600 individuals, making it the largest stock of this species and the only one in Colombia. Remarkably, there might be more adult crocodiles kept there than in the wild.

Despite the success of the captive breeding program, reintroduction of animals into the wild has been challenging. This is primarily due to the lack of a comprehensive genetic characterization that can determine whether the population is genetically viable and has no signs of inbreeding, which can result in reduced fitness at the individual and population level. To ensure the successful reintroduction of the species, it was crucial to have a robust and conclusive genetic assessment that confirms the population’s genetic health and viability.

“We felt a sense of urgency to determine the genetic viability of the population in order to proceed with the reintroduction of animals and establish new populations of the species in Colombia. Therefore, we conducted a comprehensive genetic characterization using fast-evolving molecular markers on a sample of 551 crocodiles,” explains Ana María Saldarriaga, a former researcher at the Universidad Nacional de Colombia who is currently pursuing a Ph.D. at Fordham University.

“Our findings showed that the individuals within the population possess sufficient genetic diversity and are suitable for reintroduction efforts, as well as for maintaining and enhancing the genetic variability of the ex-situ population.”

“We demonstrated that molecular data could be used to improve the management of ex-situ conservation programs well beyond what could be achieved with pedigree information alone,” she and her colleagues write in a study just published in the journal Nature Conservation.

Based on the findings of this study, the Colombian government, along with other public and private conservation institutions and agencies, can use the individuals identified in this research to initiate the establishment of new populations in regions where the species has been completely depleted.

“Today, it is widely recognized that top predators, such as crocodiles, play fundamental roles in both aquatic and terrestrial ecosystems. They have a significant impact on the nutrient cycle, regulate fish populations, and contribute to important cross-ecosystem engineering processes,” stated Mario Vargas-Ramírez, professor at the Genetics Institute of the Universidad Nacional de Colombia and director of the RFTBS.

“Therefore, the reintroduction of the Orinoco crocodile to the Orinoco region is an urgent priority. Additionally, as the Orinoco crocodile is considered an umbrella species, its recovery and conservation efforts will have a positive cascading effect, protecting a large number of species that coexist in the same environment.”

Research article:

Saldarriaga-Gómez AM, Ardila-Robayo MC, Medem F, Vargas-Ramírez M (2023) Hope is the last thing lost: Colombian captive-bred population of the critically endangered Orinoco crocodile (Crocodylus intermedius) is a genetic reservoir that could help to save the species from extinction. Nature Conservation 53: 85-103. https://doi.org/10.3897/natureconservation.53.104000

Photos by Mario Vargas-Ramírez.

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Pensoft’s science illustrator Denitsa Peneva wins first place at a prestigious international contest

“Dormice of Europe (Gliridae)” – an illustration combining watercolour and pencil – and Denitsa Peneva won at the Illustraciencia competition in the “Nature Illustration” category.

“Dormice of Europe (Gliridae)” – an illustration combining watercolour and pencil – and its author Denitsa Peneva won at the Illustraciencia competition in the “Nature Illustration” category. This year, the contest saw over 500 works.

Since 2009, the annual international event convened by the Spanish National Research Council and the Catalan Association of Scientific Communication has been recognising scientific illustrations with the aim to popularise science within the wider society.

Denitsa’s illustration depicts five dormouse species known from Europe: the Roach’s mouse-tailed or ground dormouse (Myomimus roachi), the forest dormouse (Dryomys nitedula), the European edible dormouse (Glis glis), the hazel dormouse (Muscardinus avellanarius) and the garden dormouse (Eliomys quercinus). Each of the rodents is seen on a plant that is typical either for its habitat or diet. Respectively, one of the species – which is a carnivore – is shown next to a snail.

Curiously, “Dormice of Europe (Gliridae)” was inspired by last year’s 11^th International Dormouse Conference, which took place in Svilengrad, Bulgaria. The locality was not chosen at random. It had just recently been found to house a large population of the rarest dormouse species for Europe. At the time, the Roach’s mouse-tailed or ground dormouse (Myomimus roachi), a species endemic to the Balkans, had not been encountered for almost 40 years.

You can follow the work by Denitsa on her Facebook page.

Eye for Detail: Papers in Pensoft journals sport a new look

As behaviours and needs of readers change, we strive to keep up with the times. Let’s run through what & why has changed to the PDF format.

Readers at some of the journals published by Pensoft, who have downloaded/printed a publication or ordered a physical copy of a journal issue over the last few weeks, might be in for a surprise concerning the layout of the PDF format of the articles.

Research papers published in ZooKeys demonstrating the former (left) and the current (right) article layout seen in the PDF format.

Even though it’s been years since online publishing has become the norm in how we are consuming information – including scientific publications – we understand that academia is still very much fond of traditional, often paper-based, article layout format: the one you use when accessing a PDF file or a print copy, rather than directly scrolling down through the HTML version of the article.

Even if today large orders of printed volumes from overseas are the exception, rather than the rule, we know we have readers of ours who regularly print manuscripts at home or savе them on their devices. Trends like this have already led to many journals first abandoning the physical- for digital-first, then transitioning to digital-only publication format.

Meanwhile, it is true that needs and demands have fundamentally changed in recent times.

As we speak, readers are accessing PDF files from much higher-quality desktops, in order to skim through as much content as possible.

In the meantime, authors are relying on greater-quality cameras to document their discoveries, while using advanced computational tools capable of generating and analysing extra layers of precise data. While producing more exhaustive research, however, it is also of key importance that their manuscripts are processed and published as rapidly as possible.

So, let’s run through the updates and give you our reasoning for their added value to readers and authors.

Revised opening page

One of the major changes is the one to the format of the first page. By leaving some blank space on the left, we found a dedicated place for important article metadata, i.e. academic editor, date of manuscript submission / acceptance / publication, citation details and licence. As a result, we “cleaned up” the upper part of the page, so that it can better highlight the authors and their affiliations.

Bottom line: The new layout provides a better structure to the opening page to let readers find key article metadata at a glance.

Expand as much – or as little – as comfortable

As you might know, journals published by Pensoft have been coming in different formats and sizes. Now, we have introduced the standard A4 page size, where the text is laid in a single column that has been slightly indented to the right, as seen above. Whenever a figure or a table is used in a manuscript, however, it is expanded onto the whole width of the page.

Before giving our reasons why, let’s see what were the specific problems that we address.

Case study 1

Some of our signature journals, including ZooKeys, PhytoKeys and MycoKeys, have become quite recognisable with their smaller-than-average B5 format, widely appreciated by people who would often be seen carrying around a copy during a conference or an international flight.

However, in recent times, authors began to embrace good practices in research like open sharing of data and code, which resulted in larger and more complex tables. Similarly, their pocket-sized cameras would capture much higher-resolution photos capable of revealing otherwise minute morphological characters. Smaller page size would also mean that often there would be pages between an in-text reference of a figure or a table and the visual itself.

So, here we faced an obvious question: shall we deprive their readers from all those detailed insights into the published studies?

Case study 2

Meanwhile, other journals, such as Herpetozoa, Zoosystematics and Evolution and Deutsche Entomologische Zeitschrift, had long been operating in A4 size, thereby providing their readers with a full view of the figures in their publications.

Yet, the A4 format brought up another issue: the lines were too long for the eye comfort of their readers.

What they did was organise their pages into two-column format. While this sounds like a good and quite obvious decision, the format – best known from print newspapers – is pretty inconvenient when accessed digitally. Since the readers would like to zoom in on the PDF page or simply access the article on mobile, they will need to scroll up and down several times per page.

In addition, the production of a two-column text is technologically more challenging, which results in extra production time.

Bottom line: The new layout allows journals to not sacrifice image quality for text readability and vice versa. As a bonus, authors enjoy faster publication for their papers.

Simplified font

If you have a closer look at the PDF file, you would notice that print-ready papers have also switched to a more simplistic – yet easier to the eye – font. Again, the update corresponds to today’s digital-native user behaviour, where readers often access PDF files from devices of various resolutions and skim through the text, as opposed to studying its content in detail.

In fact, the change is hardly new, since the same font has long been utilised for the webpages (HTML format) of the publications across all journals.

Bottom line: The slightly rounder and simplified font prompts readability, thereby allowing for faster and increased consumption of content.

What’s the catch? How about characters and APCs?

While we have been receiving a lot of positive feedback from editors, authors and readers, there has been a concern that the updates would increase the publication charges, wherever these are estimated based on page numbers.

Having calculated the lines and characters in the new layout format, we would like to assure you that there is no increase in the numbers of characters or words between the former and current layout formats. In fact, due to the additional number of lines fitting in an A4 page as opposed to B5, authors might be even up for a deal.

________

* At the time of the writing, the new paper layout has not been rolled out at all journals published by Pensoft. However, most of the editorial boards have already confirmed they would like to incorporate the update.

________

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Can deep learning help us save mangrove forests?

Object-oriented classification of fused Sentinel images can significantly improve the accuracy of mangrove land use/land cover classification.

Mangrove forests are an essential component of the coastal zones in tropical and subtropical areas, providing a wide range of goods and ecosystem services that play a vital role in ecology. They are also threatened, disappearing, and degraded across the globe.

One way to stimulate effective mangrove conservation and encourage policies for their protection is to carefully assess mangrove habitats and how they change, and identify fragmented areas. But obtaining this kind of information is not always an easy task.

“Since mangrove forests are located in tidal zones and marshy areas, they are hardly accessible,” says Dr. Neda Bihamta Toosi, postdoc at Isfahan University of Technology in Iran working on landscape pattern changes using remote sensing. In a recent study in the journal Nature Conservation, together with a team of authors, she explored ways to classify these fragile ecosystems using machine learning.

Comparing the performance of different combinations of satellite images and classification techniques, the researchers looked at how good each method was at mapping mangrove ecosystems.

“We developed a novel method with a focus on landscape ecology for mapping the spatial disturbance of mangrove ecosystems,” she explains. “The provided disturbance maps facilitate future management and planning activities for mangrove ecosystems in an efficient way, thus supporting the sustainable conservation of these coastal areas.”

The results of the study showed that object-oriented classification of fused Sentinel images can significantly improve the accuracy of mangrove land use/land cover classification.

“Assessing and monitoring the condition of such ecosystems using model-based landscape metrics and principal component analysis techniques is a time- and cost-effective approach. The use of multispectral remote sensing data to generate a detailed land cover map was essential, and freely available Sentinel-2 data will guarantee its continuity in future,” explains Dr. Bihamta Toosi.

The research team hopes this approach can be used to provide information on the trend of changes in land cover that affect the development and management of mangrove ecosystems, supporting better planning and decision-making.

“Our results on the mapping of mangrove ecosystems can contribute to the improvement of management and conservation strategies for these ecosystems impacted by human activities,“ they write in their study.

Research article:

Soffianian AR, Toosi NB, Asgarian A, Regnauld H, Fakheran S, Waser LT (2023) Evaluating resampled and fused Sentinel-2 data and machine-learning algorithms for mangrove mapping in the northern coast of Qeshm island, Iran. Nature Conservation 52: 1-22. https://doi.org/10.3897/natureconservation.52.89639

Illegal trade and poor regulation threaten pangolins in China

Unpermitted sellers are commonly found illegally selling pangolin scale products for the purposes of traditional Chinese medicine.

Pangolins, unique scale-covered mammals, are drastically declining in numbers across Asia and Africa, largely due to illegal trade. Part of the trade, both legal and illegal, supports the traditional Chinese medicine market, which has attracted conservation attention. The level of demand for pangolins and other animals in traditional Chinese medicine, however, hasn’t been thoroughly studied.

In a new study published in the journal Nature Conservation, Dr Yifu Wang, currently a postdoc researcher at the University of Hong Kong, investigated pangolin scale trade in China, interviewing staff in hospitals and pharmaceutical shops in two provinces (Henan and Hainan). Between October 2016 and April 2017, she and her team talked to doctors from 41 hospitals and shop owners and assistants from 134 pharmaceutical shops.

An adult Philippine Pangolin and her pup photographed in the forests of Palawan. Photo by Gregg Yan under a CC-BY-SA-4.0 license

The research found pangolin scales and their derivatives were widely available in hospitals and pharmaceutical shops across Henan and Hainan Provinces. The legislation in place, however, has not been able to prevent ongoing illegal trade in pangolin products. Her team found that 46% of surveyed hospitals and 34% of surveyed pharmaceutical shops were selling pangolin scale products illegally.

“Existing legal trade allows 711 hospitals to sell pangolin products as medicine with regulations on manufacturer, package, and national annual sale quantity,” explains Dr Yifu Wang. “However, we show that pangolin scales are under heavy demand and unpermitted sellers are commonly found illegally selling pangolin products.”

Processed pangolin scales. Photo by Dr. Yifu Wang

“Quantities of products traded by permitted legal sellers are estimated to greatly exceed the supply capacity of legal sources,” she continues.

This widespread illegal trade, coupled with the very limited legal supply capacity compared to market demand, is concerning. The researchers point to the urgent need to reduce demand from traditional Chinese medicine on pangolin scales and revise the current legal pangolin scale trade system.

“We also highlight the importance of incorporating the traditional Chinese medicine sector into combating illegal wildlife trade and species conservation beyond pangolins,” they conclude.

The researchers plan to continue investigating the pangolin scale market in China to understand the trade after COVID-19.

Research article:

Wang Y, Turvey ST, Leader-Williams N (2023) The scale of the problem: understanding the demand for medicinal pangolin products in China. Nature Conservation 52: 47-61. https://doi.org/10.3897/natureconservation.52.95916

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Protecting marine biodiversity: we take a look at science

In light of the UN’s High Seas Treaty, we look back at deep-sea science published in our journals.

Surely, March 2023 will be remembered with the historic agreement of UN member states to protect marine biodiversity in the world’s oceans.

The so-called High Seas Treaty is a legal framework for the protection of marine biodiversity and responsible and equitable use of resources of areas beyond national jurisdiction (BBJN). Its draft, published on the 5th of March 2023, is the outcome of two decades of negotiations, and is part of the international effort to protect a third of the world’s biodiversity by 2030.

An unwavering dedication to the protection and conservation of biodiversity will be required to see the firm landing of this hopeful step.

On this occasion, we look back at some impactful studies published in our journals that have made waves, hopefully in the right direction towards impactful conservation measures and actions.

Following President Barack Obama’s expansion of the largest permanent Marine Protected Area on Earth (Papahānaumokuākea Marine National Monument) in 2016, a new species of coral-reef fish was named in his honour. The fish is the only known coral-reef species to be endemic to the Monument, and, despite its small size, it carries wide-reaching cultural and political significance as a reminder of how politics go hand in hand with science.

Former President of the United States, Barack Obama, arriving on Midway Atoll Midway on September 1, 2016 to commemorate his use of the Antiquities Act to expand the boundaries of the Papahānaumokuākea Marine National Monument. Dr. Sylvia Earle gives President Barack Obama a photograph of *Tosanoides obama* on Midway Atoll, from the film “Sea of Hope: America’s Underwater Treasures” premiered on National Geographic Channel on January 15, 2017. See also the news story on National Geographic.

Other studies from our flagship zoology journal ZooKeys have focused on the benthic megafauna and abyssal fauna of the Clarion-Clipperton Zone (CCZ) in the Pacific Ocean.

The Clarion-Clipperton Zone, managed by the International Seabed Authority, has been targeted by deep-sea mining interests. In the context of heightened concern over potential biodiversity loss, scientific research is crucial for informing policy-makers and the general public about the risks and outcomes of such initiatives.

The Clarion-Clipperton Zone, central Pacific Ocean (purple box), spanning 6 milllion km². Knowledge of marine biodiversity in the area is crucial for its protection.
Image source: A. Glover at al. (2016).

The rich biodiversity of the deep sea has also been documented in big-scale taxonomic inventories and checklists in the Biodiversity Data Journal.

Such examples are the publication of 48 new echinoderm records from the CCZ made during a single 25-day cruise, marking a ~25% increase of the echinoderm species records previously available in databases. Other notable contributions are the first image atlas of annelid, arthropod, bryozoan, chordate, ctenophore and mollusc morphospecies and the first image atlas of echinoderm megafauna morphospecies inhabiting the UK-1 exploration contract area and the eastern CCZ.

The echinoderm *Amphioplus* cf. *daleus* Lyman, 1879. Image source: A. Glover at al.

*Hymenopenaeus* cf. *nereus* observed in the UK-1 exploration contract area.
Image source: Amon et al. (2017).

Going forward, the expansion of Marine Protected Areas should also ensure the implementation of policies for the methods of resource extraction and their equitable sharing and use among the world’s nations.

Over the next few years, we hope to see an ever increasing interest in biodiversity conservation - from the general public, stakeholders and policy makers, and, of course, research institutions.

 We need to love what we protect in order to be able to protect it.

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Interoperable biodiversity data extracted from literature through open-ended queries

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.

The OpenBiodiv contribution to BiCIKL

Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.

As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.

In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.

“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.

“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”
he adds.

At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.

Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL.

As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions.

Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.

Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.

On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.

*Sample of predefined SPARQL queries at OpenBiodiv.*

“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”
concludes Prof Lyubomir Penev.

***

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EU responsible for extinction domino effect on frog populations

New study shows EU frogs’ legs imports put a serious risk to frogs in Southeast Asia and Eastern Europe

**In Europe, frogs’ legs are mostly offered as appetizers. © Pixabay**

Between 2010 and 2019, total imports of frog’s legs into the EU numbered 40.7 million kg, which equals to up to roughly 2 billion frogs. While Belgium is the main importer, France is the main consumer. These insights are part of a new study, published in the journal Nature Conservation, which found “inexplicable volatility” in the trade of frog legs and an extreme dependency of the EU on other countries to meet its demand.

Leading author Dr. Auliya of the Leibniz Institute for the Analysis of Biodiversity Change in Bonn, Germany, outlines the manifold uncertainties underlying this trade: “The international trade in frogs’ legs is a black box, whether it is the lack of species-specific trade data, which would be needed to ensure sustainability, or the large-scale mislabeling in trade and the challenges to identify species when it comes to processed, skinned and frozen frogs’ legs.”

Frogs’ legs from large ranids at a large-scale reptile collector in North Sumatra, Indonesia. Photo by Mark Auliya

Frogs have a central role in the ecosystem as insect predators – and where frogs disappear, the use of toxic pesticides increases. Hence, the frogs’ legs trade has direct consequences not only for the frogs themselves, but for biodiversity and ecosystem health as a whole. The extent to which pesticide residues in frogs’ legs are traded internationally remains unclear.

In the 1970s and 1980s, India and Bangladesh were the top suppliers of frogs’ legs to Europe, but when their wild frog populations collapsed, both countries banned exports. Since then, Indonesia has taken over as the largest supplier. In the Southeast Asian country, as now also in Turkey and Albania, large-legged frog species are dwindling in the wild, one after the other, causing a fatal domino effect for species conservation. This increasingly threatens frog populations in the supplier countries.

“The EU is by far the world’s largest importer of frogs’ legs, and large-legged species such as the crab-eating grass frog (Fejervarya cancrivora), the giant Javan frog (Limnonectes macrodon) and the East Asian bullfrog (Hoplobatrachus rugulosus) are in particular demand among supposed gourmets in Europe”, points out co-author Dr. Sandra Altherr, a biologist and wildlife trade expert of the Germany-based charity Pro Wildlife.

Frozen frogs’ legs on sale in a French supermarket, August 2022. Photo by Sandra Altherr / Pro Wildlife

While commercial frog farms, like those operated in Viet Nam, may at first glance seem to be an alternative that can relieve the pressure from wild frog populations, ongoing restocking of frog farms with native species from the wild and, in the case of non-native species, such as the American bullfrog (Lithobates catesbeianus) the risk of escape, invasion and potential risk of disease spread, are serious risks for the environment.

The harvest of wild frog populations and species produced at commercial frog farms for the purpose of consumption also leaves disease control and hygiene measures by the wayside; additionally, the cross-border trade of species for consumption has led to genetic pollution and hybridization between species.

Limnonectes blythii species complex from a large-scale collector in North Sumatra. Photo by Mark Auliya

„During the course of this study, it became clear just how difficult it is to obtain concrete data on the current international trade in frogs’ legs. Specifically, relevant data are scattered across different unconnected databases,“ the researchers write in their paper.

In the course of their review, they were not able to find any published data out whether pesticide residues and other potentially toxic substances in (processed) frogs or their legs imported into the EU have been monitored. “This in itself is shocking and in view of the situation in exporting countries and the lack of transparency and management in the application of agrochemicals and veterinary medicinal substances within commercial farms, we strongly recommend that this monitoring become an urgent near-future task for importing countries,” they write.

“The complexity of issues underlying the frogs’ legs trade is not a priority policy item for the EU,” the authors conclude. They add that a listing of the most-affected frog species under CITES, the Convention on International Trade in Endangered Species of Wild Fauna and Flora, would help to monitor trade and ensure its sustainability, and the EU as the main destination should take the lead on that.

Research article:

Auliya M, Altherr S, Nithart C, Hughes A, Bickford D (2023) Numerous uncertainties in the multifaceted global trade in frogs’ legs with the EU as the major consumer. Nature Conservation 51: 71-135. https://doi.org/10.3897/natureconservation.51.93868

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