Author: Pensoft Editorial Team

BiCIKL project sums up outcomes and future prospects at a Final GA in Cambridge

On multiple occasions, the participants agreed that the Biodiversity Knowledge Hub must be the flagship outcome of BiCIKL. 

The city of Cambridge and the Wellcome Campus hosted the Final General Assembly of the EU-funded project BiCIKL (acronym for Biodiversity Community Integrated Knowledge Library): a 36-month endeavour that saw 14 member institutions and 15 research infrastructures representing diverse actors from the biodiversity data realm come together to improve bi-directional links between different platforms, standards, formats and scientific fields. Consortium members who could not attend the meeting in Cambridge joined the meeting remotely.

The 3-day meeting was organised by local hosts European Molecular Biology Laboratory (EMBL) and ELIXIR in collaboration with Pensoft Publishers.

After a welcome cocktail reception on Monday evening at Hilton Cambridge City Centre, on Tuesday, the consortium made an early start with a recap of BiCIKL’s key milestones and outputs from the last three years. All Work Package leaders had their own timeslot to discuss the results of their collaborations.  

They all agreed that the Biodiversity Knowledge Hub – the one-stop portal for understanding the complex – yet increasingly interconnected landscape of biodiversity research infrastructures – is likely the flagship outcome of BiCIKL. 

Prof. Lyubomir Penev, project coordinator of BiCIKL and founder/CEO of Pensoft Publishers at the BiCIKL’s third and final General Assembly in Cambridge, United Kingdom.

In the afternoon, the participants focused on the services developed under BiCIKL. Amongst the many services resulting from the project some were not originally planned. Rather those were the ‘natural’ products of the dialogue and collaboration that flourished within the consortium throughout the project. “A symptom of passion,” said Prof. Lyubomir Penev, project coordinator of BiCIKL and founder/CEO of Pensoft Publishers.

An excellent example of one such service is what the partners call the “Biodiversity PMC”, which brings together biodiversity literature from thousands of scholarly journals and over 500,000 taxonomic treatments, in addition to the biomedical content available from NIH’s PubMed Central, into the SIB Literature Services (SIBiLS) database. What’s more, users at SIBiLS – be it human or AI – can now use advanced text- and data-mining tools, including AI-powered factoid question-answering capacities, to query all this full-text indexed content and seek out, for example, species traits and biotic interactions. Read more about the “Biodiversity PMC” in its recent official announcement.

Far from being the only one, the “Biodiversity PMC” is in good company: from the blockchain-based technology of LifeBlock to the curation of the DNA sequences by PlutoF, the BiCIKL project consortium takes pride in having developed twelve services dedicated to FAIR and linked ready-to-use biodiversity data. 

All those services are already listed in the FAIR Data Place within the Biodiversity Knowledge Hub, where each is presented with its own video. For many services, from the same page, visitors can also download factsheets meant to serve as user guidelines. All will also be featured in the EOSC catalogue.

All services developed under BiCIKL with links to their explanatory videos:

On Wednesday, the consortium focused on BiCIKL’s activities from the Transnational and Virtual Access Pillar, which included both presentations by each open call leader and VA leader, as well as open discussions and a recap of what the teams have learnt from these experiences. 

A panel discussion took place on Thursday as part of an open event, where BiCIKL partners and ELIXIR Biodiversity and Plant Communities came together to discuss the Future of Biodiversity and Genomics data integration at the EMBL Wellcome Genome Campus.

Thursday was dedicated to an open event where BiCIKL partners and ELIXIR Biodiversity and Plant Communities came together to discuss the Future of Biodiversity and Genomics data integration at the EMBL Wellcome Genome Campus. You can find the agenda on BiCIKL’s website.

After 36 months of action, the BiCIKL project will officially end in April 2024, but does it mean that all will be done and dusted come May 2024? Certainly not, point out the partners. 

To ensure that the Biodiversity Knowledge Hub will not only continue to exist but will not cease to grow in both use and participation, the one-stop portal will remain under the maintenance of LifeWatch ERIC. 

In conclusion, we could say that an appropriate payoff for the project is “Stick together!” as put by BiCIKL’s Joint Research Activity Leader Dr. Quentin Groom.

Final words at the third and last General Assembly of the BiCIKL project.

You can find highlights from the BiCIKL General Assembly meeting on X via the #BiCIKL_H2020 hashtag (in association with #Cambridge and #finalGA)

BiCIKL keeps on adding project outcomes in own collection in RIO Journal
All research outputs, including the approved grant proposal, policy briefs, guidelines papers and research articles associated with the project, remain openly accessible from the BiCIKL project outcomes collection in RIO Journal: https://doi.org/10.3897/rio.coll.105.

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All BiCIKL project partners:

Eaten to extinction: breeding programmes begin for endangered turtles in Vietnam

Considered a delicacy in China and Vietnam, the spotted softshell turtle faces threats from overconsumption and habitat loss.

Conservationists have initiated breeding programmes in Vietnam to recover spotted softshell turtle populations threatened by overconsumption and habitat loss.

Based on a literature study, field surveys across Vietnam, and genetic screenings of collected samples, researchers estimated the range and conservation status of Pelodiscus variegatus, the spotted softshell turtle. The data were then used to model the species’ potential range in Vietnam.

Alarmingly, although several protected areas in Vietnam appear to harbour suitable habitats for the species, no populations were identified in any of the sites, indicating it is especially susceptible to extinction.

The research team releasing juvenile turtles into water.
Release of juveile turtles in Vietnaam. Credit: C. T. Pham and T. Ziegler

To recover natural populations of the species, the Institute of Ecology and Biological Resources and Cologne Zoo, Germany, initiated an in-country breeding programme. In late 2023, they released 50 young and healthy turtles to a site with suitable climate and habitat in northern Vietnam.

It is hoped that additional individuals will be reintroduced to protected areas in north-central Vietnam, the sanctuary of spotted softshell turtles, to reverse its declining trend and further contribute to the global Reverse the Red movement, a target best accomplished by applying the IUCN’s One Plan Approach to Conservation.

Softshell turtles of the genus Pelodiscus are broadly distributed from southeastern Siberia through China to Vietnam. However, their range is currently extended to Indonesia, northern Australia, western Europe, North America, Hawaii, and Mauritius as a result of human transportation and breeding activities.

The turtles are considered a delicacy in China and some Southeast Asian countries. In China alone, each year hundreds of million turtles are traded, making them the most widely consumed turtles in the world.

Traditionally, this genus had been considered monotypic with only one recognised species, the Chinese softshell turtle (Pelodiscus sinensis). However, recent research has shown that the genus is much more diverse with at least seven species known to science.

Due to their morphological similarity, widespread farming activities, overharvesting, and their aquatic lifestyle, it is often difficult to study them in their natural habitat to better understand their distribution as well as their population and conservation status.

Like other congeners, the spotted softshell turtle is facing tremendous threats, from habitat loss to overharvesting for food and genetic pollution because the Chinese softshell turtle has been farmed across the country, imperilling the native genetic sources.

As the result, the Turtle Taxonomy Working Group, the global authority on taxonomic and conservation status of turtles worldwide, provisionally classifies the species as Critically Endangered, the highest ranking for taxa most vulnerable to extinction.

Original post:

Le MD, Rödder D, Nguyen TT, The Pham C, Nguyen TQ, Ong AV, McCormack TEM, Nguyen TT, Le MH, Ngo HT, Ziegler T (2024) Climatic niche modelling and genetic analyses highlight conservation priorities for the Spotted Softshell Turtle (Pelodiscus variegatus). Nature Conservation 55: 67-82. https://doi.org/10.3897/natureconservation.55.114746

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Follow Nature Conservation on Facebook and X.

Gardeners on the front line: the key to early invasive plant detection?

A study from the United Kingdom suggests gardeners could partner with researchers to play a crucial role in preventing plant invasions.

The critical role of gardeners in identifying ‘future invaders’ – ornamental plants that could become invasive species – has been revealed by researchers from the University of Reading and the Royal Horticultural Society.

Looking to draw from the experience of Britain’s millions of gardeners, the team created an online survey where gardeners reported ornamentals that showed ‘invasive behaviour’ in their gardens.

Based on reports from 558 gardeners, 251 different plants were identified as potential invaders, reflecting the extensive variety and potential risks in domestic gardens. The team analysed the results, considering both domestic and global invasive status, and prioritised ornamental plants of concern. The result was a shortlist of plants which need their invasive potential in Britain and Ireland assessed.

The shortlisted plants include, for example: Mexican fleabane (Erigeron karvinskianus); cypress spurge (Euphorbia cyparissias); chameleon plant (Houttuynia cordata); Himalayan honeysuckle (Leycesteria formosa); and purple top (Verbena bonariensis).

Mexican fleabane. Credit: KENPEI via Wikimedia Commons
Cypress spurge. Credit: Bogdan via Wikimedia Commons
Chameleon plant. Credit: Mariko GODA via Wikimedia Commons
Purple top. Credit: Karelj via Wikimedia Commons.
Himalayan honeysuckle. Credit: H. Zell via Wikimedia Commons.

The results, published in the open-access journal NeoBiota, highlight the role of gardeners in the early detection of invasive species, a key factor in the global nature crisis. Such proactive identification could prove invaluable for future risk assessments and prevention strategies.

“The simple yet structured scheme we developed was used to prioritise which of the around 70,000 ornamental plants available to buy in the UK could be future invaders. This is crucial for focusing research efforts and resources, such as conducting formal risk assessments to explore the invasive potential of those shortlisted.”

Tomos Jones, lead author

John David, RHS Head of Horticultural Taxonomy, said: “It’s important to remember that these shortlisted plants are not yet officially invasive, and that many non-native plants that occur in the wild present no threat to our native biodiversity.”

The research team encourages gardeners to get involved in helping identify future invaders. They can report ornamental plants showing ‘invasive behaviour’ through an ongoing project called Plant Alert, run by the Botanical Society of Britain and Ireland and Coventry University.

Original source:

Jones TS, Culham A, Pickles BJ, David J (2024) Can gardeners identify ‘future invaders’? NeoBiota 91: 125–144. https://doi.org/10.3897/neobiota.91.110560

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Why two prehistoric sharks found in Ohio got new names

Research leads to rediscovery of forgotten fossils.

Until recently, Orthacanthus gracilis could have been considered the “John Smith” of prehistoric shark names, given how common it was.

Three different species of sharks from the late Paleozoic Era – about 310 million years ago – were mistakenly given that same name, causing lots of grief to paleontologists who studied and wrote about the sharks through the years and had trouble keeping them apart.

But now Loren Babcock, a professor of earth sciences at The Ohio State University, has finished the arduous task of renaming two of the three sharks – and in the process rediscovered a wealth of fossil fishes that had been stored at an Ohio State museum for years but had been largely forgotten.

Loren Babcock with a collection of Orton Museum’s fossil fishes, including several from John Newberry. Photo by The Ohio State University

In order to change the names, Babcock had to go through a process governed by the International Commission on Zoological Nomenclature (ICZN). He had to document the need to change the names, propose new names and submit them to an ICZN-recognized journal for peer review and then have the ICZN officially accept the names.

Tooth of the shark Orthacanthus lintonensis. The tooth is about 13 mm long.

“It was one of the most complex naming problems we have had in paleontology, which is probably one reason no one attempted to fix it until now,” Babcock said.

“A lot of scientists in the field have written, thanking me for doing this. We are all happy it is finally done,” he said.

One measure of the impact the renaming has had on the field: Babcock’s paper announcing the new names was just published in the journal ZooKeys on Jan. 8, but it has already been referenced on seven different Wikipedia pages.

The original Orthacanthus gracilis fossil was found in Germany and named in 1848. That species gets to keep the name.

The remaining two fossils were found in Ohio and named by the famous American paleontologist John Strong Newberry in 1857 and 1875.

Portrait of John Strong Newberry

Babcock renamed the Ohio sharks Orthacanthus lintonensis and Orthacanthus adamas, both based on the name of the place where they were originally found.

Why did Newberry give the two Ohio sharks the same name?

“He probably just forgot. It was nearly 20 years between the time the two species were named,” Babcock said.

And as far as giving it the same name as a German species: “In those days, it was really difficult to search for names that were already in existence – they did not have the internet.”

The sharks themselves were fascinating creatures, Babcock said.  They were large and creepy, nearly 10 feet long, and looked more like eels than present-day sharks, with long dorsal fins extending the length of their backs and a peculiar spine extending backward from their heads.

They lived in the fresh or brackish water of what are known as “coal swamps” of the late Carboniferous Period (323-299 million years ago) during the late Paleozoic Era. They belong to an extinct group of chondrichthyans (which includes sharks, skates and rays) called the xenacanthiforms.

Dorsal spine of Orthacanthus adamas. The spine is about 71 mm long.

Newberry was for a time the chief geologist at the Geological Survey of Ohio. He played an important role in the early growth of what is now the Orton Geological Museum at Ohio State.

Babcock, who is the current director of the Orton Museum, decided to begin the renaming process after reviewing the museum’s collection. He was surprised to see how many fossils the museum had that had been collected by Newberry, including the two prehistoric sharks.

Babcock wrote about Orton’s Newberry collection in a new article published in the Journal of Vertebrate Paleontology.

Through the years, scientists have written about how various Newberry specimens had been lost. It turns out many had been at the Orton Museum.

“No museum has a larger collection of Newberry’s fossils except for the American Museum of Natural History in New York City,” Babcock said.

“Not a lot of people are aware of that – I did not even know the extent of our collection. If you’re looking for part of the Newberry collection and can’t find it in the American Museum of Natural History, it is probably going to be here.”

Research article:

Babcock LE (2024) Replacement names for two species of Orthacanthus Agassiz, 1843 (Chondrichthyes, Xenacanthiformes), and discussion of Giebelodus Whitley, 1940, replacement name for Chilodus Giebel, 1848 (Chondrichthyes, Xenacanthiformes), preoccupied by Chilodus Müller & Troschel, 1844 (Actinopterygii, Characiformes). ZooKeys 1188: 219-226. https://doi.org/10.3897/zookeys.1188.108571

News piece originally published by the Ohio State University. Republished with permission.

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A new species of rare pseudoscorpion named after the Slovak president

Olpium caputi, named after Zuzana Čaputová, was discovered on the island Tahiti in French Polynesia

There are about 25,000 islands in the Pacific Ocean. The most remote of them are in North and East Polynesia, the Hawaiian Islands, and French Polynesia. Biologists have been attracted to these regions since the 18th century, but French Polynesia has received much less attention compared to the Hawaiian Islands.

A view of the area where Olpium caputi was found. Photo by Frédéric A. Jacq

Contributions to our knowledge of the pseudoscorpions of French Polynesia date from the 1930s and are associated with the Pacific Entomological Survey. Since then, the French Polynesian pseudoscorpion fauna has consisted of only four known species.

A female individual of Olpium caputi.

Thanks to international cooperation, a team of enthusiastic scientists has published the first discovery of a new species of pseudoscorpion from French Polynesia. Between 2017 and 2020, they studied French Polynesia’s fauna and environment for the French Polynesian Agricultural Service and as a part of a large-scale survey of arthropods. During their research work, they collected a few pseudoscorpion specimens on Huahine and Tahiti in the Society Islands.

Among them is a new species named Olpium caputi, collected by sieving moss at 1,450 m about sea level on the Mont Marau Summit, Tahiti, one of the Society Islands archipelago. Its scientific name honours Zuzana Čaputová, the President of Slovakia.

Zuzana Čaputová. Photo by Jindřich Nosek (NoJin) under a CC BY-SA 4.0 license.

“As a female leader, she takes a strong stance and supports women and scientists. Even in the 21st century, women in science or top positions are rare. The rarity of the research in French Polynesia, the uniqueness of the discovery, and the fact that the new species is a female, led us to name it after this inspiring woman who can be a role model of courage and perseverance for many women,” says Jana Christophoryová, who led the study.

The paper is published in the open-access, peer-reviewed journal ZooKeys.

The team:

Katarína Krajčovičová of Bratislavské regionálne ochranárske združenie – BROZ, Bratislava, and Jana Christophoryová of Comenius University, Bratislava, are both zoologists, who specialize in the taxonomy, distribution, and ecology of pseudoscorpions. Frédéric Jacq, botanist, and Thibault Ramage, entomologist, are independent naturalists who have been working on improving the faunistic and taxonomic knowledge of French Polynesia for over 15 years.

Research article:

Krajčovičová K, Ramage T, Jacq FA, Christophoryová J (2024) Pseudoscorpions (Arachnida, Pseudoscorpiones) from French Polynesia with first species records and description of new species. ZooKeys 1192: 29-43. https://doi.org/10.3897/zookeys.1192.111308

Earth Observation meets in-situ biodiversity monitoring: Pensoft joins the OBSGESSION project

As a leader of the Work Package 6: “Dissemination, Multi-stakeholder outreach and synergies,” Pensoft is tasked to build an involved community around OBSGESSION.

Pensoft is to contribute to the OBSGESSION consortium with expertise in science communication by taking care of stakeholders engagement, thereby supporting its goal of improved terrestrial and freshwater biodiversity monitoring. As a leader of the Work Package 6: “Dissemination, Multi-stakeholder outreach and synergies,” Pensoft is tasked to build an involved community around OBSGESSION.

Terrestrial and freshwater biodiversity has been declining at an alarming rate due various factors such as intensification of anthropogenic activities and climate change.

To help protect and preserve precious ecosystems, the new research project OBSGESSION (Observation of Ecosystem Changes for Action) launched, jointly funded under the EU programme Horizon Europe, the UK Research and Innovation (UKRI) and the University of Zurich (UZH). 

Coordinated by the Finnish Environmental Institute (Syke), OBSGESSION aims to reveal the drivers of biodiversity loss, pinpoint important indicators of ecosystem health and inform sustainability policy.

The project

OBSGESSION launched in January 2024 and will wrap up in December 2027 with the support of ~7.3 million EUR of funding, provided by the European Union’s Horizon Europe program, The UK Research and Innovation program (UKRI), and the University of Zurich (UZH).

The OBSGESSION consortium at the kick-off meeting in January 2024 (Tuusula, Finland).

The project officially kicked off with the first consortium meeting in Tuusula, Finland, between 30th January and 2nd February.

For the coming four years, the joint mission before the newly formed consortium is to integrate biodiversity data sources, such as Earth Observation, with in-situ research, and also cutting-edge ecological models. These will all be made into a comprehensive product for biodiversity management in both terrestrial and freshwater ecosystems. 

The project will also spearhead an innovative approach for assessing Essential Biodiversity Variables (EBVs) and their resilience to errors. Through purposely propagating error into biodiversity estimates and comparing the resulting models with ones using correct estimates, the EBV case studies aim to investigate model uncertainties and identify approaches that are more sensitive. Thus, they will inform policy and management about the optimal EBVs, and their key thresholds for conservation.

To demonstrate the implementation of the techniques and methodologies they are to develop within the project; and to respond to the needs of the EU Biodiversity Strategy for 2030, the consortium will focus on six distinct pilot activities:

  1. Investigating and predicting biodiversity change in the European Alps: multi-scale, multi-modal and multi-temporal investigation using remote and in-situ data integration.
  2. Improving habitat classification models: going beyond state-of-the-art in terms of accurate high-resolution mapping of Europe’s habitats, powered by machine learning.
  3. Forecasting ecosystem productivity under disturbances & climate change: incorporating remote sensing EBVs to assess metrics of ecosystem structure and health.
  4. Supporting temperate and boreal forest protection & restoration: through assessing ecosystem conditions via eDNA & image spectroscopy.
  5. Monitoring freshwater ecosystems under disturbances & climate change: utilizing the novel Thematic Ecosystem Change Indices (TECIs).
  6. Ecosystem functioning of the Kokemäenjoki estuary – assessing freshwater & transitional water quality incorporating both in-situ and Earth Observation data.

Through its pilot studies, methodological assessments, data stream integration, and investigating land use cover changes across Europe, OBSGESSION will help improve our understanding of ecosystem vulnerability across a range of specific habitat types, identify drivers and pressures to ecosystem change and improve planning and prioritization of restoration measures.

“At Pensoft, we are eager to be part of the bright OBSGESSION consortium and look forward to offering our expertise and experience in raising awareness towards the project and contributing to the high impact of the resulting outputs, methodologies and policy recommendations that aim to strengthen our understanding of biodiversity change,”

says Gabriela Popova, science communicator at Pensoft and leader of the Work Package #6: “Dissemination, Multi-stakeholder outreach and synergies” at OBSGESSION.

International Consortium

The interdisciplinary OBSGESSION consortium consists of 11 partnering organisations from seven European countries, who bring diverse expertise spanning from remote sensing and Earth observation, to freshwater ecosystems, programming and science communication. Many partners represent acclaimed scientific institutions with rich experience in collaborative EU projects.

Full list of partners:

Find more on the OBSGESSION website: https://obsgession.eu, and follow the project on X/Twitter (@obsgession_) and Linkedin (/obsgession-horizoneurope).

Towards the “Biodiversity PMC”: a literature database supporting advanced content queries

The indexing is one of the major outcomes from the partnerships within the Horizon 2020-funded project Biodiversity Community Integrated Knowledge Library (BiCIKL)

Amongst the major outcomes from the currently nearly completed Horizon 2020-funded project Biodiversity Community Integrated Knowledge Library (BiCIKL) – dedicated to making biodiversity data FAIR and bi-directionally linked – brings the SIB Literature Services (SIBiLS) database one step closer to solidifying its “Biodiversity PMC” portal and working title.

In a joint effort between the Swiss-based Text Mining group of Patrick Ruch at SIB (developing SIBiLS), the text- and data-mining association Plazi and scientific publisher Pensoft, the long-time collaborators have started feeding full-text content of over 500,000 taxonomic treatments extracted by Plazi and tens of thousands full-text articles from 40 well-renowned biodiversity journals published by Pensoft to the SIBiLS database. 

What this means is that users at SIBiLS – be it human or AI – have now gained access to advanced text- and data-mining tools, including AI-powered factoid question-answering capacities, to query all this full-text indexed content and seek out, for example, species traits and biotic interactions.

To index and directly feed the content from its 40+ academic outlets at SIBiLS, Pensoft relies on advanced and full-text TaxPub JATS XML journal publication workflow, powered by the ARPHA publishing platform. Meanwhile, Plazi uses its GoldenGate text- and data-mining software to harvest taxon treatments from over 80 journals stored at TreatmentBank and the Biodiversity Literature Repository, and then further re-used by GBIF, OpenBiodiv and now by SiBILS.

Seen as a pilot, the indexing – the partners believe – could soon be extended with other journals relying on modern publishing or converted legacy publications. 

In fact, ever since its launch in 2020, the queryable database SIBiLS has been retrieving relevant full-text papers directly from the NIH’s PubMed Central, including Pensoft’s ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal and Comparative Cytogenetics. 

However, there were still gaps left to bridge before SIBiLS could indeed be dubbed “the Biodiversity PMC”, and those have mostly been about volume and breadth of content. While the above-mentioned five journals by Pensoft had long been indexed by SIBiLS through harvesting PMC, those had been quite an exception since, several years ago, a reorganisation at PMC moved the focus of the database to almost exclusively biomedical content, thus leaving biodiversity journals out of the scope of the database.

In the meantime, while Plazi has been feeding SIBiLS a growing volume of taxonomic treatments and visual data, as it was exponentially increasing the number of publishers and journals it mined data from, a lot of biodiversity data (e.g. genetic, molecular, ecological) published in the article narratives that were not taxon treatments could not make it to the portal.

“We all know the advantages and practical uses PMC offers to its users, so we cannot miss the opportunity to incorporate this well-proven approach to navigate the data deluge in biodiversity science. Undoubtedly, it is an extremely ambitious and demanding task. Yet, I believe that, at the BiCIKL consortium, we have made it pretty clear we have the necessary expertise, know-how and aspiration to take on the challenge,”

said Prof. Lyubomir Penev, founder/CEO at Pensoft and project coordinator of BiCIKL.

“For far too long, scientific knowledge about biodiversity has been imprisoned in a continuously growing corpus of scientific outputs, which – most of the time – are published in unstructured formats, such as PDF, or as paywalled content, and often locked by both! This means that they are – at best – difficult to access and comprehend by computer algorithms. In the meantime, we need all that knowledge, in order to accelerate our understanding of the dynamics of the global biodiversity crisis and to efficiently assess the impact of climate change. This is why the need for advanced workflows and tools to annotate, mine, query and discover new facts from the available literature is more than obvious,”

added Dr. Donat Agosti, President at Plazi.

“In the course of the BiCIKL project, at SIBiLS, we started indexing a larger set of biodiversity-related contents in the broad sense, including environmental sciences and ecology, to build a new literature database, or what we now call ‘Biodiversity PMC’. Now, with the help of Plazi and Pensoft, we provide a unique entry point to half a million taxonomic treatments, which were not included into the original PubMed Central. Next on the list is to expand our network of literature sources and continue this exponential growth of queryable biodiversity knowledge to turn Biodiversity PMC into the “One Health” library. We promise to keep you posted,”

said Dr. Patrick Ruch, Group Leader at SIB and Head of Research at HES-SO, HEG Geneva, Switzerland. 

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Follow BiCIKL Project on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

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About the SIB Swiss Institute of Bioinformatics:

SIB is an internationally recognized non-profit organisation, dedicated to biological and biomedical data science. SIB’s data scientists are passionate about creating knowledge and solving complex questions in many fields, from biodiversity and evolution to medicine. They provide essential databases and software platforms as well as bioinformatics expertise and services to academic, clinical, and industry groups. With the recent creation of the Environmental Bioinformatics group, led by Robert Waterhouse, SIB is engaged in an unprecedented effort to streamline data across molecular biology, health and biodiversity. SIB also federates the Swiss bioinformatics community of some 900 scientists, encouraging collaboration and knowledge sharing.

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About Plazi:

Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To this end, Plazi maintains TreatmentBank, a digital taxonomic literature repository to enable archiving of taxonomic treatments; develops and maintains TaxPub, an extension of the National Library of Medicine / National Center for Biotechnology Informatics Journal Article Tag Suite for taxonomic treatments; is co-founder of the Biodiversity Literature Repository at Zenodo, participates in the development of new models for publishing taxonomic treatments in order to maximise interoperability with other relevant cyberinfrastructure components such as name servers and biodiversity resources; and advocates and educates about the vital importance of maintaining free and open access to scientific discourse and data. Plazi is a major contributor to the Global Biodiversity Information Facility.

Five dazzling new species of eyelash vipers discovered in Colombia and Ecuador

The groundbreaking discovery was made official in a study published in the open-access journal Evolutionary Systematics.

A group of scientists led by researchers of Khamai Foundation discovered five dazzling new species of eyelash vipers in the jungles and cloud forests of Colombia and Ecuador. This groundbreaking discovery was made official in a study published in the open-access journal Evolutionary Systematics.

Prior to this research, the captivating new vipers, now recognized as among the most alluring ever found, were mistakenly classified as part of a single, highly variable species spanning from Mexico to northwestern Peru. The decade-long study initiated with an unexpected incident wherein one of the authors was bitten by one of these previously undiscovered species.

 Distribution of the palm pitvipers of the Bothriechis schlegelii species complex, including the five new species described in Arteaga et al. 2014.

Eyelash vipers stand out due to a distinctive feature: a set of enlarged spine-like scales positioned atop their eyes. These “lashes” bestow upon the snakes a formidable and fierce appearance, yet the true purpose of this feature remains unknown. What is definite, however, is that certain populations exhibit longer, and more stylized eyelashes compared to others. The variations in the condition of the eyelashes led researchers to hypothesize the existence of undiscovered species.

The clue that led the researchers to suspect that there were new species of eyelash vipers was the fact that some populations in the cloud forests of Ecuador had almost no “lashes.” Photos by Lucas Bustamante and Jose Vieira.

Eyelash vipers are also famous for another feature: they are polychromatic. The same patch of rainforest may contain individuals of the turquoise morph, the moss morph, or the gold morph, all belonging to the same species despite having an entirely different attire. “No two individuals have the same coloration, even those belonging to the same litter (yes, they give birth to live young),” says Alejandro Arteaga, who led the study.

For some of the species, there is a “Christmas” morph, a ghost morph, and even a purple morph, with the different varieties sometimes coexisting and breeding with one another. The reason behind these incredible color variations is still unknown, but probably enables the vipers to occupy a wide range of ambush perches, from mossy branches to bright yellow heliconias.

  • Yellow-pink morph of the Rahim’s Eyelash-Pitviper (Bothriechis rahimi). Photo by Alejandro Arteaga
  • Rahim’s Eyelash-Pitviper (Bothriechis rahimi). Photo by Lucas Bustamante
  • Black-and-yellow morph of the Hussain’s Eyelash-Pitviper (Bothriechis hussaini). Photo by Alejandro Arteaga
  • Brown morph of the Shah’s Eyelash-Pitviper (Bothriechis rasikusumorum). Photo by Jose Vieira
  • “Coffee” morph of Bothriechis klebbai. Photo by Elson Meneses

Where do these new snakes live?

Three of the five new species are endemic to the eastern Cordillera of Colombia, where they occupy cloud forests and coffee plantations. One, the Rahim’s Eyelash-Pitviper, stands out for occurring in the remote and pristine Chocó rainforest at the border between Colombia and Ecuador, an area considered “complex to visit” due to the presence of drug cartels. The Hussain’s Eyelash-Pitviper occurs in the forests of southwestern Ecuador and extreme northwestern Peru. The researchers outline the importance of conservation and research in the Andes mountain range and its valleys due to its biogeographic importance and undiscovered megadiversity.

The Chocó rainforest is home to four vipers of the Bothriechis schlegelii species complex, including two new species discovered by Arteaga et al. 2024. Photo by Lucas Bustamante

What’s with the venom?

“The venom of some (perhaps all?) of the new species of vipers is considerably less lethal and hemorrhagic than that of the typical Central American Eyelash-Viper,” says Lucas Bustamante, a co-author of the study. Lucas was bitten in the finger by the Rahim’s Eyelash-Pitviper while taking its pictures during a research expedition in 2013. “I experienced intermittent local pain, dizziness and swelling, but recovered shortly after receiving three doses of antivenom in less than two hours after the bite, with no scar left behind,” says Bustamante.

Researcher Alejandro Arteaga examines the fangs of Central American Eyelash-Pitviper (Bothriechis nigroadspersus) in the Darién jungle of Panamá.

How threatened are these new species?

One of the study’s key conclusions is that four of the species in the group are facing a high risk of extinction. They have an extremely limited geographic range and 50% to 80% of their habitat has already been destroyed. Therefore, a rapid-response action to save the remaining habitat is urgently needed.

Red-wine morph of the Central American Eyelash-Pitviper (Bothriechis nigroadspersus), photographed in the Caribbean Island Escudo de Veraguas, off the coast of Panamá. Photo by Alejandro Arteaga

Who is honored with this discovery?

Two of the new species of vipers, the Rahim’s Eyelash-Pitviper (Bothriechis rahimi) and the Hussain’s Eyelash-Pitviper (B. hussaini), are named in honor of Prince Hussain Aga Khan and Prince Rahim Aga Khan, respectively, in recognition of their support to protect endangered global biodiversity worldwide through Focused On Nature (FON) and the Aga Khan Development Network. The Shah’s Eyelash-Pitviper (B. rasikusumorum) honors the Shah family, whereas the Klebba’s Eyelash-Pitviper (B. klebbai) and the Khwarg’s Eyelash-Pitviper (B. khwargi) honor Casey Klebba and Dr. Juewon Khwarg, respectively, for supporting the discovery and conservation of new species.

Turquoise morph of the Ecuadorian Eyelash-Pitviper (Bothriechis nitidus). This species is endemic to the Chocó rainforest in west-central Ecuador. Photo by Alejandro Arteaga

What is next?

Khamai Foundation is setting up a reserve to protect a sixth new species that remained undescribed in the present study. “The need to protect eyelash vipers is critical, since unlike other snakes, they cannot survive without adequate canopy cover. Their beauty, though worthy of celebration, should also be protected and monitored carefully, as poachers are notorious for targeting charismatic arboreal vipers for the illegal pet trade of exotic wildlife,” warns Arteaga. Finally, he and his team encourage the support of research on the venom components of the new species of vipers. This will promote their conservation as well as help communities that regularly encounter eyelash pitvipers.

Original source:

Arteaga A, Pyron RA, Batista A, Vieira J, Meneses Pelayo E, Smith EN, Barrio Amorós CL, Koch C, Agne S, Valencia JH, Bustamante L, Harris KJ (2024) Systematic revision of the Eyelash Palm-Pitviper Bothriechis schlegelii (Serpentes, Viperidae), with the description of five new species and revalidation of three. Evolutionary Systematics 8(1): 15-64. https://doi.org/10.3897/evolsyst.8.114527

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Assessment, monitoring, and mitigation of chemical stressors on the health of wild pollinators: Pensoft joins WildPosh

Pensoft is amongst the participants of a new Horizon Europe project aiming to better evaluate the risk to wild pollinators of pesticide exposure, enhancing their health & pollination services.

Wild fauna and flora are facing variable and challenging environmental disturbances. One of the animal groups that is most impacted by these disturbances are pollinators, which face multiple threats, driven to a huge extent by the spread of anthropogenic chemicals, such as pesticides. 

WildPosh (Pan-european assessment, monitoring, and mitigation of chemical stressors on the health of wild pollinators) is a multi-actor, transdisciplinary project whose overarching mission and ambition are to significantly improve the evaluation of the risk to wild pollinators of pesticide exposure, and enhance the sustainable health of pollinators and pollination services in Europe.

On 25 and 26 January 2024, project partners from across Europe met for the first time in Mons, Belgium and marked the beginning of the 4-year endeavour that is WildPosh. During the two days of the meeting, the partners had the chance to discuss objectives and strategies and plan their work ahead. 

This aligns with the objectives of the European Green Deal and EU biodiversity strategy for 2030, emphasising the need to reduce pollution and safeguard pollinators. WildPosh focuses on understanding the routes of chemical exposure, evaluating toxicological effects, and developing preventive measures. By addressing knowledge gaps in pesticide risk assessment for wild pollinators, the project contributes to broader efforts in biodiversity conservation.

During the kick-off meeting in Mons, WildPosh’s project coordinator Prof. Denis Michez (University of Mons, Belgium) gave an introductory presentation.

As a leader of Work Package #7: “Communication, knowledge exchange and impact”, Pensoft is dedicated to maximising the project’s impact by employing a mix of channels in order to inform stakeholders about the results from WildPosh and raise further public awareness of wild and managed bees’ health.

Pensoft is also tasked with creating and maintaining a clear and recognisable project brand, promotional materials, website, social network profiles, internal communication platform, and online libraries. Another key responsibility is the development, implementation and regular updates of the project’s communication, dissemination and exploitation plans, that WildPosh is set to follow for the next four years.

“It is very exciting to build on the recently concluded PoshBee project, which set out to provide a holistic understanding of how chemicals affect health in honey bees, bumble bees, and solitary bees, and reveal how stressors interact to threaten bee health. WildPosh will continue this insightful work by investigating these effects on wild pollinators, such as butterflies, hoverflies and wild bee species, with the ultimate goal of protecting these small heroes who benefit the well-being of our planet,”

says Teodor Metodiev, WildPosh Principal Investigator for Pensoft.

For the next four years, WildPosh will be working towards five core objectives: 

1) Determine the real-world agrochemical exposure profile of wild pollinators at landscape level within and among sites 

2) Characterise causal relationships between pesticides and pollinator health 

3) Build open database on pollinator traits/distribution and chemicals to define exposure and toxicity scenario

4) Propose new tools for risk assessment on wild pollinators

5) Drive policy and practice.

Consortium:

The consortium consists of 17 partners coming from 10 European countries. Together, they bring extensive experience in Research and Innovation projects conducted within the Horizon programmes, as well as excellent scientific knowledge of chemistry, modelling, nutritional ecology, proteomics, environmental chemistry and nutritional biology.

  1. University of Mons
  2. Pensoft Publishers
  3. Eesti Maaülikool (Estonian University of Life Sciences)
  4. BioPark Archamps
  5. French National Agency for Food, Environmental and Occupational Health & Safety
  6. French National Centre for Scientific Research
  7. Martin Luther University Halle-Wittenburg
  8. Albert Ludwigs University Freiburg
  9. UFZ Helmholtz Centre for Environmental Research
  10. University of Turin
  11. Italian National Institute of Health
  12. National Veterinary Research Institute – State Research Institute
  13. University of Novi Sad Faculty of Sciences
  14. University of Novi Sad, BioSense Institute-Research Institute for Information Technologies in Biosystems
  15. University of Murcia
  16. Royal Holloway and Bedford New College
  17. The University of Reading

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New species of 65-million-year-old shark ‘accidentally’ discovered in Alabama

The shark lived shortly after the extinction of the dinosaurs, and was discovered from a box of teeth collected over 100 years ago.

A new species of shark, which lived shortly after the mass extinction of the dinosaurs, was discovered when palaeontologist Jun Ebersole came across a 100-year-old box of teeth at the Geological Survey in Alabama, USA.

“Having documented hundreds of fossil fish species over the last decade, I found it puzzling that these teeth were from a shark that I didn’t recognise,” says Ebersole, Director of Collections, McWane Science Center, Birmingham, AL, who quickly realised the teeth belong to a new species.

New shark species tooth.
Palaeohypotodus bizzocoi tooth. Credit: McWane Science Center.

The team, consisting of Ebersole, David Cicimurri, Curator of Natural History, South Carolina State Museum in Columbia, and T. Lynn Harrell Jr., Palaeontologist and Fossil Collections Curator at the Geological Survey of Alabama in Tuscaloosa, published their discovery in the open-access journal Fossil Record.

The shark is a new species of Palaeohypotodus (pronounced pale-ee-oh-hype-oh-toe-duss), which means “ancient small-eared tooth,” in reference to the small needle-like fangs present on the sides of the teeth. Scientists believe it may have looked like a modern sand tiger shark.

Moder sand tiger shark.
Modern sand tiger. Credit: Wikimedia commons.

Living approximately 65-million-years ago in the Paleocene era, Palaeohypotodus bizzocoi was likely a leading predator as the oceans recovered following the death of the dinosaurs, when more than 75% of life on Earth went extinct.

In Alabama, much of the southern half of the state was covered by a shallow tropical to sub-tropical ocean during the Paleocene.

New shark species teeth.
Palaeohypotodus bizzocoi teeth. Credit: Ebersole et al.

“This time period is understudied, which makes the discovery of this new shark species that much more significant,” Harrell says. “Shark discoveries like this one give us tremendous insights into how ocean life recovers after major extinction events and also allows us to potentially forecast how global events, like climate change, affect marine life today.”

As part of their study of this ancient fish, the team compared the fossil teeth to those of various living sharks, like Great Whites and Makos. According to Cicimurri, shark teeth differ in shape depending on where they are located in the mouth.

“By studying the jaws and teeth of living sharks, it allowed us to reconstruct the dentition of this ancient species and showed that it had a tooth arrangement that differed from any living shark,” Cicimurri says.

Dr. Bruce Bizzoco.
The late Dr. Bruce Bizzoco (1949-2022), for whom the new species is named.
Credit: McWane Science Center.

The new species has been named Palaeohypotodus bizzocoi for the late Dr. Bruce Bizzoco (1949-2022) of Birmingham, AL. Bizzoco served as a Dean at Shelton State Community College, archaeologist, and was a long-time volunteer at McWane Science Center.

This discovery is part of an ongoing project led by Ebersole and Cicimurri to document Alabama’s fossil fishes. Together, they have confirmed over 400 unique species of fossil sharks and bony fishes, which, according to Ebersole, makes Alabama one of the richest places in the world in terms of fossil fish diversity.

Research paper

Ebersole JA, Cicimurri DJ, Harrell Jr. TL (2024) A new species of Palaeohypotodus Glickman, 1964 (Chondrichthyes, Lamniformes) from the lower Paleocene (Danian) Porters Creek Formation, Wilcox County, Alabama, USA. Fossil Record 27(1): 111-134. https://doi.org/10.3897/fr.27.e112800

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