Pensoft Editorial Team

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.

Visit can follow WildPosh on X/Twitter (@WildPoshProject), Instagram (/wildposhproject) and Linkedin (/wildposh-eu)

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.

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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Pensoft collaborates with R Discovery to elevate research discoverability

Pensoft and R Discovery’s innovative connection aims to change the way researchers find academic articles.

Leading scholarly publisher Pensoft has announced a strategic collaboration with R Discovery, the AI-powered research discovery platform by Cactus Communications, a renowned science communications and technology company. This partnership aims to revolutionize the accessibility and discoverability of research articles published by Pensoft, making them more readily available on R Discovery to its over three million researchers across the globe.

R Discovery, acclaimed for its advanced algorithms and an extensive database boasting over 120 million scholarly articles, empowers researchers with intelligent search capabilities and personalized recommendations. Through its innovative Reading Feed feature, R Discovery delivers tailored suggestions in a format reminiscent of social media, identifying articles based on individual research interests. This not only saves time but also keeps researchers updated with the latest and most relevant studies in their field.

Open Science is much more than cost-free access to research output.
Lyubomir Penev

One of R Discovery’s standout features is its ability to provide paper summaries, audio readings, and language translation, enabling users to quickly assess a paper’s relevance and enhance their research reading experience significantly.

With over 2.5 million app downloads and upwards of 80 million journal articles featured, the R Discovery database is one of the largest scholarly content repositories.

“At Pensoft, we do realise that Open Science is much more than cost-free access to research outputs. It is also about easier discoverability and reusability, or, in other words, how likely it is for the reader to come across a particular scientific publication and, as a result, cite and build on those findings in his/her own studies. By feeding the content of our journals into R Discovery, we’re further facilitating the discoverability of the research done and shared by the authors who trust us with their work,” said ARPHA’s and Pensoft’s founder and CEO Prof. Lyubomir Penev.

Abhishek Goel, Co-Founder and CEO of Cactus Communications, commented on the collaboration, “We are delighted to work with Pensoft and offer researchers easy access to the publisher’s high-quality research articles on R Discovery. This is a milestone in our quest to support academia in advancing open science that can help researchers improve the world.”

So far, R Discovery has successfully established partnership with over 20 publishers, enhancing the platform’s extensive repository of scholarly content. By joining forces with R Discovery, Pensoft solidifies its dedication to making scholarly publications from its open-access, peer-reviewed journal portfolio easily discoverable and accessible.

Two new freshwater fungi species in China enhance biodiversity knowledge

The discoveries from the southwest of the country add to the impressive diversity of freshwater fungi in China.

Researchers have discovered two new freshwater hyphomycete (mould) species, Acrogenospora alangii and Conioscypha yunnanensis, in southwestern China.

This discovery, detailed in a study published in MycoKeys, marks the addition of these species to the Acrogenospora and Conioscypha genera, further enriching the diversity of freshwater fungi known in the region.

A research team consisting of Lu Li, Hong-Zhi Du and Ratchadawan Cheewangkoon from Chiang Mai University, Thailand, as well as Vinodhini Thiyagaraja and Rungtiwa Phookamsak from Kunming Institute of Botany, China, and Darbhe Jayarama Bhat from King Saud University, Saudi Arabia, employed comprehensive morphological analysis and multi-gene phylogenetic assessments in their study.

Notably, Acrogenospora alangii was identified on submerged branches of the medicinal plant Alangium chinense, highlighting a unique ecological association.

Hostplant of *Acrogenospora alangii* growing near water body.

Freshwater fungi are highly diverse in China and frequently reported from submerged wood, freshwater insects, herbaceous substrates, sediments, leaves, foams, and living plants.

Most species are well-known as saprobes (organisms that live on decaying organisms) and they play an important role in ecological functioning as decomposers, but also can be pathogens as well as symbionts on humans and plants.

This research underscores the ecological and taxonomic richness of freshwater fungi in China, a country already recognised for its diverse fungal habitats. The findings contribute valuable insights into the roles these organisms play in freshwater ecosystems and emphasise the importance of ongoing biodiversity studies in these environments.

Research article

Li L, Du H-Z, Thiyagaraja V, Bhat DJ, Phookamsak R, Cheewangkoon R (2024) Two novel freshwater hyphomycetes, in Acrogenospora (Minutisphaerales, Dothideomycetes) and Conioscypha (Conioscyphales, Sordariomycetes) from Southwestern China. MycoKeys 101: 249-273. https://doi.org/10.3897/mycokeys.101.115209

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Spiders, snakes and pseudoscorpions: new species published in Pensoft journal

Twelve fascinating newly discovered species were published in Pensoft’s journal Zoosystematics and Evolution in January 2024.

Zoosystematics and Evolution kicked off the year with research papers introducing 12 exciting new species from around the world. The journal, published by Pensoft on behalf of Museum für Naturkunde, is known for being at the forefront of animal research and, in particular, for sharing exciting new discoveries like those below.

Four jumping spiders from India

Four new species of Phintella were discovered in India. Generally striking in appearance, the genus now has 18 recognised species in India – second only to China.

Research paper: https://doi.org/10.3897/zse.100.113049

An ethereal sea slug from British waters

Pleurobranchaea britannica, a newly discovered sea slug, is the first of its genus found in British waters. The unusual translucent creature also represents the second valid Pleurobranchaea species from European seas.

Research paper: https://doi.org/10.3897/zse.100.113707

Pleurobranchaea britannica
Pleurobranchaea britannica

A beautiful venomous snake from Thailand

In the Tenasserim Mountain Range of western Thailand, researchers discovered Bungarus sagittatus, a new species of venomous elapid snake. The name sagittatus is derived from sagittata meaning arrow, referencing the dark triangular shape on its subcaudal scales which resembles a barbed arrow.

Research paper: https://doi.org/10.3897/zse.100.116601

Bungarus sagittatus
Bungarus sagittatus

Two eels from India

Researchers described two new species, Ariosoma gracile and Ariosoma kannani, from Indian waters, based on the materials collected from the Kochi coast, Gulf of Mannar and the West Bengal coast, along the Bay of Bengal.

Research paper: https://doi.org/10.3897/zse.100.116611

Ariosoma kannani
Ariosoma gracile

An island-dwelling land snail from Australia

Xanthomelon amurndamilumila was discovered on the North East Isles, offshore from Groote Eylandt, Australia. Its conservation status is of concern on North East Island because of habitat degradation caused by feral deer.

Research paper: https://doi.org/10.3897/zse.100.113243

New fish from Türkiye

A new Eurasian minnow, Phoxinus radeki, was discovered in the Ergene River (Aegean Sea Basin). Salmo brunoi, a new species of trout, was discovered in the Nilüfer River, a tributary of the Susurluk River.

Research papers: https://doi.org/10.3897/zse.100.113467 (Phoxinus radeki),
https://doi.org/10.3897/zse.100.112557 (Salmo brunoi)

Phoxinus radeki
Salmo brunoi

An Indian pseudoscorpion

Ditha shivanparaensis may look like a scorpion, but looks can be deceiving. Rather, it is an arachnid, newly discovered from the tropical montane cloud forests or ‘sholas’ of the Western Ghats of India.

Research paper: https://doi.org/10.3897/zse.100.110020

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With all these discoveries published in January, we anticipate many more exciting new species to come from Zoosystematics and Evolution in 2024!

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Celebrating scientific excellence: Dr. Paul D. N. Hebert awarded the Benjamin Franklin Medal

Dr. Paul D. N. Hebert, known as “the father of DNA barcoding,” has been honoured with the prestigious Benjamin Franklin Medal, a testament to his trailblazing contributions to biodiversity science.

Dr. Paul D. N. Hebert. Photo credit Åge Hojem, NTNU Vitenskapsmuseet/NTNU University Museum, used under a CC BY 2.0 licence

Dr. Hebert’s innovative work has advanced our understanding of global biodiversity, making the identification of species easier, which in turn helps support global conservation efforts. By devising a method that allows the quick and efficient discerning of species, he has transformed biodiversity science.

DNA barcoding has many applications in the classification and monitoring of biodiversity. It can help protect endangered species, control agriculture pests, and identify disease vectors.

Founder and Director of the Centre for Biodiversity Genomics and Chief Executive Officer of the International Barcode of Life consortium (iBOL), Dr. Hebert is one of the leading voices of today’s biodiversity innovation and research.

Dr. Hebert is also chair of the advisory board of Pensoft’s journal Metabarcoding and Metagenomics. He has authored 13 papers in ZooKeys, substantially contributing to untangling the taxonomy of braconid wasps, butterflies, and other insects.

Acylomus ergoti, one of the many insect species Dr. Hebert has worked on.

His work has also appeared in other Pensoft-published journals, such as Biodiversity Data Journal, Nota Lepidopterologica, and Deutsche Entomologische Zeitschrift.

His innovative approach has sparked discussions and debates around the role of novel methodologies in taxonomy.

Dr. Hebert’s recognition with the Benjamin Franklin Medal demonstrates the critical role of biodiversity studies in dealing with global challenges such as the biodiversity crisis. He has inspired a generation of scientists to push the boundaries of knowledge and drive innovation in research technology.

We at Pensoft extend our heartfelt congratulations to Dr. Paul D. N. Hebert on this well-deserved recognition. He continues to lead the way in unravelling the complexities of global biodiversity.

First database of the impacts of invasive plants in Europe

Freely accessible, the database provides useful contextual information and identifies key gaps in European invasive-plant research.

A team of experts has created the first database of field studies on the impacts of invasive plants on native species, communities and ecosystems in Europe.

The dataset comprises 266 peer-reviewed publications reporting 4,259 field studies on 104 invasive species across 29 European countries. It is the first harmonised database of its kind at continental scale, and is freely accessible to the scientific community for future studies. Notably, one third of the studies focused on just five species that invade several central European countries.

Japanese knotweed (*Reynoutria japonica*) in a garden in Brastad, Lysekil Municipality, Sweden.

Published in NeoBiota, the project was mainly funded through the European Regional Development Fund (SUMHAL, LIFEWATCH, POPE). It was executed by researchers from the Spanish institutes, E s tación Biológica de Doñana, Universidad de Sevilla, Instituto Pirenaico de Ecología and Universidad de Alcalá, as well as the University of Fribourg, Switzerland.

The comprehensive database indicates that invasive plants impact other plants, animals and microbes, all trophic levels (herbivores, parasites, plants, pollinators, predators, omnivores, decomposers and symbionts) and numerous ecosystem processes.

Map of locations (red dots) of field studies on the ecological impacts of invasive plant species in Europe. Credit: Vilà et al.

More than half of the studies were conducted in temperate and boreal forests and woodlands and temperate grasslands. Major knowledge gaps are found in Baltic and Balkan countries, in desert and semi-arid shrublands, subtropical forests and high mountains.

Prof. Montserrat Vilà, coordinator of this task, highlights that the database provides information on whether the invasive species increase, decrease or have a neutral effect on the ecological variable of study. This allows investigation into the circumstances in which the invader has contrasting effects.

Himalayan balsam (*Impatiens glandulifera*). Credit: Guptaele via Wikimedia Commons, CC BY-SA 4.0.

The database will be updated as new field studies on the ecological impacts of invasive species are published. “We hope for more studies on species that are still locally rare and with restricted distribution,” Prof. Montserrat Vilà says, “this database is of interest for academic, management and policy-related purposes.”

The PLANTIMPACTSEUROPE database can be accessed at: https://figshare.com/s/0a890d22bf5632fe5cb5

Research article:

Vilà M, Trillo A, Castro-Díez P, Gallardo B, Bacher S (2024) Field studies of the ecological impacts of invasive plants in Europe. NeoBiota 90: 139-159. https://doi.org/10.3897/neobiota.90.112368

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Brand new journal Estuarine Management and Technologies streamlines innovation in ecosystems conservation

There has been an increasing need to support the exchange of research related to the conservation and sustainable management of estuarine ecosystems by means of new-age technologies and approaches.

Where freshwater rivers meet seas and oceans lies a scientifically intriguing and ecologically important type of ecosystem. As estuarine ecosystems provide various and diverse services to humanity and the planet at large, including food security and natural buffers and filters in the events of storms and water pollution, there has been an increasing need to facilitate and support the exchange of research findings and ideas related to their conservation and sustainable management by means of new-age technology and novel approaches.

This is how a team of renowned and passionate scientists, headed by Dr. Soufiane Haddout (Ibn Tofail University, Morocco), took the decision to launch a brand new open-access, peer-reviewed scholarly, aptly titled Estuarine Management and Technologies. They explain the rationale behind the journal in a new editorial, published to mark the official launch of the journal.

Having already worked closely with the scientific publisher and technology provider Pensoft on the fine touches of the concept of the new academic title, the team opted to use Pensoft’s publishing platform of ARPHA. As a result, the new journal provides a seamless, end-to-end publishing experience, encompassing all stages between manuscript submission and article publication, indexation, dissemination and permanent archiving.

Within the collaboration between the journal’s and Pensoft’s teams, Estuarine Management and Technologies will take advantage of various services offered by the ARPHA platform, including full-text automated export in machine-readable and minable JATS-XML format to over 60 relevant databases for scientific literature and data; semantically enriched and multimedia-friendly publications accessible in HTML; and rich statistics about the outreach and usage of each published article and its elements (e.g. figures and tables), including views, downloads, online mentions, and citations.

The publishing platform’s in-house indexing team will continue their close work with the journal’s editors to ensure that the scholarly outlet retains highest quality and integrity, so that it covers the criteria for indexation at additional key databases that require individual evaluation. In the meantime, ARPHA’s technical and editorial teams will provide technical and customer support to authors, editors and reviewers. The marketing and promotion team of ARPHA will be also joining forces with the journal to boost the visibility and image of the new academic title.

During the launch phase, content accepted for publication following double-blinded peer review will be made public right away for free to both authors and readers, where the journal will be operating under a continuous publication model.

Estuarine Management and Technologies welcomes studies from a wide spectrum of disciplines, including physics, chemistry, geology, biology, and hydrology, with a focus on interdisciplinarity, multifaceted approaches and holistic perspectives.

“One crucial aspect of estuarine management is the sustainable use of resources to balance conservation with human needs. Striking this delicate equilibrium requires a holistic understanding of the intricate web of ecological interactions within estuarine environments. Advanced technologies, such as isotopic techniques, environmental DNA (eDNA) analysis, can provide insights into the biodiversity of estuarine ecosystems with unprecedented precision,”
explain Dr Haddout and his colleagues in the opening editorial.

Amongst the unique features of the new journal are several additional publication types, such as Expert View, Video Paper, Rapid Communication, Mini Review and Estuarine Scientists, where these have been added to traditional publication outputs (e.g. Research Paper, Review Paper, Data Paper) to foster collaboration between researchers and other stakeholders in the field.

The journal is also running an annual Trailblazing Talent in Estuarine Management and Technologies award intended to recognise and encourage young scientists and engineers at the forefront of cutting-edge research in estuarine management and technologies. Nominations and applications are currently open.

Estuarine Management and Technologies also welcomes applications for guest editors in order to further expand the journal and its immediate expert network.

“I am delighted to see the Estuarine Management and Technologies journal already live on the ARPHA platform. We are confident that this particularly important, yet so far quite overlooked area of study will greatly benefit from this highly promising journal,”
says Prof. Lyubomir Penev, CEO and founder of Pensoft and ARPHA.

“I am pleased to announce the launch of the Estuarine Management and Technologies journal on ARPHA, a decision rooted in our commitment to advancing the field. We believe that this strategic partnership will not only enhance the visibility and accessibility of our journal, but will also foster collaboration and innovation within the estuarine management and technologies community. We expect this alliance to be a catalyst for scholarly excellence, providing a robust platform for researchers and practitioners to share insights, address challenges, and propel the field forward. Together with ARPHA, we are confident in the positive impact our journal will have on shaping the future of estuarine management and technologies.”
says Dr. Soufiane Haddout, Editor-in-Chief and founder, Estuarine Management and Technologies.

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