Category: Phytokeys

Mass digitisation of a herbarium collection: ten lessons learned from Meise Botanic Garden

The lessons were published in the open-access journal PhytoKeys.

Herbaria – collections of preserved plant specimens – are crucial in botanical research and biodiversity conservation. Digitising these collections is an important step towards making data available to all, preserving specimens by reducing the need for handling, and creating new research opportunities.

Herbarium specimens on a conveyor belt at Meise Botanic Garden.
Mass digitisation of herbarium specimens on a conveyor belt at Meise Botanic Garden, allowing the imaging of 3,000–5,000 specimens per day.

Meise Botanic Garden recently completed a six-year project to digitise approximately three million specimens of their herbarium collection. While it was a big change for their organisation, it was one they deemed necessary to bring their collection into the digital age. 

The digitisation project contributes to the Distributed System of Scientific Collections (DiSSCo) research infrastructure aiming to unify access to biodiversity and geodiversity specimens under common standards, giving users access to specimens and their data from European institutions. DiSSCo has also created a website with digitisation guides and the DiSSCo Knowledge Base. 

Several people sitting at tables working on herbarium specimens.
Joint restoration session of the herbarium team at Meise Botanic Garden.

Based on their experience, the team published ten valuable lessons they learned during the process to assist  other institutions embarking on similar digitisation projects. These lessons are available in the open-access journal PhytoKeys.

1. Knowing yourself is the beginning of all wisdom ― Aristotle

Before starting digitisation, it is important to understand the full scope of your collection. This involves detailed inventory checks and assessments of the state of the specimens. Knowing the exact number and condition of the specimens will help in accurate budgeting and planning. A detailed inventory of a representative tenth of your collection can be extrapolated to the entire collection.

2. Prioritise (if lack of money forces you to do so)

If resources are limited, prioritising which parts of the collection to digitise first is key. Consider factors such as the scientific importance of the specimens, their physical state, and stakeholder needs. It is important to note that digitising the entire collection can be more efficient than selecting subcollections, as partial digitisation can complicate management.

3. Learn from other people’s successes – and mistakes

Do not reinvent the wheel. Engage with other institutions that have undertaken similar projects to learn from their successes and mistakes. Follow existing guidelines and adapt them to fit your specific needs. If you think you have a better way of doing things, talk it over with someone with experience. 

4. Decide whether to do it yourself or have it done for you

Deciding whether to conduct the digitisation in-house or to outsource it depends on available resources. Consider the skills and availability of your staff and the costs associated with outsourcing. Some tasks, such as imaging or data transcription, might be more efficiently handled by external specialists.

5. Make a plan

A well-thought-out plan is crucial. Define workflows, procedures, and quality control mechanisms. And be specific about your requirements when outsourcing parts of the project to avoid any misunderstandings.

6. Go shopping

Ensure that all necessary supplies, such as barcodes, storage containers, and IT infrastructure, are in place before starting the digitisation process. Bulk purchasing is often cost-effective, and having everything ready will prevent delays.

7. Make your collection look its best for the photographer

Prepare the specimens for imaging by incorporating pre-digitisation curation steps like repairing damaged specimens and adding barcodes. 

8. Expect problems, particularly ones that you don’t expect

Problems will arise, from equipment malfunctions to human errors. Establish quality control processes to catch issues early. Automate checks where possible and ensure prompt human review for aspects like image focus and lighting.

9. Make your data visible – make a big deal of it

Making digitised data publicly accessible is vital. Use online portals and ensure the data adheres to FAIR principles (Findable, Accessible, Interoperable, Reusable). Publicity will increase the use and impact of your collection.

10. Save your data for the future

Make sure the digitised data is backed up in a secure, offsite archive. Long-term storage solutions should be considered to preserve the data for future use. And factor this ongoing cost into the budget.

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To read extended advice from Meise Botanic Garden, as well as four case studies, check out the full research paper below:

Original source

De Smedt S, Bogaerts A, De Meeter N, Dillen M, Engledow H, Van Wambeke P, Leliaert F, Groom Q (2024) Ten lessons learned from the mass digitisation of a herbarium collection. PhytoKeys 244: 23-37. https://doi.org/10.3897/phytokeys.244.120112 

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

¡Que Vive Centinela! A tiny new plant species reaffirms the “miraculous” survival of Western Ecuador’s ravished biodiversity

The discovery represents an inspiration for biodiversity conservation in an area the scientific community assumed to be a barren agricultural landscape of plant extinctions.

A new 5 cm-high plant species has been discovered on the western Andean slopes of Ecuador in an area where scientists once believed a rich diversity of native plants and animals had been totally destroyed.

John L. Clark with Amalophyllon miraculum. Credit @phinaea on Instagram.

The tiny plant, with iridescent foliage and white ephemeral flowers, was found in a farmer’s backyard during ongoing collaborative research expeditions in western Ecuador, led by teams of Ecuadorian and international researchers.

The expeditions resulted in the rediscovery of small forest fragments in a legendary hotspot known as Centinela. Selby Gardens research botanist, John L. Clark is the lead author of the article describing the new species in the peer-reviewed, open-access journal PhytoKeys.

The forest fragments are less than 20 miles from Santo Domingo, a major city of more than 300,000 people. Each fragment of Centinela is an isolated biodiversity island surrounded by large swaths of agricultural landscape largely devoid of forest.

Small purple plant leaf held between thumb and index finger.
Amalophyllon miraculum leaf.

A seminal publication titled “Biological extinction in western Ecuador” brought attention to the rapid loss of rainforest in western Ecuador. It was authored by the late botanists Alwyn Gentry and Calaway Dodson, Selby Gardens’ first Executive Director, whose research inspired names such as Gasteranthus extinctus in recognition of the loss of more than 70-97% of rainforests from the western Ecuadorian lowlands due to agriculture.

This discovery, amongst others, has shattered the preconception that the multitudes of life in the region had vanished entirely. The name Amalophyllon miraculum reflects the “miracle” of its discovery in the unexpected fragments of protected forests.

“The heroic efforts of local landowners who maintained small patches of forests – usually surrounding waterfalls – were instrumental in conserving these remnant forest fragments,” Clark says.

Ongoing conservation initiatives by foundations and academic institutions such as the Ecuadorian conservation NGO Fundación de Conservación Jocotoco and the Jardín Botánico Padre Julio Marrero (JBJM) of the Pontificia Universidad Católica del Ecuador are also crucial to protecting the areas.

Original source:

Clark JL, Fernández A, Zapata JN, Restrepo-Villarroel C, White DM, Pitman NCA (2024) Amalophyllon miraculum (Gesneriaceae), an exceptionally small lithophilous new species from the western Andean slopes of Ecuador. PhytoKeys 242: 307–316. https://doi.org/10.3897/phytokeys.242.118069

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Pensoft launches official Weibo account to expand global reach

The Pensoft team is looking forward to engaging in conversations with its Chinese authors, editors, and readers.

Scholarly publisher Pensoft is excited to announce it is now on Chinese social media platform Weibo. The move is aimed at fostering stronger connections with researchers, academics, and enthusiasts in China, which in turn will enhance the dissemination of scientific knowledge and facilitate international collaboration.

With over half a billion active users, Weibo is a powerful social media platform that combines the functionalities of microblogging and social networking. The Pensoft team is looking forward to engaging in real-time conversations with its Chinese audience, sharing insights, and receiving their feedback.

The launch coincides with the Dragon Boat Festival, a significant cultural event in China that commemorates the ancient poet Qu Yuan and symbolizes unity and teamwork. 

The move aims to make Pensoft’s publications and updates more accessible to Chinese researchers, allowing them to stay informed about the latest scientific discoveries and advancements. In addition, it offers an excellent opportunity for Pensoft to foster collaborations with Chinese institutions, researchers, and academic societies.

As a pioneer in open-access publishing, Pensoft will also use its Weibo account to promote the benefits of open access, making sure Chinese research reaches a global audience without paywalls.

“China, with its rapidly growing research output and a burgeoning community of scholars, represents a significant segment of the global academic landscape. Recognizing the importance of engaging with this vibrant community, Pensoft’s decision to establish a presence on Weibo underscores its commitment to inclusivity and accessibility in scientific publishing,��� says Lyubomir Penev, CEO and founder of Pensoft.

We invite you to join Pensoft’s Weibo account to learn all about our latest scientific discoveries and publishing updates.

Sun-shunning thief: new plant species robs underground fungi to survive

Tiny and highly specialised, Thismia malayana belongs to a group of plants known as mycoheterotrophs.

Researchers in Malaysia have discovered a tiny and distinctive plant that steals its nutrients from underground fungi.

Published as a new species in the open-access journal PhytoKeys, Thismia malayana belongs to a group of plants known as mycoheterotrophs. Unlike most plants, mycoheterotrophs do not perform photosynthesis. Instead, they act as a parasite, stealing carbon resources from the fungi on their roots.

Unusual brown and orange plant in leaf litter.
Thismia malayana live specimen.

The 2 cm-long plant’s unusual adaptation takes advantage of the mycorrhizal symbiosis, which is usually a mutually beneficial relationship between colonising fungi and a plant’s root system.

Several scientific photographs of an unusual brown and orange plant.
Thismia malayana.

By stealing nutrients from fungi, it can thrive in the low-light conditions of dense forest understories where its highly specialised flowers are pollinated by fungus gnats and other small insects.

A team of botanists from the Forest Research Institute Malaysia (FRIM) collaborated with local naturalists and stakeholders to make the discovery in the tropical rainforests of Peninsular Malaysia. It was there they found the miniscule species hidden amongst leaf litter and growing near tree roots and old rotten logs.

The research team identified Thismia malayana in two locations: the lowlands of Gunung Angsi Forest Reserve in Negeri Sembilan and the hilly dipterocarp forests of Gunung Benom in the Tengku Hassanal Wildlife Reserve, Pahang.

Unusual brown and orange plant with a scale showing it measures around 2 cm long.
Thismia malayana with scales (the finest grade is 0.5 mm).

Despite its small size, Thismia malayana is very sensitive to environmental changes and has been classified as Vulnerable according to the IUCN Red List criteria. Its limited distribution and the potential threat from trampling due to its proximity to hiking trails underscore the importance of continued conservation efforts.

Original source

Siti-Munirah MY, Hardy-Adrian C, Mohamad-Shafiq S, Irwan-Syah Z, Hamidi AH (2024) Thismia malayana (Thismiaceae), a new mycoheterotrophic species from Peninsular Malaysia. PhytoKeys 242: 229-239. https://doi.org/10.3897/phytokeys.242.120967

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

Now concluded Horizon 2020-funded project BiCIKL shares lessons learned with policy-makers and research funders

Within the Biodiversity Community Integrated Knowledge Library (BiCIKL) project, 14 European institutions from ten countries, spent the last three years elaborating on services and high-tech digital tools, in order to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of various types of data about the world’s biodiversity. These types of data include peer-reviewed scientific literature, occurrence records, natural history collections, DNA data and more.

By ensuring all those data are readily available and efficiently interlinked to each other, the project consortium’s intention is to provide better tools to the scientific community, so that it can more rapidly and effectively study, assess, monitor and preserve Earth’s biological diversity in line with the objectives of the likes of the EU Biodiversity Strategy for 2030 and the European Green Deal. Their targets require openly available, precise and harmonised data to underpin the design of effective measures for restoration and conservation, reminds the BiCIKL consortium.

Since 2021, the project partners at BiCIKL have been working together to elaborate existing workflows and links, as well as create brand new ones, so that their data resources, platforms and tools can seamlessly communicate with each other, thereby taking the burden off the shoulders of scientists and letting them focus on their actual mission: paving the way to healthy and sustainable ecosystems across Europe and beyond.

New BiCIKL project to build a freeway between pieces of biodiversity knowledge

Now that the three-year project is officially over, the wider scientific community is yet to reap the fruits of the consortium’s efforts. In fact, the end of the BiCIKL project marks the actual beginning of a European- and global-wide revolution in the way biodiversity scientists access, use and produce data. It is time for the research community, as well as all actors involved in the study of biodiversity and the implementation of regulations necessary to protect and preserve it, to embrace the lessons learned, adopt the good practices identified and build on the knowledge in existence.

This is why amongst the BiCIKL’s major final research outputs, there are two Policy Briefs meant to summarise and highlight important recommendations addressed to key policy makers, research institutions and funders of research. After all, it is the regulatory bodies that are best equipped to share and implement best practices and guidelines.

Most recently, the BiCIKL consortium published two particularly important policy briefs, both addressed to the likes of the European Commission’s Directorate-General for Environment; the European Environment Agency; the Joint Research Centre; as well as science and policy interface platforms, such as the EU Biodiversity Platform; and also organisations and programmes, e.g. Biodiversa+ and EuropaBON, which are engaged in biodiversity monitoring, protection and restoration. The policy briefs are also to be of particular use to national research funds in the European Union.

One of the newly published policy briefs, titled “Uniting FAIR data through interlinked, machine-actionable infrastructures”, highlights the potential benefits derived from enhanced connectivity and interoperability among various types of biodiversity data. The publication includes a list of recommendations addressed to policy-makers, as well as nine key action points. Understandably, amongst the main themes are those of wider international cooperation; inclusivity and collaboration at scale; standardisation and bringing science and policy closer to industry. Another major outcome of the BiCIKL project: the Biodiversity Knowledge Hub portal is noted as central to many of these objectives and tasks in its role of a knowledge broker that will continue to be maintained and updated with additional FAIR data-compliant services as a living legacy of the collaborative efforts at BiCIKL.

The second policy brief, titled “Liberate the power of biodiversity literature as FAIR digital objects”, shares key actions that can liberate data published in non-machine actionable formats and non-interoperable platforms, so that those data can also be efficiently accessed and used; as well as ways to publish future data according to the best FAIR and linked data practices. The recommendations highlighted in the policy brief intend to support decision-making in Europe; expedite research by making biodiversity data immediately and globally accessible; provide curated data ready to use by AI applications; and bridge gaps in the life cycle of research data through digital-born data. Several new and innovative workflows, linkages and integrative mechanisms and services developed within BiCIKL are mentioned as key advancements created to access and disseminate data available from scientific literature. 

While all policy briefs and factsheets – both primarily targeted at non-expert decision-makers who play a central role in biodiversity research and conservation efforts – are openly and freely available on the project’s website, the most important contributions were published as permanent scientific records in a BiCIKL-branded dedicated collection in the peer-reviewed open-science journal Research Ideas and Outcomes (RIO). There, the policy briefs are provided as both a ready-to-print document (available as supplementary material) and an extensive academic publication.

Currently, the collection: “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” in the RIO journal contains 60 publications, including policy briefs, project reports, methods papers, conference abstracts, demonstrating and highlighting key milestones and project outcomes from along the BiCIKL’s journey in the last three years. The collection also features over 15 scientific publications authored by people not necessarily involved in BiCIKL, but whose research uses linked open data and tools created in BiCIKL. Their publications were published in a dedicated article collection in the Biodiversity Data Journal.

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

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Visit the Biodiversity Community Integrated Knowledge Library (BiCIKL) project’s website at: https://bicikl-project.eu/.

Don’t forget to also explore the Biodiversity Knowledge Hub (BKH) for yourself at: https://biodiversityknowledgehub.eu/ and watch the BKH’s introduction video. 

Highlights from the BiCIKL project are also accessible on Twitter/X from the project’s hashtag: #BiCIKL_H2020 and handle: @BiCIKL_H2020.

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

Pensoft took a BiCIKL ride to Naturalis to report on a 3-year endeavour towards FAIR data

Three years ago, the BiCIKL consortium took to traverse obstacles to wider use and adoption of FAIR and linked biodiversity data.

Leiden – also known as the ‘City of Keys’ and the ‘City of Discoveries’ – was aptly chosen to host the third Empowering Biodiversity Research (EBR III) conference. The two-day conference – this time focusing on the utilisation of biodiversity data as a vehicle for biodiversity research to reach to Policy – was held in a no less fitting locality: the Naturalis Biodiversity Center. 

On 25th and 26th March 2024, the delegates got the chance to learn more about the latest discoveries, trends and innovations from scientists, as well as various stakeholders, including representatives of policy-making bodies, research institutions and infrastructures. The conference also ran a poster session and a Biodiversity Informatics market, where scientists, research teams, project consortia, and providers of biodiversity research-related services and tools could showcase their work and meet like-minded professionals.

BiCIKL stops at the Naturalis Biodiversity Center

The main outcome of the BiCIKL project: the Biodiversity Knowledge Hub, a one-stop knowledge portal to interlinked and machine-readable FAIR data.

The famous for its bicycle friendliness country also made a suitable stop for BiCIKL (an acronym for the Biodiversity Community Integrated Knowledge Library): a project funded under the European Commission’s Horizon 2020 programme that aimed at triggering a culture change in the way users access, (re)use, publish and share biodiversity data. To do this, the BiCIKL consortium set off on a 3-year journey to build on the existing biodiversity data infrastructures, workflows, standards and the linkages between them.

Many of the people who have been involved in the project over the last three years could be seen all around the beautiful venue. Above all, Naturalis is itself one of the partnering institutions at BiCIKL. Then, on Tuesday, on behalf of the BiCIKL consortium and the project’s coordinator: the scientific publisher and technology innovator: Pensoft, Iva Boyadzhieva presented the work done within the project one month ahead of its official conclusion at the end of April.

As she talked about the way the BiCIKL consortium took to traverse obstacles to wider use and adoption of FAIR and linked biodiversity data, she focused on BiCIKL’s main outcome: the Biodiversity Knowledge Hub (BKH).

Key results from the BiCIKL project three years into its existence presented by Pensoft’s Iva Boyadzhieva at the EBR III conference.

Intended to act as a knowledge broker for users who wish to navigate and access sources of open and FAIR biodiversity data, guidelines, tools and services, in practicality, the BKH is a one-stop portal for understanding the complex but increasingly interconnected landscape of biodiversity research infrastructures in Europe and beyond. It collates information, guidelines, recommendations and best practices in usage of FAIR and linked biodiversity data, as well as a continuously expanded catalogue of compliant relevant services and tools.

At the core of the BKH is the FAIR Data Place (FDP), where users can familiarise themselves with each of the participating biodiversity infrastructures and network organisations, and also learn about the specific services they provide. There, anyone can explore various biodiversity data tools and services by browsing by their main data type, e.g. specimens, sequences, taxon names, literature.

While the project might be coming to an end, she pointed out, the BKH is here to stay as a navigation system in a universe of interconnected biodiversity research infrastructures.

To do this, not only will the partners continue to maintain it, but it will also remain open to any research infrastructure that wishes to feature its own tools and services compliant with the linked and FAIR data requirements set by the BiCIKL consortium.

On the event’s website you can access the BiCIKL’s slides presentation as presented at the EBR III conference.

What else was on at the EBR III?

Indisputably, the ‘hot’ topics at the EBR III were the novel technologies for remote and non-invasive, yet efficient biomonitoring; the utilisation of data and other input sourced by citizen scientists; as well as leveraging different types and sources of biodiversity data, in order to better inform decision-makers, but also future-proof the scientific knowledge we have collected and generated to date.

Project’s coordinator Dr Quentin Groom presents the B-Cubed’s approach towards standardised access to biodiversity data for the use of policy-making at the EBR III conference.

Amongst the other Horizon Europe projects presented at the EBR III conference was B-Cubed (Biodiversity Building Blocks for policy). On Monday, the project’s coordinator Dr Quentin Groom (Meise Botanic Garden) familiarised the conference participants with the project, which aims to standardise access to biodiversity data, in order to empower policymakers to proactively address the impacts of biodiversity change.

You can find more about B-Cubed and Pensoft’s role in it in this blog post.

On the event’s website you can access the B-Cubed’s slides presentation as presented at the EBR III conference.

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Dr France Gerard (UK Centre for Ecology & Hydrology) talks about the challenges in using raw data – including those provided by drones – to derive habitat condition metrics.

MAMBO: another Horizon Europe project where Pensoft has been contributing with expertise in science communication, dissemination and exploitation, was also an active participant at the event. An acronym for Modern Approaches to the Monitoring of BiOdiversity, MAMBO had its own session on Tuesday morning, where Dr Vincent Kalkman (Naturalis Biodiversity Center), Dr France Gerard (UK Centre for Ecology & Hydrology) and Prof. Toke Høye (Aarhus University) each took to the stage to demonstrate how modern technology developed within the project is to improve biodiversity and habitat monitoring. Learn more about MAMBO and Pensoft’s involvement in this blog post.

MAMBO’s project coordinator Prof. Toke T. Høye talked about smarter technologies for biodiversity monitoring, including camera traps able to count insects at a particular site.

On the event’s website you can access the MAMBO’s slides presentations by Kalkman, Gerard and Høye, as presented at the EBR III conference.

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The EBR III conference also saw a presentation – albeit remote – from Prof. Dr. Florian Leese (Dean at the University of Duisburg-Essen, Germany, and Editor-in-Chief at the Metabarcoding and Metagenomics journal), where he talked about the promise, but also the challenges for DNA-based methods to empower biodiversity monitoring. 

Amongst the key tasks here, he pointed out, are the alignment of DNA-based methods with the Global Biodiversity Framework; central push and funding for standards and guidance; publication of data in portals that adhere to the best data practices and rules; and the mobilisation of existing resources such as the meteorological ones. 

Prof. Dr. Florian Leese talked about the promise, but also the challenges for DNA-based methods to empower biodiversity monitoring. He also referred to the 2022 Forum Paper: “Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms” by R. Henrik Nilsson et al.

He also made a reference to the Forum Paper “Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms” by R. Henrik Nilsson et al., where the international team provided a brief rationale and an overview of guidelines targeting the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. In the study, published in the Metabarcoding and Metagenomics journal in 2022, they also introduced a living version of these guidelines, which continues to encourage feedback and interaction as new techniques and best practices emerge.

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You can find the programme on the conference website and see highlights on the conference hashtag: #EBR2024.

Don’t forget to also explore the Biodiversity Knowledge Hub for yourself at: https://biodiversityknowledgehub.eu/ 

Celebrating taxonomic discoveries: Top 10 new species of 2023

Get to know the most exciting new species published in Pensoft journals last year.

In 2023, the world of biodiversity saw some amazing discoveries . Our taxonomy journals published hundreds of new species, so selecting a Top Ten was tough, but here we go – get to know these beautiful new species, and maybe think about all the amazing diversity that still remains unexplored on our planet.

10. The walking leaf

It’s very often that undescribed species hide in plain sight for years, but it’s easy to understand why when they look like that! Leaf insects look confusingly similar to leaves – this sophisticated camouflage provides excellent protection from predators, but also presents a challenge to researchers.

“There are around 3,500 known species of stick and leaf insects and there are currently just over 100 described species of leaf insect,” researcher Dr Sven Bradler says. This is why when Phyllium ortizi and six other leaf insect species were found, it made for a really special discovery.

Lime-green in colour, Phyllium ortizi is so far only known from Mindanao Island, Philippines.

Published in ZooKeys.

9. The spiky hedgehog

The Eastern Forest Hedgehog (Mesechinus orientalis) was discovered in southwestern China. It is a small-bodied hedgehog, smaller than most of the other species in its genus, its spines as short as 1.8-2 cm. It has a brown nose, with black whiskers that shorten towards the nose.

The species is currently known from southern Anhui and northwestern Zhejiang, where it lives in scrubland and subtropical broad-leaf evergreen forests at elevations from 30 to 700 m.

The researchers found out that genus Mesechinus, to which the new species belongs, dates back to the early Pleistocene and started appearing around 1.71 million years ago, while M. Orientalis diverged from its congeners some 1.1 million years ago.

Published in ZooKeys.

8. The bumpy salamander

Tylototriton zaimeng was found in the eponymous Zaimeng lake in Manipur, India. It is a medium-sized salamander has a massive wide head that could take up as much as a quarter of its total length. Its most distinctive feature are the knob-like warts along its body.

The salamander has an earthy-brown body with orange markings along its head and orange-brown warts down its back and sides. Its tail fades from brown at the base to yellow-orange at the tip.

Even though it has just been discovered as a species for science, locals know a lot about it and have different names for it.

Because its known range is limited and threatened by deforestation and human interference, the species should be considered vulnerable.

Published in Herpetozoa.

7. The “groins of fire” frog

An unexpected discovery, this new treefrog species was found in the Amazon lowlands of central Peru. The research team, led by Germán Chávez, was surprised that a new species could be hiding in plain sight in an otherwise well-explored part of the Amazon. No matter how many times they returned to the site, they only found two specimens, which made its scientific description challenging.

Its name, Scinax pyroinguinis, literally means “groins of fire”. It is a reference to the orange, flame-like pattern on the groins, thighs and shanks, but also to the wildfires in the area where it was found, which are a serious threat to its habitat.

Published in Evolutionary Systematics.

6. The charming carnivore

Pinguicula ombrophila is part of the butterwort family, a group of insectivorous flowering plants consisting of around 115 species. Its leaves have a sticky texture, enabling it to capture and digest small insects.

For carnivorous plants, insects can be an additional source of nutrients to help them compensate the nutrient deficiency of the substrate they’re growing in. This gives them a competitive advantage over other plants and enables them to thrive in challenging habitats.

Two striking new species of carnivorous plants discovered in the Andes of Ecuador

While the majority of butterworts are found in the northern hemisphere, this species was discovered in the elevated regions of southern Ecuador, near the Peru border. The research team found it on a nearly vertical rock face at 2,900 metres. Its name means “rain-loving butterwort”, highlighting the plant’s preference for very wet conditions.

Published in PhytoKeys.

5. The unicorn fish

Sinocyclocheilus longicornus (from the Latin words “longus”, meaning long, and “cornu”, meaning horn) comes from Southern China. It is only known from a dark vertical cave at an elevation of 2,276 m in the province of Guizhou. It is around 10-15 centimeters long and lacks pigmentation in its scales, which gives it it a ghostly whitish appearance. Since its eyes are small and probably not much help in a completely dark environment, it relies on barbels that look like tiny whiskers to feel its way around.

The researchers that found it are not quite sure what its “horn” is used for, but it might have something to do with navigating its way in the dark and dreary environment it inhabits.

Sinocyclocheilus longicornus is also featured in the SHOALS report on freshwater fish species described in 2023.

Published in ZooKeys.

4. The DiCaprio snake

snake

Sibon irmelindicaprioae was described as a new species together with four more tree-dwelling snake species from jungles of Ecuador, Colombia, and Panama. They all belong to Dipsadinae —a subfamily of snakes found in North and South America.

Also known as DiCaprio’s snail-eating snake, this species was named after actor and film producer Leonardo DiCaprio’s mother, Irmelin DiCaprio. The actor himself chose the name to honour his mother and raise awareness about the threats these snakes face.

Its habitat in Panama is affected by large-scale copper mining. The open-pit mines, some of them visible from space, make the areas uninhabitable for snail-eating snakes.

“These new species of snake are just the tip of the iceberg in terms of new species discoveries in this region, but if illegal mining continues at this rate, there may not be an opportunity to make any future discoveries,” says Alejandro Arteaga, who led the study to describe them.

Published in ZooKeys.

3. The Tolkien frog

Frog

You probably guessed it by now – this stream frog from the Ecuadorian Andes was named after J.R.R. Tolkien, the author of The Hobbit and The Lord of the Rings.

At about 66 millimeters (2.5 inches) long, Hyloscirtus tolkieni is tiny enough to fit in the palm of your hand, but that doesn’t stop it from being simply stunning. With pale pink eyes and gold-speckled toes, it looks like it came straight out of Middle-earth. It was found at an elevation of 3190 meters in Río Negro-Sopladora National Park, a protected area of páramo and cloud forests.

“The new species of frog has amazing colours, and it would seem that it lives in a universe of fantasies, like those created by Tolkien. The truth is that the tropical Andes are magical ecosystems where some of the most wonderful species of flora, funga, and fauna in the world are present. Unfortunately, few areas are well protected from the negative impacts caused by humans. Deforestation, unsustainable agricultural expansion, mining, invasive species, and climate changes are seriously affecting Andean biodiversity”, said Diego F. Cisneros-Heredia, one of the researchers behind this discovery.

Published in ZooKeys.

2. The enigmatic Nautilus

2023 was a great year for nautilus biodiversity: three species were described as new to science, including Nautilus samoaensis, which you see here. Like its name tells you, it was found off the coast of American Samoa.

Studying nautilus diversity is no easy feat – with setting spiky traps, hauling them over on board, and, eventually, burping nautiluses, it is surely a memorable experience.

Judging by the fossil record, nautiloids were once quite plentiful throughout the oceans. Today, however, they are represented by just a handful of species.

In addition, these fragile animals remain threatened by wildlife trade as they are hunted for their shells, which according to Mongabay can sell for up to about $1,000 each on the black market.

This beautiful species was also featured in the World Register of Marine Species‘ selection of the top 10 marine species published in 2023, along with another ZooKeys species.

Published in ZooKeys.

1. The electric blue tarantula

Found in Thailand’s Phang-Nga province, Chilobrachys natanicharum features an enchanting phenomenon: a neon blue-purple coloration that gives it a unique look.

There is no blue pigment in this tarantula’s body: the secret behind its striking color comes from the unique structure of its hair, which incorporates nanostructures that manipulate light in an effect that creates the blue appearance. Depending on the light, it can also appear violet.

Before it was described as a new species, Chilobrachys natanicharum was actually known to experts from the commercial tarantula trade market as “Chilobrachys sp. Electric Blue Tarantula,” but this is the first time that it’s discovered in its natural habitat.

Its name, in fact, resulted from an auction campaign, the proceeds from the auction have been channeled to bolster the education of Lahu children in Thailand and to aid impoverished cancer patients.

Published in ZooKeys.

Five new plant species with striking flowers discovered in China

The discoveries are photographed and assessed, contributing to knowledge of China’s rich flora.

With more than 30,000 native plant species, including thousands found nowhere else on Earth, China is known for its abundant flora.  New species are frequently discovered in the country due to its size and variety of ecosystems.

These five new species with distinct flowers were recently published in Pensoft’s open-access journal PhytoKeys.

Melanoseris penghuana

Melanoseris penghuana
Melanoseris penghuana
Melanoseris penghuana habitat
Melanoseris penghuana flower

Belonging to the daisy family (Asteraceae), Melanoseris penghuana was observed growing on steep grassy slopes along the valley edge of Jiulonggou, Mt. Jiaozi Xueshan, at an elevation of approximately 3,200 m.

Through data analysis from two field surveys, the conservation status of this species was classified as Vulnerable. However, located within the Jiaozi Xueshan National Nature Reserve where human disturbance is minimal, its habitat is relatively well protected.

Research paper: https://doi.org/10.3897/phytokeys.238.116343

Hydrangea xinfeniae

Hydrangea xinfeniae
Hydrangea xinfeniae flowers

Hydrangea xinfeniae belongs to the family Hydrangeaceae and was discovered in the Huagaoxi National Nature Reserve in Shuiwei Town, Sichuan Province. It grows on moist soils under the broadleaved forest at an elevation of 1,200–1,300 m.

Currently known from only three relatively small populations of the type locality, its conservation status is assessed as Data Deficient.

Research paper: https://doi.org/10.3897/phytokeys.238.114289

Prunus tongmuensis

Prunus tongmuensis
Prunus tongmuensis illustration

This new species of cherry blossom belongs to the rose family (Rosaceae). It is currently known only from Wuyishan National Park, Fujian and Jiangxi Province, where it grows in various habitats such as the margins of evergreen broad-leaved forests, valleys, or roadsides, at an altitude of 600–1,000 m.

Research paper: https://doi.org/10.3897/phytokeys.237.115098

Ophiorrhiza reflexa

Ophiorrhiza reflexa

Belonging to the madder family (Rubiaceae), Ophiorrhiza reflexa grows in moist areas under evergreen broad-leaved forests in the limestone region of Napo County, Guangxi.

Researchers found three populations of the species with more than 1,000 individuals at each site during field investigations. The three sites all belong to Laohutiao Provincial Nature Reserve, which is well-protected and not under threat. Ophiorrhiza reflexa is preliminarily assessed as Least Concern.

Research paper: https://doi.org/10.3897/phytokeys.238.116767

Ligularia lushuiensis

Ligularia lushuiensis
Ligularia lushuiensis habitat
Ligularia lushuiensis

Ligularia lushuiensis belongs to the daisy family (Asteraceae). It is currently known only from its type locality, Lushui, northwestern Yunnan, where it grows in alpine meadows at an elevation of 3,322 m.

Currently known only from a small population at its type locality, the single population researchers discovered consists of no more than 200 mature individuals. Overgrazing may threaten the habitat of this species, and it has been preliminarily categorised as Critically Endangered.

Research paper: https://doi.org/10.3897/phytokeys.238.117340

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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: