Despite the success of 2023, the Pensoft team is keener than ever to improve in every aspect in the coming year. A massive thank you to every author, editor, reviewer and reader of Pensoft’s journals, and a very happy New Year!
Through the analysis of DNA traces in the droppings of a Leislerâs bat colony, researchers at LIB have now identified over 350 different insect species that were consumed by the bats.
Adequate food supply is a fundamental need and requirement for survival. To protect a species, it is often very helpful to know what that species prefers and frequently consumes. Through the analysis of DNA traces in the droppings of a Leislerâs bat colony, researchers at LIB (Leibniz Institute for the Analysis of Biodiversity Change) have now identified an astonishingly high number âover 350â different insect species that were consumed by the bats.
Especially for small animal species and those that are nocturnal, it can be extremely difficult to determine what they feed on. Identifying small prey insects or their remains is also rarely possible down to the exact species or family. In the case of the studied bat species, there is the additional challenge that it is a forest bat species that needs to be located first. âFollowing bats equipped with radio transmitters in the forest at night is quite special,â says Martin Koch, co-initiator of the study.
Design and installation of the guano trap (3 m) and roost entrance (9 m).
Fortunately â but also complicating matters â there are about 13 different bat species living in the investigated area near Bonn, in the forests of the Natura 2000 area âWaldreservat Kottenforst.â Initially, as part of an EU Life+ project, roosts â the trees where the bats live â of the Leislerâs bats were identified, from which the studyâs starting material was then obtained. This was done using a specially developed âguano trap.â The trap consists of approximately 2.2 square meters of mosquito netting stretched rectangularly.
It was installed about 3 meters high on the tree trunk, below the entrance to the roosting cavity at about 9 meters high. During the so-called âtwilight swarmingâ after the nightly insect hunt, the bats return to the roosting cavity and initially circle the tree. They frequently perch briefly next to the cavity entrance and stick a small guano pellet to the trunk. Regularly, pellets fall and land in the mosquito netting under the cavity entrance. This âbat guanoâ was collected, fixed, and further processed in the laboratory.
âItâs fascinating how much DNA you can extract from a small amount of droppings and how much information we can draw from the DNA: from which bat species does the droppings come, and what has the bat eaten?â explains Dr. Kathrin Langen. Using the DNA contained in the droppings, our researchers were able to determine nine samples from nine different nights when only the target species swarmed around the roosting tree. On six other nights, other bats and a species of mouse were also active around the roosting tree. From the nine samples containing only the guano of the evening bat, an astonishingly rich menu was then reconstructed: the group consumed at least 126 different species of moths, 86 different species of flies and mosquitoes, 48 species of beetles, and a few dozen other various species of bugs, mayflies, caddisflies, and lacewings. Occasionally, spiders, harvestmen, lice, and other small animals were also consumed.
Timeline showing arthropod community composition at order level in the guano of N. leisleri, all three markers combined (COImldg, COIArt, 16S). With the exception of plots showing RRA assigned to major groups depending on sampling date (4C and 4F), read counts were not taken into account. A, D Number of species of each arthropod order detected at each time point; B, E Relative number of species per arthropod order as a percentage of the diet; C, F Species detected in each arthropod order, based on relative read abundances.
From the results, the team was able to deduce which of the three molecular genetic markers used worked best and provided the most species detections, a total of 358. âItâs incredibly satisfying to see what species lists come out at the end of all the lab work and bioinformatics,â says Dr. Sarah Bourlat, Head of the Metabarcoding Section at LIB, Bonn. However, the temporal course of the composition of the consumed insects was also interesting to observe: from late March to late June, the number of species in the guano steadily increases, only to decrease again by mid-August. This aligns very well with the activity patterns of certain insect groups.
The beech moth was the most frequently consumed butterfly, and a mayfly known as the transient virgin or âUferaasâ, was the most frequently consumed mayfly. The author team has listed the most important ecological parameters for the 18 key prey species in the study to contribute to better protecting the Leislerâs bat and the habitats needed by its prey insects.
Research article: Bourlat SJ, Koch M, Kirse A, Langen K, Espeland M, Giebner H, Decher J, Ssymank A, Fonseca VG (2023) Metabarcoding dietary analysis in the insectivorous bat Nyctalus leisleri and implications for conservation. Biodiversity Data Journal 11: e111146. https://doi.org/10.3897/BDJ.11.e111146
October and November 2023 were active months for the Pensoft team, who represented the publisherâs journals and projects at conferences in Europe, North America, South America, Oceania and Asia.
Letâs take a look back at all the events of the past two months.
The Biodiversity Information Standards Conference 2023
The annual gathering is a crucial platform for sharing insights, innovations, and knowledge related to biodiversity data standards and practices. Key figures from Pensoft took part in the event, presenting new ways to improve the management, accessibility, and usability of biodiversity data.
Prof. Lyubomir Penev, founder and Chief Executive Officer of Pensoft, gave two talks that highlighted the importance of data publishing. His presentation on “The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data” underscored the significance of FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. BKH is the major output from the Horizon 2020 project BiCIKL (Biodiversity Community Integrated Knowledge Library) dedicated to linked and FAIR data in biodiversity, and coordinated by Pensoft.
Prof. Lyubomir Penev, Pensoft founder and CEO.
He also introduced the Nanopublications for Biodiversity workflow and format: a promising new tool developed by Knowledge Pixels and Pensoft to communicate key scientific statements in a way that is human-readable, machine-actionable, and in line with FAIR principles. Earlier this year, Biodiversity Data Journal integrated nanopublications into its workflow to allow authors to share their findings even more efficiently.
Chief Technology Officer of Pensoft Teodor Georgiev contributed to the conference by presenting “OpenBiodiv for Users: Applications and Approaches to Explore a Biodiversity Knowledge Graph.” His session highlighted the innovative approaches being taken to explore and leverage a biodiversity knowledge graph, showcasing the importance of technology in advancing biodiversity research.
Metabarcoding and Metagenomics editor-in-chief, Florian Leese.
The theme of the conference was “Monitoring Biodiversity for Action” and there was particular emphasis on the development of best practices and new technologies for biodiversity observations and monitoring to support transformative policy and conservation action.
Metabarcoding & Metagenomicsâ editor-in-chief, Florian Leese, was one of the organisers of the “Standardized eDNA-Based Biodiversity Monitoring to Inform Environmental Stewardship Programs” session. Furthermore, the journal was represented at Pensoftâs exhibition booth, where conference participants were able to discuss metabarcoding and metagenomics research.
#geobonconf2023 was great as it linked different actors performing #biodiversity monitoring. Today we discussed #eDNA standardisation. We need formal standards, QA/QC, guidance, đharmonisation to facilitate uptake. Cool to see our @DNAquaNet practical guide in this context. pic.twitter.com/eTOtr3yug8
Following the conference, Metabarcoding & Metagenomics announced a new special issue titled âTowards Standardized Molecular Biodiversity Monitoring.â The special issue is accepting submissions until 15th March 2024.
Asian Mycological Congress2023
The Asian Mycological Congress welcomed researchers from around the world to Busan, Republic of Korea, for an exploration of all things fungi from 10-13 October.
MycoKeys Best Talk award (winner not pictured).
Titled “Fungal World and Its Bioexploitation â in all areas of basic and applied mycology,” the conference covered a range of topics related to all theoretical and practical aspects of mycology. There was a particular emphasis on the development of mycology through various activities associated with mycological education, training, research, and service in countries and regions within Asia.
As one of the sponsors of the congress, Pensoft proudly presented a Best Talk award to Dr Sinang Hongsanan of Chiang Mai University, Thailand. The award entitles the winner to a free publication in Pensoft’s flagship mycology journal, MycoKeys.
Joint ESENIAS and DIAS Scientific Conference 2023
The ESENIAS and DIAS conference took place from 11-14 October and focused on “globalisation and invasive alien species in the Black Sea and Mediterranean regions.” Pensoft shared information on their NeoBiota journal and the important REST-COAST and B-Cubed projects.
Polina Nikova receiving the NeoBiota Best Talk Award.
Polina Nikova of the Bulgarian Academy of Sciences received the NeoBiota Best Talk Award for her presentation titled “First documented records in the wild of American mink (Neogale vision von Schreber, 1776) in Bulgaria.” The award entitles her to a free publication in the NeoBiota journal.
XII European Congress of Entomology
Pensoft took part in the XII European Congress of Entomology (ECE 2023) in Heraklion, Crete, from 16-20 October. The event provided a forum for entomologists from all over the world, bringing together over 900 scientists from 60 countries.
Carla Stoyanova, Teodor Metodiev and Boriana Ovcharova representing Pensoft.
The ECE 2023, organised by the Hellenic Entomological Society, addressed the pressing challenges facing entomology, including climate change, vector-borne diseases, biodiversity loss, and the need to sustainably feed a growing world population. The program featured symposia, lectures, poster sessions, and other types of activities aimed at fostering innovation in entomology. For Pensoft, they were a great opportunity to interact with scientists and share their commitment to advancing entomological research and addressing the critical challenges in the field.
Throughout the event, conference participants could find Pensoftâs team at thir booth, and learn more about the scholarly publisherâs open-access journals in entomology. In addition, the Pensoft team presented the latest outcomes from the Horizon 2020 projects B-GOOD, Safeguard, and PoshBee, where the publisher takes care of science communication and dissemination as a partner.
Group photo of XIV International Congress of Orthopterology 2023 participants.
Hosted for the first time in Mexico, it attracted experts and enthusiasts from around the world. The congress featured plenary speakers who presented cutting-edge research and insights on various aspects of grasshoppers, crickets, and related insects.
Pensoft’s Journal of Orthoptera Research was represented by Tony Robillard, the editor-in-chief, who presented the latest developments of the journal to attendees.
Symposia, workshops, and meetings facilitated discussions on topics like climate change impacts, conservation, and management of Orthoptera. The event also included introductions to new digital and geospatial tools for Orthoptera research.
The 16th International Conference on Ecology and Management of Alien Plant Invasions
4th International ESP Latin America and Caribbean Conference
The 4th International ESP Latin America and Caribbean Conference (ESP LAC 2023) was held in La Serena, Chile, from 6-10 November. Focused on “Sharing knowledge about ecosystem services and natural capital to build a sustainable future,” the event attracted experts in ecosystem services, particularly from Latin America and the Caribbean.
Organised by the Ecosystem Services Partnership, this bi-annual conference was open to both ESP members and non-members, featuring a hybrid format in English and Spanish. Attendees enjoyed an excursion to La Serena’s historical center, adding a cultural dimension to the event.
The conference included diverse sessions and a special recognition by Pensoft’s One Ecosystem journal, which awarded full waivers for publication to the authors of the three best posters.
Magaly Aldave receiving the Best Poster Award.
Magaly Aldave of the Transdisciplinary Center for FES-Systemic Studies claimed first prize with “The voice of children in the conservation of the urban wetland and Ramsar Site Pantanos de Villa in Metropolitan Lima, Peru.” Ana Catalina Copier Guerrero and Gabriela Mallea-Rebolledo, both of the University of Chile, were awarded second and third prize respectively.
The event featured in-person and online participation, catering to a wide audience of researchers, academics, and students. It included workshops, presentations, and discussions, with a focus on enhancing understanding in biosystematics.
Pensoft awarded three student prizes at the event. Putter Tiatragu, Australian National University, received the Best Student Talk award and a free publication in any Pensoft journal for âA big burst of blindsnakes: Phylogenomics and historical biogeography of Australiaâs most species-rich snake genus.â
Helen Armstrong, Murdoch University, received the Best Student Lightning Talk for âAn enigmatic snapper parasite (Trematoda: Cryptogonimidae) found in an unexpected host.â Patricia Chan, University of Wisconsin-Madison, was the Best Student Lightning Talk runner-up for âDrivers of Diversity of Darwiniaâs Common Scents and Inflorescences with Style: Phylogenomics, Pollination Biology, and Floral Chemical Ecology of Western Australian Darwinia (Myrtaceae).â
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As we approach the end of 2023, Pensoft looks back on its most prolific and meaningful year of conferences and events. Thank you to everyone who contributed to or engaged with Pensoftâs open-access journals, and here’s to another year of attending events, rewarding important research, and connecting with the scientific community.
A post on social media asked about plant genera named for women and sparked a lively discussion with many contributors. This simple question was not as easily answered as initially thought. The resulting informal working group tackled this topic remotely during the COVID-19 pandemic and beyond. The team was motivated by the desire to amplify the contribution of women to botany through eponymy. The work of this team has so far resulted in a paper in Biodiversity Data Journal, presentations at several conferences, and a linked open dataset.
Prior to our international collaboration, no dataset was available to answer these simple questions and the required information was scattered in many different data sources. We set out to bring these data together and in doing so developed and refined our workflow. Our data paper documents this innovative workflow bringing together the various data elements needed to answer our research questions. Ultimately we created a Linked Open Data (LOD) dataset that amplified the names of women and female mythological beings celebrated through generic names of flowering plants.
During our research process we focused on pulling data from a wide variety of sources while at the same time proactively sharing the data generated as widely as possible. This was done by adding and linking it to multiple public databases and sources (push-pull) including the International Plant Name Index (hereafter IPNI), TropicosÂź, Wikidata, Bionomia and the Biodiversity Heritage Library (hereafter BHL).
Visualisation of our workflow to create a working list of flowering plant genera named for women.Â
For our list of genera, each of the protologues were reviewed to confirm the etymology or eponymy. To find the generic prologues, we searched botanical databases such as IPNI and Tropicos, openly accessible providers of digital publications and other digital libraries and websites that provide free access to such publications. Here the BHL was invaluable as the majority of protologues and many other relevant publications were openly accessible through this digital library. Where no digital publication was available we accessed scientific literature through our affiliated institutions.
For the women, our starting point was the âIndex of Eponymic Plant Names – Extended Editionâ by Lotte Burkhardt (2018). We manually extracted all genera honouring women. This dataset was supplemented with other sources including IPNI (2023), Mari Mut (2017-2021), a 2022 updated version of Burkhardtâs document (Burkhardt 2022), as well as suggestions received from colleagues and generated from our own research.
We collected the following information as structured data: information on the woman honoured, the genera named in honour of the woman, the year and place of the protologue or original publication (the nomenclatural reference), the author(s) of the genus name, and the link to the protologue or original publication if available online.
Wikidata
Wikidata was the central data repository and linking mechanism for this project as it provided structured data that can be read and edited by humans and machines and it acts as a hub for other identifiers. As such Wikidata played a central role in semantic linking and enriching of our data.
Wikidata items for the plant genera were created or enriched with information about the name, the author(s) of the genus and the year of publication. Those statements were referenced using the original publication. If the protologue was available on BHL, the BHL bibliographic or page number was added to that reference, thus creating a digital link improving access to the protologue. While undertaking this work we also collated a list of all those public domain publications that appeared to be absent from BHL. We passed on this list to BHL and requested these texts be scanned and added to BHL for the benefit of everyone.
We then added a named afterstatement to the Wikidata item for the appropriate plant genera linking that item to the Wikidata item for the woman honoured. Wikidata items for the women honoured were newly created or enriched. We researched each person and her contributions, plus information on mythological figures where necessary, and added this information to Wikidata items. Our work also included disambiguating the woman from other people with identical or similar names.
To amplify the womenâs contributions to science and to enrich the wider (biodiversity) data ecosystem, we linked to other Wikidata items and websites or databases by adding other relevant identifiers. For example if the women were botanists, botanical collectors or other naturalists, we used the author property to link the women to publications written by them. In addition, we added the women to Bionomia and attributed specimens collected or identified by them to their profiles.
Our work also included enriching Wikidata items of taxon authors. IPNI and Tropicos were searched for these author names, and websites such as BHL, the Global Biodiversity Information Facility (GBIF) or other specialist databases were consulted. Corrections or newly researched information on taxon authors was placed not just in Wikidata but was also sent together with the corresponding references to IPNI and Tropicos. This information was then used by those organizations to update these databases accordingly.
As a result of our data being placed in Wikidata it is available to be queried via the Wikidata Query Service.
Our Goal Achieved
As a result of our project, we published a dataset of 728 genera honouring women or female beings. This was a nearly twenty-fold increase in the number of genera linked to women in Wikidata. Our analysis paper on this data is forthcoming.
Notable Women
Monsonia L.
All of us came away from this research with a favourite story. One that stood out was Ann Monson, for whom Linnaeus named Monsonia. Linnaeus wrote a delightful letter to her about their creating, platonically of course, a kind of plant love-child between them, in the form of this new genus.
Translated from Latin : ââŠ.Lock these [seeds] in a pot, and place them in the window of the chamber towards the sun, when it bursts forth in February, and in the first summer the sun blooms and lasts the most beautiful Alstromeria, which no one has seen in England, and you bring forth no flowers. If it should come to pass, as I wish, if you offer our flames, I would only wish to beget with you an only child, as a pledge of my love, little Monsonia, by which you may perpetuate the fame of Lady in the kingdom of Flora, who was the Queen of Women.â
Fittonia Coem.
Two eponymous women with an interesting story are Sarah Mary Fitton and her sister Elizabeth. They wrote Conversations on Botany in 1817 accompanied by colour engravings of flowers which popularised botany with women. The genus Fittonia was named in their honour.
Chanekia Lundell
Another woman honoured in a plant genus was Mercedes Chanek, a Mayan plant collector who worked in the 1930âs for Cyrus Longworth Lundell and collected for the University of Michigan in British Honduras, today Belize. Very little is known about her life and work. However, her collections are detailed in Tropicos and Bionomia, and you can see the genus named for her by Lundell in IPNI under Chanekia.
An example of a mythological female being honoured in several plant names is that of Medusa, who has the most genera named after her, six, more than any real woman!
We hope that our data paper inspires others to use the methodology and workflow described to create other linked open datasets, e.g. celebrating and amplifying the contributions of underrepresented or marginalised groups in science.
Data paper:
von Mering S, Gardiner LM, Knapp S, Lindon H, Leachman S, Ulloa Ulloa C, Vincent S, Vorontsova MS (2023) Creating a multi-linked dynamic dataset: a case study of plant genera named for women. Biodiversity Data Journal 11: e114408. https://doi.org/10.3897/BDJ.11.e114408
Imagine having access to all the two billion biological collections of the world from your desktop! Not only to browse, but to search with artificial intelligence. We recently published a paper where we envisage what might be possible, such as searching all specimen labels for a personâs signature, studying the patterns of butterflies’ wings, or reconstructing a historic expedition.
Numbers of digital images from biodiversity collections are increasing exponentially. Herbariums have led the way with tens of millions of images available, but images of pinned insects will soon overtake plants.
Numbers of accessible images of specimens are increasing exponentially. Plants lead the way, but insects are increasing at the fastest rate. This graph was created from snapshots of the Global Biodiversity Information Facility and is undoubtedly an underestimate of the actual number of specimens for which images exist. See how this was created in Groom et al. (2023).
At one time, if you wanted access to biological collections, you had to travel. Now we are used to visiting collections online, where we can view images of specimens and their details on our desktops. Nevertheless, biological collection images are still dispersed and this limits their effective use, not just for people, but also for computers. One of the promises of making specimens digital is being able to apply machine learning to these images. Yet the real benefits of machine access to specimens can only be realised through massive access to collection images and the ability to apply these techniques to hundreds of collections and millions of specimens.
Imagine examining collections globally for the variation and evolution of wing coloration in butterflies, or studying the size and shape of leaves in research that transverses habitats and gradients of latitude and altitude.
In our paper in Biodiversity Data Journal, we examined some of the numerous uses for machine learning in digital collections. These include an enormous potential to extract traits of organisms, from the size and shape of different organs, to their colours, patterns, and phenology. Imagine examining collections globally for the variation and evolution of wing coloration in butterflies, or studying the size and shape of leaves in research that transverses habitats and gradients of latitude and altitude. We would not only be able to study the intricacies of evolution, but also practical subjects, such as the mechanics of pollination in insects, adaptations to drought in plants, and adaptations to weediness in invasive species.
Machine access to these images will also provide an unparalleled view of the history of the biological sciences, the specimens used to describe species, the evidence for evolution, the people involved and institutions that contributed. Such transparency may reveal some amazing stories of scientific exploration, but will undoubtedly also shed light on some of the less exemplary actions of colonialism. Yet if we are to redress the injustices of the past we need to have a balanced view of collections, and we should do this openly.
With such unparalleled access to collections, we could travel vicariously to times and places that are hard to reach in any other way. Fieldwork is expensive and time-consuming, and canât provide the historic perspective of collections, let alone the geographic extent. Furthermore, digital resources have the potential to democratise collections, allowing anyone the opportunity to study these collections irrespective of location.
Is such a vision of integrated digital collections possible? It certainly is! The technologies already exist, not just for machine learning, but also to create the infrastructure to provide access to millions of digital images and their metadata. Initiatives, such as DiSSCo in Europe and iDigBio in the USA are moving in this direction. Yet, we conclude that the main challenge to realising this vision of the future is a sociopolitical one. Can so many institutions and funders work together to pool their resources? Can collections in rich countries share the sovereignty of their collections with the countries where many of the specimens originated?
If you too share the dream, we encourage you to support or contribute to initiatives working in this direction, whether through funding, collaboration, or sharing knowledge. If the full potential of digital collections is to be realised, we need to think big and work together.
Research article:
Groom Q, Dillen M, Addink W, Ariño AHH, Bölling C, Bonnet P, Cecchi L, Ellwood ER, Figueira R, Gagnier P-Y, Grace OM, GĂŒntsch A, Hardy H, Huybrechts P, Hyam R, Joly AAJ, Kommineni VK, Larridon I, Livermore L, Lopes RJ, Meeus S, Miller JA, Milleville K, Panda R, Pignal M, Poelen J, Ristevski B, Robertson T, Rufino AC, Santos J, Schermer M, Scott B, Seltmann KC, Teixeira H, Trekels M, Gaikwad J (2023) Envisaging a global infrastructure to exploit the potential of digitised collections. Biodiversity Data Journal 11: e109439. https://doi.org/10.3897/BDJ.11.e109439
Content from 20 Pensoft journals will now be automatically added to ResearchGate to reach the research network’s 25 million users. Each journal will also receive a dedicated profile.
ResearchGate, the professional network for researchers, and Pensoft today announced a new partnership that will see a set of Pensoftâs open access journals increase their reach and visibility through ResearchGate â increasing access and engagement with its 25 million researcher members.
As part of this new partnership, 20 journals published by Pensoft – including the publisher’s flagship titles ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal and Research Ideas and Outcomes (RIO Journal) amongst others – will now have their content automatically added to ResearchGate upon publication to benefit from enhanced visibility and discoverability through ResearchGateâs innovative Journal Home offering. These journals will all have dedicated profiles and be prominently represented on all associated article pages on ResearchGate, as well as all other relevant touch points throughout the network.
Journal Home provides a unique opportunity for Pensoft to connect its authors with their readers. The new journal profiles on ResearchGate will provide a central location for each journal, enabling researchers to learn more, discover new article content, and understand how, through their network, they are connected to the journal’s community of authors and editors. Authors of these journals additionally benefit from having their articles automatically added to their ResearchGate profile page, giving them access to metrics, including who is reading and citing their research. These rich insights will also enable Pensoft to build a deeper understanding of the communities engaging with its journals.
âPensoft is delighted to be working with ResearchGate to provide an even greater service to our authors and readers. ResearchGate offers an innovative way for us to grow the reach and visibility of our content, while also giving us a way to better understand and engage our author and reader audiences.â
said Prof Lyubomir Penev, CEO and founder of Pensoft.
âWe couldnât be happier to see Pensoft embark on this new partnership with ResearchGate. Journal Home will not only enable Pensoft authors to build visibility for their work, but provide them and Pensoft with greater insights about the communities engaging with that research. I look forward to seeing this new collaboration developâ
said Sören Hofmayer, co-founder and Chief Strategy Officer at ResearchGate.
About ResearchGate:
ResearchGate is the professional network for researchers. Over 25 million researchers use researchgate.net to share and discover research, build their networks, and advance their careers. Based in Berlin, ResearchGate was founded in 2008. Its mission is to connect the world of science and make research open to all.
The database is a groundbreaking and pioneering initiative set to revolutionise our understanding of the rich biodiversity of Mindanao, the second-largest island group in the Philippines.
The Philippine Archipelago, with more than 7,100 islands, has one of the highest levels of endemism globally and is a hotspot for biodiversity conservation. Mindanao, the second largest group of islands in the country, is a treasure trove of terrestrial species, boasting one of the highest densities of unique flora and fauna on the planet. However, despite its ecological significance, comprehensive biodiversity records and data for the region have remained inaccessible until now.
The Mindanao Open Biodiversity Information (MOBIOS+) database aims to bridge these critical data gaps by compiling biodiversity information from the 21st century. This monumental undertaking seeks to enhance our understanding of Mindanao’s biodiversity trends, while establishing a database that is openly accessible to researchers and conservationists worldwide.
MOBIOS+ is the first of its kind and, currently, the most comprehensive attempt to create a consolidated database for the biodiversity of Mindanao based on publicly available literature. With a vast collection of biodiversity data, this database will be an invaluable resource to advance regional biodiversity research and analysis.
âIt will further facilitate the identification of species and areas that require immediate conservation prioritisation and action, addressing the urgent challenges posed by our rapidly changing planet,â the researchers behind the project write in their data paper, published in the open-access, peer-reviewed Biodiversity Data Journal.
Team members of the MOBIOS+ consortium curating the dataset.
The MOBIOS+ database, available through the Global Biodiversity Information Facility (GBIF) platform, currently comprises an impressive 12,813 georeferenced specimen occurrences representing 1,907 unique taxa. These span across ten animal classes inhabiting terrestrial and freshwater environments within the Mindanao faunal region. The project aims to continuously update the species database, complementing on-ground biodiversity efforts in Mindanao.
Diversity and distribution of species occurrence records across taxonomic groups included in the first version of the MOBIOS+ database. The diversity of species (percentage, %) according to class compared to the overall number of species recorded in the MOBIOS+ database (a); and the total number of species and the number of georeferenced occurrences per animal class (b).
Associate Professor Krizler Tanalgo of the Ecology and Conservation Research Laboratory at the University of Southern Mindanao, the project leader behind MOBIOS+, shared his thoughts on this initiative, saying:
âWe aim to democratise biodiversity information, making it readily available to researchers, policymakers, and conservation biologists. By doing so, we hope to facilitate well-informed decisions to address pressing environmental challenges, with a particular focus on the often underrepresented Mindanao region, which tends to receive limited attention in terms of research and funding.â
Distribution of biodiversity records across taxonomic groups from published papers.
âThe MOBIOS+ database is not only a testament to the dedication of the scientific community, but also a beacon of hope for the future of biodiversity conservation in Mindanao and beyond. It will support researchers and conservationists in identifying species and areas that require immediate prioritisation and action, safeguarding the unique and fragile ecosystems of this extraordinary region.â
The Biodiversity Community Integrated Knowledge Library (BiCIKL) project, funded by the European Union Horizon 2020 Research and Innovation Action under grant agreement No 101007492, has supported the publication of this work. The work is part of a special collection supported by the project and looking to demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.
Research article: Tanalgo KC, Dela Cruz KC, Agduma AR, Respicio JMV, Abdullah SS, Alvaro-Ele RJ, Hilario-Husain BA, Manampan-Rubio M, Murray SA, Casim LF, Pantog AMM, Balase SMP, Abdulkasan RMA, Aguirre CAS, Banto NL, Broncate SMM, Dimacaling AD, Fabrero GVN, Lidasan AK, Lingcob AA, Millondaga AM, Panilla KFL, Sinadjan CQM, Unte ND (2023) The MOBIOS+: A FAIR (Findable, Accessible, Interoperable and Reusable) database for Mindanao’s terrestrial biodiversity. Biodiversity Data Journal 11: e110016. https://doi.org/10.3897/BDJ.11.e110016
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You can find all contributions published in the âLinking FAIR biodiversity data through publications: The BiCIKL approachâ article collection in the open-access, peer-reviewed Biodiversity Data Journal on: https://doi.org/10.3897/bdj.coll.209.
The initiative, featured in an open-access methods paper in Biodiversity Data Journal, unites the Darwin Core (DwC) and Minimum Information about any (x) Sequence (MIxS) standards.
Biodiversity observation and research rely more and more on biomolecular data. The standardization this data, encompassing both primary and contextual information (metadata), is crucial for enabling data (re-)use, integration, and knowledge generation.
While both the biodiversity and the omics research communities have recognized the urgent need for (meta)data standards, they each have historically developed and adopted their own standards, making collaboration and data integration challenging.
The Task Group assembled a team of experts to build semantically precise and sustained interoperability between TDWGâs DwC standard, and the MIxS checklist from the GSC.
This collaborative effort culminated in a methods paper, in which they report on building sustainable interoperability between DwC and MIxS.
The paper was published in the open-access, peer-reviewed Biodiversity Data Journal, as part of a special collection, supported by the EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library), and looking to demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.
âWith representatives from established biodiversity data infrastructures, domain experts, data generators, and publishers, we – ab initio – bridged the conceptual to the application space,â
write the task group members in their paper.
To ensure the sustainability and lasting impact of this initiative, TDWG and GSC have signed a Memorandum of Understanding on creating a continuous model to synchronize their standards.
âWe trust that the activities of this TG will inspire similar activities between other metadata standards in this space, to break down silos and open a path to a more collaborative and interoperable future,â
they say in conclusion.
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Original source:
Meyer R, Appeltans W, Duncan WD, Dimitrova M, Gan Y-M, Stjernegaard Jeppesen T, Mungall C, Paul DL, Provoost P, Robertson T, Schriml L, Suominen S, Walls R, Sweetlove M, Ung V, Van de Putte A, Wallis E, Wieczorek J, Buttigieg PL (2023) Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability. Biodiversity Data Journal 11: e112420. https://doi.org/10.3897/BDJ.11.e112420
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You can find all contributions published in the âLinking FAIR biodiversity data through publications: The BiCIKL approachâ article collection in the open-access, peer-reviewed Biodiversity Data Journal on: https://doi.org/10.3897/bdj.coll.209.
For the Pensoft team, September 2023 was a busy and exciting month filled with conferences. Travelling across Europe, they promoted journals, connected with the scientific community, and rewarded exceptional research with free article publications.
Let’s take a look back at all the events of the past month.
Pensoft representatives Mrs. Boriana Ovcharova and Mrs. Anna Sapundzhieva, ready to greet attendees in the sun.
The conference looked at evolutionary adaptations from the perspective of behavioural ecology, reproduction biology, genetics, physiology, as well as nature conservation. It particularly focused on the pressing issues of wildlife research and species conservation in the context of global environmental change. Most of the â100 participants were young scientists from more than 30 countries.
The Pensoft team greeted fellow attendees with an exhibition stand and presented the conservation and ecology-focused journals Neobiota, Nature Conservation, One Ecosystem, and Biodiversity Data Journal. Pensoft also advocated for EuropaBon, who are designing an EU-wide framework for monitoring biodiversity and ecosystem services, and REST-COAST, whose mission is to provide the tools to restore environmental degradation of rivers and coasts. Within both European-funded initiatives, Pensoft is a key dissemination partner that contributes expertise in science communication, scholarly publishing, and the development of digital tools and platforms.
Joao Pedro Meireles posing with his Best Poster award.
Pensoft presented Joao Pedro Meireles from Utrecht University with the Best Poster Award for his research on pair compatibility in okapis, entitling him to a free publication in one of Pensoft’s open-access journals.
âMy study looked at pair compatibility in the zoo breeding programme of Okapi. During breeding introductions, sometimes the male becomes aggressive towards the female and we decided to investigate the potential factors. We ran a survey among all zoos that house the species in Europe and we found that differences in husbandry were linked to the aggressiveness performed by the males.â
Joao Pedro Meireles, Utrecht University
GfĂ Annual Meeting 2023
From the 12th to 16th of September, the German Centre for Integrative Biodiversity Research hosted the 52nd Annual Meeting of the Ecological Society of Germany, Austria and Switzerlandin Leipzig, Germany. The meeting welcomed more than 1,100 participants from around the world, including scientists, policymakers, educators, and environmental enthusiasts.
This yearâs meeting was held with the theme: “The future of biodiversity â overcoming barriers of taxa, realms and scales.” There was a particular emphasis on future challenges and opportunities facing biodiversity, and how to address and manage these in an interdisciplinary and integrative way.
Mrs. Boriana Ovcharova (Pensoft) with Neobiota Editor-in-Chief Prof. Dr. Ingolf KĂŒhn.
Conference participants were welcomed at the Pensoft stand, where they could learn more about the projects EuropaBon and SELINA, which deal with biodiversity, ecosystem and natural capital topics.
Also in Leipzig, the European Conference on Ecological Modellingtook place between the 4th and 8th of September. The event focused on the transformation of how societies deal with natural resources in a world where biodiversity and ecosystem services are at high risk.
The ECEM 2023 continued a series of conferences launched by the European chapter of ISEM, the International Society for Ecological Modelling. ISEM promotes the international exchange of ideas, scientific results, and general knowledge in the areas of systemsâ analysis and simulations in ecology, and the application of ecological modelling for natural resource management.
đąShutout to all attending the #ECEM23@ECEM_2023#ecological#modelling conference TODAY in Leipzig! Make sure to visit the poster session during lunch & find about the unique article types welcome to our #journal! đĄThey intend to disseminate models PRIOR TO implementation! https://t.co/dUVskYFK11
— Food & Ecological Systems Modelling Journal, FESMJ (@FESMJournal) September 5, 2023
The Bundesinstitut fĂŒr Risikobewertung team presented a poster on the Formal Model format and potential new MiDox formats, unique publication types that can be submitted to Pensoftâs Food and Ecological Modelling Journal.
118th Congress of the Italian Botanical Society
Speakers at the 118th Congress of the Italian Botanical Society.
Pensoft was proud to sponsor the 118th Congress of the Italian Botanical Society, which took place in Pisa, Italy from the 13th to 16th of September. Experts in various fields of Botany gathered to share their research on the following topics:
Journals promoted by Pensoft at the 94th Annual Meeting of the PalÀontologische Gesellschaft.
Summer may be well and truly over, but as a new academic year begins, Pensoft looks forward to attending more conferences, rewarding more incredible research, and connecting with more of the scientific community. Thank you to everyone who contributed to or engaged with Pensoftâs open-access journals this year, and hereâs to a successful final quarter of 2023.
This study, published in Biodiversity Data Journal, is an important step in creating field guides for CCZ wildlife, which will help promote sustainable practices and informed decision-making.
The demand for rare raw materials, such as cobalt, is fuelling the exploration of the deep-sea floor for mining. Commercial deep-sea mining is currently prohibited in areas beyond national jurisdiction, but companies are permitted exploratory operations in certain areas to assess their mineral wealth and measure environmental baselines. The Clarion-Clipperton Zone (CCZ) is an area of the Pacific deep-sea floor spanning up to 6 million km2, found roughly between Hawaii and Mexico. Currently, it has 17 contracts for mineral exploration covering 1.2 million km2. However, despite relatively extensive mineral exploration beginning in the 1960âs, baseline biodiversity knowledge of the region is still severely lacking. Even the most basic scientific question: âWhat lives there?â has not been fully answered yet.
Annelids found in the Clarion-Clipperton Zone.
In a new paper researchers report on the marine life of the CCZ, focusing on annelid worms. Annelids represent one of the largest group of macroinvertebrates living within the mud covering the sea floor of CCZ, both in terms of number of individuals and the number of species. Data from recent oceanographic cruises enabled researchers from the University of Gothenburg, Sweden and the Natural History Museum London to discover more than 300 species of annelids from around 5000 records. The annelid species, many considered to be new to science, were discovered through employment of traditional morphological approaches and modern molecular techniques. The current study focuses on 129 such species across 22 annelid families. Previously, the authors of this study formalized 18 new species, while altogether reporting on 60 CCZ species, including most recently 6 species in family Lumbrineridae. The lead author Helena Wiklund from University of Gothenburg comments: âTaxonomy is the most important knowledge gap we have when studying these unique habitats and the potential impact of mining operations. We need to know what lives there to inform the protection of these ecosystems.â
Bathyfauvelia glacigena.
To further understand the CCZ, scientists sail the Pacific Ocean on research expeditions that employ sampling techniques ranging from the technical, like remote-controlled vehicles that traverse the ocean floor, to the simple, like a sturdy box corer collecting sediment at the bottom.
âSadly, the soft-bodied annelids are often damaged during the collection and sediment sieving onboardâ says annelid taxonomist Lenka Neal from the Natural History Museum London. As a result, the traditional morphological approach is often of limited use when working with the deep-sea specimens, with taxonomists increasingly employing DNA techniques as well.
Bathyfauvelia ignigena.
Over the last decade, scientists have generated a large amount of annelid data. Such data are only of use when made available through publication to the wider scientific community and other stakeholders. âA priority is to make the data are FAIR, or Findable, Accessible, Interoperable and Reusable so it can be redeployed easily, if youâll excuse the pun, for future analysisâ says co-author Muriel Rabone. âThe same applies to samples, where accessibility of the specimen vouchers and molecular samples allows for reproducibility and continuation of the work. This is one step of the process. And ultimately, having more robust knowledge can lead to more robust evidence-based environmental policyâ.
An unidentified Polynoidae species.
âMore often than not, ecological papers describing biodiversity do not include a list of all the species and specimens used to make the broader ecological inferences, and even more rarely make the specimens and all associated metadata available in a FAIR way. In this study, we have made a significant and time-consuming attempt to do this, in a region of the global oceans where critical policy decisions are being made that could impact the way humanity obtains its resources and manages its environment in a sustainable way,â the researchers write in their paper, which was published in the open-access Biodiversity Data Journal.
An unidentified Cirratulidae species.
The team behind the research hope that this still partial checklist of CCZ annelids, many in too poor state of preservation to be immediately described, is a key step forward towards creating future field guides for the areaâs wildlife. Given that mining operations in the area could be imminent with the International Seabed Authority considering applications this year, the use of biological data for environmental management has become more important than ever.
This research was supported by funding from UK Seabed Resources Ltd.
Research article:
Wiklund H, Rabone M, Glover AG, Bribiesca-Contreras G, Drennan R, Stewart ECD, Boolukos CM, King LD, Sherlock E, Smith CR, Dahlgren TG, Neal L (2023) Checklist of newly-vouchered annelid taxa from the Clarion-Clipperton Zone, central Pacific Ocean, based on morphology and genetic delimitation. Biodiversity Data Journal 11: e86921. https://doi.org/10.3897/BDJ.11.e86921
