DOI: 10.3897/arphapreprints.e190520

Authors: W. Daniel Kissling, Jinhu Wang, Yifang Shi

Abstract: This deliverable, D4.10 – Demonstrator pipeline for habitat condition metric extraction and parallel and distributed computing in a cloud environment, is produced in the context of the project MAMBO (Modern Approaches to the Monitoring of BiOdiversity), funded by the European Commission through an EU Horizon Europe Research and Innovation Action (Grant Agreement No. 101060639).

HTML

XML

PDF

DOI: 10.3897/rio.12.e186726

Authors: Dominic Wanke, Daniel Whitmore

Abstract: Mountains exemplify how climate change transforms long-standing refuges into zones of loss. As species track suitable climates upslope, they confront absolute ecological limits. This commentary reflects on montane extinctions as a warning signal for broader planetary boundaries and the future of biodiversity in the Anthropocene.

HTML

XML

PDF

DOI: 10.3897/rio.12.e187550

Authors: Dimitris Koureas, Pedro Beja, Mark Blaxter, Astrid Böhne, Sarah Bourlat, Torbjørn Ekrem, Brent Emerson, Katharina Heil, José Melo-Ferreira, Ben Price, Rutger Vos, Wouter Addink, Tyler Alioto, Filippos Aravanopoulos, Jonas Astrin, Jean-Marc Aury, Ian Barnes, Claudia Bruschini, Elena Buzan, Guy Cochrane, Tamás Cserkész, Thanos Dailianis, Elza Duijm, Glenn Dunshea, Rosa Fernández, Sónia Ferreira, Giulio Formenti, Sara Fratini, Konstantinos Gkagkavouzis, Carole Goble, Michal Grabowski, Bjorn Grüning, Ivo Gut, Marta Gut, Peter Harrison, Axel Hausmann, Jacob Höglund, Laura Iacolina, Alessio Iannucci, Kjetill Jakobsen, Urmas Kõljalg, Henrik Lantz, Harris Lewin, Jan Macher, Tereza Manousaki, Fergal Martin, Ximo Mengual, Pedro Oliveira, Rebekah Oomen, Michael Raupach, Ana Riesgo, Hugues Roest Crollius, Anna Somogyi, Torsten Struck, Hannes Svardal, Ave Tooming-Klunderud, Alexandros Triantafyllidis, Olga Vinnere Pettersson, Maximilian Wagner, Patrick Wincker, Ni Yan, Jose Alonso, Ana Casino, Claudio Ciofi, Gabriela Daňková, Peter Hollingsworth, Mara Lawniczak, Camila Mazzoni, Robert Waterhouse

Abstract: The Biodiversity Genomics Europe (BGE) Project has the overarching aim of accelerating the use of genomic science to enhance understanding of biodiversity, monitor biodiversity change, and guide interventions to address its decline. The BGE Project comprises activities focused on DNA Barcoding (Barcoding Stream) and Reference Genome Generation (Genomes Stream) for eukaryotic species across Europe, bringing together two European networks: the International Barcode of Life in Europe (iBOL Europe) and the European Reference Genome Atlas (ERGA). This publication is an abridged version of the successful grant proposal developed jointly by iBOL Europe and ERGA in response to the Horizon Europe call HORIZON-CL6-2021-BIODIV-01-01. Two key strands of genomic science form the basis of this proposal: DNA barcoding - sequencing short, standardised genomic regions to tell the world’s species apart, transforming the speed of completion of the inventory of life on Earth and providing the foundations of a global bio-surveillance system for biodiversity; and genome sequencing - generating high-quality complete reference genomes for all species on Earth, transforming understanding of biodiversity at the genetic level, and delivering fundamental knowledge of how biological systems function and how species respond and adapt to environmental change. The BGE Project objectives are focused on (i) Capacity: To establish functioning biodiversity genomics networks at the European level to connect and grow community capacity to use genomic tools to tackle the biodiversity crisis; (ii) Production: To establish and implement large-scale biodiversity genomic data generation pipelines for Europe to accelerate the production and accessibility of genomic data for biodiversity characterisation, conservation, and biomonitoring; and (iii) Application: To apply genomic tools to enhance understanding of pan-European biodiversity and biodiversity declines to improve the efficacy of management interventions and biomonitoring programmes.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e188550

Authors: Yuting Tai, Tom Bucx, Mindert de Vries, Sara Pino Cobacho, Richard Marijnissen, Iris van Dongen, Rutger van der Brugge, Åse Johannessen, Fabienne Horneman, Silvia Torresan, Elisa Furlan, Andrea Critto, Alice Stocco, Caterina Dabalà, Francesca Coccon, Paolo Comandini, Silvia Frias, Ferran Bertomeu, Carles Ibáñez, Laura Puértolas Domènech

Abstract: The REST-COAST Project (Large scale RESToration of COASTal ecosystems through rivers to sea connectivity) is an EU Horizon 2020 research project (Grant agreement No. 101037097) whose overall goal is to address with effective and innovative approaches and tools the key challenges faced by coastal ecosystem restoration across Europe. The approach chosen for this project will deliver a highly interdisciplinary contribution, with the demonstration of improved practices and techniques for hands-on ecosystem restoration across several pilot sites, supported by the co-design of innovative governance and financial arrangements, as well as an effective strategy for the dissemination of results. Work Package 4 (WP4) focuses on the development of scalable adaptation-through-restoration plans (for each pilot of REST-COAST) based on adaptation pathways that incorporate ecosystem services (ESS) and biodiversity value (BDV) from NBS building blocks. It is envisaged that these plans will be suited for upscaling restoration in coastal systems worldwide, supported by the global scale analysis of coastal risks, costs and governance performed in WP 2/3/5. Deliverable 4.3 aims at providing guidelines for building adaptationthrough-restoration pathways, based on NBS and technical measures that deliver ESS and BDV gains, tested and validated at the Pilots. When using the adaptation pathway guidelines, it is important to apply them with flexibility to accommodate the specific needs and contexts of individual pilots. While it is recommended to follow the methodology in Chapter 2—‘Generic Stepwise Approach’—to develop pathways, pilots should view these methods as flexible rather than rigid, to fit their unique restoration goals, timelines, environmental and social conditions. Chapter 3—‘Restoration Pilots’—serves as a reference to provide insight from three pilots with pilot-specific approaches to build the pathways. The guidelines should be seen as a dynamic tool that can evolve based on feedback, local stakeholder input, or new scientific data, ensuring that each pilot tailors its pathway to address local uncertainties, opportunities, and challenges.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e188540

Authors: W. Daniel Kissling, Jinhu Wang

Abstract: This document is a data deliverable (D6.2) prepared for the Modern Approaches to the Monitoring of BiOdiversity (MAMBO) project, funded by the European Commission through an EU Horizon Europe Research and Innovation Action (Grant Agreement No. 101060639). The MAMBO project aims to support EU biodiversity policy and address key knowledge gaps by developing and applying innovative tools, workflows, and data products for biodiversity monitoring at multiple spatial and temporal scales.Deliverable D6.2 documents the geospatial research data products of vegetation structure metrics derived from airborne Light Detection and Ranging (LiDAR) point clouds that have been generated within the MAMBO project. The deliverable is of type ‘DATA’ and focuses on the actual datasets produced or collected during the project, rather than on the analysis or interpretation of scientific results. Its primary purpose is to support the principles of Findability, Accessibility, Interoperability, and Reusability (FAIR) by providing a structured overview of the datasets, their scope, and the platforms through which they are made publicly available.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e187633

Authors: Eeva Karjalainen, Maria Hällfors, Maria Söderholm, Nikola Ganchev, Sari Erkkilä, Satu Soini

Abstract: OBSGESSION project management guide summarises the central rules and practices agreed in Grant Agreement and Consortium Agreement. This document also describes day-to-day working practices, and thus is a living document that is updated regularly.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e187632

Authors: Maria Söderholm, Maria Hällfors, Susana Baena, Claire Brown, Marcel Buchhorn, Jorrit Scholze

Abstract: The OBSGESSION project (Observation of Ecosystem Changes for Action, https://obsgession.eu/) aims to enhance terrestrial and freshwater biodiversity monitoring and policy by new approaches for integrating data and modelling, and by developing science-based solutions. This data management plan (DMP) provides details about the data to be collected, generated, and processed in OBSGESSION, as well as other outputs. It also outlines the key principles of data management practices, as required in the Horizon Europe Programme Guideline. The project is committed to following the policies of open science and research as the foundation for all activities, including data management. Data management in the project will adhere to the FAIR principles, ensuring that data is Findable, Accessible, Interoperable and Reusable. The plan also specifies that other outputs besides data will be managed in line with these principles whenever applicable.The project will utilise a variety of data and combine biodiversity data from multiple sources. The types of data included in the OBSGESSION project are experimental, observational, statistical, and qualitative data, such as interviews. The DMP outlines the overall data management practices for the duration of the data lifecycle within the framework of the FAIR principles and provides details on planned practices and data-specific considerations. This includes, among other things, producing metadata and other documentation related to the data. The plan also presents practices for ensuring data interoperability, reusability, and publication. Relevant metadata standards have been identified to make EO data interoperable. In addition, the DMP describes the In-Situ database, OpenEO platform and Data Cubes as tools and mechanisms for implementing interoperability and (re)usability of EO and in-situ data.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e187631

Authors: Nikola Ganchev, Gabriela Popova

Abstract: Deliverable D6.2 presents a plan for shaping the dissemination, exploitation, and communication (DEC) activities of OBSGESSION. These activities are crucial for ensuring OBSGESSION’s impact and amplifying the project's influence. The Communication Plan (CP) and Plan for the Exploitation and Dissemination of Results (PEDR) is developed in M6 (June 2024) and will be updated in M24 (December 2025, D6.3) and in M40 (April 2027, D6.4) to reflect OBSGESSION's progress and maturity level, providing a targeted approach for each stage according to evolving DEC needs.Aside from defining the goals and scope of the project's communication, dissemination, and exploitation, the CP and PEDR also identify the primary stakeholder groups and key messages for each. These have been outlined based on a consortium-wide questionnaire. The plans also include the expected knowledge outputs of the project. Based on this information, D6.2 details the main communication, dissemination, and exploitation tools and evaluates their relevance to different target groups. Finally, a specific implementation plan is provided for the project's first stage of development, along with indicators for actively monitoring the effectiveness of these actions.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e187630

Authors: Joaquim Estopinan, Anne Thomas, Pierre Gaüzère, Wilfried Thuiller

Abstract: Detecting and attributing biodiversity changes is a multifaceted and demanding task. The first key challenge is gathering data on biodiversity metrics and the likely drivers that is sufficiently structured and aligned in space and time, and wide enough to cover the dynamical range of the target latent processes at play, enabling statistical inference. Demonstrating that a measure of biodiversity has significantly changed relative to a reference state — a reference which is often difficult to define due to a lack of past data — constitutes a second challenge. A third key challenge is designing an identification strategy that can isolate the contribution of multiple potential causal factors with statistical confidence.The review comprising the deliverable D3.1 addresses these three key challenges in a coherent framework, meeting the task expectations. It is entitled "Advancing Causal Inference in Ecology: Pathways for Biodiversity Change Detection and Attribution" (Schrodt et al., Methods in Ecology and Evolution, under revision). This work was achieved in collaboration with the IMPACTS synthesis group of the French Foundation for Biodiversity Research (FRB). This text provides conceptual and practical guidance on taking advantage of existing causal methods to detect and attribute changes in biodiversity. There is an emphasis on how remote sensing data can mitigate pressing issues related to confounding factors that occur across scales.By paying attention to the described challenges and relying on the suggested methods and workflow, the review introduces a solid basis to root biodiversity change studies in causal principles for better detection and attribution. The proposed manuscript is indeed highly interdisciplinary in its attempt to bring biodiversity studies closer to the science of attribution through causal inference from observational data. While this deliverable is fully autonomous, it is complemented by two perspective articles that are also under revision and a method decision tool that is under development. They cover related aspects of detection and attribution.As deliverable D3.1 format is a scientific manuscript, it is provided in its most recent version in Annex 1 below.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e187629

Authors: Gabriela Popova, Nikola Ganchev, Slavena Peneva, Kremena Kaleva

Abstract: The communication efforts of OBSGESSION kicked-off as soon as the project launched. However, to ensure proper visibility, a set of dissemination and branding tools and materials have been designed within the first three months of the project duration, ensuring broad visibility from an early stage. A project logo, social media channels and a landing page were established in time for the OBSGESSION kick-off meeting in the end of January. These formed the backbone of the project branding and public recognition. Document templates were also developed and made available to the consortium, in order to facilitate the creation and internal uptake of the project corporate identity for dissemination and reporting activities such as deliverable, milestone and presentation. Social media accounts have been established in time for the launch of OBSGESSION on X (formerly Twitter) and LinkedIn to ensure the widest possible uptake and outreach to stakeholders and other interested parties of project results, news and other announcements. The sustainability of project results and impact wil be secured through the development and maintenance of a public OBSGESSION website for a total of 9 years – 4 years of the project duration and additional 5 years after the project has ended.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e187628

Authors: Ayesha Wijesekera, Zuhail Thatey, Claire Brown, Susana Baena, Joshua Barritt

Abstract: This report provides a review of the biodiversity policy landscape at the European Union (EU) level and identifies a set of priority Essential Biodiversity Variables (EBVs) to support policy needs. Policy needs were determined based on the European 'Union's Biodiversity Strategy for 2030 (EU BDS 2030), which serves as the overarching framework for biodiversity-related policies and legislation at the EU level in response to the requirement for countries to have a National Biodiversity Strategy and Action Plan (NBSAP) as Parties to the Convention on Biological Diversity (CBD). The analysis focuses on the actions from the EU BDS 2030 as the key articulation of policy needs, and indicators to evaluate monitoring requirements. Actions were categorized based on their relevance to different stages of the policy process (e.g., planning, implementation, reporting or review), while indicators were categorized as relevant to policy reporting. Actions and indicators were also tagged by ecosystem realm (i.e., terrestrial, freshwater, marine) or as cross-cutting. The potential applicability of EBVs for broadly supporting the implementation of each of the 102 actions and sub-actions. Also, the monitoring of the 16 available indicators from the 'Strategy's dashboard, was assessed. The review found that EBVs could broadly be used to support the implementation of 37 actions and the monitoring of five indicators. These selected actions and indicators were then mapped to EBV classes and candidates based on the EBV framework by the Group on Earth Observations Biodiversity Observation Network (GEO BON). EBV candidates were ranked from high to low priority based on the total number of actions and indicators they were mapped to, both overall and within different ecosystem realms and stages of the policy process. Candidates linked to the greatest number of actions and indicators were considered the highest policy priority. Overall, the species abundance candidate ranked 1st in terms of policy priority, followed by species distributions (2nd), ecosystem distribution (3rd) and ecosystem vertical profile (4th), with markedly higher total scores than other candidates. These candidates were also consistently ranked among the top four candidates across different ecosystem realms and stages of the policy process. Taking into consideration the findings from the Europa Biodiversity Observation 'Network's (EuropaBON) User and Policy Needs Assessment, this review identified species abundances, species distributions and ecosystem distribution as priority EBVs for the development of remote sensing (RS) biodiversity products in the OBSGESSION project. The ecosystem vertical profile also ranked highly, but further assessment is recommended to determine its policy importance. While this review provides a priority set of EBV candidates based on policy needs, further prioritisation considering scientific gaps and technical feasibility for monitoring EBVs via RS will be continued under Task 1.2 as part of the Science Policy Traceability Matrix (SPTM), taking into consideration work already undertaken on RS-enabled EBVS.

HTML

XML

PDF

DOI: 10.3897/rio.12.e181653

Authors: Eva Bischoff, Rainer Buschmann, Callum Fisher, Charlotte Hoes, Katja Kaiser, André Koch, Hannah Kressig, Annekathrin Krieger, Britta Lange, Sabine von Mering, Marie Muschalek, Jana Reimer, Hilke Thode-Arora, Richard Tsogang Fossi, Simon Ville, Bernhard Wörrle, Joël Zouna

Abstract: Natural history traders have been crucial, yet under-researched contributors to museum collections. The Hamburg-based J.F.G. Umlauff family company, founded in the mid-19th century, exemplifies this significance. For nearly 100 years, members of the Umlauff family supplied zoological and ethnographic specimens to museums all over the world. During a two-day workshop, an interdisciplinary group of museum practitioners, archivists, as well as scholars from the fields of History and Cultural Studies, mapped Umlauff's impact on natural history collections, particularly in German museums, by reconstructing their global trading networks. Research questions include identifying beneficiary institutions nationally and internationally and tracing interdisciplinary procurement practices, especially for collections from colonial contexts.

HTML

XML

PDF

DOI: 10.3897/rio.12.e176590

Authors: Beatrice Bock

Abstract: Fungi exhibit diverse trophic strategies, ranging from obligate symbiosis to saprotrophy, with some taxa capable of occupying multiple ecological roles. Manually identifying trophic versatility from literature is time-consuming and difficult to scale. Here, we present a pilot workflow that automates the classification of fungal trophic modes using transformer-based language models. A curated dataset of 56 fungal ecology abstracts was manually labelled as dual (occupying multiple trophic modes) or solo (restricted to one mode) and used to fine-tune four models: BioBERT, BERT-base-cased, BERT-base-uncased and BiodivBERT. Stratified 5-fold cross-validation revealed that BioBERT and BERT-base-cased performed equally well (~ 89% accuracy, balanced precision and recall), highlighting the importance of case sensitivity in taxonomic text. BiodivBERT and uncased BERT models underperformed, indicating that domain adaptation alone is not sufficient. This pilot study emphasises reproducibility, transparency and open data integration, offering a generalisable proof-of-concept for linking literature-derived ecological information to existing fungal trait databases such as FUNGuild and FungalTraits. All code and data are openly available to support reuse and scaling to larger datasets.

HTML

XML

PDF

DOI: 10.3897/rio.12.e184961

Authors: Giuditta Parolini

Abstract: This paper discusses Intellectual Property Rights (IPR) on research data and legislations that have a direct impact on access to research data. Ensuring data access is a key requirement in the pursuit of open science and to guarantee that research can benefit society at large. Yet, legal complexities, unclear data rights, third-party IPR may transform what should be straightforward information exchange for the benefit of science and society into a frustrating experience.Examples from biodiversity science are used to illustrate legal issues regarding research data. The discussion focuses on the role legal aspects play in open science and concludes with a set of open questions regarding research data IPR and open science. This contribution is written considering the legal framework for research data in the European Union.

HTML

XML

PDF

DOI: 10.3897/rio.12.e177555

Authors: Jordy van den Berg

Abstract: The relationship between self-efficacy and self-leadership has been widely explored, with research indicating that higher perceived self-efficacy is positively associated with effective self-leadership. Self-leadership has been a focus of attention in recent studies, particularly with the increasing emphasis on the context of knowledge work, where self-leadership is associated with job performance, motivation and job satisfaction. As organisations shift towards less hierarchical and more team-based organisations, self-leadership, which involves guiding oneself through internal drive rather than external leadership, has become significant. However, much is unknown about early self-leadership development, especially as it pertains to contextual factors, such as childhood exposure to domestic violence. Specifically, prior work suggests that childhood exposure to domestic violence negatively impacts self-efficacy, but the long-term impact on self-leadership is unclear.This study explores the influence of childhood experiences with domestic violence on adult self-leadership and self-efficacy. The findings show a small, but not significant difference in the self-efficacy and self-leadership of individuals who experienced childhood domestic violence versus those who did not. This research extends leadership development research by exploring early life contextual factors as potential influences on self-efficacy and self-leadership. Practically, this study emphasises the value of trauma-informed leadership development initiatives and highlights that certain factors may buffer the long-term impacts of childhood trauma.

HTML

XML

PDF

DOI: 10.3897/rio.12.e183952

Authors: Andreea Nita, Montserrat Zamorano

Abstract: In response to climate change, the landmark Paris Agreement established a set of goals to achieve climate neutrality and limit global warming. To help investors and companies contribute to these goals, the EU adopted a taxonomy for sustainable activities and, in line with it investments, must do no significant harm, as indicated by the Recovery and Resilience Facility Regulation. Since its inception, the Environmental Impact Assessment (EIA) procedure has aimed to minimise impacts of projects that could significantly damage the environment. Certainly, there are recognised weaknesses in the EIA, but its fitness to address complex environmental challenges, such as climate change, is unmatched. Considering the importance of EIA in ensuring scaling-up sustainable energy-related investments, NetDeal focuses on providing innovative and easy-to-use methods to improve EIA worldwide and combines policy analysis and EIA assessment data into complex networks. First, we analyse models of impact assessment (IA) legislation that can make recommendations about how IA can change to fit the global effort to tackle the energy and resource crises. Second, we will expose best practice models and investigate through network-related statistical analyses the collaboration links established in each EIA stage, which are behind successful projects from the perspective of productivity, circular economy, adaptation to climate change and reaching the goal of zero net emissions. Third, using Exponential Random Graph Models, I will explore the dynamic interaction between EIA stakeholders to diagnose the organisational structures and factors that strongly influence these projects. Last, I will create an integrated multi-layer EIA framework to improve the EIA effectiveness. The findings will be translated into the economic sector and provide new instruments to facilitate a streamlined EIA procedure that facilitates the adoption of urgent measures to mitigate the current energy crisis.

HTML

XML

PDF

DOI: 10.3897/rio.12.e183261

Authors: Enriko Kroon, Ricardo Borges, Rômulo de Jesus, Stefan Kuhn

Abstract: It has been shown that it is possible to train a (simple) neural network to classify nuclear magnetic resonance spectra by a substructures either being part of the chemical structure measured or not. We now explore the interpretability of such models using techniques from explainable AI, specifically Grad-CAM. We show that those techniques do not give ideal results in the context of NMR, which would be able to identify individual peaks. On the other hand, they enable a better interpretation of the results than those metrics just based on "right or wrong". We can also confirm the result from our previous work, that the trained network performs well for pure compounds, but its generalisability to mixtures is questionable, a limitation that could only be assumed in the original study.

HTML

XML

PDF

DOI: 10.3897/rio.12.e181743

Authors: Alexandra-Maria Klein, Helge Bruelheide, Douglas Chesters, Tim Diekötter, Alexandra Erfmeier, Heike Feldhaar, Felix Fornoff, Christina Grozinger, Nina Kranke, Yu Liang, Xiaojuan Liu, Arong Luo, Yvonne Oelmann, Michael Orr, Jana Petermann, Huijie Qiao, Finn Rehling, Manuela Sann, Thomas Scholten, Andreas Schuldt, Steffen Seitz, Michael Staab, Simon Thorn, Ming-Qiang Wang, Zhi-Shu Xiao, Naili Zhang, Chao-Dong Zhu

Abstract: Biodiversity-ecosystem functioning (BEF) research has shown that ecosystem functioning and stability are closely linked to biodiversity. A cornerstone of this field is the BEF-China research platform, i.e. the world’s largest forest biodiversity experiment in subtropical China. It has demonstrated that tree diversity enhances productivity, carbon sequestration and ecosystem stability. However, the strength of these positive tree diversity effects varies widely across forests, possibly because higher trophic levels (such as herbivores and predators) mediate how biodiversity influences ecosystem functioning.To better understand how tree diversity influences higher trophic levels and their contributions to forest functioning, the German Research Foundation (DFG) is funding the project MultiTroph. MultiTroph quantifies species interactions and integrates them into food webs to understand when and why ecosystem functions change or destabilise with species loss. We expect that trophic interaction networks reveal how species share or separate their ecological roles, with more niche overlap in species-rich forests and more niche specialisation in species-poor forests.Here, we outline our conceptual framework and research goals. We are convinced that MultiTroph will expand existing BEF research and provide a more holistic understanding of the role of multi-trophic food webs in forest ecosystems.

HTML

XML

PDF

DOI: 10.3897/rio.11.e181727

Authors: Alexandra-Maria Klein, Anda Adamsone-Fiskovica, Georgina Alins, Per Angelstam, Aurelie Belveze, Jordi Bosch, Tom Breeze, Richard Comont, Elise de Groot, Lynn Dicks, Anselm Rodrigo Dominguez, György Dudás, Lotta Fabricius Kristiansen, Mariia Fedoriak, Nicola Gallai, Michael Garratt, Mikelis Grivins, Christina Grozinger, Nigel Jenner, Georgios Kleftodimos, David Kleijn, Anikó Kovács-Hostyánszki, Bodo Krauss, Sara Leonhardt, Julia Osterman, Annie Ouin, Amy Plowman, Simon Potts, Claus Rasmussen, Laura Roquer-Beni, Daniele Rossi, Maj Rundlöf, Oliver Schweiger, Henrik Smith, Jane Stout, Louis Sutter, Martin Thorsøe, George Vlontzos, Dimitry Wintermantel, Nina Kranke, Amibeth Thompson

Abstract: RestPoll is a transdisciplinary project aiming to provide society with tools to reverse wild insect pollinator declines and to position Europe as a global leader in pollinator restoration and set the future agenda for pollinator restoration worldwide. The RestPoll consortium combines the expertise of natural and social scientists, as well as representatives of NGOs, businesses and ministries. RestPoll - together with stakeholders ranging from individual land managers to public authorities - co-designs, evaluates and refines measures and cross-sectoral approaches to restore pollinators and their services. Central to RestPoll is the establishment of a Europe-wide network of pollinator restoration case-study areas with Living Labs, which are unique hubs for experimentation, demonstration and mutual learning at various spatial scales (field, farm, landscape, European scales), in landscapes dominated by intensively managed crops or grasslands. The RestPoll consortium explores, tests, evaluates and refines cross-sectoral pollinator restoration approaches to conserve biodiversity and to benefit nature and society. Our holistic approach also aims to engage in participatory planning and the development of new business models along the food value chain by engaging through newly-developed participatory approaches at diverse social, ecological and political scales. Learning outcomes are communicated to a diverse range of regional and European partners and collaborators, which allows for making a lasting impact beyond the end of the project.

HTML

XML

PDF

DOI: 10.3897/rio.11.e177579

Authors: Hideyuki Doi

Abstract: Humanity faces environmental crises on a scale that demands new scientific paradigms. While valuable, the application of artificial intelligence has largely been confined to a predictive role—a paradigm insufficient for the transformative action now required. We argue for a shift toward a generative framework, repositioning AI from an analytical tool to a facilitator of synthesis and communication. This perspective introduces a vision where advanced generative models, including text-to-video technologies, create dynamic, experiential simulations of designed ecosystems. This allows stakeholders to not only see a proposed design, but also to witness its potential dynamics, such as how a restored forest matures or how green infrastructure responds to climate events. Crucially, this approach empowers AI to act as a representative for non-human species, synthesizing data to visualize their needs. However, I emphasize the critical distinction between photorealistic visual rendering and rigorous biophysical simulation; the former must be grounded in the latter to avoid misleading outcomes. I critically examine the approach's inherent challenges, including the environmental footprint of these models, and argue for an indispensable "expert-in-the-loop" framework to guide and validate these powerful new tools. This paradigm shift has profound implications for scientific methodology and public engagement, heralding an era where interdisciplinary teams leverage AI to visualize, deliberate, and collaboratively shape a resilient planet.

HTML

XML

PDF

DOI: 10.3897/rio.11.e171663

Authors: Iro Anastasopoulou, Konstantinos Kavakakis, Vasiliki Asimogiorgou, Foteini Iatrou, Dimitra Petza, Pierluigi Carbonara, George Tserpes, Francisco Alemany, Stefanos Kalogirou

Abstract: Objective: The objective of this scoping review is to map and synthesize evidence on mitigation measures, fishing practices, and technologies to reduce endangered, threatened, and protected (ETP) species bycatch in drifting longline fisheries targeting large pelagics, summarize key concepts and findings across disciplines, and identify knowledge gaps to inform policy and research at a global scale.Introduction: Drifting longline fisheries targeting large pelagic species continue to pose a significant conservation and management challenge for ETP species. Although various types of mitigation measures, fishing practices, and technologies have been developed and utilized globally to reduce ETP bycatch, the scope and nature of field-tested evidence remain diverse and scattered.Inclusion criteria: Studies about regional measures adopted, and fishing practices and technologies tested in the field aimed at reducing ETP species in drifting longlines (LLD) for large pelagics. Both peer-reviewed and grey literature will be included. Studies published in English, Swedish, Norwegian, Greek, Spanish and Italian language and between the years 1990 and 2024 will be included. Studies related to other types of fishing gear, those that do not mention ETP species, or any type of evidence synthesis will be excluded.Methods: This scoping review will be guided by the Joanna Briggs Institute (JBI) methodology. Scopus and Web of Science databases will be used and complemented with grey literature sources, i.e. organisational websites and a web-based search engine. A team of four reviewers will conduct the screening and the data extraction processes. EndNote software, Covidence software, Microsoft Excel and Flourish platform will be used for data management, screening, extraction and presentation of the outputs. The results will be presented both graphically and in tabular form.

HTML

XML

PDF

DOI: 10.3897/rio.11.e177547

Authors: Elisaveta Kozhuharova

Abstract: The decline of wild bees is a hazard to both agricultural products and biodiversity. Since the problem, in general, is of anthropogenic origin, society must be well-informed and educated, so that adequate actions can be taken. This is valid, particularly for the future generation. The aim of this study is to investigate 1) the knowledge of children about bees and their role in the ecosystems and 2) which information sources do children rely on, and how do they assess their credibility. An interview was conducted with 60 children aged between 6 and 12. The study reveals that knowledge of facts about bees is limited. Although 70.0% of children know that bees are “useful and necessary”, and 78.3% of children think that “plants need bees”, they generally do not understand their role in ecosystems. Therefore, education about biodiversity conservation is crucial. The challenge for researchers and educators is to present well-adapted information about bees to children, with a special focus on wild bees. Media literacy is a bridge between the children and the digital world. It can be an efficient tool to create "an ecological way of thinking for biodiversity conservation" as a part of the children‘s personal value system. Children should be prepared to filter true from fake information. In the future they must be capable of advocating a competent citizenship position for biodiversity protection in policy making.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e182926

Authors: Richard Marijnissen, Dirk S. van Maren, Luis Garrote, David Santillan, Ana Iglesias, Subbiah Bharathi, Xavier Sánchez-Artús, Vicente Gracia, Manuel Espino, Agustín Sánchez-Arcilla, Luciana Villa Castrillon, Benjamin Jacob, Johannes Pein, Wei Chen, Joanna Staneva, Pushpa Dissanayake, Dennis Oberrecht, Andreas Wurpts, Reinier Schrijvershof, R.J.A van Weerdenburg, Frederica Zennaro, Fabienne Horneman, Elisa Furlan, Silvia Torresan, Andrea Critto, Christophe Briere, Julien Fornasari, Rémi Caillibotte, Claire Mahe, Alexis Beudin, Rosaria Ester Musumeci, Massimiliano Marino, Sofia Nasca, Ahmad Alkharoubi, Luca Cavallaro, Enrico Foti, Nikolay Valchev, Petya Eftimova, Elitsa Hineva, Nataliya Andreeva, Grzegorz Różyński, Morgane Jolivet, Thomas Faraon, Olivier Boutron, Mathis Cathala

Abstract: Within this portfolio of restoration interventions, we present a range of model-based projections assessing the impact of large-scale Nature-based Solutions (NbS) on enhancing Eco System Services (ESS) in various coastal systems. This deliverable applies these models to detail how these systems respond to climate change and nature-based interventions intended to mitigate climate change impacts under different Sea Level Rise (SLR) scenarios. The models range from hydro-morphological simulations of future conditions to a machinelearning approach, all aimed at demonstrating the ESS provided by restoration in the future.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e182902

Authors: Manuel Espino, Vicente Gracia, Xavier Sánchez-Artús, Maria Liste, Luis Garrote, David Santillan, Ivan Federico, Causio Salvatore, Fabienne Horneman, Silvia Torresan, Elisa Furlan, Grzegorz Różyński, Luciana Villa Castrillon, Joanna Staneva, Benjamin Jacob, Wei Chen, Bas van Maren, Richard Marijnissen, Andreas Wurpts, Pushpa Dissanayake, Rosaria Ester Musumeci, Massimiliano Marino, Petya Eftimova, Nikolay Valchev, Elitsa Hineva, Nataliya Andreeva, Bogdan Prodanov, Rémi Caillibotte, Christophe Briere, Soazig Mahe, Julien Fornasari, Agustín Sánchez-Arcilla

Abstract: nature-based approaches, while reinforcing connectivity from river basins to the sea. Deliverable D2.2 is the second technical output of Work Package 2 (WP2), building upon the storm-based modelling work presented in D2.1. While D2.1 focused on current hazard conditions and model calibration, this deliverable explores future scenarios of sea level rise, changing sediment dynamics, and increasing storm impacts. It evaluates the long-term performance of Nature-Based Solutions (NbS) through integrated hydromorpho-eco modelling and assesses their contribution to ESS delivery across seven REST-COAST pilot sites. This report supports the development of adaptive restoration strategies tailored to local contexts, while contributing to broader coastal management frameworks under climate change. By combining physical process modelling with ecological indicators and socio-economic relevance, D2.2 provides robust evidence to guide nature-based adaptation pathways across Europe’s diverse coastal systems.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e182685

Authors: Aafke Schipper

Abstract: The EU Biodiversity Strategy for 2030 aims to put biodiversity on the path to recovery by 2030. A key component of the Strategy is the development of a coherent Trans-European Nature Network (TEN-N), to increase the coherence of the existing network of Natura 2000 sites and other nationally designated protected areas by addressing gaps in the coverage of priority habitats and species. The NaturaConnect project supports the design of a TEN-N, amongst others by designing and developing a future-proof blueprint through spatial conservation prioritisation. In this context, it is key to consider multifunctionality, that is, to ensure that the TEN-N addresses not just ecological representativeness but also the ability of nature to meet societal needs or demands through the provisioning of ecosystem services (ES).The present deliverable of NaturaConnect (D4.2) provides a set of ES layers aligned with present and potential future land and climate conditions, designed for use in spatial conservation prioritisation. We generated layers for a selection of regulating and cultural ES, with a focus on climate change mitigation (carbon storage and sequestration) and adaptation (e.g., improving soil retention considering expected increases in the magnitude and frequency of heavy rainfall events), food security (crop pollination, pest control), as well as the capacity of nature to improve people’s mental and physical health by offering opportunities for recreation and experiencing nature. We quantified all ES based on common input data with regard to land systems and climate, to ensure compatibility. Where possible and relevant, we considered ES supply, demand and flow separately.We quantified carbon storage and sequestration according to a book-keeping approach, assigning typical values of the amounts of carbon stored (MgC/ha) and sequestred (MgC/ha/yr) to each land system. We considered only the supply of carbon storage and sequestration, reasoning that the demand for this service is global and considerably larger than the supply. The amounts of carbon stored and sequestered are based on values from the scientific literature and existing datasets which indicate how much carbon is stored and sequestered per land system, and how this would change if the land system underwent a transition (e.g. from forest to cropland). Output maps revealed that forests and wetlands, especially in northern Europe, are characterised by the highest carbon storage and sequestration rates. Croplands are characterised by negative sequestration rates, hence act as sources of emission.We quantified the supply of soil retention based on the ability of vegetation to prevent soil erosion induced by heavy rainfall events, using the universal soil loss equation (RUSLE) to assess soil erosion. Specifically, we quantified the soil retention service (t/ha/yr) based on how much soil loss is prevented by the current vegetation cover, defined per land system, as compared to a counterfactual situation without vegetation. We also quantified the potential additional prevention of soil loss (t/ha/yr) if the vegetation were restored from its current state to a maximum cover. We defined soil retention demand based on the amount of soil loss to be prevented in order to ensure that losses would not exceed the natural soil formation rate. Output maps revealed hotspots of actual and potential additional soil retention demand, supply and flow mainly in mountainous regions, reflecting the key role of terrain slope in determining erodibility as well as the importance of vegetation for reducing it.We modelled the supply of crop pollination based on the potential of pollinator habitat to provide pollinators and the demand based on the presence of nearby cropland in need of pollination. Using observational data from scientific literature and existing databases, we first established a quantitative relationship that estimates wild pollinator abundance in pollinator-dependent cropland (n/m2) based on various ecologically relevant covariates, including the proportion of pollinator habitat within 3 km from the cropland cell. We used this relationship to map pollinator abundance in croplands across Europe, which we subsequently attributed to the cells with pollinator habitat (i.e., the service-providing units) within 3 km from each focal cropland cell, to facilitate application of the model results in spatial conservation prioritisation. Output maps reveal high pollinator abundance values for habitat cells located in areas dominated by cropland, as these habitat cells serve multiple cropland cells, and low values when multiple habitat cells surround a single cropland cell.To assess forest recreational potential, we developed a spatial model based on people’s preferences for forests with different structural characteristics, expressed through the willingness-to-travel (WTT) indicator. Using data from a large-scale visual choice experiment conducted in 12 European countries, we estimated WTT as a function of forest management classes, combined with spatial data on canopy height and tree species diversity. The result is the first Europe-wide map of forest recreational potential, revealing particularly high values in regions with taller, more diverse, and structurally complex forests.We modelled landscape recreational potential based on the recreational opportunities associated with the land systems surrounding each grid cell. We quantify supply based on the number and diversity of land systems that provide recreational opportunities within a given distance from each focal grid cell, and the demand based on the number of potential beneficiaries within a certain distance. Well-supplied areas encompass, among others, the western Iberian peninsula (Portugal) and the Pyrenees, the Auvergne, Rhone-Alpes, and the Provence-Alpes-Cote d’Azur in France, Ireland, Scotland, the Alps and Dinarides as well as the Baltics (Estonia, Latvia), and large parts of the Scandinavian Peninsula and Finland. Demand is particularly high for the European megacities and the various conurbations and metropolitan areas.Finally, we modelled nine regulating and five cultural species-based ecosystem services provided by terrestrial vertebrate species, including, among others, carrion removal, control of pest species (bark beetles, mosquitoes) and evolutionary heritage. For each service, we modelled supply based on the number of specific vertebrate species able to provide a certain service and demand based on the land system in a grid cell assumed to be in need of the service. Resulting maps show distinct patterns for the different ES, revealing the richness of provider species in areas with demand for each service.The ES layers described in this report were primarily developed to support broad-scale spatial conservation or restoration prioritisation efforts, i.e., efforts to identify and rank planning units (in this case grid cells) based on features considered in need of conservation or restoration. In the NaturaConnect project, the ES layers will be used together with layers of other relevant variables, such as biodiversity features, habitat connectivity and the costs of conservation, to identify pan-European conservation priorities. Beyond NaturaConnect, we expect our layers to be useful in particular for national and sub-national governmental and non-state authorities responsible for land planning, as our maps can help in identifying sites where ES supply or flow are high (indicating a need for conservation) or where demand is high yet supply is low (indicating a need for restoration). This way, we expect the layers and underlying code to be useful for informing land management and conservation planning also beyond the project.

HTML

XML

PDF

DOI: 10.3897/rio.11.e160367

Authors: Rajapreethi Rajendran, Claus Weiland, Jonas Grieb, Soulaine Theocharides, Sam Leeflang, Wouter Addink, Sharif Islam

Abstract: The Distributed System for Scientific Collections (DiSSCo) is a research infrastructure to integrate European natural science collections (NSCs) digitally. The aim is to facilitate and enhance the access, management and analysis of collection assets in one unified digital collection. The Machine Annotation Services (MAS) are essential components of DiSSCo’s Digital Specimen Architecture (DSArch). These services automate the annotation of digital objects to enable labelling and categorisation of NSC's digital assets.To further advance this, a Machine Learning as a Service (MLaaS) approach was developed which provides researchers with the access to pre-trained machine-learning models for complex tasks, such as instance segmentation and morphological analysis of datasets. MLaaS enhances the DiSSCo’s scalability and flexibility and allows the integration of machine-learning tools in close alignment with the FAIR (Findable, Accessible, Interoperable, Reusable) principles.This study employs DiSSCO's MLaaS framework for the quantitative analysis of herbarium specimens. Machine-learning models, such as Mask R-CNN and YOLO11, are comparatively applied to detect and generate the pixel-level masks of plant organs in herbarium sheets. Subsequently, these models are used to reconstruct the scale in the herbarium sheet and to calculate the surface area of identified plant organs.The determination of quantitative characteristics of plant specimens, such as measuring leaf area or the timestamp of the floral transition, opens up herbarium data for reuse in the large prognosis platforms currently developed in the framework of the Common European Data Spaces. In this way, plant trait data mobilised from natural science collections can improve the predictive capability of the vegetation model components of climate-related data spaces.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e182018

Authors: Manuel Espino, Luis Garrote, David Santillan, Xavier Sánchez-Artús, Vicente Gracia, Maria Liste, Marc Mestres, Manel Grifoll, Marta Balsells, Joanna Staneva, Benjamin Jacob, Wei Chen, Luciana Villa, Pushpa Dissanayake, Mindert de Vries, Ivan Federico, Causio Salvatore, Olivier Boutron, Christophe Briere, Rémi Caillibotte, Agustín Sánchez-Arcilla

Abstract: The REST-COAST project (Large-scale RESToration of COASTal ecosystems through rivers to sea connectivity) is a Horizon 2020 research initiative funded by the European Commission under Grant Agreement No. 101037097. Its overarching aim is to restore coastal ecosystems across Europe by advancing science-based approaches to hazard mitigation and resilience, with a strong emphasis on nature-based solutions (NbS) and the sustainable delivery of ecosystem services (ESS). To meet this objective, the project adopts a multidisciplinary approach that combines modelling, monitoring, restoration, governance, and finance. Scientific development is tightly linked to practical implementation through a network of pilot sites representing diverse coastal typologies and pressures. These sites serve as laboratories for testing and validating coupled hydro-morpho-eco models capable of simulating the role of natural ecosystems in reducing risks such as coastal flooding, erosion, and saline intrusion. This deliverable, D2.1, documents the modelling work conducted under Task 2.1, focusing on present-day storm conditions. It presents the model configurations, validation procedures, and simulation outcomes used to evaluate the risk reduction potential of NbS across seven pilot sites. The work includes detailed analysis of hydrodynamic and morphodynamic processes, sediment transport, and vegetation interactions, as well as the derivation of site-specific ESS indicators. The models are tailored to local physical settings and restoration goals, and have been validated against real storm events using field and remote sensing data. D2.1 provides a robust technical foundation for assessing the effectiveness and operational relevance of ecosystem-based approaches to coastal risk management. The methods and results presented here contribute to the broader REST-COAST objective of supporting adaptive, transferable, and evidence-based coastal restoration strategies throughout Europe.

HTML

XML

PDF

DOI: 10.3897/rio.11.e174988

Authors: Camille Cornet, Kay Lucek

Abstract: We present a chromosome-level genome assembly from a female specimen of the Common Brassy Ringlet Erebia cassioides (Arthropoda, Insecta, Lepidoptera, Nymphalidae). The genome consists of a primary assembly of 546 Mb and an alternate assembly of 406 Mb. The primary assembly is scaffolded into 11 chromosomes, including the Z and the W sex chromosomes. The mitochondrial genome has also been assembled, with a length of 15.19 kb.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e181365

Authors: Marie Alavi, Pascal Koch, Laura MacDonald, Katharina Miller, Gustav Nilsonne, Gustav Nilsonne, Julia Priess-Buchheit, Jörg Scherer, Lea Škorić, Pavel Stoev, Dina Vrkic, Stephen Wyber, Nikol Yovcheva, Cemre Yucebalkan

Abstract: Advancing knowledge valorisation to enable transdisciplinary and cross-sector knowledge circulation is key to upgrading the European research landscape, resulting in economic, digital, ecological, and social benefits. That is why IP4OS advocates for a concerted Intellectual Property (IP) and Open Science (OS) approach: A complementary and supportive link between agile and fitting IP tools and the sharing of Findable, Accessible, Interoperable, and Re-usable (FAIR) research outputs (data, results, codes, etc.). IP4OS's overall goal is to empower multi-professionals and their organisations with awareness, knowledge, skills, and advocacy to valorise FAIR research outputs with effectively fitting IP tools.Firstly, IP4OS will publish a sound Synergy Framework - a Best Practice Manual mapping the relationship between IP and OS, providing recommendations for best practices. Secondly, IP4OS raises 50% more awareness in the Community of Practice (CoP) by informing about advocates, facts and figures on IP tools that support OS practices. Furthermore, IP4OS will reach 300 trained professionals and additionally (at least) 27 multipliers for multi-professional teams from all European countries via several easy-to-use and sustainable educational resources using the Synergy Framework and the Synergy Core Curriculum. Through all of IP4OS’s activities, the project builds a new CoP for IP management to support OS and addresses 15 specific professions in training who are actors, intermediaries, educators, and learners in the R&I landscape.With this approach, IP4OS is fully in line with the objectives and impact expectations of the call, namely (1) to identify the complementary synergy of IP management and OS practices by building on existing resources and practices as well as through a co-creative process of a Multi-Professional Community of Practice including experts and actors of the R&I landscape and (2) to anchor these findings in practice-oriented learning resources and bring them into practice through specialised courses to a broad community. With this process, IP4OS follows the call's core objective: the cross-over empowerment of multi-professionals and their organisations to enrich their IP practices with useful OS principles, thus emphasising value creation and utilisation in IP management and increasing European Research Area’s (ERA) benefits.IP4OS comprises a consortium with complementary expertise from IP management, knowledge transfer and education, research, libraries, and experts from small and medium-sized enterprises (SME) covering legal aspects and dissemination activities. The International Expert Advisory Board (IEAB) comprises renowned representatives from IP and industry, OS, reproducibility, training, knowledge transfer, and entrepreneurship to support the consortium. IP4OS can meet its ambitious goals due to its consortium’s and advisory board’s IP and OS experience, their already established crossover networks and infrastructures, and outstanding expertise.

HTML

XML

PDF

DOI: 10.3897/rio.11.e179253

Authors: Ronny Gey, Daniel Mietchen, Oliver Karras, Tim Wittenborg, Moritz Schubotz, Jan Bumberger

Abstract: Across essentially all fields of research, many aspects of the respective research processes – whether experimental, theoretical, empirical or outright computational – are closely related to software. Yet the process of finding software that is directly suitable or at least a good starting point for a given research task is cumbersome.This project aims to develop a community-driven system that provides potential users of research software with a diversity of pathways towards actually finding software that closely matches their research needs if such software exists. Conversely, it will provide software developers with mechanisms to make their software findable for research-related tasks and it will highlight mismatches between software supply and demand for specific tasks.To this end, we will document how various stakeholders of the research landscape have been searching for – or stumbling upon – research software so far, identify variables associated with successful search outcomes and build workflows that assist in describing software and associated concepts in a standardised fashion. These descriptions will then be aligned across various sources of relevant information and integrated into Wikidata, the knowledge graph that anyone can edit and that already contains considerable breadth and depth of information related to research, software and their interactions.While keeping an eye on similar approaches to software discovery that might work in parts of the research ecosystem, existing Wikidata content and workflows will be reviewed and built upon. Additional documentation, tooling and workflows will be developed to enrich, expand, curate, query and explore this content, both for specific use cases and with ongoing engagement of the communities involved in research software, open data or collaborative curation. Within its three years, the project seeks to establish a dedicated community overseeing a well-documented and smoothly running infrastructure for software discovery and to devise a plan for how this can be sustained for the longer term.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e180864

Authors: Sara Si-Moussi, Marianne Tzivanopoulos, Gabrielle Deschamps, Maxime Hoareau, Julien Renaud, Rémi LEMAIRE-PATIN, Wilfried Thuiller

Abstract: This deliverable outlines the creation of high-resolution (1km²) distribution maps for species and habitats across Europe, crucial for biodiversity conservation, policy compliance, and ecosystem management. Employing advanced Species Distribution Models (SDMs) and Habitat Distribution Models (HDMs), the task addressed plants, vertebrates, invertebrates, and all EUNIS Level 3 habitats.Species distribution modeling involved machine learning algorithms, carefully selected environmental variables, and spatially comprehensive occurrence datasets from GBIF, EVA, and other databases. Ensemble modeling techniques, spatial block cross-validation, and pseudo-absence generation ensured robust, reliable predictions, validated with metrics like True Skill Statistic (TSS).Habitat modeling similarly utilized environmental predictors (climate, topography, hydrography, geology, soil properties) alongside vegetation plot data from EVA and additional regional databases. Multi-class classification and ensemble forecasting methods provided high-quality predictive habitat maps validated externally and through cross-validation.Current and future scenarios (2050) were developed under varying climate and land-use trajectories (SSP1-RCP2.6, SSP3-RCP7.0), incorporating model uncertainty and expert-informed constraints. These maps support targeted conservation planning, monitoring programs, and decision-making, guiding efforts to enhance Europe's protected area network and biodiversity management.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e180863

Authors: Jeremy Dertien, Nikolaj Poulsen, Emmanuel Oceguera Conchas, Aimara Planillo, Virgilio Hermoso, Ana Ceia Hasse, Francisco Moreira, Rafaela Schinegger, Florian Borgwardt, Georg Gruber, Francesca Cosentino, Luigi Maiorano, Andrea Sacchi, Luca Santini, Néstor Fernández

Abstract: This report presents European-level terrestrial and freshwater connectivity data combining structural and functional connectivity approaches to (1) prioritise ecological connectivity for all terrestrial vertebrates, (2) assess the structural connectivity of hundreds of European Nature Information System (EUNIS) habitat types, and (3) prioritise continental corridors in river and riparian ecosystems. We designed advanced workflows for large-scale connectivity assessments in Europe and produced information that can support conservation planning at multiple levels of governance.We combined omnidirectional circuit and graph-based models to prioritise ecological corridors for 953 different terrestrial vertebrate species categorised into 30 archetype groups. These functional connectivity outputs include raster and vector spatial information covering both continuous (wall-to-wall) connectivity data and discrete ecological corridors both at 1 km resolution. Results point to the importance of connectivity within key biogeographic regions and between large protected areas in mountainous areas with nearby smaller protected areas.We produced a consistent set of maps quantifying the structural connectivity of EUNIS terrestrial habitat types across Europe. We used a probability-weighted habitat fragmentation metric that extends the classical effective mesh size to incorporate continuous-field probabilities of habitat occurrence. These data include the structural connectivity of 232 different EUNIS habitat types at 100m resolution. Overall, forest habitat types were the most structurally well connected relative to the other habitat types like heathlands and grasslands.We followed a two-step process of structural connectivity and spatial prioritization methods to design a potential freshwater ecosystem corridor network. First, we estimated riparian and river structural connectivity and created a new database of continental freshwater barriers. Second, we identified freshwater corridors that would facilitate connectivity among protected areas and suitable habitat for all species, while minimising the number of longitudinal barriers that could compromise the functionality of the corridors. The identified barriers and riparian areas in poor condition could be the focus of future restoration efforts to maximise their freshwater connectivity and functionality.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e180508

Authors: Christopher John Topping, Noa Simon Delso, James Henty Williams, Johan Axelman

Abstract: EU chemical regulation remains slow, costly, and prone to “ecological surprises” such as unforeseen negative impacts, delayed neonicotinoid bans and ongoing pollinatordecline. Current approaches create silos, overlook cumulative impacts, and trap decisions in binary “safe/unsafe” categories.A systems-first, tools-second approach can deliver faster, cheaper, and more effective decisions by prioritising simulation and systems understanding before developing regulatory tools forEnvironmental Risk Assessment (ERA). Horizon Europe’s PollinERA project demonstrates how this can work in practice: building a prototype One Systemworkflow with interoperable data and models for pollinator risk assessment; an approach that can be expanded to other environmental domains.

HTML

PDF

DOI: 10.3897/rio.11.e177037

Authors: Christoph Steinbeck, Nicole Jung, Felix Bach, Steffen Neumann, Sonja Herres-Pawlis, Johannes Liermann, Oliver Koepler, Christoph Bannwarth, Theo Bender, Thomas Bocklitz, Franziska Boehm, Christian Bonatto Minella, Frank Biedermann, Werner Brack, Ricardo Cunha, Paul Czodrowski, Franziska Eberl, Thomas Engel, Albert Engstfeld, Tillmann G. Fischer, Pascal Friedrich, Frank Glorious, Benjamin Golub, Christoph Grathwol, Rainer Haag, Johannes Hunold, Christoph Jacob, Jochen Johannsen, John Jollife, Stefan Kast, Carsten Kettner, Stefan Kuhn, Giacomo Lanza, Jan Lisec, Georg Manolikakes, Ricardo Mata, Jens Meiler, Matthias Müller, Ralph Müller-Pfefferkorn, Jochen Ortmeyer, Wendy Patterson, Jürgen Pleiss, Annalisa Riedel, Jens Riedel, Ulrich Schatzschneider, Leonie Schuster, Peter Seeberger, Johann-Nikolaus Seibert, Peter Stadler, Philip Strömert, Robert Strötgen, Patrick Théato, Nicolas Tielker, Pierre Tremouilhac, Hans-Georg Weinig, Wolfgang Wenzel, Kirsten Zeitler

Abstract: The first funding period of NFDI4Chem established a robust foundation for research data management (RDM) in chemistry by promoting FAIR data principles and creating a cohesive infrastructure to capture well-annotated data early in the lab through electronic lab notebooks (ELNs) and making this data available in public repositories. Key achievements include standardised data formats and metadata, a federated repository environment, and improved data visibility and accessibility. Training programs and outreach have significantly increased awareness and adoption of best RDM practices. In the second funding period, the consortium aims to advance these achievements by consolidating this infrastructure, developing a model for its sustainable maintenance and operation, and fostering cultural change for its widespread adoption. Goals include ensuring seamless data workflows from laboratories to open repositories, enhancing interoperability, and supporting innovative research through AI-ready data. The work plan is organised into six task areas (TAs). TA1 (Management) provides leadership and supports all other TAs in achieving their objectives. TA2 (Smart Lab) aims to develop a fully digital research environment, including an ELN as a modular platform. This environment will support data collection, management, storage, analysis, and sharing. Integrating devices and external resources will enable seamless data transfer to repositories. TA3 (Repositories) will consolidate the repository ecosystem. The goal is to integrate repositories into a federated system for better accessibility and interoperability, ensuring long-term data availability and sustainability. TA4 (Metadata, Data Standards, and Publication Standards) focuses on developing and promoting new data and metadata standards in an international community process. This includes applying ontologies to create a semantic foundation for linking research data, making it machine-readable and enabling knowledge graphs. TA5 (Community and Training) is dedicated to fostering a cultural shift towards digital chemistry through continuous engagement, collecting requirements, and providing extensive training and support through workshops and open education resources. It will promote FAIR-compliant machine learning applications, embedding RDM into academic curricula to ensure future scientists are well-versed in these practices. TA6 (Synergies and Cross-Cutting Topics) aims to enhance collaboration across NFDI consortia and beyond. This includes developing ontologies, terminology services, the search service, and other cross-cutting solutions, integrating these developments into existing infrastructure, enabling interdisciplinary data harmonisation and fostering machine learning applications.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e179513

Authors: Christopher John Topping, Johan Axelman

Abstract: A technical support document for the PollinERA Policy brief

HTML

XML

PDF

DOI: 10.3897/rio.11.e175726

Authors: António Jorge do Rosário Cruz, Fernanda Herrera-Mesías, Anna Hauprich, Dylan Thissen, Alexander Weigand

Abstract: The ultimate goal of the beelibre project is to provide a kind of “one-stop-shop” online resource, hosting within a single multi-lingual website (beelibre.lu) relevant information concerning the wild bee fauna of Luxembourg. This website will provide free and immediate access to information on the taxonomy, natural history and geographical distribution of the over 350 species of wild bees species recorded in Luxembourg. For this purpose, four sections (a.k.a “libraries”) are hosted within the website: i) a database of high-quality images taken from live bees and museum specimens (for morpho-taxonomic identification and outreach); ii) a bibliographic repository of all nationally relevant publications (for metadata analysis and knowledge exchange), incl. short summaries; iii) a pollen inventory pilot experiment aiming to uncover potential ecological interactions between regional host flowering plants and their associated wild bee pollinators and iv) a DNA barcode reference library of wild bee species from Luxembourg currently lacking reference material in BOLD systems (for molecular taxonomic identification).This initiative to produce and transfer knowledge about wild bees is aligned with Luxembourg's national action plan for pollinators and contributes directly to reducing knowledge shortfalls in relation to European bees. Therefore, all materials will be freely available to both researchers and the general public, socialising scientific knowledge to a wider audience and raising awareness on national pollinator biodiversity. With this initiative, we aim to provide a space that combines past efforts with current technology, building a platform that can be used to further assist and develop national conservation strategies protecting the wild bee fauna of Luxembourg.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e177889

Authors: Serena Rasconi, Ana Gavrilović

Abstract: Abstracts of talks presented at ParAqua Grantees Conference held in Zagreb (Croatia), 1-2 September 2025

HTML

XML

PDF

DOI: 10.3897/rio.11.e176476

Authors: Tina Heger, Stella Berger, Jonathan Jeschke, Chris Kittel, Peter Kraker, A. Makower, Daniel Mietchen, Jens Nejstgaard, Maxi Schramm

Abstract: Water is vital for life on Earth, but aquatic environments worldwide are facing critical challenges that cause severe problems for biodiversity and human well-being. These challenges include, for example, water pollution, habitat degradation, escalating water and air temperatures, salinisation of freshwaters, ocean acidification and invasive species. Since these stressors interact in complex ways, developing predictions and mitigation measures is difficult. Mesocosm experiments, offering controlled, yet realistic settings, are crucial for understanding and mitigating the impact of various stressors and their combinations on aquatic ecosystems. Mesocom facilities are key Research Infrastructures (RI), as they bridge the gap between laboratory experiments and natural systems allowing studies of highly complex environments comparable to natural ecosystems, while still offering controlled and replicated settings not available in natural systems.The AQUACOSM-RI consortium, comprising over 60 individual state-of-the-art mesocosm facilities at 28 host institutions across Europe, has therefore been instrumental in advancing aquatic environmental research across climate zones including marine, brackish and freshwater ecosystems. In addition, the EU H2020-INFRAIA projects AQUACOSM (CORDIS No. 731065) and AQUACOSM-plus (CORDIS No. 871081, www.aquacosm.eu) have developed a virtual network beyond Europe of presently > 85 host institutions with > 120 aquatic mesocosm facilities around the world, www.mesocosm.org. However, the rich, yet disconnected resources in aquatic mesocosm-based experimental research and mitigation approaches need to be combined in a modern, visible and accessible way.The project AQUANAVI (Navigating Grand Challenges and their Mitigation using Aquatic Experimental RIs) aims to enhance existing efforts by creating an interactive atlas of aquatic mesocosm facilities and related mesocosm-based experimental research. Integrating data, publications, reports and information on mesocosm facility capacities generated by the AQUACOSM consortium and other mesocosm facilities in Europe and beyond, AQUANAVI will facilitate fast discovery of resources and unused potentials of available mesocosm facilities in a modern, visible and accessible way that is presently not available. Such a multidimensional tool is expected to enable novel collaborations and a much faster setup and execution of connected and/or distributed experiments and efficient development of environmental mitigation strategies. Built upon the AQUACOSM-RIs and their encompassing data and information repository as well as scientific and technical competence, while also leveraging related infrastructures like AnaEE, EMBRC, JERICO-RI and eLTER, AQUANAVI will provide a comprehensive resource platform to more effectively explore available resources for aquatic experimental research.AQUANAVI will bridge this wealth of scientific data, expertise and mesocosm facility information through Hi Knowledge, an innovative analysis and visualisation platform that merges Wikidata, Open Knowledge Maps,and Scholia. Hi Knowledge harnesses the semantic capabilities of Wikidata to rapidly construct a FAIR and open corpus for a domain, based on a sophisticated conceptual classification system. Subsequently, Hi Knowledge incorporates visualisation components from Open Knowledge Maps and Scholia, allowing researchers to smoothly navigate information using cutting-edge visualisation techniques, artificial intelligence and knowledge synthesis methods.Open and collaborative by design, AQUANAVI’s architecture will engage a broad range of research communities. By consolidating data and information from diverse RIs, the platform will leverage and enhance the AQUACOSM and related research infrastructures, securing the reusability and interoperability of existing data collections and better exploration of existing RIs in the future. Compliant with FAIR principles and EOSC requirements, AQUANAVI will ensure the long-term sustainability and openness of its resources, enriching both the ENVRI services portfolio and the broader scientific community. In summary, AQUANAVI will empower researchers and stakeholders to implement measures to mitigate the effects of climate change and other Grand Challenges facing aquatic environments, serving as a key resource within and beyond the European research area.

HTML

XML

PDF

DOI: 10.3897/rio.11.e176120

Authors: Christos Arvanitidis, Olga Ameixa, Alberto Basset, Eva Chatzinikolaou, Claudia Coman, Berta Companys, Francesco De Leo, Klaas Deneudt, Federico Drago, John Eriksson, Tiziana Ferrari, Teodor Georgiev, Giovanni Giuliano, Stefan Gruber, Jens Habermann, Katharina Heil, Tim Hubbard, Cristina Huertas Olivares, Georgios Kotoulas, Dimitris Koureas, Natalia Manola, Vanessa Marrocco, Nicolas Pade, Ana Portugal Melo, Antonello Provenzale, Fotis Psomopoulos, Niels Raes, Susie Robinson, Patrick Ruch, Dick Schaap, Adrian Stanica, Tassos Stavropoulos, Heliana Teixeira, Peter van Tienderen, Costas Tsigenopoulos, Robert Waterhouse, Giuseppe Aprea, Michel Boër, Ana Casino, Laurent Delauney, Jonathan Ewbank, Ana Lillebø, Michael Mirtl, Jana Pavlic-Zupanc, Lyubomir Penev, Jaume Piera, Paraskevi Pitta, Ingrid Puillat, David Richter, Diana Stepanyan, Anton Ussi, Jan Węsławski, Gabriela Zuquim

Abstract: The interdependence of human, animal, plant and ecosystem health necessitates systemic, cross-domain collaboration to address global challenges, such as emerging diseases, climate change and biodiversity severe change. Through the Crete Declaration, Europe’s (e-)infrastructures, organisations and projects that focus on the functioning of our biosphere commit to jointly advancing the One Health approach. In doing so, the signatories aim to strengthen Europe’s resilience and leadership through the sharing of data and expertise, the development of innovative solutions and the promotion of evidence-based policies.

HTML

XML

PDF

DOI: 10.3897/rio.11.e174994

Authors: Bernabé Moreno, Lloyd Peck, Melody Clark, Katherine Dunlop, David Barnes, Bodil Bluhm, Markus Molis, Amanda Ziegler, Jack Longsden, Ainsley Hatt, Èric Jordà Molina, Terri Souster

Abstract: Predicting how benthic assemblages respond to ocean warming remains a central challenge in marine ecology. Artificial units of habitat such as settlement plates have long been used to study marine lithophilic assemblage dynamics under natural and experimental conditions. Recently, heated settlement plate (HSPl) experiments have been deployed in polar and temperate seas to simulate likely near-future thermal regimes in situ. We convened a one-day hybrid workshop bringing together researchers who pioneered HSPl approaches with a broader international community of benthic researchers including project managers, senior scientists and early career researchers. The workshop aimed to: i) share experiences and outcomes from existing HSPl deployments; ii) identify technical and logistical challenges; iii) prioritise emerging research questions and applications; and iv) scope pathways for future collaborations and funding. Participants outlined desirable minimum standards for imaging and metadata in HSPl photosampling, compared design choices and replication strategies; and highlighted context-specific considerations for polar vs. temperate sites (e.g. ice scouring, permitting frameworks, diver safety considerations). A preliminary research agenda was developed spanning community assembly processes, trait-mediated responses, priority effects under warming and the integration of HSPl imagery with automated pipelines for analysis and data FAIRness. The workshop represents a first step towards building a cohesive global network to coordinate cross-site experiments, promote open protocols and data sharing and enable meta-analyses that will strengthen the understanding of how marine environmental change affects lithophilic assemblages across ecosystems.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e175173

Authors: Cristina Galván, Elvira Ramos, Araceli Puente

Abstract: Coastal zones are complex socio-ecological systems that present significant challenges for sustainable management. In this study, a bow-tie approach was applied to the coast of Cantabria to analyse the connections between drivers of change, biodiversity loss, and socio-economic consequences. The two most prominent drivers identified by stakeholders were large-scale tourism and harbour infrastructure development. These were associated with biodiversity impacts, including species and habitat loss, and the spread of non-native invasive species facilitated by human activities. Stakeholders and scientists identified multiple consequences of biodiversity change across ecological, social, economic, and governance dimensions. Based on the bow-tie analysis, a set of prevention and mitigation measures was proposed to enhance governance responses and reduce biodiversity-related damage in the study area.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e174999

Authors: Toke Thomas Høye, Mario V Balzan, Simon Potts, Oliver Schweiger, Pavel Stoev

Abstract: Pollinators are critical to Europe’s biodiversity, food security, and ecosystem resilience. Yet, their populations are declining due to habitat loss, climate change, and pesticide use. Under Article 10(2) of the Nature Restoration Regulation, Member States must improve pollinator diversity and reverse the decline of pollinator populations at the latest by 2030 and thereafter achieve an increasing trend of pollinator populations, measured at least every six years from 2030, until satisfactory levels are achieved. The MAMBO project (Modern Approaches to the Monitoring of Biodiversity) can potentially contribute to this goal through its development and demonstration of cutting-edge technologies, including artificial intelligence (AI) and insect camera traps, that can support how pollinators are monitored across Europe. This policy brief outlines MAMBO’s innovations, highlights emerging opportunities, and recommends actions for integrating these tools into EU PoMS.

HTML

XML

PDF

DOI: 10.3897/rio.11.e171656

Authors: Daniel Mietchen, Sheeba Samuel

Abstract: Computational notebooks like Jupyter have transformed scientific and educational workflows in computational fields by combining code, text, and visualizations. They have also become a popular mechanism to share computational workflows. However, ensuring their reproducibility remains a persistent challenge due to often insufficiently documented direct and indirect dependencies, missing data, and inconsistencies in execution environments. Existing datasets lack the multimodal, fine-grained structure needed for AI applications. FAIRJupyter4AI aims to address this gap by creating a large-scale, AI-ready corpus of Jupyter notebooks enriched with executable code, markdown, outputs, and structured annotations. The project integrates these into a hybrid knowledge graph (KG) that incorporates symbolic, statistical, and execution-based representations. Key objectives include: curating diverse notebooks (initially Python, later R, with provisions for additional languages); automating reproducibility testing; building a KG for cross-notebook queries; training AI models for tasks like error repair and notebook generation; and fostering community use via APIs and integration with community platforms like NFDI or Hugging Face.The project will be implemented using the infrastructure established by the NFDI Basic Service Jupyter4NFDI, in the upcoming Integration Phase of which (October 2025-September 2027) the applicants are actively involved. Its central JupyterHub provides cross-consortial and cross-institutional access to scalable computing and data resources and associated software stacks for both research and training purposes.The FAIRJupyter4AI work programme is structured around five interlinked work packages: (1) Data Collection & Curation, (2) Reproducibility Assessment, (3) Knowledge Graph Development (4) AI Model Training, and (5) Communication, Community & Sustainability. Key innovations include continuous updates and enrichment pipelines (avoiding static snapshots), unifying multimodal content for AI, and bridging reproducibility with AI. Building on prior work involving 27,000+ notebooks and the FAIR Jupyter Knowledge Graph, FAIRJupyter4AI will curate, annotate and release over 20,000 notebooks that are research-related and openly licensed. In addition, we will share a metadata corpus for 50,000 research-related notebooks, along with open-source tools, models, and associated documentation. By making Jupyter notebooks metadata FAIR, reusable, and machine-understandable, this project will set a new standard for reproducible and AI-enhanced computational science, and it will open up new opportunities for learning and teaching about computational reproducibility across multiple domains of research.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e173903

Authors: Cristina Galván, Elvira Ramos, Araceli Puente

Abstract: Coastal zones are complex socio-ecological systems that present significant challenges for sustainable management. In this study, a bow-tie approach was applied to the coast of Cantabria to analyse the connections between drivers of change, biodiversity loss, and socio-economic consequences. The two most prominent drivers identified by stakeholders were large-scale tourism and harbour infrastructure development. These were associated with biodiversity impacts, including species and habitat loss, and the spread of non-native invasive species facilitated by human activities. Stakeholders and scientists identified multiple consequences of biodiversity change across ecological, social, economic, and governance dimensions. Based on the bow-tie analysis, a set of prevention and mitigation measures was proposed to enhance governance responses and reduce biodiversity-related damage in the study area.

HTML

XML

PDF

DOI: 10.3897/rio.11.e172117

Authors: Grigorios Skouradakis, Thanos Dailianis, Panayota Koulouri

Abstract: This study performs a bow-tie analysis concerning biodiversity change in the Broad Belt Transect of Heraklion Bay (BBT12) in the framework of MARBEFES project. Heraklion Bay is currently undergoing changes mostly due to climate change, tourism and urbanisation. This affects the marine environment via marine heat waves, mass mortality events and tropicalisation. Introduction of invasive species is on the rise in the area and together with the transformation of typical Mediterranean rocky reefs to barren reefs is leading to an ecosystem shift and significant changes in biodiversity. In addition, tropicalisation can also be linked to the reduction of marine biological resources affecting the local fisheries. Furthermore, recent studies of macrobenthic communities of soft-bottom habitats in the area contribute to understanding the spatial and temporal trends and changes in biodiversity due to multiple environmental and human-induced disturbances. These changes reduce the ecosystemic resilience and can affect ecosystem services we take for granted. Within the framework of the project, stakeholders of Heraklion BBT have been surveyed and interviewed and their views concerning balance between nature, society and economy have also been incorporated into the bow-tie analysis. Their main concern for Heraklion BBT is the extensive development of large-scale tourism in the area. All these pressures have negative effects on the marine environment of the area and socio-economic impacts on the population of the area. Having this in mind, prevention and mitigation measures are presented.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e173693

Authors: Tom Breeze, W. Daniel Kissling, Maria Lumbierres, Joana Santana, Alejandra Morán-Ordóñez, Roy Van Grunsven, Tim Hirsch, Tree Robionson, Simon Potts, Ian McCallum, Ute Jandt, Cesar Capinha, Jessica Junker, Pavel Stoev, Camino Liquete, Henrique M. Pereira

Abstract: Although biodiversity monitoring costs are widely cited as a constraint, there have been very few assessments of these costs and even fewer studies have assessed the potential benefits of this monitoring. Here, we synthesise available evidence, alongside a comprehensive assessment of the costs of proposed biodiversity monitoring to explore the relative costs, benefits risks and opportunities in biodiversity monitoring. We find that the costs of biodiversity monitoring, €0.5bn-€3.6bn/year, are greatly outweighed by the combined economic benefits and opportunities arising from the availability of co-ordinated, high-quality data, which are estimated to be >€25.2bn/year.

HTML

XML

PDF

DOI: 10.3897/rio.11.e171643

Authors: Kesang Wangchuk

Abstract: The International Center for Integrated Mountain Development (ICIMOD) organised a two-day consultative workshop in Phuntsholing, Bhutan, focusing on human-wildlife conflict (HWC) management in the Himalayan mid-hills, a region often overlooked in favour of the foothills where human-elephant conflicts dominate. The workshop brought together key officials from Bhutan, India and Nepal to synthesise discussions across five thematic areas: Gender and Social Inclusion (GESI), Stakeholders and Partnerships, Risk Management, Monitoring and Evaluation (M&E) and Sustainability and Scaling of Solutions.The meeting highlighted stark gender disparities in HWC impacts, with women disproportionately affected due to their roles in resource collection and agriculture, yet marginalised in decision-making. Socio-cultural norms, caste hierarchies and financial constraints further restricted their participation. Children, the elderly and persons with disabilities also faced heightened risks. Stakeholder mapping identified NGOs, international donors, the private sector and media as crucial partners in mitigation, with varying degrees of involvement across countries. Risk management strategies emphasised species-specific deterrents, gender-inclusive rapid response teams and landscape-level interventions.Community-driven M&E systems, supported by technology (e.g. drones, AI cameras), were deemed essential for tracking conflict trends and intervention effectiveness. Sustainability hinged on strengthening local ownership, assured funding and policy integration. Persistent challenges included gender inequity, conflicting stakeholder interests and weak M&E systems. Future directions advocate for institutional reforms (e.g. gender quotas), alternative livelihoods and transboundary collaboration. The workshop underscored the need for inclusive, adaptive strategies to foster sustainable human-wildlife co-existence in the Himalayan mid-hills.

HTML

XML

PDF

DOI: 10.3897/rio.11.e163817

Authors: Laurel Haak, Katherine Skinner, Kristen Ratan

Abstract: Research activities utilise and depend on interlocking infrastructures – tools, standards, protocols, and other systems and structures at local, national, and international scales that enable researchers to collaborate, analyze and share data and software, and discuss their research findings. Despite growing policy momentum towards open science, a significant challenge persists: a substantial portion of research infrastructure remains inherently closed or restrictive. This lack of openness undermines transparency, integrity, limits reproducibility, and constrains researchers’ ability to fully engage with each other. In this paper, we examine how research infrastructures can be designed to embed open principles throughout their development and operation, borrowing elements from Manufacturing Principles, Systemic Service Design, and Open Science frameworks. We propose an open-by-design reference framework for infrastructure builders and guidance for enabling, making visible, and incentivizing specific elements of “openness” within research infrastructures that are prerequisites for a thriving research and knowledge ecosystem.

HTML

XML

PDF

DOI: 10.3897/rio.11.e169264

Authors: Talia Karim, Erica Krimmel, Holly Little, Lindsay Walker

Abstract: A two day cyberinfrastructure alignment workshop was held in May 2025 as part of the "Community-driven enhancement of information ecosystems for the discovery and use of paleontological specimen data" project, which is funded under the United States National Science Foundation (NSF) Geosciences Open Science Ecosystem (GEO OSE) programme. Participants with expertise in informatics, technical cyberinfrastructure development and management and geo- and biological sciences were invited to foster a shared and increased understanding across this broad-community of the needs for palaeontological specimen data. This report describes the activities and outcomes of the workshop and how they will contribute to final deliverables for the grant funded project.

HTML

XML

PDF

DOI: 10.3897/rio.11.e163757

Authors: Geraint Tarling, E Abrahamsen, Yevgeny Aksenov, Madeline Anderson, Carol Arrowsmith, Chelsey Baker, Chris Barry, Anna Belcher, Mar Benavides, Milo Bischof, Emma Boland, Mike Bowes, J Brearley, Peter Brown, Amanda Burson, Sammie Buzzard, Nathan Callaghan, Arthur Coët, Kathryn Cook, Sarah Coombs, Chris Evans, Sophie Fielding, Elaina Ford, Isabelle Fournier, Jennifer Freer, E Garcia-Martin, VR Ghosh, Sarah Giering, Alanna Grant, Huw Griffiths, Ruta Hamilton, Katharine Hendry, Simeon Hill, Nathan Hubot, Aidan Hunter, Nadine Johnston, Anna Katavouta, Ezra Kitson, Melanie Leng, Isabel Lewis, Katrin Linse, Stephen Lofts, Clara Manno, Adrian Martin, Alice Marzocchi, Edward Mawji, Daniel Mayor, Rebecca McKenzie, Andrew Meijers, Michael Meredith, David Munday, M Pereira, Alexandra O'Brien, Justyna Olszewska, Stuart Painter, Julien Palmiéri, Shailee Patel, Amy Pickard, Jessica Richt, Stefanie Rynders, Rachael Sanders, Ryan Saunders, Andrew Shepherd, Thomas Slater, Bryan Spears, Gabriele Stowasser, Amy Swiggs, Laura Taylor, Petra ten Hoopen, Sally Thorpe, Tracey Timms-Wilson, Maud van Soest, Hugh Venables, Zoe Wright, Andrew Yool, Emma Young

Abstract: The export of elements (particularly carbon, nitrogen and phosphorus) from the Poles critically supports global marine biodiversity and major fisheries as well as the sequestration of atmospheric carbon to the deep ocean. Ecosystem processes regulate this export, but major uncertainties remain in terms of how and by how much. Progress on understanding key ecosystem interactions is hindered by lack of data and their representation in Earth system models is poor. The two polar regions share similarities in environmental extremes which make them sensitive to the impacts of climate change. They both receive nutrients from multiple and diverse sources and the delivery of these nutrients to other oceans is regulated by similar ecosystem processes. However, the extent to which these ecosystem processes will be modified by climate change is unclear and urgently needs to be determined. BIOPOLE will determine how polar ecosystems regulate the balance of carbon and nutrients in the world’s oceans and, through it, their effect on global fish stocks and carbon storage. It will address this challenge by integrating ambitious fieldwork campaigns and innovative modelling in a multidisciplinary and highly coordinated approach. BIOPOLE will capitalise on world-leading capabilities and infrastructure in ocean and high-latitude research, including cutting-edge land-based facilities, state-of-the-art polar research vessels and innovative autonomous instrumentation. Collaboration with national and international partners will further strengthen BIOPOLE’s multidisciplinary approach and efficient use of infrastructure. BIOPOLE’s legacy will be the first assessment of the global impact of polar ecosystems on biogeochemical cycling and fish stocks; technologically-novel approaches and strong partnerships between leading international science groups.

HTML

XML

PDF

DOI: 10.3897/rio.11.e168765

Authors: Christos Arvanitidis, Boris Barov, Montserrat Gonzalez Ferreiro, Gabriela Zuquim, Declan Kirrane, Cristina Huertas Olivares, Federico Drago, Nicolas Pade, Alberto Basset, Klaas Deneudt, Dimitrios Koureas, Natalia Manola, Daniel Mietchen, Ana Casino, Lyubomir Penev, Yannis Ioannidis

Abstract: This white paper represents the collective perspectives of a network of legal entities based in Europe and with global interests, which includes biodiversity, ecology, and engineering communities, aiming to strengthen Science, Technology, and Innovation (STI) efforts toward achieving the United Nations (UN) Sustainable Development Goals (SDGs). With their combined expertise and through European initiatives such as the Research Infrastructures, the e-Infrastructures, the European Open Science Cloud (EOSC), the Digital Twin projects and academic publishers, these communities provide a base for collaboration in strategically contributing to the implementation of the Kunming-Montreal Global Biodiversity Framework targets. Furthermore, these communities seek to forge an international alliance to further integrate biodiversity conservation into the UN Summit of the Future priorities and the post-SDG agenda.

HTML

XML

PDF

DOI: 10.3897/rio.11.e167869

Authors: Elena Delgado Rivera, Lucas de Moncuit, Christos Arvanitidis

Abstract: LifeWatch ERIC’s Gender Equality Plan (2025–2027) sets out a clear roadmap for promoting gender equality and equity throughout the organisation. As a continuation of the first plan published in 2022, this updated version introduces more focused and ambitious measures. It reflects LifeWatch ERIC's ongoing commitment to creating a fair, inclusive and respectful working environment for everyone, regardless of gender identity, sexual orientation, age, ethnicity, disability or other personal characteristics.The plan is aligned with the European Commission's requirements for Horizon Europe and aims to make gender aspects an integral part of our internal policies, decision-making, human resources and research activities. Rather than introducing separate or additional measures or programme, the GEP aims to reinforce the LifeWatch ERIC Culture Principle by integrating new measures with existing policies, procedures and best practices that have an impact on equality and diversity in the organisation. Ultimately, this plan goes beyond compliance and represents a broader commitment to organisational excellence, fairness and responsibility, recognising that true innovation can only occur when diversity is fully embraced and supported at all levels.

HTML

XML

PDF

DOI: 10.3897/rio.11.e164067

Authors: Sara Klingenfuß, Manuel John, Tuulikki Halla, Theresa Klara Loch, Philipp Mack, Barbara Meyers, Ronja Mikoleit, Taru Peltola

Abstract: The forest understory plays a central role in ecological processes and human experiences of forests, yet it often remains overlooked in forest management and conservation. In this interdisciplinary workshop, researchers from Finland and Germany came together to explore the understory through multiple lenses—ecological, cultural, social, and sensory. The participants acknowledged and discussed diverse forms of knowledge related to the understory, from scientific to traditional and place-based, to better understand the many ways people relate to it. Through shared readings, discussion, and direct engagement in the forest, we reflected on how the understory shapes foraging practices, sense of place, human–nature relationships, and alternative forest economies. We discussed what it means to "know" the understory, who holds this knowledge, and how it influences forest governance. This report brings together the key themes, questions, and ideas that emerged, highlighting the understory not only as a biological layer, but as a space where ecological, cultural and political dimensions meet. In doing so, we aim to provoke rethinking dominant forest perspectives and encourage more inclusive and relational ways of valuing and managing European forests.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e167290

Authors: Jurate Lesutiene, Andrius Šiaulys, Arturas Razinkovas-Baziukas

Abstract: This study employs a bow-tie risk analysis framework to examine four critical biodiversity loss processes in Lithuanian coastal waters: blue mussel decline, commercial fishery stock reduction, dune habitat loss, and eutrophication. The framework identifies human activities, resulting pressures, preventive controls, mitigation measures, and consequences across ecological, economic, and social dimensions. The analysis reveals distinct temporal patterns of risk occurrence. The invasive round goby caused rapid blue mussel eradication, with ineffective monitoring and preventive controls leading to habitat degradation and ecosystem service losses. Commercial fishery stocks, particularly cod and pikeperch, have experienced long-term decline due to overfishing combined with climate change impacts, resulting in economic losses and trophic cascade effects. Coastal dune habitats require continuous management to maintain their UNESCO cultural landscape status, with climate change and tourism presenting significant pressures. Finally, eutrophication remains a persistent challenge, with Lithuania still needing substantial nutrient reduction to meet Baltic Sea Action Plan targets. Climate change further complicates management efforts across all four areas. The study highlights the effectiveness of the bow-tie approach in integrating diverse stakeholder perspectives and identifying critical control points for biodiversity conservation and ecosystem management in coastal environments.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e167392

Authors: Anita Franco, Katie Smyth, Michael Elliott

Abstract: Marine biodiversity is adversely affected by many human activities and their pressures. As such, there is the need for a cause-consequence-response method to objectively address the risks associated with those adverse changes. Such a method is the ISO-accredited Bow-tie technique as an objective and structured approach giving the causes, preventative control measures, mitigation and compensation measures and consequences of changes to biodiversity. Here, the Bow-tie method underpinned by the cause-consequence-response DAPSI(W)R(M) framework was used and adapted to help managers map out risks to biodiversity requiring management of the human activities and their relevant pressures, in specific case study areas (termed Broad Belt Transects, BBTs). Instead of using restrictive proprietary software, a more-flexible template framework was developed in Microsoft PowerPoint to allow a broad user base. This employed standardised lists of elements (and further adapted during the application process) allowing the development of unique, but standardised and directly comparable Bow-ties for all BBTs. The methods of developing the template and standardised lists are described together with the techniques used to help quantify this usually qualitative approach. The successful application of the Bow-tie method in case studies from the European seas shows the adaptability of this approach in ways wider than the original policy-driven risk-assessment use. Although designed for European seas, the approach and standardised lists are sufficiently generic for adoption in wider areas worldwide.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e167014

Authors: Dorota Kołbuk, Julie Bremner, Ashley Cahillane, Valentina Di Gennaro, Tasman Crowe

Abstract: In this study we apply the bow-tie risk analysis framework to map the causes and consequences of decline or loss of five key Irish Sea ecosystem components: intertidal sandflats and mudflats, burrowing fauna including Dublin Bay prawn Nephrops norvegicus, blue mussel Mytilus edulis, commercially harvested fish, and wintering waterbirds. Main activities exerting multiple pressures on the Irish Sea ecosystem include energy production from offshore wind farms, tourism and leisure, fishing, transport, agriculture, urban and industrial uses, and waste treatment and disposal. All of them can contribute to decline in condition or loss of critical habitats and biota, leading to significant ecological, economic and sociocultural consequences. Understanding these consequences is essential for designing appropriate management responses. The bow-tie approach allows to identify management risks and highlights the most impactful control points for intervention to prevent or mitigate adverse biodiversity events.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e166451

Authors: Lorenzo Latini, Giorgio Massaro, Stefania Coppa, Jacopo Giampaoletti, Giuseppe de Lucia, Alessia Dinoi, Paolo Magni

Abstract: The Gulf of Oristano Area, located on the central-western coast of Sardinia (Italy, Mediterranean Sea), is a highly diverse and ecologically valuable region. This area features a mosaic of habitats, supports rich biodiversity, and sustains traditional fishing practices. It is also protected under various international and EU conservation frameworks. However, despite its ecological importance, the Gulf Area faces growing pressures from human activities such as overfishing, eutrophication, habitat loss, and the introduction of non-native species. This study applies a bow-tie risk analysis framework to identify key drivers, pressures, and consequences associated with three central ecological events: species decline and loss, habitat change, and increased competition with non-native species. Stakeholder consultations and standardized classification systems inform the assessment, highlighting the interplay between legal fishing, tourism, aquaculture, pollution, and infrastructure development. The analysis identifies both prevention and mitigation measures, such as spatial planning, environmental monitoring, citizen science, and sustainable tourism and fisheries initiatives. While the environmental regulation of the Gulf of Oristano Area provides a basis for ecosystem protection, persistent challenges – such as enforcement, fragmented governance, and low stakeholder engagement – hinder effectiveness. To ensure ecological integrity and socio-economic resilience in the central-western Sardinian coast, this study underscores the need for strengthened integrated coastal zone management, alignment with EU strategies, and investment in adaptive and participatory conservation approaches.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e165615

Authors: Elena Delgado Rivera, Christos Arvanitidis

Abstract: LifeWatch ERIC’s Gender Equality Plan (2025–2027) sets out a clear roadmap for promoting gender equality and equity throughout the organization. As a continuation of the first plan published in 2022, this updated introduce more focused and ambitious measures. It reflects our ongoing commitment to creating a fair, inclusive, and respectful working environment for everyone, regardless of gender identity, sexual orientation, age, ethnicity, disability, or other personal characteristics.The plan is aligned with the European Commission's requirements for Horizon Europe and aims to make gender aspects an integral part of our internal policies, decision-making, human resources and research activities. Rather than introducing separate or additional measures or programs, the GEP aim to reinforce the LifeWatch ERIC Culture Principle by integrating new measures with existing policies, procedures and best practices that have an impact on equality and diversity in the organization. Ultimately, this plan goes beyond compliance and represents a broader commitment to organizational excellence, fairness, and responsibility, recognizing that true innovation can only occur when diversity is fully embraced and supported at all levels

HTML

XML

PDF

DOI: 10.3897/rio.11.e165316

Authors: Quentin Groom, Tim Adriaens, Tom August, César Capinha, Ana Cardoso, Katharina Dehnen-Schmutz, Franz Essl, Alexandra Franklin, Marina Golivets, João Gonçalves, Louise Hendrickx, Dave Hodgson, Toke Høye, Philip Hulme, Sabrina Kumschick, Bernd Lenzner, Eva Malta-Pinto, Angeliki (F) Kelly Martinou, Sofie Meeus, Tom Myers, Nicolas Noé, Ana Novoa, Michael Pocock, Anna Poimala, Cristina Preda, Petr Pyšek, Lien Reyserhove, Laurentiu Rozylowicz, Anna Sapundzhieva, Cândida Vale, Joana Vicente, Nikol Yovcheva, Agnes Zolyomi, Helen Roy

Abstract: The overarching objective of OneSTOP is to pioneer an innovative and joined-up approach to biosecurity for terrestrial invasive alien species, strengthening the interconnections between animal, plant, human and environmental health. OneSTOP aims to harness current technologies and citizen science, while overcoming challenges posed by dispersed and fragmentary processes, policies, and knowledge, to deliver methods for identification, early detection and surveillance of invasive alien species. OneSTOP aims to achieve transformative results to minimise the introduction, establishment and spread of invasive alien species by integrating cutting-edge detection methods, underpinned by prioritisation and robust models, alongside stakeholder engagement to inform harmonised policies and facilitate knowledge exchange. The outcomes will be relevant for invasive alien species policy, noting the importance of enhancing collaboration and coordination across local, national, and regional scales, recognising that geographic boundaries do not confine the impact of these species. By adopting a holistic and interconnected approach, OneSTOP seeks to establish a strategy to achieve rapid and transformative progress in detecting, eradicating and controlling invasive alien animals and plants, ultimately contributing to a more secure and resilient environment. Throughout, OneSTOP is based upon the strategic actions recommended for integrated governance of biological invasions in the recently published IPBES Thematic assessment report on invasive alien species and their control (IPBES 2023).

HTML

XML

PDF

DOI: 10.3897/rio.11.e163815

Authors: Gonzalo Bravo, Gregorio Bigatti, Mariana Lozada, Luke Thompson, Juan Livore, María Mendez, Lorena Arribas, Lino Bigatti, Tyler Christian, Erasmo Macaya, Edgardo Londoño-Cruz, Nicolas Moity, Juan Cruz-Motta, Augusto Flores, Gabriela Vélez-Rubio, Maria Palomo, Cesar Cordeiro, Franciane Pellizzari, Maritza Cárdenas-Calle, La Daana Kanhai, Ivonne Vivar Linares, Patricia Gil-Kodaka, Linsey Martinez, Pablo Sugliano, Agostina Trigo, Juan Zottola, Dulce Blanco, Matias Tricase, Nadia Bravo, Mariana Degrati, Camila Tavano Formigo, Frank Muller-Karger, Enrique Montes

Abstract: The Marine Biodiversity Observation Network Pole to Pole of the Americas (MBON Pole to Pole) brought together 30 participants from 10 countries in Patagonia, Argentina, to strengthen observing capacity of coastal biodiversity across the Americas. The network held a five-day workshop focused on three core components: standardized rocky intertidal photo-quadrat surveys, low-cost environmental DNA (eDNA) sampling, and affordable plankton imaging tools. Participants included researchers, park rangers, and conservation practitioners fostering a collaborative and inclusive environment. Key outcomes included field validation of protocols, identification of context-specific methodological adaptations (e.g., for low tidal amplitude areas), adoption of novel tools for monitoring marine life, and strategies for broader participation and data harmonization. The workshop highlighted the potential of simple, replicable methods to support long-term monitoring, and emphasized the value of shared protocols, tools, and open data for building a more connected and resilient regional observation network.

HTML

XML

PDF

DOI: 10.3897/rio.11.e152094

Authors: Frank Twum Aboagye, Mawutor Kwame Ahiabu, Maame Ekua Acquah, Queenstar Quarshie, Naa Kumah, Hannah Akahoho, Nfayem Imoro, Abena Enninful, Bill Egyam, Yvonne Ashong

Abstract: The emergence of COVID-19, caused by SARS-CoV-2, led to the widespread use of antigen rapid diagnostic tests (AgRDTs) due to their speed, affordability and ease of use. However, the diagnostic sensitivity of AgRDTs has been inconsistent across emerging SARS-CoV-2 variants, with some variants exhibiting reduced detection rates. Thus, AgRDTs have been unreliable in detecting the different variants of SARS-CoV-2. This study explores the molecular mechanisms responsible for this variability, focusing on structural changes in the viral spike (S) and nucleocapsid (N) proteins and how these changes affect antigen-antibody interactions. Using structural biology techniques, such as X-ray crystallography and cryo-electron microscopy, molecular virology approaches like whole genome sequencing, immunoassays including ELISA and surface plasmon resonance (SPR) and computational modelling tools for molecular dynamics simulations, this research will uncover specific mutations that impact diagnostic sensitivity. The results of this study will provide information for the development of next-generation AgRDTs with enhanced sensitivity across diverse viral variants, thereby supporting global efforts in pandemic surveillance and control.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e163734

Authors: Tiina Salo, Marie C. Nordström

Abstract: The Archipelago Sea in the northern Baltic Sea suffers from multistressor perturbations, including ones related to local nutrient loading as well as consequences from global climate change. In this study, we use the bow-tie risk analysis framework to examine and illustrate how these drivers, eutrophication and climate change, contribute to biodiversity loss and associated implications of this in the Archipelago Sea. The bow-tie approach indicates both causes and ecological, economic, and social consequences of a problem as well as measures to prevent and mitigate the identified causes and consequences. For the Archipelago Sea, the bow-tie approach illustrated highly interlinked impacts of agriculture and aquaculture-driven eutrophication and climate change in degrading marine communities in the Northern Baltic Sea. Similarly, the consequences of this biodiversity loss were complex and highly interlinked. Many of the marine communities in the study area are highly connected, and as this may propagate the degradation of biodiversity and ecosystem services, future assessments should aim to include both trophic and non-trophic interactions in the bow-tie risk analysis. The study also highlights the need to prevent and mitigate multiple drivers of biodiversity loss simultaneously in order to reduce and stop the ongoing degradation of marine habitats and the ecosystem services they support.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e161262

Authors: Laura Garzoli, Alena Gsell, Silke Van den Wyngaert

Abstract: Many parasites produce resting spores to survive host absence or adverse conditions. Insights into the environmental triggers for switching between active and resting phases is crucial for understanding host-parasite dynamics in nature. Zoosporic fungi from the Chytridiomycota phylum, known as chytrids, are widespread parasites of phytoplankton, impacting bloom dynamics and influencing key processes in aquatic ecosystems. Though chytrids produce resting spores, the triggers for their germination remain poorly understood. A previous study found that germination could be induced in cold, dark-stored spores by exposing them to increased temperature and light. To disentangle the effects of temperature, light, and host presence, we conducted a microcosm experiment with the phytoplankton-chytrid model system Staurastrum sp. – Staurastromyces oculus. Resting spores were stored for 3 months at 4°C or 16°C in darkness or light. They were then exposed to combinations of temperature (4°C or 16°C), light (light or dark), and host presence (with or without host). Using automated fluorescence microscopy, we imaged and quantified resting spores, germination, and new infections daily for the first 5 days, and at days 7, 10, and 14. Our preliminary results indicate that an increase in temperature following 4°C storage is a primary trigger for germination, while light does not appear to significantly influence the process, as infections were observed even in dark conditions. Interestingly, the highest infection rate occurred in spores stored and incubated at 16°C with light. These findings suggest that multiple pathways can induce germination in chytrid resting spores, primarily through temperature shifts or host presence.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e160986

Authors: Martyna Budziak, Doris Ilicic, Hans-Peter Grossart, Wojciech Krztoń, Edward Walusiak, Janusz Fyda, Elżbieta Wilk-Woźniak

Abstract: Fungal parasitism is attracting growing attention in phytoplankton ecology because of its outstanding importance for aquatic food webs and energy cycling. However, relatively few studies have addressed baseline data on occurrence and environmental factors associated with chytrid parasite infections in natural ecosystems. This work provides insights into occurrence, prevalence, and dynamics of parasitic infections by studying three shallow, freshwater bodies during the growing season over a period of six years. Data were collected each year from April to October, monthly or fortnightly from a central point of each waterbody from 2019 to 2024. Chytrids were detected in each of the studied waterbodies, infecting species of green algae, diatoms, and cyanobacteria. General linear model (GLM) indicated that major factors driving the occurrence of chytrid infections were water temperature, nitrates, phosphates and pH. However, recurring and prevalent infections were observed in only one waterbody, which is classified as a natural, undisturbed aquatic ecosystem. The recorded infection prevalence (IPC) ranged between 0% and 20%, while the mean infection severity remained low throughout the study. Infections were highest in summer (June-August) and were most prominent during cyanobacterial blooms, although the most infected group of phytoplankton was green algae (Desmodesmus spp.). GLM revealed a significantly positive correlation between IPC and water temperature, precipitation and cyanobacterial bloom. Overall, our results demonstrate that a combination of abiotic and biotic parameters drives the occurrence of parasitic infection more than just indicated by the magnitude of the prevalence alone.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e159590

Authors: Alicia Kling, Julia Osterman, Tomasz Kiljanek, Dimitry Wintermantel

Abstract: Pesticide effect studies on pollinators focus predominantly on the Western honeybee, Apis mellifera, which is also the only species for which EU regulations require risk assessment. Reliance on A. mellifera as the only model species for pollinators has been widely criticized, as its life history traits may lead to differences in pesticide sensitivity and exposure compared to other species. Therefore, current guidelines by EFSA recommend testing also on bumblebees and solitary bees, which has been done in practice almost exclusively on the generalist species Bombus terrestris and Osmia bicornis. Oligolectic bee species remain largely overlooked, which is concerning as they have experienced greater range reductions than generalist species. In addition, pesticide risk to pollinators is typically assessed for individual compounds or products, even though in reality pollinators are exposed to a mixture of several pesticides where synergistic effects may occur.Here, we present a protocol for a semi-field experiment that assesses the effects of two pesticides and their combination on the oligolectic Osmia brevicornis and the generalist O. bicornis. Conducted as part of the EU project WildPosh, the experiment builds on laboratory studies investigating pesticide impacts on pollinator health and is designed to test the effects of realistic exposure levels. Specifically, the experiment, for which we detail the methodology here, tests the insecticide Mospilan SG (a.i. acetamiprid), the fungicide Folicur (a.i. tebuconazole), and their combination. The study follows a full-factorial design using 40 flight cages across four spray treatments—Mospilan SG, Folicur, their combination, and a negative control — with 10 cages per treatment. Adult bees of both species will be exposed to the spray treatments for a minimum of 7 days and various endpoints regarding fitness (i.e., survival and reproduction) as well as foraging behavior of the two species and pollination success will be assessed. The results of this experiment will provide information on whether the spray treatments differentially affect the generalist species O. bicornis and the closely related oligolectic species O. brevicornis, and on any interactions between the insecticide and the fungicide at realistic exposure levels.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e159547

Authors: Marianna Garfí, Kurt Ziegler-Rodriguez, Eva Gonzalez-Flo, Joan García

Abstract: In recent decades, interest in bio-based products has grown significantly due to rising concerns about eco-friendly and sustainable alternatives to synthetic polymers and conventional energy sources. These bio-derived materials have the potential to substitute products obtained from fossil fuels, including plastics, additives, colourants and energy carriers like hydrogen (H₂). Additionally, within the framework of a circular bioeconomy, bio-based products can help decrease waste generation, lessen environmental harm, and enhance the efficient use of resources (Chrispim et al., 2024).The EU Horizon 2020 PROMICON project has developed a Social Life Cycle Assessment (S-LCA) (ISO, 2024; UNEP, 2020) to evaluate the social implications along the life cycle of four bio-based products (additives, bioplastics, pigments, and hydrogen) generated by microbiomes.

HTML

XML

PDF

DOI: 10.3897/rio.11.e154645

Authors: Michael Meredith, Katharine Hendry, E. Povl Abrahamsen, J. Alexander Brearley, Emma Young, David Munday, Hugh Venables, Anna Hogg, Benjamin Wallis, Katrien Van Landeghem, Filipa Carvalho, Andrew Yool, Amber Annett, Alberto Naveira Garabato, Mark Inall, Katy Sheen, Andrew Fleming, Estelle Dumont, Oskar Głowacki, Carlos Moffat, Neil Fraser, Sarah Gille, Matthew Alford, Rebecca Jackson, Katherine Retallick

Abstract: Mixing of the ocean around Antarctica is a key process that exerts influences over large scales and in multiple ways. By redistributing heat in the ocean, it exerts strong influences on the Antarctic Ice Sheet, with implications for sea level rise globally. Similarly, the redistribution of ocean heat affects the production of sea ice in winter and its melt in summer, with consequences for climate. Mixing also affects the distribution of nutrients in the ocean, with direct impacts on the marine ecosystem and biodiversity and with consequences for fisheries.It was long thought that mixing of the seas close to Antarctica was predominantly caused by winds, tides and the loss of heat from the ocean especially in winter. However, we recently discovered that when glaciers calve in Antarctica, they can trigger underwater tsunamis. These are large (multi-metre) waves that move rapidly away from the coastline and when they break, they cause sudden bursts of very intense mixing. Simple calculations indicated that the net impact of these underwater tsunamis could be as strong as winds, and much more important than tides, in driving mixing. It was also argued that they are likely to be relevant everywhere that glaciers calve into the sea, including Greenland and across the Arctic. As our ocean and atmosphere continue to heat up, it is very possible that glacier calving will become more frequent and intensify, increasing further the impact of underwater tsunamis on large-scale climate, the cryosphere and ecosystems.This is an exciting new avenue of scientific investigation and many key questions remain unanswered. We need to know how widespread and frequent the generation of underwater tsunamis is, how far they travel from the coastline before breaking, and how variable this is. We need to measure what impacts the extra mixing has on ocean temperature and nutrient concentrations, and to determine what this means for the cryosphere and ocean productivity. There is a pressing need to include the effects of underwater tsunamis in the computer models that are used for projecting future ocean climate and ecosystem conditions and to determine the feedbacks between climate change and the generation of more underwater tsunamis.To answer these questions, our project will deploy innovative techniques for measuring the ocean and ice in close proximity to a calving glacier, including robotic underwater vehicles and remotely-piloted aircraft, and cutting-edge deep-learning techniques applied to satellite data. We will use advanced computer simulations to fully understand the causal mechanisms responsible for the creation and spread of the underwater tsunamis and their impacts on ocean climate and marine productivity. We will make our developments in computer simulation available to the whole community of users, for widespread uptake and future use.This project will have significant benefits for academics seeking to predict the future of Antarctica and its impacts on the rest of the world, for Governments and intergovernmental agencies seeking to understand how best to respond to climate change, and for the curious general public wanting to learn more about the extremes of the planet and why they matter. The fieldwork will be especially photo- and video-genic and will lead to outstanding outreach and impact opportunities, and we will work with media agencies seeking to tell compelling stories about the extremes of the Earth.

HTML

XML

PDF

DOI: 10.3897/rio.11.e154845

Authors: Abigail Goben, Kristin Briney

Abstract: While funders and publishers continue to expand requirements for data management planning and sharing, few books have been written for academic researchers and research trainees to help them understand both introductory or discipline-specific concepts and practices. In this annotated bibliography, we review currently available English-language data management books and identify the limitations and opportunities for future publications.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e158720

Authors: Jesus Lozano-Fernandez, Marc Domènech, Attila Ibos, Thomas Marcussen, Torsten H. Struck, Rebekah Oomen, Astrid Böhne, Rita Monteiro, Laura Aguilera, Marta Gut, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler S. Alioto, Leanne Haggerty, Swati Sinha, Fergal Martin, Diego De Panis

Abstract: The reference genome of Gluvia dorsalis is the first of its order Solifugae (sun spiders), offering insights into adaptations to arid environments and the evolutionary history of arachnids. The entirety of the genome sequence was assembled into 5 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 787 Mb, composed of 51 contigs and 10 scaffolds (including the mitogenome), with contig and scaffold N50 values of 38 Mb and 199 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/rio.11.e156738

Authors: Max Korbmacher

Abstract: In the proposed project, we expect to improve diagnosis and treatment for patients suffering from neurodegenerative diseases by establishing a new biomarker based on deep learning and big data outputs. We will use brain age, a neuroimaging-derived marker of brain health which has previously rarely been tested longitudinally, but not in neurodegenerative disorders. The analyses will help to assess treatment response as well as stratifying and sub-typing neurodegenerative disease, based on brain structural characteristics in addition to multiple other markers of disease expression.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e158692

Authors: Minmin Pan, Stamatina Roussou, Peter Lindblad, Jens Krömer

Abstract: Phototrophic microbial communities – groups of tiny organisms whose energy for growth comes from light – play a significant role in global primary production by absorbing carbon dioxide and nitrogen gas. With the growing challenges of energy demands and environmental concerns, researchers are exploring scientifically designed (synthetic) phototrophic communities as a promising alternative to traditional energy generation methods. These consortia can efficiently convert CO₂ and N₂ gases, along with water and solar energy, into bioenergy products, offering a potential solution to today’s energy and sustainability problems.In this context, the development of synthetic phototrophic communities has attracted increased attention due to their ability to divide tasks among different species, allowing them to function more efficiently and remain stable. However, challenges remain, particularly in maintaining balance among strains and ensuring stable performance in environments that do not replicate the complex natural conditions in which these consortia typically thrive.To address these challenges, recent PROMICON studies have focused on how cyanobacteria interact with purple nonsulfur bacteria (PNSB). These bacteria, including Rhodopseudomonas palustris (R. palustris), have shown potential in producing biohydrogen and lipids by capturing nitrogen in oxygen-free environments. Nevertheless, a key limitation is that they need a carbon-based food source (e.g., acetate) to produce energy. A promising approach to overcome this issue involves growing R. palustris with cyanobacteria, which can pull carbon dioxide from the air and turn it into the organic carbon that R. palustris needs to thrive.

HTML

XML

PDF

DOI: 10.3897/rio.11.e152859

Authors: Florencia Yannelli, Kristiina Visakorpi, Anni Arponen, Carlos Arnillas, Javiera Chinga Chamorro, Mariana Chiuffo, Sharon Collinge, Roger Cousens, Kadambari Devarajan, Ken Ehrlich, marilyn grell-brisk, Rebecca Kariuki, Heather Kharouba, Andrea Monica Ortiz, Ana Prado-Valladares, Helen Regan, Florian Schnabel, Bruno Soares, Gisela Stotz, Michael Williams, Marc W. Cadotte

Abstract: The sixth mass extinction and the ongoing biodiversity and climate crises demand urgent action from ecologists and environmental scientists (EESs). Despite their critical role in addressing these challenges, EESs face unclear professional responsibilities towards society, local communities and ecosystems. The 2024 ANdiNA workshop was held in Conguillío National Park in Chile, within Wallmapu the ancestral land of the Mapuche people. It gathered global EESs to explore the roles, obligations and accountability of professionals in this field. The discussions focused on the evolving responsibilities of EESs amidst the environmental crises, as well as the need for clearer frameworks to guide their actions.Key questions included the scope of EESs' professional activities, how their obligations should adapt during times of crisis and whether they should be held accountable for scientific mistakes that lead to negative societal outcomes. The workshop explored the potential for creating a codified framework, such as an oath or manifesto, to clarify EESs' professional responsibilities. Participants highlighted the importance of integrating financial, intellectual, ethical and institutional dimensions in defining these roles, particularly in how EESs engage with local communities and society.Emerging themes included the need for a shared framework to align EESs' actions, exemplified by the Conguillío Statement, which encourages collaboration, inclusivity and ethical engagement with communities, especially Indigenous ones. The workshop also emphasised the importance of solution-orientated, transformative research and advocacy, calling for a shift in how EESs approach their roles as agents of change. By critically reflecting on their responsibilities, the workshop provided a foundation for re-imagining the role of EESs in the face of global environmental crises, urging systemic, collaborative approaches to safeguarding both nature and humanity.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e157676

Authors: Davide Raho, Andrea Tarallo, Ilaria Rosati

Abstract: This poster presents the ParAqua database, the first structured initiative aimed at centralising and harmonising data on zoosporic parasites of algae by integrating in situ observations, genetic data from NCBI, and literature sources. The database includes standardised information on parasite and host taxonomy, observation variables, genetic identifiers, and bibliographic metadata. Built with controlled vocabularies (Darwin Core, LifeWatch Traits Thesaurus, Dublin Core), the platform features a user-friendly web application offering structured query tools, a navigable data table, CSV downloads, and a stateless RESTful API for programmatic access. This resource supports researchers in identifying knowledge gaps and advancing parasitological and ecological studies. This work was presented as a poster at the CNR-IRET Conference held in Rome, February 18–19, 2025.

HTML

XML

PDF

DOI: 10.3897/rio.11.e156054

Authors: Mihael Ichim, Ruxandra Crețu, Valentin Grigoras, Madalina Popa, Ancuța Raclariu-Manolică, Camelia Stefanache

Abstract: Herbal food supplements produced from medicinal and aromatic plants (MAPs) are becoming increasingly popular to complement synthetic pharmaceuticals. This category of products is regulated under more lenient food product regulations rather than the stringent rules applicable to medicines. The effectiveness and safety of these products rely on various factors, including the varying phytochemical composition of the original plant material, potential adulteration, substitution and contamination from biological and chemical sources. The SAFEMAPS scientific research project aims to provide integrated analytical solutions that enhance the compliance and quality of food supplements derived from aromatic and medicinal plants. This project seeks to improve the safe use of these products by consumers, while promoting the sustainable exploitation of plant biodiversity. Within this project, an experimental model will be developed to assess the identity, authenticity, traceability and quality of herbal food supplements. This model includes analytical solutions that integrate phytochemical and molecular genetic analyses. The proposed solutions will prioritise the needs of the food supplements industry, particularly regarding the quality and compliance of herbal products sold in Romania and across the European single market. These solutions will also tackle various aspects of the supply chain, including growers or collectors of medicinal and aromatic plants, processors, importers and final consumers.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e157339

Authors: Soulaine Theocharides, Sam Leeflang, Wouter Addink, Sharif Islam

Abstract: Biodiversity research relies on physical specimens stored in natural science collections, which serve as enduring reservoirs of data about organisms and their environments. However, these reservoirs remain siloed. The concept of Digital Specimen addresses the challenges posed by the vast amount of disconnected digital biodiversity data available today. The existing approach involves converting analogue records into digital replicas stored in local databases, leading to isolated and fragmented datasets that are difficult to integrate and utilise efficiently. The Digital Specimen aims to overcome this by establishing an interconnected network of digital objects on the Internet. Digital Specimens are FAIR Digital Objects (FDOs), structured digital entities that adhere to the FAIR principles: Findable, Accessible, Interoperable, and Reusable. FDOs have the potential to enhance the accessibility and interoperability of data from natural science collections by providing unique identifiers, descriptive metadata, and defined operations. DiSSCo utilises the FDO framework to enhance the accessibility and interoperability of biodiversity research data from natural science collections. FDOs facilitate seamless data exchange by providing structured digital objects with unique identifiers, descriptive metadata, and defined operations. As part of making Digital Specimens FDOs, DiSSCO implemented FDO records, metadata records associated with a Persistent Identifier, which further enable machine actionability. A Digital Object repository was developed for the purposes of storing and acting upon digital specimens. Three technological pillars compose the repository: a relational database stores the latest version of the digital specimen and is used for retrieving specimens by their identifier; an indexing solution provides full search capabilities on digital specimens; and a document store holds previous versions of a digital specimen for provenance purposes. There are three ways a user may interact with the digital object repository: a REST API; a user-friendly web portal; and a DOIP server.To ingest data from multiple source systems, a harmonised data model was developed, called OpenDS. Built upon existing international standards like DarwinCore and ABCD, OpenDs accommodates complex structures necessary to capture information about multiple taxonomic identifications, events, agents, and relationships to other data sources. DiSSCo has decided to adapt the GBIF Unified Model (UM) for specimen data, ensuring interoperability and avoiding the development of potentially competing standards. By aligning with the GBIF UM, DiSSCo enhances interoperability with GBIF and promotes the establishment of a unified data modelling standard within the biodiversity community, facilitating seamless data exchange and integration with data aggregators like GBIF.

HTML

XML

PDF

DOI: 10.3897/rio.11.e156185

Authors: Denis Michez, Michel Bocquet, Philippe Bulet, Marie-Pierre Chauzat, Pilar De la Rúa, Reet Karise, Tomasz Kiljanek, Alexandra Klein, Marion Laurent, Elli Leadbeater, Marika Mänd, Anne-Claire Martel, Teodor Metodiev, Marija Miličić, Julia Osterman, Robert Paxton, Simon Potts, Sara Reverte, Marie-Pierre Rivière, Oliver Schweiger, Deepa Senapathi, Olga Tcheremenskaia, Simone Tosi, Ante Vujic, Dimitry Wintermantel, Mark Brown

Abstract: Wild fauna and flora are facing variable and challenging environmental disturbances. One of the animal groups that is most impacted by this, concerns pollinators. Pollinators face multiple threats, but the spread of anthropogenic chemicals (i.e. pesticides) form a major potential driver of these threats. WildPosh is a multi-actor, transdisciplinary project whose overarching mission and ambition are to significantly improve the evaluation of risk to pesticide exposure of wild pollinators, and enhance the sustainable health of pollinators and pollination services in Europe. As chemical exposure varies geographically, across cropping systems, inside the crop system and among pollinators, we will characterise exposure by doing fieldwork in 4 countries representing the four main climatic European regions, Mediterranean, Atlantic, Continental and Boreal climate in Germany, England, Estonia and Spain. We will also develop experiments in controlled conditions on different species of bees, syrphid flies, moths and butterflies, and collect in silico data on their traits and on toxicity of pesticides. With WildPosh, we aim to achieve the following objectives:1. Determining the real-world agrochemical exposure profile of wild pollinators at landscape level, within and among sites;2. Using integrated and controlled laboratory and semi-field experiments to characterise causal relationships between pesticides and pollinator health;3. Building an open database on pollinator traits/distribution and chemicals to define exposure and toxicity scenarios by developing databases on ecological traits and the spatial distribution of pollinators in relation to their potential exposure to pesticide;4. Proposing integrated systems-based risk assessment tools for risk assessment for wild pollinators; and5. Driving policy and practice through interactive innovation, meeting the need for monitoring tools, novel and innovative screening protocols for practice and policymaker use.

HTML

XML

PDF

DOI: 10.3897/rio.11.e155393

Authors: Elizabeth Adams, Natalie Raia, Saebyul Choe, Isaac Wink, Doug Curl

Abstract: State geological surveys create and steward valuable long-term earth and environmental science datasets and often serve as physical archives for material samples. Often funded directly through state legislatures, these agencies face varying degrees of support, nuanced regulations and public-serving missions that direct their research and day-to-day operations. Scientists at state geological surveys produce a range of outputs: datasets that may be stored internally, through an institutional repository or disseminated to broader community repositories and publications that may include both grey and peer-reviewed literature. This paper discusses a workshop held at the Kentucky Geological Survey to introduce researchers to data management, sharing and stewardship practices and to better understand obstacles to implementing such practices.

HTML

XML

PDF

DOI: 10.3897/rio.11.e146649

Authors: Lachlan Fetterplace, Emilia Benavente Norrman, Kristin Öhman, Filip Bohlin, Lisa Sörman, Daniel Rooth, Peter Ljungberg, Sara Königson

Abstract: Electronic monitoring (EM) using video cameras is valuable for documenting fisheries catch and bycatch, but it remains challenging to implement in small-scale fisheries. Current barriers include high costs, technical installation needs and limited power supply on small vessels. In addition, as most EM systems on the market are difficult to quickly move between vessels, they do not allow for random data collection, which may be required to obtain reliable estimates of bycatch across a fleet. Basic EM systems available, designed for use in small-scale fisheries, are image-based, have low frame rates and are not always capable of recording in high enough video quality to identify species with high precision.The Swedish small-scale fishery consists of over 700 boats (under 12 m length), with key target species including cod, herring, sprat and flatfish. To meet monitoring requirements and to gather sufficient data for machine-learning applications, we created the HafsAuga MobileEM: a low-cost mobile multi-camera, GPS and remote data offload system for recording data on fisheries catch, bycatch and effort. It records video (up to 60 fps), is compact (~ 2 kg) and deployable in under 30 minutes. Designed to be simple to operate and install, it is modifiable and allows users to connect to a vessel's 12v power or to an internal battery to record high-quality video footage continuously for over a week. This system is ideal for use in small-scale fisheries and also well-suited to situations where fleets need to be randomly sampled by quickly moving EM systems between vessels.Here, we describe the HafsAuga MobileEM system and outline its use in Sweden, where it has been in use since 2020. To date, twenty Swedish vessels have had mobile systems mounted on them and over 1000 fishing days have been successfully recorded. The HafsAuga MobileEM provides an innovative new EM tool with potential applications in fisheries in other regions.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e155925

Authors: Tatjana Čelik, Tjaša Lokovšek, Elena Bužan, Astrid Böhne, Rita Monteiro, Rosa Fernández, Nuria Escudero, Marta Gut, Laura Aguilera, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler S Alioto, Leanne Haggerty, Swati Sinha, Fergal Martin, Chiara Bortoluzzi

Abstract: The reference genome of the False ringlet (Coenonympha oedippus) will serve as a valuable resource for uncovering the genetic mechanism underlying the species′ adaptability to two ecologically distinct habitats. Through this genome we might be able to determine whether (i) each ecotype is monophyletic, indicating that the ecological divergence represents an early stage of speciation, (ii) the ecotypes have evolved through divergent evolution of habitat preference, or (iii) the differences between ecotypes are solely due to phenotypic plasticity or epigenetic variation. This reference genome is also a prerequisite for the planning, design, and implementation of conservation measures for this endangered species, taking into account its intraspecific diversity. Furthermore, it holds broader implications for population genomic studies of the species-rich genus Coenonympha, which includes some of the most endangered butterfly taxa in Europe. The complete genome sequence was assembled into 30 contiguous chromosomal pseudomolecules (sex chromosomes included). This chromosome-level assembly encompasses 0.39 Gb, composed of 385 contigs and 62 scaffolds, with contig and scaffold N50 values of 2.8 Mb and 14.2 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e155484

Authors: Jaume Pellicer, Teresa Garnatje, Daniel Vitales, Oriane Hidalgo, Joan Vallès, Alfredo García-Fernández, Arnoldo Santos-Guerra, Astrid Böhne, Rita Monteiro, Rosa Fernández, Nuria Escudero, Wellcome Sanger Institute Tree of Life Management Samples and Laboratory Team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, Abitha Thomas, Benjamin Jackson, Jonathan MD Wood, Kerstin Howe, Mark Blaxter, Shane McCarthy, Leanne Haggerty, Swati Sinha, Fergal Martin, Chiara Bortoluzzi

Abstract: The reference genome of Cheirolophus tagananensis, locally known as the Cabezón de Taganana, will provide an exceptional opportunity to establish a new framework to develop comparative genomic tools. These tools will help uncover the genetic basis of rapid plant radiations and microevolutionary adaptation processes of insular species on oceanic islands. This genomic resource will also contribute to facilitate the establishment of better informed in situ and ex-situ conservation strategies for this narrow endemic in the face of potential habitat degradation, and support taxonomic studies to better understand genetic diversity at the population, species, and genus levels. A total of 16 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 0.62 Gb, composed of 421 contigs and 235 scaffolds, with contig and scaffold N50 values of 4.0 Mb and 36.5 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e155364

Authors: Evelyn Underwood, Gabrielle Aubert, Daniel Veríssimo

Abstract: This factsheet series describes the available sources of funding for the Trans-European Nature Network (TEN-N) and characterises their relevance to the costs involved in setting up the network. Each factsheet outlines the relative strengths and limitations of each source of funding or finance in relation to protected areas and connectivity projects. The review looks at both public funding through EU sources and private finance options.Public funding opportunities are available for ecological connectivity, but lack of post-project funding as well as protected area under-resourcing are key challenges. EU funds are often still underdelivering on funding for biodiversity and there are bottlenecks to access to some EU funding opportunities. The suggestions for private finance instruments vary from proven mechanisms such as the “user pays-principle" applied to protected areas, to conceptual instruments in initial stages of development such as resilience bonds. Even though private finance is still in its early stages, it has the potential to considerably scale-up the finance available for nature in Europe. Land management tools, such as strategic and targeted use of conservation easements, land banks, habitat banks, and legal compensation obligations, can be used to repurpose land for nature goals, including the creation of ecological corridors. These tools are being increasingly used for ecological connectivity, but the current small-scale and fragmented initiatives should increase.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e155085

Authors: Salvador Carranza, Daniel Fernández-Guiberteau, Laura Blasón, Rosa Fernández, Rita Monteiro, Astrid Böhne, Laura Aguilera, Marta Gut, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler Alioto, Leanne Haggerty, Swati Sinha, Fergal Martin, Diego De Panis

Abstract: Malpolon monspessulanus is a large, rear-fanged snake widely distributed across Mediterranean habitats, where it plays an essential ecological role by controlling populations of small vertebrates. The reference genome of this species offers a crucial resource for uncovering the genomic foundations underlying venom evolution in rear-fanged snakes. A total of 23 contiguous chromosomal pseudomolecules (21 autosomes and two sex chromosomes) were assembled from the genome sequence. This chromosome-level assembly encompasses 1.8 Gb, composed of 140 contigs and 60 scaffolds, with contig and scaffold N50 values of 32.7 Mb and 121.9 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e154801

Authors: Elena Buzan, Aja Bončina, Boštjan Pokorny, Nuria Escudero, Rosa Fernández, Astrid Böhne, Rita Monteiro, Laura Aguilera, Marta Gut, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler Alioto, Leanne Haggerty, Fergal Martin, Diego De Panis

Abstract: The reference genome of Rupicapra rupicapra (subsp. rupicapra) provides insights into the genetic makeup that enabled this iconic mountain ungulate to adapt to its harsh environment, including its ability to survive in extreme weather and high altitudes—factors that are increasingly important in the face of climate change. A total of 29 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 2.62 Gb, composed of 124 contigs and 76 scaffolds, with contig and scaffold N50 values of 77 Mb and 101 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e154773

Authors: Franc Janžekovič, Elena Buzan, Aja Bončina, Nuria Escudero, Rosa Fernández, Astrid Böhne, Rita Monteiro, Laura Aguilera, Marta Gut, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Tyler Alioto, Leanne Haggerty, Fergal Martin, Diego De Panis

Abstract: The reference genome of Apodemus agrarius provides a valuable resource for phylogenetic studies of rodents, particularly mice, and for understanding factors that influence the geographical distribution of the species across East Asia and East Europe. A total of 25 contiguous chromosomal pseudomolecules were assembled from the genome sequence (23 autosomes and 2 sex chromosomes). This chromosome-level assembly encompasses 2.6 Gb, composed of 242 contigs and 60 scaffolds, with contig and scaffold N50 values of 35 Mb and 119 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e154462

Authors: Katerina Vasileiadou, Tereza Manousaki, Thanos Dailianis, Grigorios Skouradakis, Emmanouela Vernadou, Danae Karakasi, Astrid Böhne, Rita Monteiro, Rosa Fernández, Nuria Escudero, Genoscope Sequencing Team, Alice Moussy, Corinne Cruaud, Karine Labadie, Lola Demirdjian, Benjamin Istace, Arnaud Couloux, Patrick Wincker, Pedro H Oliveira, Jean-Marc Aury, Leanne Haggerty, Swati Sinha, Fergal Martin, Chiara Bortoluzzi

Abstract: Pinctada radiata, commonly known as the Gulf pearl oyster, is a species of pearl oyster found primarily in the warm waters of the Red Sea, the Persian Gulf, and parts of the Indian Ocean. Pinctada radiata contributes to marine ecosystems by filtering water, which helps maintain water quality and supports other marine life. This species is the first bivalve Lessepsian migrant, having migrated from the Red Sea to the Mediterranean Sea via the Suez Canal. The reference genome of Pinctada radiata could help identify genes enabling adaptation to varying temperatures and salinities, facilitating survival in diverse and newly colonized habitats allowing comparisons with other bivalves to uncover shared and unique genetic adaptations. Additionally, the genome could support targeted management practices and conservation initiatives, such as habitat restoration and selective breeding, ensuring the long-term sustainability of P. radiata. The entirety of the genome sequence was assembled into 14 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 0.93 Gb, composed of 220 contigs and 44 scaffolds, with contig and scaffold N50 values of 8.1 Mb and 63.8 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e154439

Authors: Katerina Vasileiadou, Tereza Manousaki, Thanos Dailianis, Grigorios Skouradakis, Emmanouela Vernadou, Danae Karakasi, Astrid Böhne, Rita Monteiro, Rosa Fernández, Nuria Escudero, Genoscope Sequencing Team, Alice Moussy, Corinne Cruaud, Karine Labadie, Lola Demirdjian, Emilie Téodori, Simone Duprat, Patrick Wincker, Pedro H Oliveira, Jean-Marc Aury, Leanne Haggerty, Swati Sinha, Fergal Martin, Chiara Bortoluzzi

Abstract: Arca noae, also known as the Noah's Ark clam, is a bivalve mollusk found in the shallow coastal waters of the Mediterranean Sea and the eastern Atlantic Ocean. This species plays a crucial ecological role by filtering plankton and organic particles from the water, helping maintain water quality and supporting nutrient cycling in marine ecosystems. It is also an important food source for various marine predators, including fish and crustaceans, thereby contributing to the coastal food web. Arca noae is notably resilient to environmental stressors, such as temperature fluctuations, changes in salinity, and pollution, making it a valuable model species for studying how bivalves adapt and respond to stress. While it is not commonly harvested commercially, Arca noae is of great interest to marine researchers due to its ability to thrive in diverse coastal habitats. The reference genome of Arca noae will thus provide important evolutionary insights. The entirety of the genome sequence was assembled into 19 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.5 Gb, composed of 257 contigs and 119 scaffolds, with contig and scaffold N50 values of 20.5 Mb and 84.7 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/rio.11.e140548

Authors: Florencia A. Yannelli, Wayne Dawson, Mark van Kleunen, Jonathan M. Jeschke, Tina Heger

Abstract: In this contribution of the Hypothesis Description series, we provide an overview of one of the longest-standing hypotheses in invasion science: Darwin's naturalisation hypothesis. We present a brief summary of past definitions and propose the revised definition “high phylogenetic distance between non-native species and the recipient community increases invasion success”. This formulation follows the basic form ‘subject – relationship – object’, enabling clarity for future research and computational applications in invasion biology. We also provide formalised definitions for previous formulations of the hypothesis and identify both related and opposite hypotheses to Darwin’s naturalisation hypothesis.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e153920

Authors: Petros Lymberakis, Danae Karakasi, Manolis Papadimitrakis, Rita Monteiro, Astrid Böhne, Rosa Fernández, Nuria Escudero, Genoscope Sequencing Technical Team, Alice Moussy, Corinne Cruaud, Karine Labadie, Sophie Mangenot, Caroline Belser, Lola Demirdjian, Swati Sinha, Leanne Haggerty, Fergal Martin, Patrick Wincker, Pedro H. Oliveira, Tom Brown

Abstract: The Acomys minous reference genome offers a crucial resource for uncovering phylogenetic relationships within the genus and its complex phylogeographic history . The entirety of the genome sequence was assembled into 20 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 2.35 Gb, composed of 297 contigs and 113 scaffolds, with contig and scaffold N50 values of 29.3 Mb and 113 Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e152862

Authors: Marc Ventura, Nati Franch, Rosa Fernández, Javier Palma-Guerrero, Astrid Böhne, Rita Monteiro, Laura Aguilera, Marta Gut, Tyler S Alioto, Francisco Câmara Ferreira, Fernando Cruz, Jèssica Gómez-Garrido, Leanne Haggerty, Fergal Martin, Tom Brown

Abstract: The reference genome of Valencia hispanica, a critically endangered actinopterygian species endemic to the Iberian Peninsula, is key to unravelling its genetic architecture and adaptation to freshwater ecosystems. This genomic resource will enable targeted conservation efforts and shed light on the species' essential role in ecological dynamics, including its contributions to algal biomass regulation and role in the aquatic food web while also highlighting the challenges it faces from habitat degradation and invasive species. Furthermore, it offers opportunities to gain valuable insights into the evolutionary paths within the Valenciidae family, significantly advancing our comprehension of genetic diversity and adaptability in aquatic ecosystems. The entirety of the genome sequence was assembled into 24 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 1.29Gb, composed of 99 contigs and 28 scaffolds, with contig and scaffold N50 values of 38.3Mb and 56.9Mb, respectively.

HTML

XML

PDF

DOI: 10.3897/rio.11.e147364

Authors: Salomé Landel, Michel Guiraud, Ana Casino, Katharine Worley

Abstract: The European Research Infrastructure DiSSCo (Distributed System of Scientific Collections) aims to digitally unify all European natural science assets, to ensure that collection data are easily findable, accessible, interoperable and reusable (FAIR). 170 institutions across more than 23 countries are involved in this ambitious objective of transforming a fragmented landscape of collections into an integrated knowledge base, enabling researchers to use and interconnect different collections.Research Infrastructure (hereinafter referred as to RI) cost calculation can be multifaceted and complex. DiSSCo is both a central team and a coordinated network responsible for supplying the infrastructure’s services. The RI linked costs are spread all over Europe and connect thousands of people. As the extended DiSSCo perimeter encompasses a wide range of services - from physical access, to digitisation on demand and consulting services - distributed amongst a great number of partners, cost information is spread across centralised and decentralised areas.The following article outlines the first “centralised” cost calculation exercise for DiSSCo and concludes that the DiSSCo Central Hub office would need a minimum annual budget of 1.4 million euros to be operational. This would not change between the construction and the operation phases. Furthermore, the DiSSCo Central Hub IT team would need a budget of 2.2 million euros to finalise all IT systems under the construction phase (if the construction phase lasts two years, it would cost around 1.1 million euros per year) in order to develop the digital services that will facilitate access to NSC data. The annual cost to operate these services would be around 1.2 million euros per year. This budget will evolve according to funding opportunities, the enlargement of the membership and the implementation of a business model open to new sources of income. As is often the case, research infrastructures grow over time and the more DiSSCo becomes known and recognised, the more it will attract users and the more its budget will increase.In order to calculate the RI linked costs, which are spread all over Europe, we developed a cost calculation methodology that has been distributed amongst all the 170 DiSSCo partner institutions. Twenty-seven institutions responded to the exercise. This allows for a first shared understanding on how to calculate DiSSCo related costs. It also provides the first figures on a cost-per-hour or a cost-per-service basis and it opens the door for the pricing of DiSSCo services. Finally, such a methodology also aims at guaranteeing a fair service pricing, based on the same principles and variables.

HTML

XML

PDF

DOI: 10.3897/rio.10.e134825

Authors: Tom August, Mario Balzan, Paul Bodesheim, Gunnar Brehm, Lisette Cantú-Salazar, Sílvia Castro, Joseph Chipperfield, Guillaume Ghisbain, Alba Gomez-Segura, Jérémie Goulnik, Quentin Groom, Laurens Hogeweg, Chantal Huijbers, Andreas Kamilaris, Karolis Kazlauskis, Wouter Koch, Dimitri Korsch, João Loureiro, Youri Martin, Angeliki Martinou, Kent McFarland, Xavier Mestdagh, Denis Michez, Charlie Outhwaite, Luca Pegoraro, Nadja Pernat, Lars Pettersson, Pavel Pipek, Cristina Preda, David Rolnick, Tobias Roth, David Roy, Helen Roy, Veljo Runnel, Martina Sasic, Dmitry Schigel, Julie Sheard, Cecilie Svenningsen, Heliana Teixeira, Nicolas Titeux, Thomas Tscheulin, Elli Tzirkalli, Marijn van der Velde, Roel van Klink, Nicolas Vereecken, Sarah Vray, Toke Thomas Høye

Abstract: The InsectAI COST action will support insect monitoring and conservation at the national and continental scale in order to understand and counteract widespread insect declines. The Action will bring together a critical mass of researchers and stakeholders in image-based insect AI technologies to direct and drive the research agenda, build research capacity across Europe and support innovation and application.There is mounting evidence that populations of insects around the world are in sharp decline. Understanding trends in species and their drivers is key to knowing the size of the challenge, its causes and how to address it. To identify solutions that lead to sustainable biodiversity alongside economic prosperity, insect monitoring should be efficient and provide standardised and frequently updated status indicators to guide conservation actions.The EU Biodiversity Strategy 2030 identifies the critical challenge of delivering standardised information about the state of nature and image-based insect AI can contribute to this. Specifically, the EU Nature Restoration Law will likely set binding targets for the high resolution data that cameras can provide. Thus, outputs of the Action will contribute directly to EU policies implementation, where biodiversity monitoring is considered a key component.The InsectAI COST Action will organise workshops, conferences, short-term scientific missions, hackathons, design-sprints and much more, across four Working Groups. These groups will address how image-based insect AI technologies can best address Societal Needs, support innovation in Image Collection hardware, create standardised approaches for Image Processing and develop novel Data Analysis and Integration methods for turning data into actionable insights.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e148125

Authors: Serena Rasconi, Laura Garzoli, Ana Gavrilović

Abstract: Abstracts of talks presented at ParAqua Conference held in Dubrovnik (Croatia), 16-17 April 2024

HTML

XML

PDF

DOI: 10.3897/rio.11.e145727

Authors: Ohad Graber-Soudry, Florian Weissbach, Maja Jensen

Abstract: The European Spallation Source ERIC relies on in-kind contributions from its Members, including technical components, R&D and services, which are vital to its construction and operation. The complex nature and delivery of in-kind contributions have posed significant accounting challenges. Following a comprehensive review in collaboration with external advisors, the European Spallation Source ERIC has adopted a harmonised approach that aligns the treatment of in-kind contributions with cash contributions, enhancing transparency towards stakeholders, compliance with accounting principles and the robustness of financial reporting. The experience of the European Spallation Source ERIC in addressing these complexities offers valuable insights for other ERICs and organisations with similar scopes, promoting effective and transparent management of in-kind contributions. This commentary aims to contribute to the broader understanding of managing in-kind contributions by sharing the European Spallation Source ERIC's experience and lessons learned.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e147255

Authors: Joan García, Eva Gonzalez-Flo

Abstract: The widespread use of petrol-based plastics has led to an environmental problem, as these materials are prone to abandonment, breaking down into microplastics and nanoplastics that harm living organisms. While biodegradable plastics are seen as a solution, their global production still remains modest at 1.3 million tons in 2022 (vs. 400 million tons of petrol-based plastics). Moreover, many such plastics fail to biodegrade efficiently under all environmental conditions (marine, soil, rivers, etc.). Polyhydroxyalkanoates (PHA) are a type of bioplastics naturally produced by microorganisms. They are a promising alternative because they degrade completely in soil, water, and marine environments. However, their industrial production is still limited and needs further research and investment to scale up.Commercially produced PHA is nowadays highly energy-intensive and relies heavily on organic raw materials and clean water, which conflicts with the EU’s goals for a circular, sustainable economy. The current production process is far away from the zero emissions neutral carbon strategy. The EU Horizon 2020 PROMICON project has developed an innovative method that uses photosynthetic microorganisms (cyanobacteria) to produce PHA efficiently. This process uses sunlight, absorbs CO2, and requires minimal organic resources, aligning perfectly with EU bioeconomy goals.

HTML

XML

PDF

DOI: 10.3897/rio.10.e137412

Authors: Christine Christian, Gilbert Gwilliam III, Matt von Konrat, June Ahn, Colleen Bailey, Daniel Dodinval, Elizabeth R. Ellwood, Kate Golembiewski, Lila Higgins, Camille Jones, Vanessa Martinez, Miguel Ordeñana, Gregory Pauly

Abstract: Participatory science and "amateur" participation in scientific data collection and work has been common for hundreds of years, but has become a more formalised field of practice in recent decades. The inclusion and reliance on informally trained members of the public in scientific endeavours has especially helped connect natural history collections to the general public. In recent decades, the term used to describe these participants — citizen scientists — was intended to unite formal and informal scientists as global citizens working towards a common goal. However, the term 'citizen' today has negative connotations for many members of the public and can have a polarising effect on certain individuals. Given that the nature of participatory science is to be inclusive and inviting, it is time to change this terminology. The term 'community' science has been suggested as an alternative by some practitioners and programmes. This self-awareness within the scientific community is important, but lacks impact without input from the community members potentially participating in these programmes. We addressed this knowledge gap by posing the question of term preference to groups of volunteers who have attended participatory science activities from the Field Museum of Natural History (Chicago, Illinois, USA) and the Natural History Museum of Los Angeles County (Los Angeles, California, USA) from 2019 to 2023. A majority of respondents showed a clear preference for the term 'community' over 'citizen' science. This was especially true for younger individuals and those who belong to ethnic groups other than White. This information can impact which terms are used for specific programme populations and supports community involvement in selecting terminology and in project design. We advise stopping use of the term 'citizen' in all participatory science programmes and adopting terminology that is most appropriate depending on region, research, audience and activity. Moreover, participant populations should be solicited to hear their voices.

HTML

XML

PDF

DOI: 10.3897/rio.10.e134189

Authors: Vixey Douglas

Abstract: Animal-transmitted diseases such as rabies represent a barrier to successful rewilding and threaten continued human-wildlife co-existence. In North America, population growth and human settlement expansion lead to encounters with wild mammals which have the potential to transmit rabies to domestic dogs and humans. The recent development of gene drives mediated by CRISPR-Cas9 allows for ecosystem engineering at unprecedented scales given the potential to spread new traits through wild populations with biased inheritance exceeding the pattern of classical Mendelian dominant genes. This study of a possible red fox rabies immunity gene drive project contributes a novel proposal to the existing academic conversation about suitable applications of gene drive technology in wild animal populations, such as projects to fight malaria and Lyme disease. Noting the unique characteristics of rabies, such as the dire mortality rate in humans once symptoms arise, as well as the tendency for rabid wild animals to lose their fear of humans, it appears to be a suitable target for eventual eradication via gene drive to spread immunity through wild mammal reservoir populations. Introducing heritable rabies immunity into North American red fox populations through gene drive represents a strategy to both battle rabies and adjust the ecology of (sub)urban environments. Given this review of the project's possible implementation and expected outcomes, providing inherited rabies immunity to wild red fox populations in North America via gene drive appears both feasible and sensible. Similar projects may be used to eradicate comparable infectious diseases from other wild animal populations, with likely benefits to human patients, wildlife and ecosystems.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e144611

Authors: Guy Ziv, Catriona Willoughby, Denise Hick, Arjan Gosal, Rosemary Wool, Chunhui Li, Jiaqi Ge, Paul Evans, Michael Beckmann, Anne Paulus, Meike Will, Birgit Mueller, Tomáš Václavík, Tomáš Čejka, Tomáš Čejka, Ruth Delzeit, Ornella Dellaccio, Jon Stenning, Anna Cord, Stephanie Roilo, Sanja Brdar, Joan Masó, Yoni Gavish, Danny Hooftman, James Bullock

Abstract: This Deliverable provides a roadmap to expansion of BESTMAP towards a operational pan-European modelling platform, as well as explore via pilot analyses several areas for improvement and future research. Considering new case studies, we analyse the locations where models parameterized in those regions can transfer to cover the most area. We conclude that in future case studies, they should be located in northern Spain, north-west Italy, central Italy, Montenegro/Albania, and Bulgaria. Testing if one can model water quality at the European scale, our modelling shows the NDR model (used in BESTMAP CS work) has generally good performance at EU scale, despite it being a rather simple process-based model. There is an overestimation of Nitrogen at low N, and underestimation of Phosphate at high P, which need to be considered in future work.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e144610

Authors: Cristina Domingo-Marimon, Joan Maso

Abstract: The BESTMAP dashboard, a pivotal element of the H2020 BESTMAP project, stands as a vital instrument for disseminating project findings and fostering informed decision-making processes. This platform enables exploration, analysis, and reporting on the outcomes of biophysical models, offering users valuable insights into various environmental factors. This deliverable offers a comprehensive overview of the dashboard's architecture, outlining its seamless integration into diverse environments. It also provides updates on the dashboard's final status, its content, and the creation of e-learning courses aimed at guiding users in effectively utilizing the tools and features available within the dashboard.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e144609

Authors: Pavel Stoev, Boris Barov, Gabriela Popova, Maria Mincheva, Milica Trajković, Dajana Vujaklija, Guy Ziv, Jodi Gunning, Michael Beckmann, Anne Paulus, James Bullock, Paul Evans, Tomáš Václavík, Cristina Domingo-Marimon, Anna Cord, Stephanie Roilo

Abstract: In order to enhance the visibility of BESTMAP project and its outcomes and to explore potential common activities and complementarities with other projects, initiatives, networks, and policy makers at EU level, the Plan of Engagement is developed and it will act as the strategy for creating a bridge between BESTMAP and all the other relevant projects or institutions. This document is an updated version of the Milestone 12 Plan of Engagement and it will serve as a strategic channel of relationship-building processes with identified related parties from now on. External relationships and engagement with relevant parties is a continuous process between BESTMAP and other parties. Therefore, the Plan of Engagement is considered as a living document that will be extended and changed as the engagement with all parties evolved.

HTML

XML

PDF

DOI: 10.3897/arphapreprints.e144185

Authors: Tomáš Čejka, Paul Evans, James Bullock, Guy Ziv, Stephanie Roilo, Tomáš Václavík

Abstract: Insights into potential policy outcomes may be biased if based on an unrepresentative selection of case study information. As case studies are a central element of the BESTMAP project, evaluating their representativeness in the wider EU context is one of the major tasks of WP5 - Upscaling. In this Deliverable, we first briefly describe the principles of meta-models of ecosystem services and biodiversity that were developed as part of Task 5.2 to upscale predictions of ecosystem services beyond case studies. Second, we report on the development of a distance metric used to determine case study representativeness, i.e. the degree of similarity in conditions between BESTMAP case studies and NUTS3 regions across Europe. Third, we describe the transferability diagrams that we used to obtain the relationship between the predictive power of the meta-models and the distance metric, which were then used to determine the threshold within the distance metric (similarity of conditions) that corresponds to a model prediction that we considered reliable (R 2>0.5 ). Fourth, for each ecosystem service and biodiversity, we present a series of transferability maps based on the set threshold to identify the transferability potential of BESTMAP models to NUTS3 regions across Europe. Finally, we discuss the limitations and challenges of our approach used to determine case study representativeness and the transferability potential of ecosystem service models.

HTML

XML

PDF