DOI: 10.3897/arphapreprints.e214299

Authors: Marta Leon, Ana Casino, David Dopazo, Laura Tilley

Abstract: This guide describes the design, positioning and operational strategy of the Taxonomic e-Services and Expertise Marketplace developed under the TETTRIs project. The Marketplace is conceived as a structured and navigable index that enhances the discoverability, accessibility and mobilisation of taxonomic expertise and services across Europe. It addresses the fragmentation of taxonomic capacity by providing a centralised, FAIR-aligned platform that supports expert registration, structured metadata, and linkage with research infrastructures and knowledge aggregators. The document outlines the platform architecture and information schema, defines target audiences and value propositions, and presents a phased strategy for adoption, engagement and long-term sustainability. It also describes pathways for future interoperability, including persistent identifiers, metadata alignment and potential API-based access, while clarifying governance, data management and ethical considerations. By connecting expertise supply with scientific, policy and applied demand, this guide supports the effective use of taxonomic knowledge to address biodiversity challenges at European and global scales.

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DOI: 10.3897/arphapreprints.e214297

Authors: Marta Leon, Tom Dijkema, Wouter Addink

Abstract: This document describes the pilot implementation of a marketplace for taxonomic e-services, designed to provide a curated, FAIR-compliant online catalogue for taxonomists, researchers, students and citizen scientists. It describes the objectives during implementation, the design process and the development process followed, as well as the final result and suggestions for further improvement. Aim of the pilot was to create a useful and accessible platform for connecting supply and demand of taxonomic e-services with focus on trustworthiness, interoperability, and open science principles, sustainable through CETAF. The service includes both a front-end application for user interaction and a back-end application for managing service descriptions and ensuring FAIR principles compliance. The pilot implementation supports the registration of a wide variety of taxonomic e-services to assist taxonomists with their daily job. The marketplace for taxonomic e-services is implemented as part of a CETAF marketplace (https://marketplace.cetaf.org/) that will also include a taxonomic expertise component, developed in another task in the TETTRIs project. The marketplace has a modern, responsive design with pages for searching, viewing, and suggesting e-services, styled in the TETTRIs theme, hosted and curated by CETAF. Its back-end is powered by Cordra, an open-source digital object store with built-in support for persistent identifiers utilising the Handle system. The data model was built using JSON-LD and aligned with schema.org and FAIR principles.

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DOI: 10.3897/arphapreprints.e214296

Authors: Marta Leon, Anton Güntsch, Walter G. Berendsohn, David Fichtmüller

Abstract: Our analysis of the landscape of local taxonomies and infrastructures providing aggregated taxonomic information has identified the matching process for scientific organism names as the core element of linking taxonomic resources. Name matching is considered the primary requirement for integrating datasets containing scientific names of organisms across the Internet, and for enabling science-based semantic linking of organism-related data. We also found wide variation in user requirements as well as in the offered functionalities for this process. As a consequence, a single, universally applicable workflow does not exist, but rather a number of approaches that depend on the specific user interest. This document presents a detailed concept and a demonstrator implementation of an interactive user guide for name matching of scientific organism names, as well as background information and general recommendations. The goal is to enable local users to verify and link their usage of names to other such resources, particularly to aggregated taxonomic datasets. Local users that want to apply name matching include everybody from individual researchers with their spreadsheets (such as those used in ecological studies) to curators of national or regional taxonomic databases. The technical implementation demonstrated includes a user interface for formulating queries as well as the underlying database that holds information on publicly available taxonomic datasets, name matching services, and the data and functionality provided by their combination. The focus is on functionality accessible by simple means, but information on available technical resources (APIs, R packages, Reconciliation Interfaces) is also included.

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DOI: 10.3897/arphapreprints.e214295

Authors: Marta Leon, Anton Güntsch, Andreas Müller

Abstract: EU-Nomen is a centralized, expert-curated taxonomic backbone designed to standardize species names across Europe, supporting scientific research, biodiversity monitoring, and policy-making. Initially developed under the EU-funded PESI project, EU-Nomen integrates data from major taxonomic sources—Euro+Med PlantBase, Fauna Europaea, ERMS, and Index Fungorum—into a unified structure. Hosted at FUB-BGBM and maintained by VLIZ, the infrastructure harmonizes nomenclature and taxonomy using a refined merging workflow based on the EDIT Platform for Cybertaxonomy. This modernized workflow replaces an earlier SQL script-based approach that was inefficient and difficult to maintain. Key features of the updated system include modular imports, automated validation, round-trip data consistency checks, and semi-automated taxonomic merging guided by source priorities. EU-Nomen supports open data directives and provides programmatic access via web services, ensuring interoperability with European biodiversity platforms. Recent enhancements include the integration of new data (e.g., bryophytes, lichens, and animal common names) and increased automation that allows more frequent releases. Together, these developments position EU-Nomen as a critical infrastructure for managing and delivering authoritative European taxonomic information.

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DOI: 10.3897/arphapreprints.e214294

Authors: Marta Leon, Conrad Gillett, Marco Bonifacino, Hanna Laakkonen, Sofie Meeus, Gunilla Ståhls

Abstract: This deliverable describes the implementation of species-level online access to European reference collections and the creation of pilot virtual reference collections (VRCs) for selected pollinator taxa within the TETTRIs project. Species-level metadata on entomological collections and pollinator subcollections were collected through a structured survey of European institutions and published as collection descriptors in the Global Registry of Scientific Collections (GRSciColl), enabling online discovery of collection holdings even where specimens are not fully digitised. In parallel, curated VRCs were developed from expertly identified specimens and published through the DiSSCo DiSSCover portal, providing high-quality diagnostic images to support species identification, research and biodiversity monitoring. Together, these approaches demonstrate scalable methods for improving access to natural history collections and strengthening their use in pollinator identification, research and monitoring across Europe.

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DOI: 10.3897/arphapreprints.e214292

Authors: Marta Leon, Luc Willemse

Abstract: The role of natural history collection as reference collection for research purposes and as benchmark collection for additional identification is highlighted and their stakeholders indicated. The identification process and its challenges are explained. Important features that determine the quality of both physical and virtual reference and benchmark collections are discussed. Several categories of measures to improve the quality of both physical and virtual collections and thereby optimising their use are reviewed and summarised in a set of recommendations.

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DOI: 10.3897/arphapreprints.e212343

Authors: Vincent Kalkman

Abstract: This document describes the availability of training data for image and sound recognition models of European animals, focusing on species groups for which an EU Red List is available, on species groups included in the EU pollinator initiative and on alien invasive species of Union concern. It compares the availability of training data with the goals set by ourselves at the start of the MAMBO project, analyses gaps and discusses possible ways to address these gaps in the next few years.

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DOI: 10.3897/arphapreprints.e212342

Authors: Vincent Kalkman

Abstract: In less than a decade image and sound recognition models have become the most widely used tool for the identification of both plants and animals. Part of this development was made possible due to work done in work packages 3.1 (image) and 3.2 (sound) of the EU Horizon MAMBO project.

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DOI: 10.3897/arphapreprints.e212341

Authors: Maria Mincheva, Pavel Stoev

Abstract: Effective communication, dissemination, and exploitation are crucial for clearly conveying research results and bridging the gap between science, policy, industry, and the public. European projects like MAMBO prioritise the effective distribution of outcomes to achieve significant societal impact. MAMBO’s strategy emphasises raising awareness and promoting activities, while dissemination ensures broad access to knowledge. Exploitation focuses on enabling stakeholders to leverage results for societal, commercial, or political purposes.

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DOI: 10.3897/arphapreprints.e212340

Authors: Raya Chakarova, Pavel Stoev, Slavena Peneva

Abstract: The aim of this document is to present MAMBO’s visual identity, website, and promotional materials as key tools in the communication and dissemination activities of the project.

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DOI: 10.3897/arphapreprints.e212264

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

Abstract: This document illustrates several examples of deploying a workflow (with Jupyter Notebooks) on a compute cluster for deriving a consistent set of habitat condition metrics from LiDAR for EU habitat monitoring.

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DOI: 10.3897/arphapreprints.e212344

Authors: W. Daniel Kissling, Yifang Shi, Jinhu Wang, Agata Walicka, Charles George, Jesper Moeslund, France Gerard

Abstract: This document is a report (deliverable D4.2) prepared for the Modern Approaches to the Monitoring of BiOdiversity (MAMBO) project (Høye et al., 2023), funded by the European Commission through an EU Horizon Europe Research and Innovation Action grant (No. 101060639). The MAMBO project aims to support EU biodiversity policy and address knowledge gaps by providing solutions to biodiversity monitoring through the design and development of novel tools and technologies. This report identifies the challenges for upscaling habitat condition metrics derived from LiDAR point clouds collected with crewed aircraft through (sub)national airborne laser scanning (ALS) surveys, as well as Red, Green and Blue (RGB) and Near-Infrared (NIR) imagery and LiDAR point clouds collected with affordable unmanned aerial vehicles (UAV, i.e. drones).

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DOI: 10.3897/rio.12.e199260

Authors: Tom Breeze, Riccardo Bommarco, Alexandra-Maria Klein, Ignasi Bartomeus, David Kleijn, Jochen Kantelhardt, Maximilian Koppenberg, Miranda Meuwissen, Henrik Smith, Carla Stoyanova, Mark Brady, Florence Damiens, Teodor Metodiev, Jelena Meinila, Joanna Tusznio, Carlos Ruiz Carreira, Henning Schaak, Sebastian Bekker, Jake Bishop, Shon Ferguson, Klara Fischer, Małgorzata Grodzińska-Jurczak, Hajnalka Szentgyörgyi, Helena Hansson, Romina Rader, René Van Der Wal, Richard Walters, Xiu-shan Li, Zhang Ying, Elena Carp, Simon Potts

Abstract: VALOR is a multi-actor project that will develop a comprehensive systems based approach to develop a deeper understanding of the cascading impacts of pollinator shifts from flower to fork (and beyond). Our work spans seven localised “focal regions” across Europe, where we will explore the impacts of pollinator shifts on ecosystems, farm businesses and local communities through primary research and modelling. These will be supported by broader synthesis and modelling tasks to determine the impacts of pollinators on value chains, international trade and nutrition and highlight the risks to ecosystems and natural capital across Europe, under different co-developed future scenarios. VALOR aims to empower actors to better understand their relationship with pollinators and will produce a number of co-developed tools for landowners businesses and policymakers to better understand these risks and easily undertake their own studies by replicating our methods and employing our models. Throughout the project, VALOR will work through our existing networks of policy and business collaborators to maximise the engagement with our outcomes, datasets and tools, build synergies with the wider pollinator research community and effectively mainstream pollinators into decision-making at all levels throughout Europe.

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DOI: 10.3897/arphapreprints.e200563

Authors: W. Daniel Kissling, France Gerard, Pierre Bonnet

Abstract: This deliverable (D5.3) reports on the technical training activities conducted within the MAMBO project to support the uptake and application of remote sensing-based habitat monitoring tools and workflows developed in Work Package 4. Instead of a single technical workshop as originally planned, two complementary training events were organised to address different user needs and levels of expertise.

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DOI: 10.3897/rio.12.e193918

Authors: Erica Zaja, Will Brownlie, Rajabu Hamisi, Maja Arsic, Adelaide Asante, Hilary Barraclough, André Bationo, Martin Blackwell, Dana Cordell, James Elser, Oluwole Fatunbi, Kwame Frimpong, Elise Gallois, Enam Gbekor, Kailyn Harris-Gilliam, Philip Haygarth, Ludwig Hermann, Kenneth Irvine, Issy Lewis, Ning Liu, Vincent Logah, Kaushik Majumdar, Muneta Grace Manzeke-Kangara, Eric Mensah, Malika Mezeli, Michael Miyittah, Innocent Muhwezi, Frederick Otu-Larbi, Richard Padi, Kasper Reitzel, Seth Robinson, Collins Tay, Francis Tetteh, Louis Tetteh, Shamie Zingore, Bryan Spears

Abstract: Phosphorus sustains global food production and is, therefore, of crucial importance to human nutrition and health. However, its mismanagement can lead to water pollution and environmental degradation in addition to low crop yields. In many parts of sub-saharan Africa, phosphorus deficiency constrains agricultural productivity and exacerbates food insecurity. Despite these challenges, phosphorus remains a fragmented topic in global and African policy. To address these issues, the 8th Sustainable Phosphorus Summit (SPS8) was convened in Africa for the first time. SPS8 took place in Accra, Ghana, between 30th September and 3rd October 2025. The Summit was an international collaboration, with co-conveners from the Council for Scientific and Industrial Research (CSIR) – Ghana, the Forum for Agricultural Research in Africa (FARA), The UK Centre for Ecology & Hydrology West Africa Office, Lancaster University and Rothamsted Research. In this paper, we give a detailed overview of the key messages and insights that emerged from highlight talks, lectures, working groups and field trips. We also discuss and reflect on the challenges of delivering an inclusive summit, from designing solutions to benefit-sharing. SPS8 demonstrates that inclusive, cross-sector knowledge-exchange events are crucial to support and enable phosphorus sustainability on the continent of Africa and globally and to enable the next generation of interdisciplinary phosphorus researchers.

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DOI: 10.3897/arphapreprints.e198827

Authors: James Henty Williams

Abstract: This deliverable is a review of ethical and security implications of activities and research undertaken as part of the PollinERA project. This ESP is a ‘living document’ and will be updated if additional ethical and security issues are identified and detail actions needed to ensure compliance with EU and national regulations.

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DOI: 10.3897/arphapreprints.e197166

Authors: Martin Jung, Maximilian Wolschlager, Louise O'Connor, Matea Osti, Carla Freund, Kyle J Brumm, Piero Visconti

Abstract: Ambitious commitments under the European Biodiversity Strategy for 2030, including protecting at least 30% of land area and restoring 20% of ecosystems, are an opportunity to halt and reverse biodiversity loss. Achieving these objectives would benefit from coordinated, integrated and biodiversity-inclusive spatial planning approaches to identify where conservation and restoration actions will be most effective and resilient. Systematic conservation planning (SCP) provides such a framework, but its outputs are often complex and need to be translated into actionable and interpretable information for decision makers. Here in the context of the NaturaConnect project, we developed stand-alone policy support tools designed to bridge this gap between science, policy and practice, specifically tailored to the implementation of the EU Biodiversity Strategy in the terrestrial realm. Specifically, we developed two interactive platforms, described in this deliverable: NaturaConnector and PriorityCheck. Both tools are web-based and enable to visualise spatially explicit prioritisation outputs generated using the prioritizr R-package. We produced multiple spatial scenarios reflecting different objectives and planning assumptions, allowing exploration of trade-offs and synergies across different scenarios. NaturaConnector provides a web-based interface that enables users to explore our prioritisation outputs interactively and to better understand the implications of alternative planning strategies. It allows users to compare different scenarios, adjust planning criteria, and visualise how priorities shift under different objectives, assumptions, and implications in terms of performance across a range of ecological, geographic and socio-economic indicators. To facilitate uptake and dissemination, the platform also includes a link to downloadable infosheets for 39 countries and 10 biogeographic regions. The infosheets showcase consensus prioritization outputs as well as an assessment of the performance of the spatial planning solutions with some key takeaways specific to each country or geographic region. PriorityCheck is an online tool that enables users (stakeholders, practitioners, and experts) to engage directly with the prioritisation outputs, including querying the species and habitats composition at each site, and provide spatially explicit feedback to the research team on selected priority areas, regarding their implementation challenges, feasibility, and local relevance and value for conservation or restoration. Based on this spatially-explicit feedback entered by stakeholders and regional experts on PriorityCheck, we then further refined and improved the spatial prioritisation outputs.

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DOI: 10.3897/rio.12.e194808

Authors: Nicolae Manta, Cristina Preda, Laurentiu Rozylowicz, Steluta Manolache, Ioana-Minodora Sirbu, Marius Skolka, Cristian Ioja, Iulia Miu, Andreea Nita, Mihai Nita, Iulian Niculae, Mihaela Urziceanu, Eugenia Nagoda, Alina Cislariu, Petronela Camen-Comanescu, Marian Mirea, Lavinia Pindaru, Marius Matache, Paulina Anastasiu

Abstract: Invasive alien species (IAS) represent one of the most significant threats to biodiversity in Romania and across the European Union. Despite the adoption of EU Regulation 1143/2014 on the prevention and management of the introduction and spread of IAS, its effective implementation at national level requires substantial institutional, scientific and operational capacity building. Here, we present a comprehensive national project, COMPLIAS Consolidarea Sistemului National de Management al Speciilor Alogene Invazive din Romania in Conformitate cu Cerintele UE / Strengthening the National Management System for Invasive Alien Species in Romania in Compliance with EU Requirements, SMIS 337191, funded under the Sustainable Development Programme (PDD/216, Priority 2, Specific Objective RSO 2.7) and implemented by the University of Bucharest in partnership with the Ministry of Environment, Waters and Forests of Romania. The project addresses all major obligations under EU Regulation 1143/2014 through seven interconnected work packages: (WP1) updating the regulatory and strategic framework, including the revision of the Invasive Alien Species Action Plan (IAS action plan); (WP2-WP4) comprehensive inventory and mapping of invasive alien species (plants, vertebrates and invertebrates) across Romania; (WP5) developing an early detection and border control system for IAS; (WP6) species distribution modelling, impact assessment and piloting eradication and control techniques for priority IAS; and (WP7) public awareness and stakeholder engagement campaigns. The project will also produce legally binding outputs, including a revised IAS action plan approved by Ministerial Order and mandatory country reports to the European Commission. This paper describes the project's objectives, methodological approach, expected outcomes and its contribution to the EU Biodiversity Strategy for 2030.

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DOI: 10.3897/arphapreprints.e194246

Authors: Carla Stoyanova, Teodor Metodiev

Abstract: This document is a deliverable for the PollinERA project, funded under the European Union’s Horizon Europe (HE) Research and Innovation Action under grant agreement No. 101135005. The purpose of this document is to present a detailed Plan for the Exploitation and Dissemination of Results (PEDR) of the PollinERA project, along with a communication strategy (CS), based on the preliminary plans in Section 2.2 of the PollinERA proposal.

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DOI: 10.3897/arphapreprints.e194245

Authors: Michael Rubinigg

Abstract: This Data Management Plan (DMP), prepared as part of the deliverables of the EC REA (Grant Agreement 10135005) funded project “Understanding pesticide-pollinator interactions to support EU environmental risk assessment and policy” (PollinERA), represents a plan for data management agreed upon by the PollinERA consortium. This plan is in line with the policies of the consortium partner’s organisations, as defined by the organisation’s data management policies, and with the requirements of the sponsor, as defined in the Horizon Europe research and innovation funding programme.

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DOI: 10.3897/arphapreprints.e192871

Authors: Camille Venier-Cambron, Nuno Garcia, Anandi Sarita Namasivayam, Niek Scherpenhuijzen, Alex Levering, Peter Verburg, Marta Cimatti, Moreno Di Marco

Abstract: D5.2 Spatial data for land-use and climate scenarios including TEN-N options and constraints

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DOI: 10.3897/arphapreprints.e192870

Authors: Martina Marei Viti, Henrique Miguel Pereira

Abstract: The implementation of the Trans-European Nature Network (TEN-N) requires a robust monitoring framework capable of tracking biodiversity trends across its extension and evaluating the effectiveness of protection and management actions that the network entails. This report contributes to this objective by identifying optimal strategies for the spatial design of an EU-wide biodiversity monitoring network, evaluating alternative stratification frameworks, and assessing how existing monitoring infrastructures can be integrated into a TEN-N monitoring system. The report comprises three analytical components and a cross-cutting synthesis. Chapter 1 assesses how alternative spatial sampling designs and network sizes influence the performance of an ex novo EU-wide biodiversity monitoring. Results show that network size is the dominant determinant of monitoring performance, particularly for common species and habitats, with performance converging across sampling designs at very small and very large network sizes. However, stratified sampling consistently outperformed random and grid-based approaches at intermediate network sizes, offering higher efficiency by maximising representativeness for a given level of effort. The importance of spatial design increased markedly when focusing on rare species and habitats. In these cases, stratified sampling improved coverage by up to 10% compared to alternative designs, reflecting its ability to distribute sampling effort more evenly across environmental conditions where rare entities are more likely to occur. Even under high sampling effort, however, rare species remained substantially more difficult to capture than rare habitats, highlighting inherent limits of probabilistic designs for monitoring rare biodiversity. Beyond representativeness, Chapter 1 also shows that no sampling design fully captures the full range of interacting anthropogenic pressures relevant for trend attribution, although stratified designs perform best overall. Climate and land-use gradients were most readily represented, while pressures with highly localised patterns, such as biological invasions, were consistently underrepresented. Together, these findings indicate that a stratified core monitoring network provides the most efficient foundation for EU-wide monitoring, but should be complemented by targeted modules to adequately address rare entities and complex pressure gradients. Building on these results, Chapter 2 examines whether refining the definition of strata, rather than changing the allocation method, can further improve monitoring performance. Alternative stratification frameworks were tested, based on combinations of environmental conditions, land protection intensity and ecological connectivity. Results show that modifying the stratification framework does not substantially alter overall network performance, with environmental stratification remaining the best-performing option. However, integrating conservation-relevant layers into the stratification framework enables the monitoring system to more directly address TEN-N assessment needs, particularly by facilitating systematic comparisons across gradients of protection and ecological connectivity. The choice of stratification layers therefore represents a key design decision with important implications for TEN-N monitoring. Chapter 3 assesses how existing pan-European biodiversity monitoring schemes can support a future TEN-N monitoring network. While these schemes represent among the best extensive monitoring efforts across the European Union, spatial gaps remain, particularly in Northern, Southern and Eastern Europe, as well as strong representativeness gaps of rare habitats and species. The comparison of existing monitoring schemes with ex novo monitoring networks of sites distributed across environmental strata suggested that an ex novo network could achieve comparable results with substantially less monitoring effort and cost. However, strategic gap-filling and expansion of the existing network could address the monitoring needs of rare entities. These results reinforce the need for targeted monitoring modules to adequately address the monitoring needs of rare species. The synthesis presented in Chapter 4 integrates insights from across the research and outlines implications for TEN-N monitoring. Two key principles emerge as essential: Assessing TEN-N effectiveness requires monitoring across conservation efforts; Existing monitoring schemes provide a foundation but must be complemented by a core stratified network and targeted monitoring modules. Together, the results provide an evidence base for designing a representative TEN-N monitoring network. This report therefore offers practical guidance for the European Commission and Member States in developing an EU-wide biodiversity monitoring strategy that supports the implementation, evaluation, and long-term success of the Trans-European Nature Network.

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DOI: 10.3897/rio.12.e187033

Authors: Katharina Heil, Tyler Alioto, Astrid Böhne, Tom Brown, Eli Chadwick, Physilia Chua, Christian de Guttry, Diego De Panis, Carole Goble, Ivo Gut, Marta Gut, Nick Juty, Seanna McTaggart, Laura Najera-Cortazar, Joana Paupério, Tomasz Rewicz, Felix Shaw, Stian Soiland-Reyes, Robert Waterhouse, Peter Woollard, Rutger Vos

Abstract: Biodiversity genomics is converging from historically separate approaches — DNA barcoding and reference genome sequencing — into an integrated digital ecosystem driven by shared data stewardship principles: transparent provenance, persistent identifiers and interoperable repositories. We demonstrate how these workflows can operate within a unified informatics architecture spanning data generation, validation, publication and reuse. We describe coordinated infrastructure, including the European BOLD mirror, ERGA Genome Tracking Console and metadata platforms COPO and PlutoF. These systems employ harmonised validation pipelines, shared metadata standards that bridge the Darwin Core and Genomic Standards Consortium vocabularies and automated data exchange amongst ENA, UNITE and GBIF. Workflows in Galaxy, Nextflow and Snakemake are registered in WorkflowHub as Research Object Crates (RO-Crates), ensuring reproducibility and complete provenance. Key outcomes include comprehensive data flow documentation, automated quality control using BUSCO and ERGA Assembly Reports and robust specimen-to-data linkage. We identify challenges in metadata harmonisation, distributed tracking, collaborative attribution and infrastructure sustainability and provide recommendations for addressing them through existing platforms and emerging RO-Crate standards. This work establishes practical foundations for treating biodiversity molecular data as a continuum, demonstrating how FAIR principles can scale to continental initiatives.

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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).

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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DOI: 10.3897/arphapreprints.e179513

Authors: Christopher John Topping, Johan Axelman

Abstract: A technical support document for the PollinERA Policy brief

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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.

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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.

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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.

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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.

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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.

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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.

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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).

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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DOI: 10.3897/rio.10.e138341

Authors: Fernando Ascensão, Pedro Cardoso, Rui Rebelo, Mário Boieiro, Alice Nunes, Sergio Chozas, Inês do Rosário, Adriana Príncipe, Cristina Máguas, Cristina Branquinho, Paulo Borges

Abstract: Much of the work developed on biodiversity dynamics due to climate change focuses on large scales. Yet, we know that small scale is critical to fully understand biodiversity change, particularly for plants and small or less mobile organisms which might seek refuge in sites that keep specific microclimatic and biotic conditions dampening the effects of large-scale changes. The project BASS - Biodiversity Assessment at Small Scales - aims to explore the intricate relationships between small-scale environmental variations in space and time and biodiversity patterns. Central to our study is researching how microclimatic conditions, such as potential solar radiation, influence species occurrence, abundance, community composition and biotic interactions within a Mediterranean context. Our objectives include gaining a deeper understanding of the effects of localised environmental conditions and their change in time on biodiversity, providing critical data for an under-researched Mediterranean Biodiversity Hotspot region, and examining the dynamics of small-sized species, particularly plants and invertebrates. We have established a network of 16 fixed sampling points across the Lisbon University field station - Herdade da Ribeira Abaixo (HRA), Grândola (South Portugal): eight with high and eight with low potential solar radiation. Each of these plots will serve as a 'mesocosm' for detailed ecological studies in the next decades. This framework will support a variety of research projects each focusing on different taxa and questions, including Masters' theses, PhD dissertations and independent studies, thereby fostering a collaborative research environment. By integrating previously collected data during the last three decades with new findings, we aim to offer valuable insights into the processes underlying ecosystem functioning and change at small spatial scales. This project not only addresses fundamental ecological questions, but also contributes to sustainable landscape management and biodiversity conservation efforts.

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DOI: 10.3897/arphapreprints.e142876

Authors: Laetitia Navarro, Francesca Cosentino, Virgilio Hermoso, Luigi Maiorano, Maria Paniw, Eloy Revilla, Andrea Sacchi, Luca Santini, Zulima Tablado, Wilfried Thuiller

Abstract: This report presents an overview of data identification and documentation related to biodiversity, ecosystem services, and the associated drivers, pressures, and response mechanisms. While not systematic nor exhaustive, our effort of data identification and documentation allowed us to describe more than 100 datasets and databases on European biodiversity (most datasets), ecosystem services, the drivers and pressures affecting them, and the mechanisms put in place to address these. These datasets represent nearly 2000 variables and metrics that can be used directly by researchers, land managers and decision-makers, for example for spatial planning in conservation or for further integration into biodiversity and ecosystem services models.Moreover, we also evaluate the completeness of biodiversity data (occurrence, trait and biotic interactions) in Europe across four terrestrial vertebrate classes, and assess potential drivers of data completeness. Despite Europe being one of the richest continents for biodiversity data globally, there are substantial data gaps in species distribution, trait, and species interactions, particularly in Eastern Europe, and for reptiles and amphibians. Results highlight how this heterogeneity in data availability is strongly associated with socioeconomic factors.We found that freshwater systems, data on ecosystem functions and population abundances are overall still under-represented in large-scale biodiversity data repositories and catalogues such as the ones that we consulted to build our metadatabase. In contrast, most of the metrics identified can be classified as species traits (both functional and life-history traits) although those also largely related to static data. By design, most of the datasets that we describe are openly available and easily accessible. Nevertheless, they also vary greatly in formats and standardization efforts which would impair a smooth integration into open workflows that could support the wider adoption of the tools that projects such as NaturaConnect could develop.Moreover, knowledge gaps are unevenly distributed within the European continent showing a strong taxonomic but also geographic bias. Amphibian and reptile data are strongly under-sampled compared to mammals and birds considering the species distribution (Wallacean shortfall), biological traits (Raunkiæran shortfall), and trophic interactions data (Eltonian shortfall).Some general recommendations in the view of these results are: i) there is a need to promote the publication of open protocols that describe in a standardized way the inputs and outputs of models used for decision-making and research in biodiversity conservation and that would limit the risk for redundancy, overestimations and circularity when integrating several datasets from various sources and disciplines; and ii) priority areas for data collection are located in southern and eastern Europe, which are strongly under-sampled compared to central and northern Europe (e.g., France, United Kingdom). Addressing these issues is crucial for advancing biodiversity conservation and ecosystem service management across Europe.

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DOI: 10.3897/rio.10.e131260

Authors: Irene Terry, Thomas Marler

Abstract: The island of Guam’s only gymnosperm and historically one of the island’s most abundant trees, Cycas micronesica, has been devastated by high mortality due primarily to the armoured scale Aulacaspis yasumatsui. This cycad-specific scale pest invaded Guam in 2003 and, in only a few years, this pest caused over 90% mortality to maturing trees and 100% mortality to seedlings. In 2015, C. micronesica was listed under the United States Endangered Species Act. Continuous surveillance of tree mortality throughout the island showed extreme decline in health until recent surveys have demonstrated that there has been improved tree health with little evidence of leaf herbivory on some remaining trees. Suggested explanations for this observed reduction in scale herbivory include some form of resistance in the surviving trees or a biocontrol agent (or several agents) that previously existed or has been introduced unintentionally and is controlling the scale to a greater degree. A combination of resistance and biocontrol are possibly both involved. We discuss in depth these possibilities and then propose experimental approaches that will help resolve this question.

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DOI: 10.3897/rio.10.e135978

Authors: Emily Veltjen, Pieter Asselman, Wim Baert, Steve Baeyen, Lise Beirinckx, Liselot Breyne, Dimitri Brosens, Tim Claerhout, Sari Cogneau, Karen Cox, Laura Cuypers, Lynn Delgat, Philippe Desmeth, Jordi de Raad, Lore Esselens, Maria-Rose Eves Down, Philippe Helsen, Frederik Leliaert, Kenny Meganck, Zjef Pereboom, Nathalie Smitz, Gontran Sonet, Maarten Trekels, An Vanden Broeck, Charlotte Van Driessche, Aaike De Wever

Abstract: DNA collections are a valuable type of Natural Science collection, enabling the validation of past research, serving as a source for new genomic studies and supporting ex situ conservation. The DiSSCo Flanders DNA collection working group, aiming to advance and "unlock" their DNA collections, identified the need for: 1) actively sharing best practices regarding the management of DNA collections; and 2) providing guidance on how to bring theory into practice. By combining best practice examples from within the working group with available literature and brainstorming ideas, the working group co-created two outputs, referred to as: the "Challenges" and the "Key". The Challenges are a list of obstacles to DNA collection management, which shape the structure of the linked Key and can also be used to spark discussion amongst stakeholders. The Key is a tool that guides users through the maturation process of their DNA collection in a standardised way. It stimulates holistic growth, breaks down the needed work into manageable steps and helps to decide priorities during the process. Furthermore, the Key facilitates communication with both internal stakeholders and external DNA collection managers. The Key distinguishes itself from other self-assessment tools in several ways: it includes (re)investigation of the collection’s purpose and context; it is specialised for DNA collections; it delivers concrete goals linked to relevant information and shared experience; and it is inclusive, targeting all Natural Science DNA collections, regardless of their context or size.

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DOI: 10.3897/arphapreprints.e140771

Authors: Martina Marei Viti, Miguel Fernandez, Rafaela Schinegger, Carina Seliger, Georg Gruber, Florian Borgwardt, Hildegard Meyer, Irene Lucius, Heini Kujala, Maria Hällfors, Risto Heikkinen, Thiago Cavalcante, Aino-Maija Määttänen, Marie-Caroline Prima, Sara Si-Moussi, Marianne Tzivanopoulos, Gabrielle Deschamps, Florian Barnier, Wilfried Thuiller, Miguel Araújo, Bárbara Pais, Francisco Moreira, Zulima Tablado, Marcello D'Amico, Sanne Evers, Virgilio Hermoso, Laetitia Navarro, Maria Paniw, Eloy Revilla, Dagmar Haase, Manuel Wolff, Sebastian Sebastian Scheuer, Peer von Döhren, Banjamin Labohm, Piero Visconti, Henrique Pereira

Abstract: This milestone report compiles mid-term findings from the six case studies of the NaturaConnect project, each serving as a critical testing ground to understand the practical implications of TEN-N across diverse environmental and socio-political contexts and different spatial scales. These mid-term reports represent a starting point for identifying commonalities and challenges among case studies, offering guidance on the design and implementation of TEN-N.

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DOI: 10.3897/rio.10.e129578

Authors: Zoe Ryan, Emily Clark, Beatrice Cundiff, Joslyn Nichols, Maya Mahoney, Nkosi Evans, Thomas Campbell, Danny Kreider, Matt von Konrat

Abstract: Over the last decade, access to global data has become increasingly critical for research, allowing insights into diverse biological, environmental and societal questions at a macro scale. Digitisation has greatly enhanced the use of herbarium data in the analysis of species distributions and ecological niche modelling. Yet, sources on modelling and mapping methodology using open-source software is greatly lacking for beginners. We have created a replicable and thorough tutorial to visualise species occurrence data and exploratory analysis that was developed by undergraduates with broad backgrounds and levels of experience. This tutorial integrates the open-source programmes QGIS, MaxEnt and R to develop distribution maps, using bryophytes as a case study, to promote the accessibility of open-source software and remote access learning. This tutorial has already set the foundation for further research into distribution modelling of rare Illinois bryophytes to better understand the potential impact of climate change.

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DOI: 10.3897/arphapreprints.e139236

Authors: Joana Bores, Hildegard Meyer, Evelyn Underwood, Mila Sirychenko, Wouter Langout, Peer von Döhren, Daniel Veríssimo, Balázs Horváth, Kenny Meganck, Alina Blaga, Måns Ingvarsson, Gabrielle Aubert, Barbara Herrero, Matea Osti, Anouk Puymartin

Abstract: The EU Biodiversity Strategy for 2030 aims to halt and reverse biodiversity loss besides other through the creation of the Trans-European Nature Network (TEN-N). This report, part of the NaturaConnect project, presents a comprehensive review of governance frameworks and land-use policies across European Union member states aimed at supporting the effective implementation of TEN-N. Using the Political Economy Analysis (PEA) framework, the report evaluates the economic, political, and social factors influencing policy reforms. It identifies key governance challenges such as weak regulations, unsustainable land use, and limited conflict management, alongside existing ecological connectivity frameworks. Data was gathered through literature reviews, interviews, surveys, and case studies from Finland, France, Portugal, Doñana in Spain, Halle-Leipzig in Germany, and countries in the Danube-Carpathian region.Our findings reveal that while many countries have national strategies for ecological connectivity, legal gaps and poor implementation persist, impeding progress. However, successful practices from countries like Germany and Portugal offer governance models. Furthermore, the report highlights opportunities to strengthen ecological connectivity through improved public funding mechanisms, private financing, and targeted interventions for regulatory reform, stakeholder engagement, and sustainable land use.This report provides valuable insights into the pathways of change and interventions necessary to enhance ecological connectivity and the role of Green and Blue Infrastructure in achieving biodiversity goals. The outcomes of this study are pivotal for shaping the future of European biodiversity conservation efforts and guiding the effective planning and governance of TEN-N.

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DOI: 10.3897/arphapreprints.e138574

Authors: Martin Jung, Marco Davoli, Thiago Cavalcante, Louise O'Connor, Alessandra D'Alessio, Mata Cimatti, Michela Pacifici, Jutta Beher, Piero Visconti, Moreno Di Marco, Heini Kujala

Abstract: The expansion of area-based conservation measures, such as protection and restoration efforts, as well as the design of multi-functional green and blue infrastructure, are widely seen as instrumental in halting or reversing further biodiversity decline. Europe has a long history of protection for biodiversity such as through the Natura 2000 program, however there still remain several gaps in sufficiently conserving the various aspects of biodiversity (e.g. species, ecosystems, functions & services) across Europe. Given the legal, political and societal challenges in negotiating the expansion of any new areas, it is key that these are done in strategic way and make use of best-available data to identify which areas would have the highest potential to contribute meaningfully to the conservation of biodiversity. Methods from systematic conservation planning (SCP) can be used to identify where such areas could be located under various assumptions and future narratives and can help to contribute to the design of a Trans-European Nature Network (TEN-N). In this report we 1) review previous SCP applications at various spatial and temporal grains across Europe and guiding principles for identifying conservation area expansions, 2) outline a methodology building on Favourable Reference Values (FRVs) to quantitatively identify the level of ambition for ensuring the long-term persistence of species of conservation priority, 3) describe a way to account for resilience towards future climates so as to ensure that protected areas play their role now and in the future, 4) describe how different parameters and datasets can be robustly integrated in a SCP problem formulation so as to identify where to best conserve, restore or manage European landscapes across different variants. By doing so this report provides a methodological basis on how to plan for a more coherent pan-European wide TEN-N. The TEN-N variants can inform on areas with high potential for local implementation, opportunities for cross-border conservation collaborations, or regions where future funding for conservation and restoration could be allocated across European member states. Furthermore, the TEN-N variants will be closely inspired by European policy targets and definitions and can thus serve as feasibility assessment of European Biodiversity policies under different scenarios.

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DOI: 10.3897/rio.10.e137296

Authors: Ricardo da Silva Ribeiro

Abstract: The National Council for Scientific and Technological Development (CNPq) and Confap announced the launch of the 5th edition of the Protax programme aimed at supporting the advancement of human resources in biological taxonomy. The funding for the programme has been increased from R$6 million (equivalent to 1,1 million US dollars) to R$14 million ($2,5 million), making grants of up to R$400,000 ($73 thousand) per project available. However, it is important to note that the programme primarily emphasises human resources, overlooking the crucial need for funding fieldwork, which plays a vital role in taxonomic research in diverse ecosystems like the Amazon. To ensure the success of Protax, a comprehensive approach including dedicated funds for expeditions and biological collections is essential.

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DOI: 10.3897/rio.10.e137763

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

Abstract: A network of European organisations is coordinating a workshop in New York (USA) on September 26, 2024, as part of the Science Summit 2024 at the 79th Session of the UN General Assembly (UNGA79). This network represents active communities from the fields of biodiversity, ecology, and engineering. It aims to strengthen science, technology, and innovation efforts to achieve the UN Sustainable Development Goals (SDGs).These communities, through European initiatives like the European Research Infrastructures, the European Open Science Cloud (EOSC), and Digital Twin projects, have selected the Kunming-Montreal Global Biodiversity Framework (K-M GBF) as a testbed for contributing to the SDGs. Their collective focus is on the network shared impact rather than individual projects. By examining a common approach to the K-M GBF, they aim to enhance their contributions to the framework's strategic goals, particularly its 2030 and 2050 targets.In this direction, the network: Recognises the contribution and rights of indigenous peoples and local communities as custodians of biodiversity and holders of traditional knowledge for the conservation, restoration, and sustainable use of ecosystems. By adhering to the Open Science principles of “Findable Accessible Interoperable Reusable” (FAIR) and “Collective Benefit, Authority to Control, Responsibility, Ethics” (CARE), and by being consistent with the practices adopted by the scientific community, the members of the network promote traceability of their work and of the materials they use, including those provided by indigenous peoples.Implements a variety of approaches to improve biodiversity monitoring, management, and protection. It promotes multi- and cross-disciplinary, integrative approaches to enhance its contribution to many of the Framework objectives. Its members support research on biodiversity at all levels of the biological organisation, from single-celled organisms, through collections and specimen data and up to the scale of ecosystems, as well as on how biodiversity responds to climate change. A key role in this process is already being played by the biodiversity Research Infrastructures, both in the EU and globally, through bi- and multi-directional linking and an increased interoperability of their data holdings, the provision of advanced access to semantically structured FAIR data, the provision of single points of access to federated data discovery from different data domains, thus supporting multi-disciplinary research addressing questions of high complexity and importance to society.All organisations in the network are committed to the three principal objectives of the Convention on the Biological Diversity, namely conservation, sustainable use, and fair sharing of benefits derived from the utilisation of natural resources. They contribute significantly to the three above principal objectives of the CBD, by: (a) making biodiversity information readily available and developing systems to support decision making and conservation efforts that directly contribute to our ability to live sustainably with nature, as concerns the first of the principal objectives above; (b) identifying priorities and targets and raising awareness of the need to streamline efforts among scientific and societal actors, are critical elements towards the second objective; (c) developing technologies to enable the sharing of data, services and other products related to genetic resources, which are used in combination with any other type of resource or product (e.g. taxonomic, literature, environmental, etc.), are included among the activities to achieve the third principal objective. Contributes to the achievement of the K-M GBF objectives through science, technology and innovation, based on scientific evidence, traditional knowledge, and innovative practices. This support is translated into activities such as: (a) providing solutions for research, data sharing and management, and scientific computing solutions to researchers, learners, policy makers, public administrations and businesses; (b) developing standard operating procedures, implementing standards, and promoting open science principles to enhance research integrity, accuracy and accountability in science; (c) providing federated research services, resources, and other research products to promote multidisciplinary knowledge and innovation; (d) creating models (e.g. of climate and human activity related land-use changes in biodiversity dynamics and ecosystem services), automated data flows (from sensors to data systems) and integration (e.g. biodiversity data flows combined with environmental and human activity variables; (e) building digital twins for informed decision making, such as the European Digital Twin of the Ocean (European DTO), with assured connectivity to newly collected high quality environmental and biodiversity data; (f) providing training and capacity building services for innovative tools.Supports the consideration of the ecosystem approach principle in the implementation of the K-M GBF, with a number of activities being developed by the network: (a) providing virtual representations of the ocean and land, integrating observations, modelling, and digital infrastructures, and creating digital twins that allow the scientific community to simulate and study “what if” scenarios; (b) developing and implementing technologies that enable a cross-domain, multidisciplinary approach to the study of biodiversity and ecosystems; (c) promoting ecosystem-based approaches to biodiversity management and habitat conservation in innovative publications venues (e.g. Nature Conservation, Biodiversity Data Journal, One Ecosystem, etc.).Promotes collaboration and synergies between the Convention on Biological Diversity and its Protocols, as well as with other biodiversity-related conventions, relevant multilateral agreements and international organisations and processes, as this will facilitate the implementation of the K-M GBF. The network is developing a variety of work, including: (a) collaborating with bodies and organisations responsible for the implementation of the CBD and its Protocols (e.g. IUCN, IPBES, European Commission) to co-design and co-develop research resources and products to support their mandates; (b) establishing strong links with policy actors such as the European Commission and the European Parliament, the JRC and others. Participate in social, scientific and technical initiatives in the European arena, such as the European Green Deal, the EU Knowledge Centre for Biodiversity and its Science Service for Biodiversity, the Biodiversity Knowledge Hub, the EU Pollinators Initiative and the EOSC. Developing links with the private sector through the Science/Business initiative, cooperation with the European Environmental Bureau (EEB), and the EOSC Digital Innovation Hub (EOSC DIH); (c) integrating and sharing of computational resources and expertise will not only advance the frontiers of scientific knowledge, but also ensure that data-driven research initiatives around the world are well supported.Contributes to the understanding and researching of the links between biodiversity and health. Particular emphasis will be placed on the following activities: (a) participating in initiatives and projects such as the EOSC Health Cluster, a platform for interdisciplinary research, EC projects such as B4Life, B-Cubed and BioAgora by publishing research that investigates how biodiversity affects human health; (b) using data from multiple sources to numerically demonstrate the links between human and environmental health, in the context of the One Health concept; (c) using digital twins to create Virtual Research Environments (VREs) that generate knowledge on how biodiversity patterns derived from taxa and habitats interact with patterns derived from data and information on their health; (d) publishing the results of the research, such as studies on zoonotic diseases, biodiversity and mental health, and the benefits of ecosystem services for public health. During the workshop, the participants will present their collective contribution to the implementation of the K-M GBF and invite international and regional stakeholders to present their expectations on the above topic. Based on stakeholder input, the network will publish a white paper outlining its approach.Finally, these communities will issue an open call to forge an international alliance to further integrate biodiversity conservation into the priorities of the UN Summit of the Future agenda priorities and the post-SDG agenda.

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DOI: 10.3897/rio.10.e133454

Authors: Yann Hautier, Kathryn Barry, Mariet Hefting, Marijke van Kuijk, Edwin Pos, Betty Verduyn, Rola Johannes, George Kowalchuk, Merel Soons

Abstract: Extreme climate events such as floods and droughts are becoming increasingly frequent and intense across the world. Future climate scenarios predict both an increase in individual extreme events, as well as chronic changes in climatic seasonality. Yet, the combined and relative effects of these pressures on ecosystems remain unknown. Concurrently, human-induced ecological disruption is accelerating species extinction rates, which are estimated to be 100 to 1000 times greater than pre-human levels. This is alarming as greater biological diversity is thought to buffer ecosystem functioning against extreme climate events, thereby safeguarding the provisioning of essential ecological services that contribute to human well-being. However, how and to what extent biodiversity buffers ecosystems against climate variability remains unclear. We recently constructed experimental grassland communities in a mesocosm-based field design representing a realistic gradient of plant diversity. Both extreme events (drought and flood) and a change in seasonality of precipitation are manipulated in a full factorial design to quantify the effects of future seasonal shifts and extremes in precipitation. We will: 1) determine to what extent higher biological diversity ensures that grasslands can continue to provide multiple ecosystem services even in the context of climate change and 2) unravel the fundamental mechanisms by which this is achieved including species asynchrony and positive species interactions. Results of our experimental approach will advance our understanding of the buffering potential of plant diversity and contribute to the development of strategies for sustainable service provisioning of our ecosystems in the face of climate change.

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DOI: 10.3897/rio.10.e131405

Authors: H. Michael G. Lattorff

Abstract: Pollination of crop plants is highly valued as it contributes to productivity in terms of quality and quantity. Globally, pollination is valued at more than USD 500 billion. The primary pollinators are insects and amongst them, bees. The Western honeybee (Apis mellifera) is a very generalist pollinator that is managed. Honeybees contribute up to 50% of the pollination of various crop plants. Pollinators are at risk due to land-use/land-cover changes and agricultural pesticide input.In a recently published study, research on honeybees in runner bean (Phaseolus coccineus L.) in Poland is presented. In one part of the study, the actual foraging of honeybees in beans is recorded, along with the time of day, abundance and time spent on flowers. The second part of the study investigated several apiaries concerning the potential poisoning of bees by means of pesticide exposure. The authors recorded the fitness of colonies, flight activity, behaviour, productivity and pesticide residues in bees.The manuscript, unfortunately, has several scientific flaws that are outlined in this commentary. These flaws, particularly those related to experimental planning and data collection and analysis, have the potential to compromise the conservation of pollinators. The misguidance in the implementation of measures to protect pollinators and pollination services is a cause for concern and should motivate us to address these issues.

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DOI: 10.3897/arphapreprints.e132163

Authors: Marit Schnepf, Simone Prestes Dürrnagel, Giacomo Laghetto, Teresa Pastor, Carol Ritchie

Abstract: NaturaConnect is a Horizon Europe research project, which aims to work closely with key stakeholders to co-develop tools and build capacity that will assist European Union Member States to design a resilient, coherent, and well-connected network of protected and conserved areas – the Trans-European Nature Network (TEN-N). The project aims to elicit stakeholder visions and to tailor knowledge and tools, resulting from engagement and dissemination efforts across Europe and in six specific case study areas. This report provides an overview of the stakeholder engagement during the first half of the project, outlines the capacity building approach and briefly discusses the main communication activities. An overview of applied methods in the stakeholder analysis, results from the stakeholder mapping and an evaluation of the engagement activities conducted until end of 2023 are described. Capacity building is a crucial project component in developing knowledge, understanding, skills and competences for users of the NaturaConnect frameworks, data and tools. The capacity building evaluation of this report focuses on the NaturaConnect Learning Platform and the NaturaConnect Training Needs Assessment. This mid-term report assesses engagement activities conducted until date in order to address any identified bottlenecks. The capacity building part provides an overview of applied methods and tools for assessing training needs and describes key features of the NaturaConnect Learning Platform.

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DOI: 10.3897/rio.10.e129357

Authors: Christiane Werner, Ulrike Wallrabe, Andreas Christen, Laura Comella, Carsten Dormann, Anna Göritz, Rüdiger Grote, Simon Haberstroh, Mazin Jouda, Ralf Kiese, Barbara Koch, Jan Korvink, Jürgen Kreuzwieser, Friederike Lang, Julian Müller, Oswald Prucker, Alexander Reiterer, Jürgen Rühe, Stefan Rupitsch, Helmer Schack-Kirchner, Katrin Schmitt, Nina Stobbe, Markus Weiler, Peter Woias, Jürgen Wöllenstein

Abstract: Global climate change threatens ecosystem functioning worldwide. Forest ecosystems are particularly important for carbon sequestration, thereby buffering climate change and providing socio-economic services. However, recurrent stresses, such as heat waves, droughts and floods can affect forests with potential cascading effects on their carbon sink capacity, drought resilience and sustainability. Knowledge about the stress impact on the multitude of processes driving soil-plant-atmosphere interactions within these complex forest systems is widely lacking and uncertainty about future changes extremely high. Thus, forecasting forest response to climate change will require a dramatically improved process understanding of carbon and water cycling across various temporal (minutes to seasons) and spatial (leaf to ecosystem) scales covering atmosphere, biosphere, pedosphere and hydrosphere components.Many relevant processes controlling carbon and water exchange occur at small scales (e.g. rhizosphere, single leaf) with a high spatial and temporal variability, which is poorly constrained. However, interactions and feedback loops can be key players that amplify or dampen a system’s response to stress. Moreover, spatial and temporal scaling rules for these non-linear processes in structurally and functionally diverse ecosystems are unknown. Legacy effects, for example, altered response after previous stress and retarded recovery of forests after climate extremes, are not captured in state-of-the-art models. Currently, we are lacking the appropriate and interconnected measurement, data assimilation and modelling tools allowing for a comprehensive, real-time quantification of key processes at high spatio-temporal coverage in heterogeneous environments. Moreover, since climate impacts are highly unpredictable with respect to timing and location, future research will require novel mobile, easily deployable and cost-efficient approaches. ECOSENSE, therefore, assembles expertise from environmental and engineering sciences, both being excellently paired at the University of Freiburg.Our interdisciplinary research project will investigate all relevant scales in a next-generation ecosystem research assessment (ECOSENSE). Our vision is to detect and forecast critical changes in ecosystem functioning, based on the understanding of hierarchical process interaction. In the first phase, ECOSENSE will explore these process interactions by investigating pools and fluxes of water and carbon, i.e. CO2 exchange, isotope discrimination and volatile organic compounds (VOC), as well as stress indicators by remotely and in situ sensed chlorophyll fluorescence.To address these research tasks, ECOSENSE will develop, implement and test a distributed, autonomous, intelligent sensor network, based on novel microsensors tailored to the specific needs in remote and harsh forest environments. They will measure the spatio-temporal dynamics of ecosystem pools and fluxes in a naturally complex structured forest system with minimal physiological impact. Measured data will be transferred in real-time into a sophisticated database, which will be explored for process analysis, conducted by Artificial Intelligence and close to real-time process-based ecosystem models for now- and forecasting applications. Thereby, ECOSENSE will: i) break new ground for integrative ecosystem research by identifying hierarchies and interactions of abiotic and physiological processes of forest carbon and water exchange, ii) provide a profound understanding of complex ecosystem responses to environmental stressors and iii) enable the prediction of process-based alterations in ecosystem functioning and sustainability.Our novel ECOSENSE toolkit, tested and validated in controlled climate extreme experiments and our ECOSENSE Forest, will open new horizons for rapid assessment in vast and remote ecosystems. Thereby, ECOSENSE will allow for a unique avenue of data acquisition and, consequently, for unprecedented scale-crossing ecosystem understanding and modelling.

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DOI: 10.3897/rio.10.e124288

Authors: Mathias Dillen, Laura Abraham, Ann Bogaerts, Sofie De Smedt, Henry Engledow, Frederik Leliaert, Maarten Trekels, Steven Dessein, Quentin Groom

Abstract: This Data Management Plan outlines a comprehensive strategy for handling, storing, and sharing of data generated by digitisation projects of the herbarium at Meise Botanic Garden with Index Herbarium code BR. Its purpose is to establish clear guidelines for both staff and external users, specifying the terms governing data usage and storage. It aims to prioritise the FAIR principles (Findable, Accessible, Interoperable and Reusable), ensure responsible data management, facilitate long-term preservation, uphold legal and ethical obligations, all while aligning with the research excellence mission of Meise Botanic Garden. This plan serves as a guiding document to effectively and efficiently achieve these goals.

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DOI: 10.3897/rio.10.e124168

Authors: Franziska Taubert, Tuomas Rossi, Christoph Wohner, Sarah Venier, Tomáš Martinovič, Taimur Khan, Julian Gordillo, Thomas Banitz

Abstract: European grassland management has often favoured high production through frequent mowing and heavy fertilisation over biodiversity conservation, which is typically supported by less intensive management. Besides management, climate change and extremes are increasingly affecting grassland productivity and biodiversity, requiring timely adaptation of management practices. Here, we describe the development of a prototype Digital Twin (pDT) of grassland biodiversity dynamics intended to support researchers, farmers or regulatory decision-makers in monitoring the current state of selected grassland sites and projecting their future state under various management and climate scenarios.

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DOI: 10.3897/rio.10.e125523

Authors: Otso Ovaskainen, Patrik Lauha, Julian Lopez Gordillo, Ossi Nokelainen, Anis Rahman, Allan Souza, Jussi Talaskivi, Gleb Tikhonov, Aurélie Vancraeyenest, Ari Lehtiö

Abstract: Bird populations respond rapidly to environmental change making them excellent ecological indicators. Climate shifts advance migration, causing mismatches in breeding and resources. Understanding these changes is crucial to monitor the state of the environment. Citizen science offers vast potential to collect biodiversity data. We outline a project that combines citizen science with AI-based bird sound classification. The mobile app records bird vocalisations that are classified by AI and stored for re-analysis. Additionally, it shows a shared observation board that visualises collective classifications. By merging long-term monitoring and modern citizen science, this project harnesses the strength of both approaches for comprehensive bird population monitoring.

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DOI: 10.3897/rio.10.e125450

Authors: Simon Rolph, Chris Andrews, Dylan Carbone, Julian Lopez Gordillo, Tomáš Martinovič, Nick Oostervink, Dirk Pleiter, Kata Sara-aho, John Watkins, Christoph Wohner, Will Bolton, Jan Dick

Abstract: Digital twin approaches have the potential to revolutionise usage, planning and management of cultural ecosystem services i.e. the non-material benefits people obtain from ecosystems, including recreation, tourism, intellectual development, spiritual enrichment, reflection and aesthetic experiences.Here, we outline our blueprint for a prototype digital twin (pDT) for cultural ecosystem services. The pDT consists of two modelling components; a recreation potential model to quantify the cultural ecosystem services of the physical landscape and species distribution models to quantify the biodiversity component.It is envisaged that the digital twin will be used primarily by two user types: 1. those who wanted to enjoy the area and potentially contribute to citizen science programmes and 2. people who want to inform or make evidence-based management decisions (land managers, policy-makers, researchers).

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DOI: 10.3897/rio.10.e124579

Authors: Taimur Khan, Ahmed El-Gabbas, Marina Golivets, Allan Souza, Julian Gordillo, Dylan Kierans, Ingolf Kühn

Abstract: Invasive alien species (IAS) threaten biodiversity and human well-being. These threats may increase in the future, necessitating accurate projections of potential locations and the extent of invasions. The main aim of the IAS prototype Digital Twin (IAS pDT) is to dynamically project the level of plant invasion at habitat level across Europe under current and future climates using joint species distribution models. The pDT detects updates in data sources and versions of the datasets and model outputs, implementing the FAIR principles. The pDT’s outputs will be available via an interactive dashboard. All input and output data will be freely accessible.

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DOI: 10.3897/rio.10.e124978

Authors: Tobias Frøslev, Robin Boyd, Dmitry Schigel

Abstract: Advancements in environmental DNA (eDNA) metabarcoding have revolutionised our capacity to assess biodiversity, especially for cryptic or less-studied organisms, such as fungi, bacteria and micro-invertebrates. Despite its cost-effectiveness, the spatial selection for sampling sites remains a critical challenge due to the considerable time and resources required for processing and analysing eDNA samples. This study introduces a Biodiversity Digital Twin Prototype, aimed at optimising the selection and prioritisation of eDNA sampling locations. Leveraging available eDNA data and integrating user-defined criteria, this digital twin facilitates informed decision-making in selecting future sampling sites. Through the development of an associated data formatting tool, we also facilitate the accessibility and utility of DNA metabarcoding data for broader conservation efforts. This prototype will serve multiple end-users, from researchers and monitoring initiatives to commercial enterprises, by providing an intuitive interface for interactive exploration and prioritisation, based on estimated complementarity of future samples. The prototype offers a scalable approach to biodiversity sampling. Ultimately, this tool aims to refine our understanding of global biodiversity patterns and support targeted conservation strategies through efficient eDNA sampling.

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DOI: 10.3897/rio.10.e124988

Authors: Vladimir Mikryukov, Kessy Abarenkov, Thomas Jeppesen, Dmitry Schigel, Tobias Frøslev

Abstract: Phylogenetic diversity (PD) represents a fundamental measure of biodiversity, encapsulating the extent of evolutionary history within species groups. This measure, pivotal for understanding biodiversity's full dimension, has gained recognition by major environmental and scientific organisations, including the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Unlike traditional taxonomic richness, PD offers a comprehensive, evolutionary perspective on biodiversity, essential for conservation planning and biodiversity management. This manuscript describes the development of a BioDT (Biodiversity Digital Twin) prototype, aimed at facilitating the calculation and visualisation of biodiversity metrics from global, dynamic data sources. By utilising the PhyloNext pipeline and integrating with global phylogenetic and species occurrence databases like the Open Tree of Life (OToL) and the Global Biodiversity Information Facility (GBIF), the prototype aims to significantly reduce computation time and enhance user interaction. This enables dynamic visualisation and potentially hypothesis testing, making it a valuable tool for researchers, monitoring initiatives, policy-makers and the public. The prototype's development focuses on improving the PhyloNext pipeline's scalability and creating a more intuitive user interface, expanding its utility for conservation efforts and biodiversity exploration. Our work illustrates the potential impact of the BioDT prototype in supporting diverse user groups in visualising and exploring PD, thus contributing to more informed decision-making in conservation and biodiversity management.

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DOI: 10.3897/rio.10.e125167

Authors: Jürgen Groeneveld, Tomas Martinovic, Tuomas Rossi, Ondrej Salamon, Kata Sara-aho, Volker Grimm

Abstract: Honey bees are vital to human well-being and are under multiple stresses. We need to be able to assess the viability and productivity of honey bee colonies in different landscapes and under different management and climate-change scenarios. We have developed a prototype digital twin, HONEYBEE-pDT, based on the BEEHAVE model, which simulates foraging, population dynamics and Varroa mite infestation of a single honey bee colony. The main input data are land-cover maps and daily weather data. We have developed the pDT for simulating large areas and have tested it for the whole of Germany. We have also developed a web-based GUI that users can use to run the pDT for specific sites. Hive weight data from hundreds of hives will be used for calibration and validation.

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DOI: 10.3897/rio.10.e125192

Authors: Desalegn Chala, Erik Kusch, Claus Weiland, Carrie Andrew, Jonas Grieb, Tuomas Rossi, Tomas Martinovic, Dag Endresen

Abstract: Amidst population growth and climate-driven crop stresses such as drought, extreme weather, fungal and insect pests, as well as various crop diseases, ensuring food security demands innovative strategies. Crop wild relatives (CWR), wild plants in the same genus as the crop as well as wild populations belonging to the same species as the crop, offer novel genetic resources crucial for enhancing crop resilience against these stress factors. Here, we introduce a prototype digital twin (pDT) to aid in searching and utilising CWR genetic resources. Using the MoDGP (Modelling the Germplasm of Interest) tool, the pDT enables mapping geographic areas where stress-tolerant CWR populations can be found. With its graphical user interface, it offers flexibility in selecting genetic resources from CWR tailored to enhance resilience of various crops against diverse stress factors.

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DOI: 10.3897/arphapreprints.e129021

Authors: Francisco Moreira, Filipe S. Dias, Jeremy Dertien, Ana Ceia Hasse, Luis Borda-de-Água, Silvia Carvalho, Miguel Porto, Francesca Cosentino, Luigi Maiorano, Andrea Sacchi, Luca Santini, Florian Borgwardt, Georg Gruber, Nikolaj Poulsen, Rafaela Schinegger, Carina Seliger, Néstor Fernández

Abstract: Ecological connectivity is key to maintaining a coherent and resilient network of protected areas in the EU. The EU Biodiversity Strategy for 2030 has identified the unhindered movement of species, nutrients and ecological processes across connected landscapes as a key feature of a coherent Trans-European Nature Network (TEN-N) of protected and conserved areas. However, to date, streamlined guidance on planning for and implementing connectivity measures specifically at the European scale has been limited. This report presents a coherent methodological framework and guidelines for mapping functional and structural connectivity at the European scale, as part of the Horizon Europe NaturaConnect project, which is supporting EU Member States in developing a coherent TEN-N of protected and conserved areas. It describes key ecological connectivity concepts and approaches; outlines methods and tools for estimating connectivity; presents an overview of connectivity projects across Europe; identifies connectivity priorities, gaps and challenges following a stakeholder consultation process; and provides practical and operational guidelines for implementing ecological connectivity for conservation projects ranging from regional to national and European levels. The guidelines present a strategic blueprint aimed at enhancing ecological connectivity across Europe, and address the specific challenges and opportunities related to planning ecological connectivity in the European context. This report has been written for practitioners and individuals involved in the management and administration of protected areas and ecological connectivity projects across Europe. This includes professionals working in TEN-N implementation at national or regional levels, others involved in spatial planning outside protected areas, and professionals engaged in the implementation of connectivity projects and protected area management.

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DOI: 10.3897/arphapreprints.e128550

Authors: Martin Baptist, Richard Marijnissen, Grzegorz Różyński, Rosaria Ester Musumeci, Massimiliano Marino, Laura Borzi, Agata di Stefano, Morgane Jolivet, Alice Stocco, Fabienne Horneman, Silvia Rova, Silvia Torresan, Elisa Furlan, Caterina Dabalà, Francesca Coccon, Andrea Critto, Fabio Pranovi, Ferran Bertomeu, Carles Ibáñez, Nuno Caiola, Elitsa Hineva, Nataliya Andreeva, Petya Eftimova, Bogdan Prodanov, Valentina Doncheva, Nikolay Valchev, Shylee Berg, Mathis Cognat

Abstract: This deliverable presents the generation of EUNIS habitat maps for Europe as a whole and for each of the pilot areas in REST-COAST. Subsequently, it presents the assignment of semi-quantitative scores for the contribution of each EUNIS (sub)habitat to the five key ecosystem services applying the rank scale 0 (none), 1 (very low contribution), 2 (low contribution), 3 (medium contribution), 4 (high contribution) to 5 (very high contribution). It also describes the assignment of the IUCN Red List of Habitats to each of the depicted EUNIS (sub)habitats in the pilot areas. And finally, to assess coastal system behaviour and restoration effects on ecosystem services and biodiversity gains under climate change, a homogenised score card methodology is presented to overcome the problem of comparing minor changes (some percents) with major changes (tens of percents) in the total scores for ESS or BDV in each pilot area.

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DOI: 10.3897/rio.10.e127123

Authors: Nico Eisenhauer, Cordula Vogel, Luiz A. Domeignoz Horta, Ana Bonato Asato, Zarah Janda, Simone Cesarz

Abstract: Soil is the basis for life on Earth as we know it. Healthy and stable soil is a prerequisite for well-functioning terrestrial ecosystems and has, thus, been proposed to play a key role in plant diversity–ecosystem functioning relationships. The overall objective of this sub-project is to study multidimensional soil stability as affected by plant diversity in a long-term plant diversity experiment. We designed three coordinated work packages (WPs) to comprehensively assess soil multistability to environmental fluctuations and climate extremes by considering the biological, chemical and physical dimensions that are key for soil functioning. We will use all unique facilities and approaches of the Jena Experiment Research Unit by combining synthesis of long-term data in the Main Experiment and the ΔBEF Experiment with performing new soil analyses in the DrY Experiment, the ResCUE Experiment and a joint CoMic Experiment, to gain a better mechanistic understanding of plant diversity–ecosystem functioning relationships. In close collaboration with other sub-projects, we will assess biological, chemical and physical soil properties and stability indicators that will be used to calculate soil multifunctionality and multistability indices. In WP1, we will build on three unique datasets to explore short-term and long-term effects of plant diversity on the stability of soil (microbial) properties. In WP2, we will combine different datasets and approaches to explore if plant diversity effects on the magnitude and stability of soil properties increase with abiotic and biotic stresses. In WP3, we will combine measurements of the above-mentioned dimensions of soil stability to explore if plant diversity increases the stability of multiple soil properties under hot drought. This sub-project is at the heart of the Research Unit by testing the overarching hypotheses outlined in the Coordination Proposal of the Jena Experiment, contributing to all main experiments, sharing data and performing joint sampling campaigns with all sub-projects and, at the same time, introducing a novel concept of soil multistability as affected by plant diversity and climate extremes. We propose to use a combination of simple, high-throughput (e.g. bait-lamina test) and more sophisticated methods (e.g. extracellular polymeric substances analyses) to be able to investigate temporal dynamics of soil processes and their mechanistic basis. Taken together, the results of the three WPs will provide new insights into the stabilising mechanisms of soil properties in the long term and in relation to climate extremes through plant diversity.

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DOI: 10.3897/arphapreprints.e128158

Authors: Helge Bruelheide, Ute Jandt, Néstor Fernández, Andres Marmol-Guijarro, Bruno Smets, Marcel Buchhorn, Lori Giagnacovo, Giorgia Milli, Borja Jimenez-Alfaro, Jose Manuel Álvarez-Martínez

Abstract: The report demonstrates the potential workflows to leverage monitoring data on biodiversity to assess the status of two selected habitats of the Habitats Directive, Nardus grasslands (EU habitats directive Annex I 6230*) and forest dominated by Fagus sylvatica on acidic soils (habitat 9110).

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DOI: 10.3897/rio.10.e126532

Authors: Andrea Weeks, Elizabeth Collins, Twanelle Majors, Zack Murrell, Deborah Paul, Matthew Sheik, David Shorthouse, Shawn Zeringue-Krosnick

Abstract: We created and delivered a workshop and symposium series for biologists at all career stages focused on the skills and practices needed to sustain natural history specimen attribution and citation. The name of the workshop and symposium series, SISRIS, reflected our ultimate goal of effecting community-level change by sharing skills and practices that can support inclusive and sustainable (collections-based) research infrastructure for systematics. We report here the rationale for SISRIS, its learning objectives for participants and its results, including the assessment of outcomes from three iterations of the workshop held in 2023. The SISRIS workshops and symposia were held in person at the annual meeting of the Association for Southeastern Biologists in Winston-Salem, North Carolina and Botany 2023 in Boise, Idaho. A stand-alone SISRIS workshop was held online later to accommodate individuals who were unable to travel to the in-person events.

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DOI: 10.3897/rio.10.e127485

Authors: Christopher John Topping, Agnieszka Bednarska, Emilio Benfenati, Jordan Chetcuti, Noa Delso, Xiaodong Duan, Andreas Focks, Ryszard Laskowski, Anna Lombardo, Luna Marcussen, Teodor Metodiev, Michael Rubinigg, Maj Rundlöf, Fabio Sgolastra, Carla Stoyanova, Gregor Sušanj, James Williams, Elżbieta Ziółkowska

Abstract: PollinERA aims to reverse pollinator population declines and reduce the harmful impacts of pesticides. It addresses the call through four objectives: SO1 filling ecotoxicological data gaps to enable realistic prediction of the source and routes of exposure and impact of pesticides on pollinators and their sensitivity to individual pesticides and mixtures. SO2 developing and testing a co-monitoring scheme for pesticides and pollinators across European cropping systems and landscapes, developing risk indicators and mixture exposure information. SO3 developing models for predicting pesticide toxicological effects on pollinators for chemicals and organisms, environmental fate, toxicokinetic/ toxicodynamic, and population models. SO4 developing a population-level systems-based approach to risk and policy assessment considering multiple stressors and long-term spatiotemporal dynamics at the landscape scale and generating an open database for pollinator/pesticide data and tools.This will be achieved through developing knowledge and protocols for a broad range of toxicological testing, feeding to in silico models (QSARS, toxicokinetic/toxicodynamic, and population). Using a strong stakeholder co-development approach, these models will be combined in a One System framework taking a systems view on risk assessment and policy evaluation, including an international monitoring program.The One System framework is based on EFSA’s system ERA view, expanding on the tools used for bees to include butterflies, moths and hoverflies. The consortium partners are experts in the field needed for this development and are well-placed to facilitate the uptake of tools by European bodies to guarantee the project's future impact.Expected impacts target Destination impacts of better understanding and addressing drivers of biodiversity decline, interconnected biodiversity research using digital technologies, and understanding the biodiversity and health nexus at the ecosystem level.

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DOI: 10.3897/rio.10.e118851

Authors: Sabine von Mering, Erik Stolze, Katja Kaiser, Mareike Petersen

Abstract: Linked open data on collection agents contribute to increased discoverability, accessibility and transparency of natural history collections. Despite major efforts to digitise and open up museum and university object collections, related information is often stored in internal resources. This paper describes a project conducted at the Museum für Naturkunde Berlin (MfN) contributing to its collection disclosure and development initiatives. Information on historical collectors and other collection agents was transferred from the internal MfN collector wiki to Wikidata. For a total of 600 collection agents, existing Wikidata items were enriched or new items created.Special emphasis was put on linking these people to the Museum, to document their affiliation with the MfN, its collection and its archive. Within the project, an open participatory approach was taken. Several Wikidata edit-a-thons were organised to test this collaborative and innovative format for possible future application by the Museum. By opening up institutional silos and openly sharing data on agents connected to museum holdings, these data become more widely accessible and reusable, for example, as a resource for transdisciplinary provenance research.

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DOI: 10.3897/rio.10.e126586

Authors: Donat Agosti, Laurence Bénichou, Ana Casino, Lars Nielsen, Patrick Ruch, Puneet Kishor, Lyubomir Penev, Patricia Mergen, Christos Arvanitidis

Abstract: Knowledge about biodiversity is largely embedded in a daily growing corpus of over 500 million pages of biodiversity literature that is not machine-actionable. It is thus not open to building a biodiversity knowledge graph, or facilitating the use of artificial intelligence tools. This hinders the completion of a much-needed taxonomic name reference system, prevents the discovery of the biotic interactions underpinning the prediction and understanding of global change trends and consequences, viral spillovers, annotation of genes with their respective phenotypes, and their citations in various domains dealing with biological species such as conservation, agriculture, medicine, life sciences and industry, necessary to achieve the objectives of the Green Deal and address the targets identified in the Global Biodiversity Framework. This Policy Brief highlights key actions that can liberate the scientific data published, exploit their use , promote an enhanced way to publish, and ultimately foster excellence and innovation in biodiversity science, monitoring and conservation.

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DOI: 10.3897/rio.10.e126588

Authors: Lyubomir Penev, Quentin Groom, Ana Casino, Boris Barov

Abstract: A new community of research infrastructures has joined forces to provide scientists with seamless access to the plethora of data, services and tools in biodiversity research. New levels of technological innovation and interoperability between infrastructures foster unprecedented access to biodiversity data across all data domains and the entire research lifecycle, thus advancing open science practices and strengthening Europe's position in the global biodiversity research landscape. This policy brief highlights the potential benefits derived from enhanced connectivity and interoperability among various types of biodiversity data, fostering innovation and advancements in biodiversity science, monitoring, conservation, and policy development.

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DOI: 10.3897/rio.10.e121892

Authors: Wouter Los

Abstract: The original vision on what later became LifeWatch ERIC started about a quarter of a century ago in 1996. In those days, the promise of digital technologies entered biodiversity and ecosystem research. Not only by digitiing relevant information, but also with applications to process such data. While several (inter)national initiatives embarked on specific topics, there was also an idea that the upcoming view on grid computing provided attractive solutions for federated data sources, together with a strong computing capacity. This paper presents the history from conception to early actions, until actual preparations towards a research infrastructure on the European scale.

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DOI: 10.3897/arphapreprints.e125515

Authors: Simon Rolph, Chris Andrews, Dylan Carbone, Julian Lopez Gordillo, Tomas Martinovic, Nick Oostervink, Dirk Pleiter, Kata Sara-aho, John Watkins, Christoph Wohner, Jan Dick

Abstract: Digital twin approaches have the potential to revolutionise usage, planning and management of cultural ecosystem services i.e. the non-material benefits people obtain from ecosystems, including recreation, tourism, intellectual development, spiritual enrichment, reflection, and aesthetic experiences. Here we outline our blueprint for a prototype digital twin (pDT) for cultural ecosystem services. The pDT consists of two modelling components; a recreation potential model to quantify the cultural ecosystem services of the physical landscape and species distribution models to quantify the biodiversity component. It is envisaged that the digital twin will be used primarily by two user types 1. those who wanted to enjoy the area and potentially contribute to citizen science programs and 2. people who want to inform or make evidence-based management decisions (land managers, policy makers, researchers).

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DOI: 10.3897/rio.10.e120483

Authors: Alex Borisenko, Robert Young, Robert Hanner

Abstract: The adoption of environmental DNA approaches as a standard tool for biodiversity monitoring leads to the increase in the number of eDNA-based species occurrence records; however, considerable disparity remains in the nature and quality of associated information, much of it unpublished and/or poorly parametrised. A robust system for tracking biological materials from their point of origin through laboratory analyses is required to connect inferred taxon occurrences with analytical history and provenance data. The bulk of eDNA research is currently driven by small-scale operations where the tasks of digitisation, organisation and cross-referencing field records with laboratory analytical data and biomaterial sample location, are often performed manually and disconnected.We present an integrative, full-stack data management solution that provides a structured ontological concept, a minimalist data schema for eDNA research and a software application prototype designed to facilitate real-time digitisation, parsing, annotation and archival of eDNA data. The system tracks the provenance and analytical history of biological samples through a structured hierarchy of events, linked with associated digital file attachment archives, such as images and raw sequence files, and with inferred taxonomic occurrence records. The data entry process is compartmentalised and incorporated into the corresponding stages of standard operations used in fieldwork, biological collection management and laboratory analysis. Resulting data records can be integrated into various output formats required for large-scale analytics, publication and/or submission to global data aggregators. The prototype is implemented on the Microsoft 365 platform as a relational database (Access) linked to cloud-based data tables (SharePoint) and a set of associated data conversion spreadsheets (Excel). The system is designed primarily around the data management needs of small research labs; however, it is scalable to larger institutions and inter-institutional academic networks.

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DOI: 10.3897/arphapreprints.e123365

Authors: Douglas Spencer, Alexandra Marques, Clara Veerkamp, Martijn van der Marel, Peter Verburg, Anandi Sarita Namasivayam, Moreno Di Marco, Martin Jung, Heini Kujala, Louise O'Connor, Piero Visconti, Aafke Schipper

Abstract: Opportunity costs, the foregone economic benefits from alternative activities or uses of a resource on a particular site, represent one of multiple options to approximate costs of nature conservation and can be used alongside biodiversity and ecosystem services data in spatial conservation prioritisation analyses. However, such cost data are not yet available across Europe. We created a European opportunity cost layer for productive (arable, pastoral and forestry) and urban lands at a spatial resolution of 1 km2, using land, resource, and residential rents. We mapped the opportunity costs of productive lands based on (sub)national land and resource rent data, which we allocated to the grid level based on gridded agricultural and forestry production data combined with country-specific commodity prices. We converted empirical data on property rents specific to housing type and city into area-standardised and city-specific rents and then applied these values to all cities and urban area within the respective country. When multiple cities from a single country were represented in the empirical dataset, a mean value of all the corresponding cities was used.

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DOI: 10.3897/rio.10.e121887

Authors: Wouter Los, Magdalena Năpăruş-Aljančič, Tatyana Bileva, Eva Chatzinikolaou, Ohad Graber-Soudry, Lucas de Moncuit, Marta Neto, Graziano Pesole, Maria Vallejo Abascal, Dafinka Grozdanova

Abstract: A distributed research infrastructure such as LifeWatch ERIC necessitates close cooperation among the various components that constitute the research infrastructure and contribute to the overall services, facilities and resources it offers to the user community. In-kind contributions are non-monetary contributions, consisting of labour, services, facilities and access to resources, typically provided by the distributed components of the research infrastructure. The financing for in-kind contributions is usually provided by the national funding agency on behalf of the LifeWatch member country or by the member directly, with a value being accredited towards the member's funding obligations to LifeWatch ERIC. The management and validation of in-kind contributions towards shared objectives are integral to the legal framework supporting LifeWatch ERIC. This involves a rigorous assessment process to verify each in-kind contribution. This short article outlines that process and explores the function of the In-Kind Contributions Committee (IKCC) at LifeWatch ERIC.

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DOI: 10.3897/rio.10.e120626

Authors: Laurence Livermore, Holly Little, Jillian Goodwin, Sylvia Orli, Helen Hardy, Frederik Berger, Emily Braker, Jacqueline Chapman, Lauren Cohen, Sharon Grant, Jesse Grosso, David Jennings, Austin Mast, Gary Motz, Gil Nelson, Nelson Rios, Vincent Rossi, Franziska Schuster, Rebecca Snyder, Kira Sobers, Patrick Sweeney, Kimberly Watson, Alyson Wilkins, Jennifer Zaspel, Breda Zimkus, Diane Zorich

Abstract: Many larger museums and archives have begun to implement a centralized approach to digitization of collections by creating Digitization Coordinator positions. This new effort has initiated a singular vision for digitization that incorporates priorities, workflows, and resources to greatly improve the efficiency and throughput of digitization in collections. Smaller institutions are now starting to see the benefit of creating a more structured cross-disciplinary approach to digitization, allowing for better awareness and resourcing of digitization needs.The workshop brought together natural sciences digitization professionals from the USA and EU, highlighting lessons learned and best practices to realize the benefits of a coordinated approach including advocacy for digitization, accelerating digitization efficiency and, ultimately, increasing digital collections access and usability to address societal challenges, such as biodiversity decline. Insights, lessons learned and initial thoughts on best practices are described, and the supporting workshop resources are shared so that others can benefit.

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DOI: 10.3897/rio.10.e119943

Authors: Christos Arvanitidis, Alberto Basset, Peter van Tienderen, Cristina Isabel Huertas Olivares, Cristina Di Muri, Lucas de Moncuit, Wouter Los

Abstract: LifeWatch ERIC has embarked on its new destination towards upgrading and (co-)constructing its Infrastructure as a response to the needs of its target communities and stakeholders. Through an industrialisation process, all independent data, software components, publications and other types of research products contributed by the Member Countries will be consolidated and integrated to enable collaborative development. The Technology Readiness Level of LifeWatch ERIC will be raised to level 9. This process is described in its new Strategic Working Plan on its second implementation period (2022-2026). Accordingly, this topical collection of papers includes articles which describe the main outcomes, that is the deliverables of this new Strategic Working Plan. The deliverables published in this topical collection are not of a confidential nature and are developed in the form of a standard, structured template.

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DOI: 10.3897/rio.10.e107393

Authors: Tina Heger, Jonathan Jeschke, Maud Bernard-Verdier, Camille Musseau, Daniel Mietchen

Abstract: This paper provides a brief overview of a major hypothesis in invasion biology: the enemy release hypothesis. Building on a summary of different previous definitions, we provide the following revised definition: “A reduced pressure by enemies in the non-native range contributes to invasion success.” Further, we suggest formalizing the hypothesis in the basic form ‘subject - relationship - object’ to allow for disambiguating the different existing meanings and enhancing their usability by machines.

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