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/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 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/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/arphapreprints.e182452

Authors: Emad Al-Helaly

Abstract: This study utilizes multi-temporal remote sensing images and Geographic Information Systems (GIS) to analyze and document significant land cover changes in the Bahr Al-Najaf depression, Najaf Governorate, Iraq, over a 23-year period (2002–2025)1.A systematic methodology was employed, featuring the use of Landsat series (TM, ETM+, OLI/TIRS). Following rigorous preprocessing for radiometric and geometric consistency 3, the images were subjected to supervised classification using the robust Random Forest algorithm4. The primary land cover classes analyzed include shallow water, deep water, dry soil, wet soil, and buildings. The post-classification comparison method was applied across multiple time intervals (e.g., 2002 vs. 2015, 2023 vs. 2025) to quantify the dynamics of change. The results were validated with field visits to document classification accuracy and identify water sources.The findings reveal a highly dynamic environment, marked by severe fluctuations in water bodies. The study documents periods of significant drought and water scarcity, particularly noting the near-disappearance of shallow water and increased dry land presence by 2015. This decline is attributed to reduced rainfall, excessive groundwater depletion from random drilling, and high evaporation rates exacerbated by temperatures reaching 500 C. Conversely, the analysis also notes an expansion in water area between 2003 and 2023, considered the largest in decades. Furthermore, there has been an evident increase in anthropogenic changes, specifically the growth of built-up areas (buildings), driven by agricultural and tourism projects, which has led to waterlogging, deterioration of vegetation cover, and potential conflict with efforts to establish the area as a nature reserve. Continuous monitoring is essential for controlling the fate of this biologically and ecologically vital area.

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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/arphapreprints.e176591

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/arphapreprints.e175020

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.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, Andres Marmol-Guijarro, 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/arphapreprints.e166452

Authors: Gorgias AIKPON, Jean Cossi Ganglo

Abstract: The spread of species worldwide, previously governed by natural processes, is now largely influenced by globalization, trade development, and human movement. Some species become invasive, causing major concerns due to their negative impacts on natural ecosystems and biodiversity. This study employs a methodological approach combining bibliometric analyses and the PRISMA protocol. Using VOSviewer and R, we analyzed scientific literature on invasive alien species. Results reveal a sustained growth in scientific publications, reflecting researchers' increasing interest in this issue. However, a crucial observation emerges: most research is not integrated into national policies with concrete management measures. The results shows a growing scientific focus on invasive species, indicating their significance as a research subject. Despite this academic attention, a critical gap exists between fundamental research and practical management strategies. An urgent need exists to bridge the divide between scientific research on invasive species and practical management programs at local, regional, and national levels. This approach is essential to safeguard biogeographical regions already impacted and preserve non-invaded areas.

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DOI: 10.3897/arphapreprints.e162936

Authors: Suvarna Khadakkar, Ashish Tiple, Ashish Kumar Jangid, Arun Khurad

Abstract: Studies on scarab (Insecta: Coleoptera: Scarabaeidae) seasonality from central Indian province are sparse, particularly from tropical dry deciduous forests. Our study of seasonal distribution of scarabs in Bor forest, a tropical dry deciduous forest of central India, led to a collection of 72 species belonging to 35 genera under seven subfamilies namely, Aphodiinae, Cetoniinae, Dynastinae, Melolonthinae, Rutelinae, Scarabaeinae and Orphnini. Subfamily Scarabaeinae is found to be the most speciose with 36 species under 14 genera. Genus Onthophagus is the most speciose genus with 15 species. Subfamily Orphninae found to be the least diverse with a single species. Season and weather parameters shaped the scarab beetle assemblages in the tropical dry deciduous Bor forest. Scarab species richness is found to be positively and significantly related to the mean temperature (β=0.03±0.01 SE, p<0.05) and to the mean precipitation (β=0.03±0.01 SE, p<0.05). Constrained by logistics, we could not identify optimum temperature or precipitation values on which the scarab species richness can be highest for both the fitter models

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DOI: 10.3897/arphapreprints.e160486

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/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/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/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, Javier Palma-Guerrero, 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/arphapreprints.e154400

Authors: Suvarna Khadakkar, Ashish Tiple, Arun Khurad

Abstract: Though economically important, the field of description of larval morphology and taxonomy of Scarabs is restricted to a very few publications specifically from India. This study was planned to study and document the morphology of developmental stages of one of the most commonly occurring species of scarab, Holotrichia fissa (Coleoptera: Scarabaeidae: Melolonthinae) from central India. Here we describe in detail the morphological characteristics of egg, first, second and third instar larva and pupa along with notes on biology of the species. The details of third instar larva are described focussing on the structure of Cranium, Antenna, Labrum, Clypeus, Epipharynx, Mandibles, Maxilla, Thorax, Abdomen, and Raster pattern. This study adds to the knowledge of morphology of the developmental stages the species.

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DOI: 10.3897/arphapreprints.e153920

Authors: Petros Lymberakis, Danae Karakasi, Manolis Papadimitrakis, Rita Monteiro, Astrid Böhne, Rosa Fernández, Nuria Escudero, Jean-Marc Aury, 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/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/arphapreprints.e142661

Authors: Suvarna Khadakkar, Ashish Tiple, Arun Khurad

Abstract: Detailed description of IIIrd Instar larva and pupa of Phyllognathus dionysius is described along with notes on biology and distribution. Beetles belonging to the family scarabaeidae are economically important as crop pests. Grubs of P. dionysius are polyphagous and known to feed on roots of Jowar, Bajra, Maize, Turmeric, Sugarcane and Paddy while adults are nocturnal in habit and feed on foliage of Ficus sp. For the study, grubs of P. dionysius were collected from dung pads from the Bor forest of Maharashtra, central India. Collected grubs were reared in rearing pots in the laboratory under optimum temperature and humidity. Our knowledge of developmental stages of scarabs lags behind our knowledge of the adults especially in the fields of morphology and taxonomy. In this study, we provide diagnostic characters for identification of the immature stages in brief. Biology of the species is described on the basis of its coprophagous behaviour. Life cycle of P. dionysius completed in 145-163 days with prepupal period of 24-36 hours and pupal period of 9-11 days.

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DOI: 10.3897/arphapreprints.e140771

Authors: Martina 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/arphapreprints.e140550

Authors: Florencia 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.e139236

Authors: Joana Bores, Hildegard Meyer, Evelyn Underwood, Mila Sirychenko, Wouter Langhout, 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, Marta 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/arphapreprints.e132939

Authors: Matt von Konrat, Yarency Rodriguez, Colleen Bailey, Gilbert Gwilliam III, Christine Christian, Blanka Aguero, June Ahn, Zoe Albion, James Allen, Colin Bailey, Erryn Blake, Winnie Blake, Gwen Blake, Laura Briscoe, Jessica Budke, Thomas Campbell, Matt Chansler, Dina Clark, Robin Delapena, Michael Denslow, Shari Ellis, Elizabeth Ellwood, Belle Ens, Nkosi Evans, Alejandra Fabian, Wyatt Gaswick, Kate Golembiewski, Sharon Grant, Kimberly Hansen, Brittany Janney, Janeen Jones, Zachary Kachian, Lucia Kawasaki, Olivia Leek, Kacee Kellum, Crystal Maier, Austin Mast, Joann Martinec, Paul Mayer, Melissa Mladek, Ainun Nadhifah, Christopher Neefus, Mary Nodulman, Margaret Oliver, Kelsey Overberg, A. Townsend Peterson, Ayesha Qazi-Lampert, Carl Rothfels, Robert Salm, Dawn Schreiner, Matthew Schreiner, Eric Tepe, Maureen Turcatel, Amelia Vega, Heaven Wade, Dianne Weinand, Kate Webbink, Todd Widhelm, Miranda Zwingelberg

Abstract: A comprehensive overview of volunteer-driven public programs focused on activities to enhance natural history collections (NHCs) is provided. The initiative revolves around the WeDigBio events and the Collections Club at the Field Museum, aiming to deepen the public's connection with scientific collections, enhance participatory science, and improve data associated with natural history specimens. The implementation and journey of these programs are outlined, including surveys conducted from 2015 through 2021 to gauge participant motivation, satisfaction, and the impact of these events on public engagement with NHCs. Results show trends in on-site and virtual volunteer participation over the years, especially during the peak period of the COVID-19 pandemic. The majority of participants expressed high satisfaction, indicating a willingness to continue participating in similar activities. The surveys revealed a shift towards more altruistic motivations for participation over time, with increased emphasis on supporting the Field Museum and contributing to the scientific community. The success of participatory science events demonstrates the potential of volunteer-driven programs to contribute meaningfully to the preservation, digitisation, and understanding of biodiversity collections, ultimately transforming spectators into stewards of natural history. From 2015 to present participants celebrate a significant milestone, with over a thousand community scientists contributing to the inventorying, collection care, curation, databasing, or transcription of 286,071 specimens, objects or records. We also discuss accuracy and quality control as well as a checklist and recommendations for similar activities.

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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/arphapreprints.e129598

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. Digitization has greatly enhanced the use of herbarium data in the analysis of species distribution data and ecological niche modeling. Yet, sources on modeling and mapping methodology using open source software is greatly lacking for beginners. We have created a replicable and thorough tutorial to visualize species occurrence data and exploratory analysis that was developed by undergraduates with broad backgrounds and levels of expereince. This tutorial integrates the open-source programs 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 modeling of rare Illinois bryophytes to better understand the potential impact of climate change.

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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/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/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/arphapreprints.e125077

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

Abstract: European grassland management has often favored high production through frequent mowing and heavy fertilization 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/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/arphapreprints.e119131

Authors: Ana Ceia-Hasse, Judy Shamoun-Baranes, Néstor Fernández, Henrique Pereira, César Capinha

Abstract: A relevant number of ecological questions raised by policymakers, managers, and citizens often pertain to the short-term future (e.g., the coming days or weeks). In this sense, short-term ecological and biological forecasts can make substantial and practical contributions to achieving policy objectives and benefit society broadly. Specifically, short-term forecasts of Essential Biodiversity Variables (EBVs) and Essential Ecosystem Service Variables (EESVs) can support decision-making by stakeholders from multiple sectors, enabling to anticipate ecological transformations and support proactive, informed decisions that promote conservation, economic activities, and human well-being.The aim of this task was to demonstrate how a European Biodiversity Observation Network can support the generation of short-term spatial forecasts of ecological and biological phenomena relevant to the Bioeconomy Strategy and to EU citizens at large. Our specific objectives included showcasing 1) a computational workflow that enables the production of days-ahead forecasts for distinct ecological or biological phenomena and 2) a specialized computational workflow for days-ahead forecasts of bird aerial biomass. The first, (‘generic’) workflow, is exemplified using two case studies: i) forecasting the fruiting of a wild mushroom of commercial and recreational relevance, and ii) forecasting the life stage of relevance for surveillance of an invasive pest species important for agriculture. These case studies aim to demonstrate specific, tangible contributions that short-term ecological forecasting can make towards the sustainable use of bio-based economy sectors, ecosystem protection, and anticipation of ecological risks. Beyond aligning with the EU Bioeconomy Strategy, our three forecasting targets also offer relevant contributions to a wider range of EU strategies and policies.We actively involved stakeholders in defining the end-products and in the development of computational modelling approaches of the workflows. This process entailed two distinct approaches. For the generic forecasting workflow, we engaged in a participatory process from the project's start, focusing on stakeholders involved in mushroom foraging and experts in mycology and ecological modelling. For the bird aerial biomass forecasting workflow, we built upon substantial developments that predated the project, with our engagement primarily drawing on insights and input from earlier initiatives. The two workflows serve complementary purposes in terms of the primary data they use. While the first (generic) workflow is based on the growing body of opportunistic biodiversity observation data, particularly from citizen science initiatives, the second workflow requires highly specialized radar data from weather stations. However, both workflows use predictor data from weather observations and forecasts and employ machine learning algorithms to correlate these data with observed variations in the phenomena being forecasted.

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DOI: 10.3897/arphapreprints.e115172

Authors: Mark Brown, Matthias Albrecht, Pilar De la Rúa, Sara Hellström, Alexandra-Maria Klein, Denis Michez, Francesco Nazzi, Robert Paxton, Edward Straw, Dimitry Wintermantel, Simon Potts

Abstract: Managed bees and other pollinators are exposed to a wide variety of stressors and these often act in combination. Historically, most risk assessments and research have focused on the impacts of individual stressors on honey bees. However, there is broad scientific consensus that there is a need for a systems-based risk assessment approach and a post-approval monitoring system. This should consider: multiple interacting stressors; a variety of pollinator species (including different subspecies, sexes, castes and life history stages); field studies as well as laboratory studies; and a diversity of end-points (molecular, physiological, behavioural, developmental, reproductive and colony health). The PoshBee project has made a significant step in our understanding of how the interactions between agrochemicals, pathogens and nutrition impact different bee species.

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DOI: 10.3897/arphapreprints.e114920

Authors: Mathias Dillen, Andreas Plank

Abstract: In this task, the aim is to develop a workflow that should facilitate the linking process of collector name strings to PIDs for those collectors. Such a workflow should help scale up the number of links being made, make the process more efficient and should take advantage as much as possible of existing work and infrastructures, so as not to reinvent the wheel. As such, the work can be roughly split into a few subtasks:- Make existing linking workflows more easily implementable in other contexts and by other infrastructures. This includes finding ways for such workflows to produce links that can easily be published, i.e. in a standardised format compatible with existing infrastructure. The suitability of different infrastructures for making established links available should also be assessed.- Establish, document and improve the comprehensiveness, findability and interoperability of the content in PID-minting resources, in particular Wikidata as it can be edited openly.- Refine the decision making process of establishing links, by implementing and improving the methods that can be used to validate potential links.In this document, the focus lies on linking people. We will propose a workflow to 'roundtrip' links established through the Bionomia platform back to the collections holding the attributed specimens, as well as making them available for use by other BiCIKL infrastructures. We will also refine existing automated linking workflows and pilot the new functionalities on the (botanical) collections of the task partners. These refinements will be influenced by an assessment of the current state of Wikidata, investigated through shape expressions constructed from commonly used queries and from Wikidata records which have been linked in previous efforts such as the Botany Pilot, Bionomia and published specimen data to GBIF.

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DOI: 10.3897/arphapreprints.e114048

Authors: Maëlle Wannier

Abstract: The Digital Botanical Gardens Initiative (DBGI) embarks on an innovative journey to curate, manage, and disseminate digital data from living botanical collections, with an emphasis on mass spectrometric evaluations of chemodiversity. Using semantic web technology, this data is linked with relevant metadata, propelling ecosystem research and guiding biodiversity conservation efforts. Central to the success of DBGI is the creation of an interactive platform for both humans and machines to assimilate this knowledge. This report outlines our efforts to design the prototype of a data visualization portal intended to evolve into the DBGI dashboard. Starting with a Plotly Dash application, the project transitioned to a Node.js application leveraging Javascript, HTML, and CSS for enhanced customization. This provides a basis for future improvements, some of which are proposed in the report.

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DOI: 10.3897/arphapreprints.e112382

Authors: Bryony Willcox, Deepa Senapathi, Mark Brown, Simon Potts

Abstract: In the real world, pollinators face multiple interacting pressures, and so response options must be tailored to this. To date, most attention has been on characterising the risks to managed pollinators from single stressors, though recently more attention has been paid to risks from multiple stressors (e.g., pesticides, pathogens and poor nutrition). The PoshBee project has developed a policy brief providing recommendations on options that mitigate against multiple stressors.

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DOI: 10.3897/arphapreprints.e112175

Authors: Mark Brown, Philippe Bulet, Marie-Pierre Chauzat, Alexandra-Maria Klein, Anina Knauer, Marika Mand, Denis Michez, Francesco Nazzi, Robert Paxton, Oliver Schweiger, Jane Stout, Orlando Yanez, Simon Potts

Abstract: Policies and management practices for managed bees and other pollinators are increasingly reliant on the availability of high quality data in order to inform them. This in turn requires the widespread adoption of state-of-the-art standardised methods and approaches so that new data and knowledge are both robust and trustworthy. The PoshBee project has developed, tested, and validated a wide range of new tools. These include, but are not limited to: experimental protocols, monitoring tools, technological tools and practice guides. The wide scale application of these, and other tools will help ensure that researchers, risk assessors, policymakers, beekeepers, and agri-food industry are producing data to the highest standards in a way that increases comparability and transparency.

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DOI: 10.3897/arphapreprints.e107394

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

Abstract: The enemy release hypothesis is a major and well-known hypothesis in invasion biology. Building on a summary of different previous definitions, we provide the following revised definition: “A reduced pressure by enemies in the non-native range positively affects 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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DOI: 10.3897/arphapreprints.e107169

Authors: Wouter Addink, Niki Kyriakopoulou, Lyubomir Penev, David Fichtmueller, Ben Norton, David Shorthouse

Abstract: United and coordinated efforts of biodiversity data infrastructures are needed to bring together various data forms from many different scientific areas. Biodiversity data are considered of great importance and use when they form a network of knowledge that can be seamlessly integrated and presented to various audiences, promoting both research and education. The Biodiversity Community Integrated Knowledge Library (BiCIKL) project seeks to maximise the potential of integrated data sources by striving to connect fragmented data derived from biological, paleontological, and geological specimens and collections, as well as all derived information such as literature in the form of taxonomic treatments, research papers etc., taxonomic information and molecular sequences provided by these infrastructures, under the umbrella of common digital practices and policies in curation, data sharing and open data access over different scientific fields. One of the main goals of BiCIKL is to create bi-directional links between various data types, a process enabled by: a) the adoption of globally unique and persistent identifiers upon agreement among all stakeholders, that link to digital specimen objects, collections, taxonomic treatments, people, sequence data and taxa, and b) implementation of the best practices for the generation, management and curation of interlinked data by the host infrastructures. At the same time, infrastructures should be readily discoverable and accessible by end users, providing data that enable re-usability. In this manual we give an overview of the best practices and their associated recommendations for infrastructures on making the most out of their services and data, for establishing a network of knowledge with other infrastructures, for servicing researchers, data providers and other end users. These guidelines have been developed in collaboration with the infrastructures through Technical RI Forum meetings organised in the context of the BiCIKL project. Practices and recommendations were divided into six categories: 1) modalities of access, 2) building communities and trust, 3) technology and standards, 4) versioning of APIs and their data, 5) bi-directional linking between infrastructures and 6) API design patterns and naming conventions. A second division into three user groups (Infrastructures, Data providers, Users e.g. Researchers, Developers and Citizen scientists) is presented in Appendix I.

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DOI: 10.3897/arphapreprints.e107168

Authors: Wouter Addink, Sharif Islam, Mathias Dillen, Anton Güntsch, Soulaine Theocharides

Abstract: Persistent Identifier (PID) systems are the foundation for achieving the FAIR Guiding Principles (“findable, accessible, interoperable and reusable”). As FAIR data and connecting different data classes (i.e. specimens, genomics, observations, taxonomy and publications) are essential aspects of the BiCIKL project, we need a PID system at least at the European level to create and maintain identifiers for the digital representation of specimens and samples, called Digital Specimens (DS) (Hardisty et al. 2022). The PID system provides the mechanism to ensure that identifiers are globally unique, persistent and resolvable. This system should also manage associated metadata, facilitate provenance, enable discovery, manage states and the life cycle of the PID, link to other derived data and digital content, and allow content providers to enforce metadata constraints. For the successful provision of a PID system, this design document has been created to guide us during the implementation and operation phases. The document is based on an earlier milestone (MS28) that was used for discussion and evaluation with potential end-users.

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DOI: 10.3897/arphapreprints.e107167

Authors: Kessy Abarenkov, Allan Zirk, Guy Cochrane, Vishnukumar Kadhirvelu, Joana Pauperio, Olaf Bánki, Jerry Lanfear, Filipp Ivanov, Timo Piirmann, Raivo Pöhönen, Urmas Kõljalg

Abstract: This deliverable report includes description of the work steps towards building a web interface for the reporting of errors and gaps in sequenced material source annotations as part of the Task 8.3 of BiCIKL. Beta version of the web interface has been published and is available for the registered users of PlutoF platform.

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DOI: 10.3897/arphapreprints.e107166

Authors: Soulaine Theocharides, Niki Kyriakopoulou

Abstract: Work package 11 of the BiCIKL project involves developing software tools to support a FAIR experience for members of the biodiversity research community. The package overall focuses on Findability, by providing tools to search and answer questions, and Accessibility, through developing links across various biodiversity data sources and research tools. Task 11.2 specifically involves prediction of new links using machine learning. We chose to demonstrate the functionality of machine learning link prediction with plant-pollinator interactions. This type of interaction was chosen due to the wealth of data available, particularly on the Global Biotic Interactions (GloBI) database, as well as this kind of interaction’s ecological and economic significance. The result was a RESTful API capable of predicting plant-pollinator interactions among a predefined set of species. Predictions are made on-the-fly, at the time of the request. The GitHub repository for the API can be found here: https://github.com/DiSSCo/BiCIKL_Linkages_APIThe API takes either a plant or a pollinator as inputs, and outputs potential matches based on a user-defined confidence score. The API’s prediction is powered by a random forest classifier stored on disk. The classifier was trained on the taxonomic hierarchy of observed plant-pollinator pairs obtained from the GloBI database. When evaluating the likelihood of an interaction, the trained classifier looks at the taxonomic hierarchy of both the plant and pollinator and outputs a confidence score. What pairs are returned is determined by the minimum confidence score set by the user.

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DOI: 10.3897/arphapreprints.e106369

Authors: Christos Arvanitidis, Ron Dekker, Andreas Petzold, Niklas Blomberg, Giovanni Lamanna, Rudolf Dimper, Cristina Isabel Huertas Olivares, Ana Mellado, Matthew Viljoen, Sally Chambers, Montserrat González, Sophie Viscido

Abstract: The Special Collection of articles on the Science Projects of the EOSC Future project, funded by the European Commission, refers to one of the essential components of the project. This editorial article explains how the Science Projects fit to the EOSC Future, the way their concept has been developed and evolved during the preparation and the implementation of the project and it also makes an introduction to the templates developed by the Science Projects as a plan to carry out their activities.

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DOI: 10.3897/arphapreprints.e105207

Authors: Dylan Nguyen

Abstract: With an alarmingly high rate of Long COVID, it is essential to address the lack of understanding of the pathogenesis and susceptibility to Long COVID. This study aims to investigate how symptoms and immunological markers of Long COVID are correlated in order to develop better biomarkers and inform strategies to accurately identify patients at high risk for developing Long COVID. It has been found that underlying health conditions increase the likelihood of developing Long COVID. Additionally, certain symptoms during COVID-19 infection have been linked to Long COVID. However, the immune system activity has not been well investigated for its correlation to the susceptibility and severity of Long COVID symptoms. In our study, human subjects from the United States and United Kingdom will be followed for a year, where they will be tested weekly for the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), draw blood for immune system activity analysis, and report symptoms bidaily. Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) will be used to detect and quantify the presence of SARS-CoV-2. Qualitative information about participants will be collected via the ZOE Health Study app to enable the collection of clinical metadata such as symptoms. This study’s unique and sizeable prospective cohort will provide critical knowledge about the susceptibility of patients to Long COVID by pre-existing symptomatology and immune markers. Moreover, we will better understand the possible mechanisms and pathogenesis of the disease.

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DOI: 10.3897/arphapreprints.e104881

Authors: David Kleijn, Ignasi Bartomeus, Vincent Bretagnolle, Kati Häfner, Felix Herzog, Jochen Kantelhardt, Erik Öckinger, Simon Potts, Giulia Riedo, Anna Sapundzhieva, Lena Luise Schaller, Nikol Yovcheva

Abstract: Agricultural expansion and intensification are key drivers of biodiversity decline. There is mounting evidence that modern farming impacts the effectiveness of protected areas as one of the key instruments of biodiversity conservation through, for example, eutrophication, pesticide emissions or increasing access to remote areas [1]. This is increasingly acknowledged and in many countries conservation efforts now include farmed lands and engage farmers to enhance biodiversity on their lands. This benefits farmland biodiversity which, especially in Eurasia, supports some highly threatened species groups [2]. However, farmland biodiversity is also functionally important as it provides a wide range of ecosystem services. Examples are natural pest regulation, pollination, carbon sequestration, human well-being, water purification and cultural services. Agricultural management influences the provision of a wide range of ecosystem services and therefore, contributes to food security and mankind’s ability to sustain itself in the mid to long term. There is clear evidence that enhancing farmland biodiversity promotes the delivery of specific ecosystem services [3]. For example, enhancing wild pollinators and natural enemies through the provision of semi-natural habitat enhances productivity of many crops [4, 5]. However, only a few ecosystem services, such as pollination, pest control and nutrient cycling, may provide private benefits to farmers. Other services, such as carbon sequestration, biodiversity conservation, health benefits and water purification, are public goods which are poorly captured by markets [6].

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DOI: 10.3897/arphapreprints.e104251

Authors: Hannah Moersberger, Juliette G. C. Martin, Jessi Junker, Ivelina Georgieva, Joachim Maes, Ian McCallum, Henrique M. Pereira, Aletta Bonn

Abstract: In order to assess user and policy needs related to biodiversity monitoring and data, the EuropaBON project invited national experts to fill in this survey in August 2021. The survey was tailored to the national level and aimed at identifying current monitoring efforts, data flows from collection to reporting, data uptake by policymaking, challenges and roadblocks, as well as biodiversity variables and indicators for a desirable future. On behalf of the European Commission (DG Environment) and EuropaBON, the surveys were sent out to all national focal points of the European Environment Information and Observation Network (Eionet) as well as key national agencies. Eionet is a partnership network of the European Environment Agency (EEA) and its 38 member and cooperating countries to gather and develop data, knowledge, and advice to policy makers about Europe's environment. The results of our surveys form the basis for the analysis of the EuropaBON User and Policy Needs Assessment (DOI) and inform the design of the Europa Biodiversity Observation Network and its work programme. We published the original responses of survey sections A and B in the annex of the User and Policy Needs Assessment. Responses of section C were synthesised in the assessment.

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DOI: 10.3897/arphapreprints.e104168

Authors: Hannah Moersberger, Juliette G. C. Martin, Jessi Junker, Ivelina Georgieva, Joachim Maes, Ian McCallum, Henrique M. Pereira, Aletta Bonn

Abstract: In order to assess user and policy needs related to biodiversity monitoring and data, the EuropaBON project invited European experts to fill in this survey in August 2021. The survey was tailored to the European level and aimed at identifying current monitoring efforts, data flows from collection to reporting, data uptake by policymaking, challenges and roadblocks, as well as biodiversity variables and indicators for a desirable future. On behalf of the European Commission (DG Environment) and EuropaBON, the surveys were sent out to key European agencies (e.g., DG ENV, DG AGRI, DG CLIMA, EEA, Eurostat, Biodiversa+). The results of our surveys form the basis for the analysis of the EuropaBON User and Policy Needs Assessment (DOI) and inform the design of the Europa Biodiversity Observation Network and its work programme. We published the original responses of survey sections A and B in the annex of the User and Policy Needs Assessment. Responses of section C were synthesised in the assessment.

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DOI: 10.3897/arphapreprints.e103105

Authors: Carolina Corrales, Samantha Luciano, Jonas J. Astrin

Abstract: Biobanks are curated collections of biological samples that are preserved at the molecular level, usually frozen, along with associated data, and managed to high scientific standards. We conducted a 'landscape analysis'—based both on a community survey and a literature review—to determine commonalities, information gaps, and challenges in the various workflows of biodiversity and environmental biobanks. The survey was completed by 55 institutions from more than 20 countries. Its results were compared to other collection-based surveys and complemented by literature research in the areas of general biobank management, staffing, sample handling, storage, (cryo-/)preservation, policies, databases, and networking. We illustrate the strengths and weaknesses of biodiversity and environmental biobanks and provide some basic recommendations for improving biobank procedures. In general, we found that increased efforts are needed to standardise biobank workflows or individual workflow components. While general, organism-independent biobanking guidelines already exist, more detailed guidance documents to date mostly address only human biobanking, or a narrow range of biodiversity. We hope to start closing that gap by providing an overview of current protocols and practices in biodiversity and environmental biobanking in form of a handbook, to which the present work is directly related. The handbook is available open-access under https://doi.org/10.3897/ab.e101876.

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DOI: 10.3897/arphapreprints.e102530

Authors: Jessi Junker, Pedro Beja, Lluís Brotons, Miguel Fernandez, Néstor Fernández, W. Daniel Kissling, Maria Lumbierres, Anne Lyche Solheim, Joachim Maes, Alejandra Morán-Ordóñez, Francisco Moreira, Martin Musche, Joana Santana, Jose Valdez, Henrique Pereira

Abstract: EuropaBON harnesses the power of modelling Essential Biodiversity Variables (EBVs) to integrate different reporting streams, data sources, and monitoring schemes, and measure biodiversity change across multiple dimensions in space and time. Therefore, EBVs are at the core of the project and form the basis for several of the tasks feeding into the co-design of a biodiversity monitoring system for Europe. In this document, we describe the stepwise process of identifying and specifying the EBVs in the EBV list presented in this deliverable. We further provide a summary of the characteristics of the EBVs identified for EuropaBON, in terms of their desired spatial- and temporal resolutions, as well as the taxonomic/ ecosystem scope to be measured.

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DOI: 10.3897/arphapreprints.e101323

Authors: Matthew J Allan, Robin Dean, Alexandra-Maria Klein, Dimitry Wintermantel, Matthias Albrecht, Janine Schwarz, Anina Knauer

Abstract: Under the terms of the PoshBee agreement, the members tasked with delivering Work Package 7 carried out semi-field and field studies on honey bees, bumble bees and solitary bees. These studies involved the exposure of the bees to more than one stressor, for example a fungicide and an insecticide or a fungicide and a nutritional deficiency. This is in contrast to the conventional study design where one stressor or product alone is assessed.These studies built upon recommendations by the European and Mediterranean Plant Protection Organisation (EPPO), European Food Safety Authority (EFSA), Prevention of Honeybee Colony Losses (COLOSS), and the Organisation of Economic Co-operation and Development (OECD). The team of researchers incorporated several innovative approaches in designing and carrying out the studies. In the authors’ view both the quality and quantity of data required for ecotoxicology studies can be improved by adoption of novel methods, including electronic means and artificial intelligence, and the design, manufacture and use of equipment specifically for such studies. Several examples are described.It is the intention of the team to include in this document practical advice for workers who are not familiar with such studies.

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DOI: 10.3897/arphapreprints.e99679

Authors: Elena Velado-Alonso, Ignasi Bartomeus, Kira Keini, Suresh Chithathur, Anna Sapundzhieva, Alexandra Korcheva, David Kleijn

Abstract: Communication and dissemination are key elements to maximise SHOWCASE project impact and ensure long‐term effects. For that, an effective communication strategy is essential to convey the principles and best practices to integrate biodiversity in farm management to favour farmers’ livelihoods while promoting conservation in agricultural landscapes. Current discourses around biodiversity, nature conservation and farming are contradictory with each other and not always engaging for SHOWCASE stakeholders. Thus, an inspirational narrative has been developed in the first months of the project by WP4 “Communicating the benefits of agrobiodiversity through multistakeholder knowledge exchange”, task 4.1. SHOWCASE narrative explains in an effective manner 1) why people care about biodiversity; 2) what we can do, and; 3) how we can do it better.

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DOI: 10.3897/arphapreprints.e96718

Authors: Heidi Murray

Abstract: The Florida Keys Mosquito Control District (FKMCD) is an independent taxing district in Monroe County, Florida. The mission of FKMCD is to protect the community and visitors of the Florida Keys from mosquito-borne disease and prevent nuisance mosquitoes from impacting the quality of life of its citizens and the local economy. The State of Florida requires mosquito control programs to provide recorded evidence of mosquito activity prior to pesticide application. Surveillance is an appropriate method to record the abundance and mosquito species present in an area to determine if adulticide applications are necessary. Mosquito surveillance traps have been set by FKMCD since 1998. Trapping is conducted throughout the District to document species composition and abundance.  Mosquito surveillance is used for operational decisions for both nuisance mosquitoes and disease vectors.This data set includes previously unreported mosquito trapping results in Monroe County, Florida. This data set includes trap results collected from CDC light traps and BG Sentinel traps set weekly on Vaca Key, Flamingo Island, Key Colony Beach, Fat Deer Key, Crawl Key, Long Point Key, Grassy Key, Long Key, and Lower Matecumbe Key from January 1, 2018 through December 31, 2021.

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DOI: 10.3897/arphapreprints.e93511

Authors: Anna Sapundzhieva, Alexandra Korcheva, Georgi Zhelezov

Abstract: The following report presents the initial project branding and marketing products that showcase the project’s visual identity and overall corporate appearance.As a foundation of the future effective communication activities, a sound set of working dissemination tools and materials is crucial to be established within the first months of the project. A project logo, project promotional materials, overall visual identity package, and a public website (www.showcase-project.eu) were developed in the first 4 months of the project duration in order to form the main tools of project public visibility and internal communication.The project is provided with a logo that has been communicated and coordinated with all project partners. Dissemination materials such as the SHOWCASE brochure and poster were produced for raising awareness and engaging stakeholders at events. A project brand manual was created and circulated among project partners in order to provide a consistent visual representation of the project. A set of corporate templates was also produced and made available to the consortium partners to facilitate future dissemination and reporting activities such as letters, milestones and deliverable reports, PowerPoint presentations, etc. The project website is developed as the main dissemination channel.The longer‐term impact of the project's results will be secured by maintaining the website for a minimum of 5 years after the end of the project.

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DOI: 10.3897/arphapreprints.e93510

Authors: Lena Luise Schaller, Verena Scherfranz, Kati Häfner, Fabian Klebl, Jabier Ruiz, Jochen Kantelhardt, Annette Piorr

Abstract: Regulatory and incentive instruments for biodiversity management on farms (Short summary for practitioners)

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DOI: 10.3897/arphapreprints.e93509

Authors: Anna Sapundzhieva, Alexandra Korcheva, Nikol Yovcheva

Abstract: Communication, dissemination and exploitation play a vital role within SHOWCASE as the main means of ensuring knowledge transfer and uptake of results during the project lifetime and after the project is concluded. The project’s strategic objectives and target groups, as well as the key messages and narratives that the project aims to communicate serve as an orientation in the project’s actions in the relevant field. The current Plan for Exploitation and Dissemination of Results (PEDR) has been developed to define target-specific objectives and outline concrete implementation actions.The SHOWCASE PEDR represents a document that aims to guide the communication and dissemination efforts to target project-relevant audiences, convey clear, understandable, coordinated and effective messages, and reach out project results to all interested parties within the various stakeholder groups.The plan presents the different communication and dissemination tools, structured in an implementation plan according to the different target groups and different stage of development of the project. It also provides a list of tailored key performance indicators (KPI) for the project’s outreach activities that aim to provide a means to quantitatively monitor the effectiveness of dissemination activities. Indicative time schedule for implementation and updates is provided.In addition, this document will identify key project results, which will be a subject of exploitation.

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DOI: 10.3897/arphapreprints.e93508

Authors: Alexandra Korcheva, Anna Sapundzhieva, Ignasi Bartomeus

Abstract: The SHOWCASE DMP is structured into five sections, which aim to establish the scope and terms of use of research data within the project in accordance with the Horizon 2020 requirements of data management.The first section provides an introduction to the plan, which outlines the main data management practices that SHOWCASE would implement throughout the five-year project duration, as well as aspects of sustainable management of results and data after the conclusion of the project period.The second section of the document provides an overview of the commitments that SHOWCASE has made in relation to handling data in a controlled and transparent way, and ensuring an open access to research data and results in line with the EU’s Open Research Data Pilot and FAIR data management.The third section describes the details of data management within the project, focusing on different aspects of the process - from data collection, through data processing, to storage and access provision. The section features information on personal data protection in accordance with the General Data Protection Regulation (GDPR), as well as a break-down of the research data usage into project work packages. Recommendations for relevant data management practices are described in the section.The fourth section includes an overview of the specific data management details for the project work packages. The specific data formats and data management requirements of work packages are described.The fifth section of the DMP features concluding remarks on the data management strategy adopted by the project, and it outlines future updates and additions to the plan, which are going to be presented at a later stage of the project’s development.

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DOI: 10.3897/arphapreprints.e93507

Authors: Andrew Ruck, Erik Öckinger, Rene van der Wal, Alice Mauchline, Amelia Hood, Simon Potts, Michiel Wallis De Vries, Sabrina Gaba, Vincent Bretagnolle

Abstract: This report was researched and written between April and December 2021 by researchers at the Swedish University of Agricultural Sciences (SLU), with support from partners at the University of Reading (UK), De Vlinderstichting (Netherlands), and Centre National de la Recherche Scientifique (CNRS, France). The report consists of a review of existing 'citizen science’ approaches to monitoring biodiversity on farmland, in which we introduce a typology of five different types of approach, and highlight the strengths and weaknesses of these. This forms part of the project “SHOWCASing synergies between agriculture, biodiversity and Ecosystem services to help farmers capitalising on native biodiversity” (SHOWCASE). SHOWCASE aims to encourage the widespread uptake of biodiversity-friendly farming practices across Europe, both through identifying effective incentives for farmers, and gathering further evidence of the ecosystem services provided by increased levels of biodiversity. The project receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No.862480. In particular, this report fulfils Deliverable 3.8 within SHOWCASE: “A review of existing citizen science approaches to monitoring farmland biodiversity, including an overview of the different statistical approaches to handling citizen science data”. We at SLU are grateful to all SHOWCASE partners for their contributions.

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DOI: 10.3897/arphapreprints.e93506

Authors: Lena Luise Schaller, Verena Scherfranz, Kati Häfner, Fabian Klebl, Jabier Ruiz, Jochen Kantelhardt, Annette Piorr

Abstract: This document represents Deliverable 2.1 “Overview of regulatory and incentive instruments for biodiversity management on farms” within WP2 „Identifying incentives to promote biodiversity and ecosystem services in agricultural landscapes“ of the EU Horizon 2020 project SHOWCASE. It reports the outcomes of WP2 Task 2.1 “Evaluating regulatory and incentive instruments for biodiversity management on farms”.In the 1st and 2nd chapter, the report gives a short introduction of the deliverable’s objectives, the tasks addressed, the report’s outline and the main focus of the literature review.Chapter 3 gives an overview of the main laws governing biodiversity protection in the European Union. The main elements of the Birds and Habitats directives are presented, alongside other biodiversity laws and policies, with a focus on the obligations and requirements they set on agriculture in order to protect European native wildlife. Chapter 3 also covers the features of the EU’s Common Agricultural Policy that operate as a regulatory baseline for all beneficiaries of farm subsidies, i.e., cross-compliance and greening requirements under the current CAP and the new conditionality in the CAP 2023-2027.Chapter 4 gives an overview of economic and non-economic approaches potentially promoting farmers’ pro-biodiversity behaviour. Whereas economically oriented approaches imply positive or negative monetary flows – compensation payments or rewards vs. penalties – to motivate farmers to implement biodiversity-friendly management practices or to prevent them from harming biodiversity, partnerships and networks steer farmers’ behaviour through agreeing on a common goal and working towards it by sharing resources, skills and risk. With regards to the agricultural focus of SHOWCASE, Chapter 4 looks in more detail at the incentives provided by the Common Agricultural Policy (CAP) of the European Union. This covers both the current and future CAP, with an overview of how the novel eco-schemes can provide new incentives for farmers to adopt biodiversity friendly practices.Chapter 5 looks into how the combination of regulatory frameworks and incentives operate in practice for farmers in the EU. To this end, grey literature and European Commission publications related to farming for biodiversity have been reviewed. A specific focus is set on biodiversity-friendly farming in Natura 2000 sites, as central exemplary areas of continuous and long-lasting efforts in biodiversity conservation. This is followed by revising some of the main conclusions from very recent grey literature assessing the successes and failures of the CAP in relation to biodiversity.Chapter 6 provides an overview of approaches that have already been implemented to incentivize farmers’ pro-biodiversity behaviour. Based on grey literature, various types of approaches – i. e. focusing on plot or farm level, land tenure or the entire value chain, building on organic farming or including market-based, value-based or measure-based mechanisms – were identified within the EBA countries, further EU member states and selected western countries outside the EU. In sum, 62 examples of pro-biodiversity schemes were included in the further analysis representing highly divergent incentivizing mechanisms and the most important agricultural systems of the EBAs as well as in consequence serving as an information platform for further EBA scheme design activities.Based on the preceding chapters and their focus on result-based approaches, Chapter 7 casts a critical eye on their suitability with regards to various regulatory, policy, social and administrative contexts also considering potential national differences. On the international level, WTO requirements such as Green Box rules are a limiting factor with regards to result- based payment modalities and thus scheme design. On the national and regional level, issues to be considered include long-term availability of funding, guaranteeing additionality if requested, stakeholders’ and decision-makers’ attitudes towards agri-environment-climate measures in general as well as towards result-oriented approaches specifically, availability of suitable indicators and IT-systems, access to extension services and profound know-how of farmers and public authorities regarding the interlinkages between biodiversity and farming practices. On individual level, farmers’ trust in involved institutions and their willingness to participate are additionally discussed as highly relevant factors affecting the suitability of result- based approaches.In Chapter 8 a structured overview on factors influencing farmers’ willingness to promote biodiversity by implementing voluntary biodiversity measures is presented. Based on the review of scientific literature, the chapter describes several determinants which have been identified along three scales, i.e. 1) society, community and landscape, 2) farm scale, and 3) farmers’ intrinsic factors. The main influencing factors at the first scale range from the design of policies, to economic aspects, to socio-cultural norms. The second scale encompasses relevant farm characteristics, such as farm type and size to field conditions. For the farmers’ intrinsic factors age, education, experience, and self-identity play an important role. However, it is important to make a distinction between farmers’ willingness to participate in schemes and their actual behaviour, because the latter is determined by their ability to do so.Chapter 9 closes the Deliverable by giving an outlook on the further use of the results for scientific analyses within SHOWCASE, supporting mainly the work of designing interventions in WP1 and of developing surveys and model designs in WP2, as well as providing a basis for communication and policy recommendation material for WP4.

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DOI: 10.3897/arphapreprints.e93505

Authors: Vincent Bretagnolle, Sabrina Gaba, Amelia Hood, Simon Potts

Abstract: SHOWCASE’s first step is to create a European network of local Experimental Biodiversity Areas (EBAs), that will be used to co-develop (though to varying degrees) and test successful strategies for better integrating biodiversity into farming. EBAs are located across a wide range of agro-ecosystems and represent farming systems undergoing both intensification as well as agricultural abandonment. Rather than creating new sites for the network, the approach in SHOWCASE was that EBAs would be developed mostly from existing collaborations between scientists and practitioners. The first work Package of SHOWCASE, WP1, has built in the 10 countries an experimental and knowledge exchange network in agricultural landscapes across Europe. Existing collaborations include LTSER platforms from eLTER RI, farmer cooperatives, farming research organisations and conservation organisations. These are well-established multi-actor networks already undertaking knowledge exchange, participatory research and innovation activities. Then, participatory approaches with farmers, administrators and other stakeholders are defining operational biodiversity targets at field/farm/regional level by discussing the types and extents of biodiversity indicators that should be used. WP1 thus is building our EBA network, with each EBA serving both as a local testbed for developing and implementing novel interventions and as a knowledge exchange hub. This is a pan-European network of Experimental Biodiversity Areas. In these EBAs multi-actor communities (growers, extension workers, researchers, NGOs, citizens etc.) work together to co-develop, co-manage, co-monitor and co-evaluate biodiversity innovations to enhance farm production, wildlife protection, livelihood quality and resilience of social-ecological production systems. These multi-actor communities will i) identify and prioritise local or regional challenges of biodiversity-agricultural production trade-offs, and ii) co-formulate and test potential solutions. However, to add value at the European level and allow up- scaling and out-scaling of solutions, it is essential to have a common framework and set of core standardised methodologies and measures used by all EBAs. EBAs are expected to be somewhat representative of Europe, in terms of biogeography, farming system or agricultural intensification/abandonment. However, all EBAs are starting from different points. One main target was to develop the network of EBAs based on a core approach, though place-based, in order to provide local solutions to local challenges. A conceptual representation of an EBA is given below illustrating how each EBA will be the fundamental base and operational platform integrating the various Tasks of WP1.

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DOI: 10.3897/arphapreprints.e86743

Authors: Urmas Kõljalg, R. Henrik Nilsson, Arnold Tobias Jansson, Allan Zirk, Kessy Abarenkov

Abstract: Species have intrinsic value but also partake in a long range of ecosystem services of major economic value to humans. These values have proved hard to quantify precisely, making it all too easy to dismiss them altogether. We outline the concept of the species stock market (SSM), a system to provide a unified basis for valuation of all living species. The SSM amalgamates digitized information from natural history collections, occurrence data, and molecular sequence databases to quantify our knowledge of each species from scientific, societal, and economical points of view. The trading system will necessarily be unlike that of the regular stock market, but the looming biodiversity crisis implores us to finally put an open and transparent price tag on symbiosis, deforestation, and pollution

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DOI: 10.3897/arphapreprints.e86423

Authors: Aubrey Moore, Matthew Siderhurst

Abstract: Coconut rhinoceros beetle, a major pest of coconut and oil palms, is causing severe economic and environmental damage following recent invasions of several Pacific islands. Population suppression and eradication of this pest requires location and destruction of active and potential breeding sites where all life stages aggregate. Three search tactics for discovering breeding sites have been used with limited success: visual search by humans, search with assistance from detector dogs, and search by tracking CRB adults fitted with radio transmitters.Here we suggest a fourth search tactic: releasing CRB adults fitted with harmonic radar tags to locate breeding sites. Our idea is to find static end points for tags which accumulate at breeding sites, rather than active tracking of individual beetles. We plan to use commercially available hand-held harmonic radar devices. If we are successful, this technique may be useful for locating other insects which aggregate, such as hornets and other social insects.

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DOI: 10.3897/arphapreprints.e86014

Authors: Maria Auxiliadora Mora-Cross, Adriana Morales-Carmiol, Te Chen-Huang, María Barquero-Pérez

Abstract: Essential Biodiversity Variables (EBVs) make it possible to evaluate and monitor the state of biodiversity over time at different spatial scales. Its development is led by the Group on Earth Observations Biodiversity Observation Network (GEO BON) to harmonize, consolidate, and standardize biodiversity data from varied biodiversity sources. This document presents a mechanism to get baseline data to feed the Species Traits Variable Phenology or other biodiversity indicators by extracting species characters and structure names from morphological descriptions of specimens and classifying such descriptions using machine learning (ML).A workflow that performs Named Entity Recognition (NER) and Classification of morphological descriptions using ML algorithms was evaluated with excellent results. It was implemented using Python, Pytorch, Scikit-Learn, Pomegranate, Python-crfsuite, and other libraries applied to 106,804 herbarium records from the National Biodiversity Institute of Costa Rica (INBio). The text classification results were almost excellent (F1 score between 96% and 99%) using three traditional ML methods: Multinomial Naive Bayes (NB), Linear Support Vector Classification (SVC), and Logistic Regression (LR). Furthermore, results extracting names of species morphological structures (e.g., leaves, trichomes, flowers, petals, sepals) and character names (e.g., length, width, pigmentation patterns, and smell) using NER algorithms were competitive (F1 score between 95% and 98%) using Hidden Markov Models (HMM), Conditional Random Fields (CRFs), and Bidirectional Long Short Term Memory Networks with CRF (BI-LSTM-CRF).

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DOI: 10.3897/arphapreprints.e84517

Authors: Hannah Moersberger, Juliette G. C. Martin, Jessi Junker, Ivelina Georgieva, Silke Bauer, Pedro Beja, Tom Breeze, Lluís Brotons, Helge Bruelheide, Néstor Fernández, Miguel Fernandez, Ute Jandt, Christian Langer, Anne Lyche Solheim, Joachim Maes, Francisco Moreira, Guy Pe'er, Joana Santana, Judy Shamoun-Baranes, Bruno Smets, Jose Valdez, Ian McCallum, Henrique M. Pereira, Aletta Bonn

Abstract: In this report, we present the analysis of the different available biodiversity data streams at the EU and national level, both baseline biodiversity data and monitoring data. We assess how these biodiversity data inform and trigger policy action and identify the related challenges the different European countries and relevant EU agencies face and the solutions to overcome them. To do this, we consulted with more than 350 expert stakeholders from policy, research and practice. The assessment identified a fragmented biodiversity data landscape that cannot currently easily answer all relevant policy questions. Quantity and quality of biodiversity baseline datasets differ for the different countries, ranging from non-existent biodiversity monitoring due to capacity issues, to regular monitoring of ecosystem processes and state. By engaging stakeholders and experts in both member states and non-member states and from several EU bodies, we identified key challenges and ways to address these with targeted solutions towards building a joint European Biodiversity Monitoring Network. Solutions include focussing on cooperation and coordination, enhanced data standardisation and sharing, as well as the use of models and new technologies. These solutions can however only be realised with dedicated funding and capacity building, in coordination with all stakeholders in partnership.

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DOI: 10.3897/arphapreprints.e83854

Authors: Melanie Pivarski, Matt von Konrat, Thomas Campbell, Ayesha Qazi-Lampert, Laura Trouille, Aimee Davis, Selma Aburahmeh, Joseph Aguilar, Cosmin Alb, Ken Alferes, Ella Barker, Kelli Boulware, Sicong Cao, Christine Christian, Arturo Corona Jr., Kaltra Demiri, Daniel Evans, Connor Flavin, Victoria Gogol, Elizabeth Heublein, Edward Huang, Jake Hutchinson, Cyrus Jackson, Odaliz Jackson, Michi Kirihara, Annette Kowalczyk, Alex Labontu, Briajia Levi, Sylvie Martin-Eberhardt, Joann Martinec, Pansy Nguyen, Sarah Nolimal, Victoria Reese, Joannie Rodriguez, Yarency Rodriguez, Jacob Shuler, Jasmine Silvestre, Glenn Simpson, Gabriel Somarriba, Rogers Ssozi, Tomomi Suwa, Cheyenne Syring, Keith Thompson, Caitlin Vaughn, Mario Viramontes, Chak Shing Wong

Abstract: Globally, thousands of institutions house nearly three billion scientific collections offering unparalleled resources that contribute to both science and society. For herbaria alone - facilities housing dried plant collections - there are over 3,000 herbaria worldwide with an estimated 350 million specimens that have been collected over the past four centuries. Digitization has greatly enhanced the use of herbarium data in scientific research, impacting diverse research areas, including biodiversity informatics, global climate change, analyses using next-generation sequencing technologies, and many others. Despite the entrance of herbaria into a new era with enhanced scientific, educational, and societal relevance, museum specimens remain underused. Natural history museums can enhance learning and engagement in science, particularly for school-age and undergraduate students. Here we outline a novel approach of a natural history museum using touchscreen technology that formed part of an interactive kiosk in a temporary museum exhibit on biological specimens. We provide some preliminary analysis investigating the efficacy of the tool, based on the Zooniverse platform, in an exhibit environment to engage patrons in the collection of biological data. We conclude there is great potential in using crowd‐sourced science coupled with online technology to unlock data and information from digital images of natural history specimens themselves. Sixty percent of the records generated by community scientists (citizen scientists) were of high enough quality to be utilized by researchers. All age groups produced valid, high quality data that could be used by researchers, including children (10 and under), teens, and adults. Significantly, the paper outlines the implementation of experiential learning through an undergraduate mathematics course that focuses on projects with actual data to gain a deep, practical knowledge of the subject, including observations, the collection of data, analysis, and problem solving. We here promote an intergenerational model including children, high school students, undergraduate students, early career scientists and senior scientists, combining experiential learning, museum patrons, researchers, and data derived from natural history collections. Natural history museums with their dual remit of education and collections-based research can play a significant role in the field of  community engagement and people-powered research. There also remains much to investigate on the use of interactive displays to help learners interpret and appreciate authentic research.

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DOI: 10.3897/arphapreprints.e81371

Authors: Atsuya Yamamoto, Kota Tabata, Tomohiro Fukushige, Takuya Inoue, Hiroaki Furutsu, Michihisa Hiroya, Minoru Kanaiwa

Abstract: Length-weight relationships (LWRs) were estimated for ten freshwater fish species such as a species of crucian carp, gin-buna, Carassius langsdorfii Temminck & Schlegel, 1846, lake minnow Phynchocypris percnura (Pallas, 1814), a species of stone loach Barbatula toni (Dybowski, 1869), Japanese smelt Hypomesus nipponensis McAllister, 1963, masu salmon Oncorhynchus masou (Brevoort, 1856), rainbow trout O. mykiss (Walbaum, 1792), whitespotted char Salvelinus leucomaenis (Pallas, 1814), ninespine stickleback Pungitius pungitius (Linnaeus, 1758), a species of sculpin, hana-kajika, Cottus nozawae Synder, 1911, and a species of goby Rhinogobius sp. OR. Specimens were collected once a month except snowy season from Abashiri River basin, eastern Hokkaido, between June 2007 to November 2011. Fish were captured by the electrofisher (Smith-Root, Model 12-b). The estimated allometric coefficient b values ranged from 2.790 (ninespine stickleback ) to 3.294 (the sculpin), and r2 values ranged from 0.772 (lake minnow) to 0.994 (the goby). All the LWRs were highly significant, with p < 0.001. Besides, the study provides the first estimates of LWRs for the stone loach, Japanese smelt, masu salmon, whitespotted char, the sculpin, and the goby.

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DOI: 10.3897/arphapreprints.e81337

Authors: Tomáš Václavík, Fanny Langerwisch, Guy Ziv, Jodi Gunning, Arjan Gosal, Michael Beckmann, Anne Paulus, Felix Wittstock, Anna Cord, Stephanie Roilo, Cristina Domingo-Marimon, Anabel Sanchez, Annelies Broekman, Dajana Vujaklija

Abstract: This document is the first version of the Guidelines and protocols harmonizing activities across case studies of the H2020 BESTMAP project. It is intended to be updated in month 40 (D1.8).

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DOI: 10.3897/arphapreprints.e81207

Authors: Henrique M. Pereira, Jessi Junker, Néstor Fernández, Joachim Maes, Pedro Beja, Aletta Bonn, Tom Breeze, Lluís Brotons, Helge Bruehlheide, Marcel Buchhorn, César Capinha, Cher Chow, Karolin Dietrich, Maria Dornelas, Grégoire Dubois, Miguel Fernandez, Mark Frenzel, Nikolai Friberg, Steffen Fritz, Ivelina Georgieva, Anne Gobin, Carlos Guerra, Sigrid Haande, Sergi Herrando, Ute Jandt, W. Daniel Kissling, Ingolf Kühn, Christian Langer, Camino Liquete, Anne Lyche Solheim, David Martí, Juliette G. C. Martin, Annett Masur, Ian McCallum, Marit Mjelde, Jannicke Moe, Hannah Moersberger, Alejandra Morán-Ordóñez, Francisco Moreira, Martin Musche, Laetitia M. Navarro, Alberto Orgiazzi, Robert Patchett, Lyubomir Penev, Joan Pino, Gabriela Popova, Simon Potts, Anna Ramon, Leonard Sandin, Joana Santana, Anna Sapundzhieva, Linda See, Judy Shamoun-Baranes, Bruno Smets, Pavel Stoev, Leho Tedersoo, Liis Tiimann, Jose Valdez, Sara Vallecillo, Roy H. A. Van Grunsven, Ruben Van De Kerchove, Dani Villero, Piero Visconti, Claudia Weinhold, Annika M. Zuleger

Abstract: Observations are key to understand the drivers of biodiversity loss, and the impacts on ecosystem services and ultimately on people. Many EU policies and initiatives demand unbiased, integrated and regularly updated biodiversity and ecosystem service data. However, efforts to monitor biodiversity are spatially and temporally fragmented, taxonomically biased, and lack integration in Europe. EuropaBON aims to bridge this gap by designing an EU-wide framework for monitoring biodiversity and ecosystem services. EuropaBON harnesses the power of modelling essential variables to integrate different reporting streams, data sources, and monitoring schemes. These essential variables provide consistent knowledge about multiple dimensions of biodiversity change across space and time. They can then be analyzed and synthesized to support decision-making at different spatial scales, from the sub-national to the European scale, through the production of indicators and scenarios. To develop essential biodiversity and ecosystem variables workflows that are policy relevant, EuropaBON is built around stakeholder engagement and knowledge exchange (WP2). EuropaBON will work with stakeholders to identify user and policy needs for biodiversity monitoring and investigate the feasibility of setting up a center to coordinate monitoring activities across Europe (WP2). Together with stakeholders, EuropaBON will assess current monitoring efforts to identify gaps, data and workflow bottlenecks, and analyse cost-effectiveness of different schemes (WP3). This will be used to co-design improved monitoring schemes using novel technologies to become more representative temporally, spatially and taxonomically, delivering multiple benefits to users and society (WP4). Finally, EuropaBON will demonstrate in a set of showcases how workflows tailored to the Birds Directive, Habitats Directive, Water Framework Directive, Climate and Restoration Policy, and the Bioeconomy Strategy, can be implemented (WP5).

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DOI: 10.3897/arphapreprints.e72231

Authors: Mark Brown, Tom Breeze, Philippe Bulet, Marie-Pierre Chauzat, Iliyana Demirova, Joachim de Miranda, Alexandra-Maria Klein, Marika Mand, Teodor Metodiev, Denis Michez, Franceso Nazzi, Peter Neumann, Robert Paxton, Simon Potts, Jane Stout, Gail Turney, Orlando Yañez

Abstract: PoshBee is a 5-year funded project (2018-2023) that aims to support healthy bee populations, sustainable beekeeping, and consequently pollination for crops and wildflowers across Europe. To do this we take a range of approaches, from the laboratory to the field, from molecules to ecosystems, and from fundamental science to risk assessment. This document is an edited version of the original funding proposal that was submitted to the European Commission.

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