DOI: 10.3897/rio.12.e198587

Authors: Camille Musseau, Jessica Bathe-Peters, Jan Krzystolik, Jörn Geßner

Abstract: The Baltic sturgeon Acipenser oxyrinchus, once widespread in rivers draining to the Baltic Sea, was extirpated by overfishing and habitat degradation and is now the focus of a basin-wide restoration programme. Since 2006, more than seven million hatchery-reared juveniles have been released in Baltic rivers, yet the movements, habitat use and survival of stocked fish remain poorly quantified. HaffStör aims to close these knowledge gaps and to provide an operational basis for adaptive, cross-border management of the recovering population in the Oder River–Szczecin Lagoon system (Germany/Poland).The project combines movement ecology, conservation biology and social sciences in four interconnected work packages. First, we optimise rearing protocols, comparing juveniles produced under different degrees of environmental control (ambient vs. static recirculating aquaculture systems), coupled with behavioural experiments on habitat choice and anti-predator responses. Second, we release tagged juveniles in the Lower Oder and Szczecin Lagoon and track their movements using active and passive acoustic telemetry, complemented by habitat mapping and benthic sampling, to identify key migration routes, habitat utilisation and zones of overlap with human activities, mainly associated with fisheries and navigation. Third, we develop and test a standardised, cost-effective monitoring framework, based on passive gears, fishery-independent surveys and environmental DNA, aligned with Bern Convention guidelines and intended to be transferable to other Baltic catchments. Fourth, we establish cooperation with commercial fisheries through targeted outreach to initiate structured by-catch reporting, co-designed surveys and joint project activities.By integrating ecological and fishery data, HaffStör will deliver robust estimates of juvenile survival and mortality drivers, refine release and monitoring strategies and generate spatially-explicit assessments of by-catch risk. Beyond new scientific insights into Baltic sturgeon ecology, the project seeks to strengthen stewardship amongst local communities and practitioners and to support evidence-based, transnational governance for this flagship migratory species.

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DOI: 10.3897/arphapreprints.e203736

Authors: Willem Boone, Dorien Aerts, Nelle Meyers, Carlota Muñiz, Klaas Deneudt, Hanneloor Heynderickx

Abstract: The southern North Sea is an intensively used marine region where multiple human activities and environmental pressures overlap. This case study applies a Bow-tie risk analysis to a broad belt transect extending from the Belgian coast to the Dogger Bank, aiming to identify the causes and consequences of biodiversity change in an intensively used marine area. Based on stakeholder consultations, three types of human activities were identified as key drivers behind biodiversity change: tourism and leisure, extraction and cultivation of living resources, and offshore production of energy. These activities were linked to several overlapping pressures that resulted in the identification of four main biodiversity hazards; biodiversity decline, habitat degradation, altered movement, and ecological community change. Spatial planning and legislative frameworks were recognised as overarching prevention measures of biodiversity change, while multiple mitigation measures remain in place to minimise the nature and economic based consequences that are linked to the activity-pressure pathways. Our findings underscore the utility of the Bow-tie method as a communicative and analytical tool, particularly in densely utilized marine areas where the multifunctional spatial use intensifies biodiversity hazards.

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DOI: 10.3897/rio.12.e193918

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

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

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DOI: 10.3897/rio.12.e194808

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

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

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DOI: 10.3897/rio.12.e187033

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

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

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DOI: 10.3897/rio.12.e187550

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

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

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DOI: 10.3897/arphapreprints.e188550

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

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

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DOI: 10.3897/rio.11.e171663

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

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

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DOI: 10.3897/arphapreprints.e182018

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

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

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DOI: 10.3897/rio.11.e176476

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

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

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DOI: 10.3897/rio.11.e176120

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

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

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DOI: 10.3897/rio.11.e174994

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

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

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DOI: 10.3897/arphapreprints.e175173

Authors: Cristina Galván, Elvira Ramos, Araceli Puente

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

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DOI: 10.3897/arphapreprints.e173903

Authors: Cristina Galván, Elvira Ramos, Araceli Puente

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

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DOI: 10.3897/rio.11.e172117

Authors: Grigorios Skouradakis, Thanos Dailianis, Panayota Koulouri

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

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DOI: 10.3897/arphapreprints.e173693

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

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

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DOI: 10.3897/rio.11.e163757

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

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

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DOI: 10.3897/rio.11.e168765

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

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

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DOI: 10.3897/arphapreprints.e167290

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

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

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DOI: 10.3897/arphapreprints.e167392

Authors: Anita Franco, Katie Smyth, Michael Elliott

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

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DOI: 10.3897/arphapreprints.e167014

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

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

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DOI: 10.3897/arphapreprints.e166451

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

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

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DOI: 10.3897/rio.11.e163815

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

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

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DOI: 10.3897/arphapreprints.e163734

Authors: Tiina Salo, Marie C. Nordström

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

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DOI: 10.3897/rio.11.e154645

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

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

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DOI: 10.3897/arphapreprints.e157676

Authors: Davide Raho, Andrea Tarallo, Ilaria Rosati

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

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DOI: 10.3897/arphapreprints.e157339

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

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

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DOI: 10.3897/rio.11.e146649

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

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

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DOI: 10.3897/arphapreprints.e154462

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

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

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DOI: 10.3897/arphapreprints.e154439

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

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

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DOI: 10.3897/arphapreprints.e152862

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

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

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DOI: 10.3897/rio.11.e147364

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

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

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DOI: 10.3897/rio.10.e134825

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

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

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DOI: 10.3897/rio.10.e135978

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

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

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DOI: 10.3897/rio.10.e127927

Authors: Hideyuki Doi, Tatsuya Saito

Abstract: Environmental DNA (eDNA) analysis has transformed our understanding of aquatic ecosystems, but traditional methods often lack insights into organismal health. The emerging field of environmental protein (eProtein) analysis offers a novel approach to monitoring the physiological status of aquatic organisms. Recent advancements in proteomic technologies have enabled the detection and characterization of stress-responsive proteins in water samples, providing valuable insights into organismal health and environmental stressors. This perspective paper explores the potential of eProtein analysis for monitoring aquatic organism health, disease dynamics and reproductive cycles. Methodological advancements in protein extraction and mass spectrometry have enhanced the sensitivity and specificity of eProtein analysis, facilitating comprehensive molecular profiling and biomarker identification. By integrating eProtein analysis into aquaculture management and environmental monitoring, researchers can proactively manage fish health, mitigate disease outbreaks and safeguard aquatic ecosystems. Future research directions include refining extraction methods, establishing standardized protocols and leveraging interdisciplinary collaborations to maximize the potential of eProtein analysis for aquatic research and conservation.

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DOI: 10.3897/arphapreprints.e138026

Authors: Andrea Tarallo, Giuseppe Turrisi, Davide Raho, Ilaria Rosati

Abstract: This paper presents the collaborative efforts of Working Group 1 (WG1 - Occurrence and detection of zoosporic parasites) and Working Group 2 (WG2 - Drivers underlying the dynamic of zoosporic diseases) within the ParAqua COST Action, a research initiative focused on understanding zoosporic parasites and their interactions with algae. Initially conceived as an interactive web page, one of the deliverables of WG1 has evolved into a centralised database for data gathered by the scientific community of ParAqua. In this paper we present a summary of our work, carried out from July 2022 to October 2023. After gathering and analysing community needs, we have harmonised data collection, designed and implemented the database structure. The upcoming steps involve the data upload and integration process into the database and creating a Graphical User Interface to query the database. The paper focuses on the methodology and discusses the challenges faced during the activity. As part of our commitment to promoting the practices of open science, we wrote this paper to document the entire process of the database development. Our aim is to provide a clear pathway for others to expand, challenge, and refine our database designing process, encouraging a dynamic exchange of ideas that propels the field forward. In a broad sense, this research contributes to the understanding of algae-parasite interactions, by providing a unique experience of data mobilisation and integration in the field of algae parasites research.

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DOI: 10.3897/rio.10.e137296

Authors: Ricardo da Silva Ribeiro

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

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DOI: 10.3897/rio.10.e137763

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

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

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DOI: 10.3897/arphapreprints.e131654

Authors: Grace Kotnik, Lisa Morales, Bastiaan Willem Ibelings, Mridul Thomas, Alena Gsell, Dedmer van de Waal

Abstract: Poster showing the experimental design for a laboratory assay for sinking rates of chytrid infected diatom Asterionella formosa.

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DOI: 10.3897/rio.10.e130474

Authors: Gabriela Ioana-Toroimac

Abstract: Our report synthesizes information on (i) restoration projects along the Lower Danube River in order to show their hydrological effects and (ii) reference conditions of sites in order to better understand the evolution of riparian wetlands under present-day conditions.Our report (i) concluded on the difficulty to successfully restore the hydrology of the Lower Danube wetlands and (ii) pointed out restrictive factors for the terrestrialization of wetlands and islands in reference conditions.Overall, the report is a state of the art that shows a general picture of the present-day hydrological conditions of the Lower Danube’s wetlands.

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DOI: 10.3897/rio.10.e124978

Authors: Tobias Frøslev, Robin Boyd, Dmitry Schigel

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

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DOI: 10.3897/rio.10.e124988

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

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

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DOI: 10.3897/rio.10.e126660

Authors: Gonzalo Bravo, Gregorio Bigatti, María Bagur, Erasmo Macaya, Nelson Valdivia, Ariel Rodriguez, Mariela Gauna, Ian Walker, Juan Pablo Livore, María Mendez, Rocío Nieto Vilela, Fernando Lima, Rui Seabra, Enrique Montes

Abstract: The Marine Biodiversity Observation Network Pole to Pole of the Americas (MBON Pole to Pole) conducted two workshops on 27-31 March 2023 and 22-26 January 2024 in the Argentinian Patagonia aiming to enhance capacity for long-term monitoring of rocky intertidal communities in Argentina and Chile by applying novel and easy-to-use methods for biodiversity observing. In these workshops, participants received training on the collection and processing of benthic photo-quadrat imagery and their analysis using open-source artificial intelligence applications. Workshop participants included park rangers, undergraduate and graduate students and scientists. These training activities covered theoretical concepts of rocky shore ecology and field exercises. The workshops promoted collaboration and knowledge exchange between users of biodiversity data and ecologists resulting in the development of a standardised biodiversity monitoring protocol for rocky intertidal communities available in the Ocean Best Practices System of the Intergovernmental Oceanographic Commission of UNESCO. Participants learned to identify dominant species and functional groups (e.g. macro-algal taxa, molluscs, barnacles) commonly present in these habitats and their zonation patterns along elevation gradients, capture high-quality benthic photographs using quadrat frames and cameras provided by the MBON Pole to Pole and compute percentage cover estimates of observed taxonomic groups using open-source automated classifiers. Emerging recommendations underscored the importance of actively involving park rangers in survey efforts and facilitating communication with decision-makers managing Marine Protected Areas. These activities were endorsed by the UN Decade as contributions to the Marine Life 2030 programme towards increasing capacity in the implementation of coordinated, standardised and sustained biodiversity observing efforts in the Americas.

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DOI: 10.3897/arphapreprints.e128742

Authors: Tena Radočaj, Oliver Barić, Serena Rasconi, Irena Vardić, Jurica Jug-Dujaković, Ana Gavrilović

Abstract: One of the biggest challenges in the microalgae industry is the lack of reliable methods to detect and avoid biological contaminants, including parasites, which can affect cell growth and consequently lead to crash of the culture. In recent years, the metabarcoding approach has been widely used to study diversity and distribution of microalgae communities and is also a promising tool for contaminant detection in routine biomonitoring. The aim of this article presents steps of DNA extraction for molecular analysis of microalgae communities.

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DOI: 10.3897/rio.10.e126532

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

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

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DOI: 10.3897/rio.10.e118851

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

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

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DOI: 10.3897/rio.10.e121892

Authors: Wouter Los

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

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DOI: 10.3897/arphapreprints.e124344

Authors: Milos Stupar, Wejden Gongi, Silke Van den Wyngaert, Alexandra Kraberg, Albert Reñé, Serena Rasconi

Abstract: The objective of this methodological paper is to outline a microscopy protocol for detecting and observing fungal zoosporic parasites of phytoplankton in natural environments, with potential applications in algal biotechnology to enhance the success and sustainability of algal cultivation endeavors. The fluorescent dual staining with wheat germ agglutinin (WGA) and Calcofluor White (CFW) showcased during the Training School "Identification and detection of zoosporic parasites" in Neuglobsow (Germany) from 16th till 18th of May 2023 and organized and funded by COST Action ParAqua (European Cooperation in Science and Technology) illustrated its ease of implementation and suitability for diverse natural and artificial systems.

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DOI: 10.3897/rio.10.e120483

Authors: Alex Borisenko, Robert Young, Robert Hanner

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

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DOI: 10.3897/rio.10.e119782

Authors: Catherine Borremans, Jennifer Durden, Timm Schoening, Emma Curtis, Luther Adams, Alexandra Branzan Albu, Aurélien Arnaubec, Sakina-Dorothée Ayata, Reshma Baburaj, Corinne Bassin, Miriam Beck, Katharine Bigham, Rachel Boschen-Rose, Chad Collett, Matteo Contini, Paulo Correa, Carlos Dominguez-Carrió, Gautier Dreyfus, Graeme Duncan, Maxime Ferrera, Valentin Foulon, Ariell Friedman, Santosh Gaikwad, Chloe Game, Adriana Gaytán-Caballero, Fanny Girard, Michela Giusti, Mélissa Hanafi-Portier, Kerry Howell, Iryna Hulevata, Kiamuke Itiowe, Chris Jackett, Jan Jansen, Clarissa Karthäuser, Kakani Katija, Maxime Kernec, Gabriel Kim, Marcelo Kitahara, Daniel Langenkämper, Tim Langlois, Nadine Lanteri, Claude Jianping Li, Qi-Ran Li, Pierre-Olivier Liabot, Dhugal Lindsay, Ali Loulidi, Yann Marcon, Simone Marini, Ashley Marranzino, Miquel Massot-Campos, Marjolaine Matabos, Lenaick Menot, Bernabé Moreno, Marcus Morrissey, David Nakath, Tim Nattkemper, Monika Neufeld, Matthias Obst, Karine Olu, Alexa Parimbelli, Francesca Pasotti, Dominique Pelletier, Margaux Perhirin, Nils Piechaud, Oscar Pizarro, Autun Purser, Clara Rodrigues, Elena Ceballos Romero, Brian Schlining, Yifan Song, Heidi Sosik, Marc Sourisseau, Bastien Taormina, Jan Taucher, Blair Thornton, Loïc Van Audenhaege, Charles von der Meden, Guillaume Wacquet, Jack Williams, Kea Witting, Martin Zurowietz

Abstract: Imaging is increasingly used to capture information on the marine environment thanks to the improvements in imaging equipment, devices for carrying cameras and data storage in recent years. In that context, biologists, geologists, computer specialists and end-users must gather to discuss the methods and procedures for optimising the quality and quantity of data collected from images. The 4th Marine Imaging Workshop was organised from 3-6 October 2022 in Brest (France) in a hybrid mode. More than a hundred participants were welcomed in person and about 80 people attended the online sessions. The workshop was organised in a single plenary session of presentations followed by discussion sessions. These were based on dynamic polls and open questions that allowed recording of the imaging community’s current and future ideas. In addition, a whole day was dedicated to practical sessions on image analysis, data standardisation and communication tools. The format of this edition allowed the participation of a wider community, including lower-income countries, early career scientists, all working on laboratory, benthic and pelagic imaging.This article summarises the topics addressed during the workshop, particularly the outcomes of the discussion sessions for future reference and to make the workshop results available to the open public.

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DOI: 10.3897/rio.10.e121887

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

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

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DOI: 10.3897/rio.10.e120626

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

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

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DOI: 10.3897/rio.10.e119943

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

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

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DOI: 10.3897/rio.10.e107393

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

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

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DOI: 10.3897/rio.10.e119805

Authors: Daniel Mietchen, Jonathan Jeschke, Tina Heger

Abstract: Hypotheses play a central role in the scientific process, yet the way they are introduced often leaves much room for interpretation, which makes it difficult to use them later on: to study and test them, to delineate their scope and to explore the relationships they have to other hypotheses or concepts, to datasets, methodologies or other resources. Here, we introduce a new article type in RIO that is dedicated to them: Hypothesis Descriptions. Such articles combine a specific verbal definition of a hypothesis with a concise description of its components and provide pointers to prior work as well as alignments with formal ways of knowledge representation, optionally including relevant nanopublications. With this format, we aim to facilitate the study of hypotheses in and of themselves, to improve their testability along with the documentation and interpretability of such tests, and to stimulate efforts towards standardization and automation in this space.

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DOI: 10.3897/rio.10.e114366

Authors: Edmund Schiller, Karin Wiltschke-Schrotta, Eva Häffner, Jutta Buschbom, Frederik Leliaert, Breda Zimkus, John Dickie, Suzete Gomes, Chris Lyal, Daniel Mulcahy, Alan Paton, Gabi Droege

Abstract: We present two different typologies of legal/contractual information in the context of natural history objects: the Biodiversity Permit/Contract Typology categorises permits and contracts, and the Typology of Legal/Contractual Terms for Biodiversity Specimens categorises the terms within permits and contracts. The Typologies have been developed under the EU-funded SYNTHESYS+ project with the participation of experts from outside the consortium. The document further addresses a possible technical integration of these typologies into the Distributed System of Scientific Collections (DiSSCo). The implementation in the DiSSCo data model is outlined and a concrete use case is presented to show how conditions, e.g. the Typology of Legal/Contractual Terms, can be introduced into the DiSSCo Electronic Loans and Visits System (ElViS). Finally, we give an outlook on the next steps to develop the typologies into a standard that supports compliance with legal and contractual obligations within the wider community of natural science collections.

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DOI: 10.3897/rio.10.e117217

Authors: Salomé Landel, Gaël Lymer, Markus Pasterk, Michel Guiraud, Katharine Worley

Abstract: A key consideration during the preparatory phase project DiSSCo Prepare – which laid the foundations for the future Research Infrastructure DiSSCo (Distributed System of Scientific Collections) – was the need to establish a small number of alternative viable financial contribution models and a scalable formula which could be presented to potential funders, with a view to obtaining the minimum financial contribution necessary for DiSSCo to operate, as well as considering how the RI could grow with increased national funding.This report briefly explains the ERIC funding framework – as chosen for DiSSCo – and its legal constraints, in order to explain the key role played by national member contributions in the viability of an ERIC. An essential annex of the statutes that will be signed by all members of the ERIC is the member fee calculation. A proposal for the DiSSCo member fee calculation is set out in this document and is based on three main indicators: economic power (GDP), annual spending in research and development and population size. In the context of DiSSCo – and to ensure the ERIC can function – these indicators are connected to a fixed baseline fee of €50,000, in order to guarantee a minimum significant annual contribution from each participating country and avoid contributions that will be more expensive to manage than to benefit from. This baseline is multiplied by contribution factors which propose different ways to weight the various indicators.The method is established on an ideal scenario, whereby all 27 EU members, as well as the UK, Iceland, Norway and Switzerland sign the DiSSCo statutes and agree to the proposed member contribution calculation, amounting to €4.5 million for the annual budget of the ERIC. This scenario remains highly unlikely; therefore, a scaled approach has been envisaged, meaning the initial engagement of some countries will allow DiSSCo to begin its operation and implement its business strategy, whilst the growth of the ERIC and its activities is likely to evolve proportionally to the number of national members it is able to engage.This report also looks at the ways in which funding could be distributed amongst the DiSSCo members in order to implement decentralised services.

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DOI: 10.3897/rio.10.e118241

Authors: Dimitrios Koureas, Laurence Livermore, Wouter Addink, Eva Alonso, Jose Alonso, Ana Casino, François Dusoulier, Vânia Ferreira, Jonas Grieb, Quentin Groom, Sharif Islam, Urmas Kõljalg, Gaël Lymer, Karol Marhold, Carole Paleco, Stefaan Pijls, Serge Scory, Ben Scott, Claus Weiland, Katharine Worley

Abstract: The Distributed System of Scientific Collections (DiSSCo) is a pan-European Research Infrastructure (RI) initiative. DiSSCo aims to bring together natural science collections from 175 museums, botanical gardens, universities and research institutes across 23 countries in a distributed infrastructure that makes these collections physically and digitally open and accessible for all forms of research and innovation. DiSSCo RI entered the ESFRI roadmap in 2018 and successfully concluded its Preparatory Phase in early 2023. The RI is now transitioning towards the constitution of its legal entity (an ERIC) and the start of its scaled-up construction (implementation) programme. This publication is an abridged version of the successful grant proposal for the DiSSCo Transition Project which has the goal of ensuring the seamless transition of the DiSSCo RI from its Preparatory Phase to the Construction Phase (expected to start in 2025). In this transition period, the Project will address five objectives building on the outcomes of the Preparatory Phase project:1) Advance the DiSSCo ERIC process and complete its policy framework, ensuring the smooth early-phase Implementation of DISSCo;2) Engage & support DiSSCo National Nodes to strengthen national commitments;3) Advance the development of core e-services to avoid the accumulation of technical debt before the start of the Implementation Phase;4) Continue international collaboration on standards & best practices needed for the DiSSCo service provision; and5) Continue supporting DiSSCo RI interim governance bodies and transition them to the DiSSCo ERIC formal governance.The Project’s impact will be measured against the increase in the RI's overall Implementation Readiness Level (IRL). More specifically, we will monitor its impact towards reaching the required level of maturity in four of the five dimensions of the IRL that can benefit from further developments. These include the organisational, financial, technological and data readiness levels.

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DOI: 10.3897/rio.10.e114485

Authors: Kiara Lasch, Sabine Gollner, Alex Oude Elferink, Siren Rühs, Francesca Sangiorgi, Erik van Sebille, Junjie Wang

Abstract: The ocean's significance encompasses crucial ecosystem services including climate regulation, oxygen production and food supply. The ocean is also a major player in the global economy. However, human activities continue to harm the ocean, jeopardising these vital functions. In July 2022, the United Nations Ocean Conference adopted a political declaration entitled "Our ocean, our future, our responsibility," emphasising the need for sustainable ocean management and protection. However, an important initial question arises: who are the “Our”? or, rephrased “Whose ocean” is it? This study presents first answers to this question, based on interviews with ocean professionals from diverse backgrounds. Their responses showcased the complexity of the issue, with differing opinions on ocean “ownership” and “control”. Despite the diversity of perspectives, a shared emphasis emerged: shifting from profit-driven decision-making to prioritising marine ecosystem health. Proposed approaches to build a sustainable relationship between people and the ocean include promoting ocean literacy and marine research and ensuring global accountability. These voices offered valuable insights towards ocean sustainability, guiding future academic, educational and policy-making efforts.

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DOI: 10.3897/rio.9.e113299

Authors: Samuel C. Bernardes, Thomas von Rintelen, Serena Alexander, Fiona Lorenz, Kristina von Rintelen

Abstract: Specimens in natural history museums are a valuable resource for biological research, such as taxonomic, biodiversity or evolutionary studies. However, the quality of DNA and even morphological characters can decrease over time, depending on previous fixation and long-term preservation methods. In recent years, advances in DNA extraction and sequencing techniques have allowed researchers to obtain DNA from museum specimens, even when the DNA was very fragmented. Extraction methods should ideally be morphologically non-destructive, leaving diagnostic characters intact for future taxonomic studies. Here, we assess whether the whole-body extraction widely used for several taxa would be destructive for small crustaceans kept in wet collections. We extracted the DNA from over 70 small (1-3 cm) and relatively fragile shrimps collected during the last 30 years by using: i) a piece of abdominal tissue and ii) from the entire remaining body of the animal. We photographed several samples before and after the lysis, focusing on taxonomically relevant characters. Although DNA concentration was higher in the whole-body extractions, the presence of intact DNA was not correlated to the amount of lysed tissue. The resulting genomic libraries had little to no difference in yield. The taxonomically relevant characters were primarily preserved in larger specimens, whereas smaller specimens (< 1.5 cm) became too fragile to handle or were damaged. We conclude that this method must be carried out carefully in smaller crustaceans, depending on size and taxon. We advise against using it with type specimens as the advantages do not outweigh the risks. Our experiment may provide future research with quantitative and qualitative evaluations to help scientists weigh their decisions when extracting DNA from wet collection material.

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DOI: 10.3897/rio.9.e114134

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

Abstract: AquaticVID is a low-cost, long battery life video camera system for use in a wide-range of aquatic research applications. The system can be deployed for multiple day recording on a single charge, is submersible to depths of down to 950 m and can be constructed quickly using easily sourced off-the-shelf materials. The system is essentially ‘plug-and-go’, as assembly and preparation for deployment takes < 30 minutes without the need for technical build or programming skills. All of the electrical components are interchangeable with parts from multiple manufacturers and the camera system can be adapted to fit a variety of waterproof enclosure sizes depending on power and data storage requirements. Here, we describe three versions of the AquaticVID in detail and give examples of above and below water research undertaken with the system. The small size and extended battery times, coupled with ease of use and low cost (US$ 268–540) make the AquaticVID a useful option for numerous aquatic research applications.

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DOI: 10.3897/rio.9.e115796

Authors: Loïc Van Audenhaege, Vincent Mahamadaly, David Price, Alexandre Sneessens, Hayley Cawthra, Clément Delamare, Valentin Danet, Simon Delsol, Rodolphe Devillers, Iason-Zois Gazis, Isabel Urbina-Barreto

Abstract: For the past decades, photogrammetry has been increasingly used for monitoring spatial arrangement or temporal dynamics of submerged man-made structures and natural systems. As photogrammetry remains a nascent technique for data collection in the underwater environment, acquisition workflows have evolved constrained by specific methodological practicalities (e.g. euphotic environments vs. deep-sea waters). The annual GeoHab conference gathers a world-wide range of scientists interested in mapping and is, therefore, an adequate event to set up a state-of-the-art workshop on (underwater) photogrammetry. More specifically, a preliminary survey identified the overall lack of photogrammetry knowledge from the audience. A programme was conceptualised to explore within a day theoretical concepts, sampling design and practicalities and a wide range of case studies in various underwater environments. Furthermore, we provided manual training on data acquisition and processing. In overall, a post-survey demonstrated the audience’s satisfaction despite a remaining lack of confidence for implementing their own photogrammetry studies. As this workshop gathers a diversity of materials and a training relevant for a scientific audience, it sets the stage for a reproducible event and leaves room for future improvements. Finally, it provided relevant materials and discussions that enabled us to identify the aspects limiting photogrammetry methodology across scientific applications and institutes, in order to work towards standardisation.

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DOI: 10.3897/rio.9.e113968

Authors: Silvia Paoletti, Bob Rumes, Nino Pierantonio, Simone Panigada, Romain Jan, Thomas Folegot, Anita Schilling, Nicolas Riviere, Vincent Carrier, Antoine Dumoulin, David Van Hamme, Gildas Marquis-Laisné, François-Antoine Bruliard, Félix Petitpierre, Damien Demoor

Abstract: With the continuous intensification of marine traffic worldwide, whale-vessel collisions at sea (or “ship strikes”) have become one of the primary causes of mortality for cetaceans and a widely recognised cause of concern for human safety and economic losses. The Mediterranean Sea is a global hotspot for whale-vessel collisions, with one of the highest rates involving large cetaceans, especially the endangered fin whales (Balaenoptera physalus) and sperm whales (Physeter macrocephalus). Evidence indicates that both species are experiencing higher chances of a fatal collision than what predictions have estimated so far, with ship strikes being the main human-induced threat in the area. Regional and international organisations have stressed the need to address the issue by investigating the projected impacts of ship strikes on whale populations and by identifying possible mitigation measures to reduce chances of collision. Amongst the most popular and feasible options, there is the improvement of animal detection during navigation. Here, we present SEADETECT, a LIFE project that aims at developing an automated detection system to reduce vessel collision risk with marine mammals and unidentified floating objects (UFOs), combining state-of-the-art and novel technologies with existing approaches in the study of large whale ecology. This detection system consists of three elements; an automated onboard detection system composed of several sensors, a real-time passive acoustic monitoring (PAM) network at sea and a real-time detection-sharing and alert system (REPCET®). In this paper, we propose the development of a mitigation measure framework tailored for the issue of collision with fin and sperm whales in the north-western Mediterranean Sea, but that has the transferability features necessary for its application in other high-risk areas for ship strikes worldwide.

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DOI: 10.3897/rio.9.e115454

Authors: Helen Hardy, Lisa French, Josh Humphries, Sabine von Mering, Peter Giere, Frederik Berger, Anne Koivunen, Jonas Grieb, Martin Vipp, Vincent Smith

Abstract: As a highly decentralised research infrastructure, the Distributed System of Scientific Collections (DiSSCo) will need to develop cross-institutional teams, adopting work practices where individual staff are intensively working collectively on common tasks in a distributed environment. These flexible and distributed working practices will be essential to the delivery of the research infrastructure across a wide range of delivery partners and a geographically dispersed set of scarce resources and skills, particularly in more technical roles. Since work to consider secondment and distributed working in DiSSCo was first envisaged, there has been a step change in distributed working owing to the Covid-19 pandemic and lockdowns or other restrictions to where work could take place. This report examines distributed team working practices and how they have changed, through interviews with a range of key roles across DiSSCo Prepare institutions. It briefly examines key project management and technical team delivery techniques. It documents how some of these approaches have been piloted within DiSSCo Prepare for the development, testing and delivery of DiSSCo Policy and Digital Maturity tools. Finally, bringing this together with previous work on secondment policies and practices for DiSSCo, we make recommendations about how secondment and distributed team working can be approached to enhance DiSSCo capabilities and the likelihood of successful implementation of the research infrastructure.

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DOI: 10.3897/rio.9.e112231

Authors: Charlene da Silva, Toufiek Samaai, Sven Kerwath, Luther Adams, Katie Watson, Anthony Bernard, Grant van der Heever, Andrea Angel, Stefan Schoombie, Guilherme Frainer, Mari-Lisa Franken, Adam Rees, Angus Paterson

Abstract: The inaugural Computer Vision for Marine Scientists workshop was held at the 17th South African Marine Science Symposium, with the primary goal of establishing a community of practice for computer vision (CV) in marine sciences in South Africa. The one-day hybrid event, attended by 97 people, covered the principles of artificial intelligence (AI) techniques required for evaluating video and photographic imagery through presentations, practical demonstrations and interactive discussions. The recordings of the workshop sessions are available online, providing an opportunity to reach marine researchers both regionally and globally. The workshop highlighted that many scientists have begun to incorporate CV and AI into their research activities; however, there is little national coordination and the extent of research is lagging behind international trends. To support image-based AI research in South Africa, it is critical to maintain and expand the network established during the workshop. This would enable a more collaborative and successful approach to incorporating CV technology in the country's marine research initiatives, ultimately leading to ground-breaking discoveries and advancements in the field.

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DOI: 10.3897/arphapreprints.e115410

Authors: Fausto Favero, Lieke Hüsken, Jochen Hinkel, Heleen Vreugdenhi, Umberto Pernice, Michael Sedlmeier

Abstract: This deliverable is the first contribution of Work Package 3 to the REST-COAST Project. The overarching purpose of REST-COAST is to provide the tools to address some of the key challenges faced by coastal ecosystems restoration. To achieve this objective, REST-COAST will improve coastal restoration practice and techniques through new hands-on restoration pilot projects, co-design effective governance arrangements and policies, and generate new tools and data for risk reduction assessment. In addition to these activities, Work Package 3 will design innovative financial arrangements and bankable business plans to support the implementation and thescaling up of coastal ecosystem restoration.

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DOI: 10.3897/arphapreprints.e115409

Authors: Gabriela Popova, Iliyana Demirova, Boris Barov

Abstract: The main goals of WP6 Dissemination, exploitation and social transformation tools, are to establish and maintain a distinct project identity, as well as to maximise the impact of project results by marketing andcommunicating them to stakeholders and the broader public. To ensure the efficient communication, Pensoft has developed a number of promotional materials reflecting the REST-COAST corporate identity, aswell as a project website.

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DOI: 10.3897/rio.9.e114548

Authors: Louise Ahl, Luca Bellucci, Philippa Brewer, Pierre-Yves Gagnier, Elspeth Haston, Laurence Livermore, Sofie De Smedt, Helen Hardy, Henrik Enghoff

Abstract: There are approximately 1.5 billion specimens kept in European Natural History Collections. The mission for the Distributed System of Scientific Collections (DiSSCo) is to unite all these specimens into a one-stop e-science infrastructure of digital specimens. This is a monumental digitisation task and criteria for how to prioritise this effort are, therefore, crucial for the success of the project. In this report, we have reviewed the literature and designed and conducted surveys of the digitisation plans and criteria used by DiSSCo Partners to understand the prioritisation criteria used in the digitisation of natural history collections. As an attempt to provide some guidance for the digitisation of specimens, we suggest that an organisation (e.g. DiSSCo or an individual institution) that is planning to digitise natural history collections considers four categories of prioritisation criteria: Relevance, Data quality, Cost and Feasibility.

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DOI: 10.3897/rio.9.e114370

Authors: Mohamed Ahusan, Nuria Rico-Seijo, Farah Amjad, Erika Gress, Shafiya Naeem, Toufiek Samaai, Kaveh Samimi-Namin, Lucy Woodall, Paris Stefanoudis

Abstract: The Nekton Maldives Taxonomic Workshop took place at the Maniyafushi Research Station in the Maldives between 12 and 23 February 2023. This workshop had two primary objectives. Firstly, it aimed to identify species from biological samples and underwater imagery collected during the Nekton Maldives Mission in 2022. Secondly, it sought to facilitate training and knowledge exchange sessions between early career researchers from the Maldives and international taxonomists. These sessions were designed to share knowledge and introduce fundamental taxonomy concepts and enhance practical identification skills for common reef benthic groups and major zooplankton taxonomic groups. A total of 24 people from 10 different countries were directly or indirectly involved with the workshop comprising nine taxonomic experts, eleven trainees and four organisers. Collectively, we identified 278 biological specimens including potentially undescribed species of hydroids, black corals, sponges and octocorals, 318 morphotypes for underwater footage and zooplankton composition congruent with previous reports from the Indian Ocean Region. Next steps will involve depositing the specimens into a more a permanent facility to facilitate the process of specimen description and knowledge transfer.

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DOI: 10.3897/arphapreprints.e114825

Authors: Carles Ibáñez, Alba Alemany, Ferran Bertomeu, Silvia Frias, Judith Molero, Roberto Merciai, Laura Puertolas

Abstract: Coastal regions provide some of the most productive and biodiverse environments with an important and often underappreciated carbon storage potential. At the same time, they are among the areas of highest population density, natural assets, and cultural heritage in the world, yet are experiencing significant social, economic and environmental challenges, exacerbated by climate change and human pressures.The Rest-Coast Project (Large scale RESToration of COASTal ecosystems through rivers to sea connectivity) is an EU Horizon 2020 research project (Grant agreement No. 101037097) whose overall goal is to address with effective and innovative tools the key challenges faced by coastal ecosystem restoration across Europe. The approach chosen for this project will deliver a highly interdisciplinary contribution, with the demonstration of improved practices and techniques for hands-on ecosystem restoration across several pilot sites, supported by the co-design of innovative governance and financial arrangements, as well as an effective strategy for the dissemination of results.

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DOI: 10.3897/arphapreprints.e114824

Authors: Carla Danelutti, Emmi Lindqvist, Maria del Mar Otero, Mindert de Vries, Albert Vos, Nuno Caiola, Vicente Gracia, Nil Alvarez, Laura Puertolas, Jaime Ordonez, Silvia Torresan, Caterina Dabalà, Francesca Coccon, Grzegorz Różyński, Nikolay Valchev, Nataliya Andreeva, Elitsa Hineva, Olivier Boutron, Rosaria Ester Musumeci, Massimiliano Marino, Christophe Briere, Julien Dalle, Margot Defoort-Levkov, Margot Ahr, Yael Salame-Rubin, Simon Nemtzov, Avi Uzan

Abstract: Coastal regions provide some of the most productive and biodiverse environments with an important and often underappreciated carbon storage potential. At the same time, they are among the areas of highest population density, natural assets and cultural heritage in the world, yet are experiencing significant social, economic and environmental challenges, exacerbated by climate change and human pressures.The REST-COAST project (Large scale RESToration of COASTal ecosystems through rivers to sea connectivity) will demonstrate to what extent upscaled coastal restoration can provide a low-carbon adaptation, reducing risks and providing gains in biodiversity for vulnerable coastal ecosystems, such as wetlands or sea grass beds. By overcoming present technical, economic, governance and social barriers to restoration upscaling, REST-COAST will develop the large scale river-coast connectivity and increase the nearshore accommodation space for the resilient delivery of coastal ecosystem services (ESs). The selected ESs (risk reduction, environmental quality and fish provisioning) touch urgent coastal problems such as the erosion/flooding during recent storms or the accelerating coastal habitat degradation that seriously affects fisheries and aquaculture. Combining new techniques, risk assessments, innovative financial/governance arrangements and homogeneous metrics for ESs and biodiversity, REST-COAST will develop a systemic approach to coastal restoration based on a scalable coastal adaptation plan.

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DOI: 10.3897/rio.9.e113991

Authors: Gabriela Ioana-Toroimac, Gabriela Moroșanu, Dana Constantin, Cătălina Stoica, Ionuț Șandor

Abstract: In the context of the requirements of the Water Framework Directive to reinstate a river’s good ecological status after being severely altered by human pressures, river restoration became a major topic in the last decade in the EU and the number of projects implemented especially on hydromorphology increased. However, it is still uncertain whether these restoration measures have positive cumulative effects, i.e. hydromorphological effectiveness, when compared to reference conditions and expectations of stakeholders, because of inconsistent methodologies. Therefore, the goal of our project is to develop a methodology to evaluate the hydromorphological effectiveness of river restoration, based on standardised indicators, at various spatial scales, appropriate for implemented measures and for restored river types, weighting the expectations of actors and adapted to case studies in Romania. This methodological protocol could become also a useful tool to create a strategy and make decisions in the practice of river restoration. Moreover, this kind of analysis could contribute to clarifying the issue of standards in environmental projects.

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DOI: 10.3897/rio.9.e113906

Authors: Dimitrios Koureas, Laurence Livermore, Eva Alonso, Wouter Addink, Maria Judite Alves, Ana Casino, Luís Curral, Henrik Enghoff, Michel Guiraud, Helen Hardy, Jana Hoffmann, Salomé Landel, Carole Paleco, Mareike Petersen, Serge Scory, Vincent Smith, Claus Weiland, Karsten Wesche, Matt Woodburn

Abstract: The Distributed System of Scientific Collections (DiSSCo) is a new world-class Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI aims to create a new business model for one European collection that digitally unifies all European natural science assets under common access, curation, policies and practices that ensure that all the data is easily Findable, Accessible, Interoperable and Reusable (FAIR principles). DiSSCo represents the largest ever formal agreement between natural history museums, botanic gardens and collection-holding institutions in the world.DiSSCo entered the European Roadmap for Research Infrastructures in 2018 and launched its main preparatory phase project (DiSSCo Prepare) in 2020. DiSSCo Prepare is the primary vehicle through which DiSSCo reaches the overall maturity necessary for its construction and eventual operation. DiSSCo Prepare raises DiSSCo’s implementation readiness level (IRL) across the five dimensions: technical, scientific, data, organisational and financial. Each dimension of implementation readiness is separately addressed by specific Work Packages (WP) with distinct targets, actions and tasks that will deliver DiSSCo’s Construction Masterplan. This comprehensive and integrated Masterplan will be the product of the outputs of all of its content related tasks and will be the project’s final output. It will serve as the blueprint for construction of the DiSSCo RI, including establishing it as a legal entity.DiSSCo Prepare builds on the successful completion of DiSSCo’s design study, ICEDIG and the outcomes of other DiSSCo-linked projects such as SYNTHESYS+ and MOBILISE.This paper is an abridged version of the original DiSSCo Prepare grant proposal. It contains the overarching scientific case for DiSSCo Prepare, alongside a description of our major activities.

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DOI: 10.3897/rio.9.e113378

Authors: Helen Hardy, Laurence Livermore, Paul Kersey, Ken Norris, Vincent Smith

Abstract: UK natural science collections hold over 137 million items, an unrivalled source of data about 4.56 billion years of planetary development and hundreds of years of biological change, including the differences made by humans — but the scientific, commercial, and societal benefits of these collections are constrained by the limits of physical access, and by highly fragmented digitisation efforts with less than 10% digitally available. Following work with Frontier Economics in 2021, which showed potential for £2 billion in benefits to the UK economy from digitising all UK natural science collections, in 2022–23 the Natural History Museum London worked, with analytical support from McKinsey and Company, to understand the impact of what has already been digitised and shared by UK natural science collections — what is the demand for these data, what are they used for, and how does this deliver efficient, effective and impactful research?This study focuses on usage via the Global Biodiversity Information Facility, the largest source of relevant usage data, examining 7.6 million records from twelve UK institutions. While these UK collections data are just 0.3% of total GBIF occurrences, they are cited in 12% of peer reviewed publications citing GBIF data, showing the disproportionate impact of UK collections data and the historical, geographical, and taxonomic richness that they bring. Researchers have already benefited from more than £18 million of efficiency savings from digital UK specimen data. Data from natural science collections held in the UK are uniquely impactful resources, vital to a future in which people and planet thrive, and a step change in the pace of digitisation is needed to unlock their potential for researchers, policymakers, and society.

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DOI: 10.3897/rio.9.e108807

Authors: Stefano Larsen, Jose Manuel Alvarez-Martinez, Jose Barquin, Maria Cristina Bruno, Laura Concostrina Zubiri, Luca Gallitelli, Micael Jonsson, Monika Laux, Giorgio Pace, Massimiliano Scalici, Ralf Schulz

Abstract: Europe has committed to upscale ecosystems protection to include 30% of land and sea. However, due to historical overexploitation of natural assets, the available area for biodiversity protection is severely limited. Riparian zones are natural ecotones between aquatic and terrestrial ecosystems, contributing disproportionately to regional biodiversity and providing multiple ecosystem functions and services. Due to this and their branching geometry, riparian networks form a vast system of ‘blue-green arteries’ which physically and functionally connect multiple ecosystems over elevation gradients, despite covering a relatively small area of the basin. Hence, RIPARIANET argues that developing approaches able to optimise the spatial conservation of natural stream-riparian networks represent a flagship example of biodiversity protection in the EU. Although the integrity of riparian zones is fundamental for the achievement of multiple EU environmental objectives, the lack of a standardised framework for biodiversity assessment and protection across Member States has led to extensive impairment of riparian areas and frequent stakeholder conflicts.The main objective of RIPARIANET is to leverage the increasing resolution of remote sensing information to provide practitioners with evidence-based guidance and approaches to biodiversity conservation. Key questions include: i) how can we remotely assess riparian integrity and identify areas which provide effective connectivity allowing species biodiversity and ecosystem functions to persist through meta-ecological processes? ii) how can we disentangle the influence of local- and network-scale stressors and processes on riparian biodiversity to better implement river basin management schemes? iii) to what extent do currently existing protected areas in rivers account for the geometry of riparian networks and their multifunctionality?We will address these questions in riparian networks within six river basins in Europe, including Boreal, Continental, Alpine, Temperate and Mediterranean systems. First, we will gather local needs and interests from key stakeholders together with satellite imagery and GIS environmental data for all basins. Then, riparian and river ecosystems functions will be modelled and ecological hotspots will be identified through a GIS-based multi-criteria approach, including stakeholder inputs. Then, we will collect in situ data to assess multiple biodiversity and stressors at the local scale and, subsequently, scale-up this information to the network scale using geostatistical tools and advanced modelling. This knowledge will be conveyed to managers at local and EU scales in the form of decision-support tools allowing decision-makers to identify protection gaps and ecological hotspots along riparian networks, based on multiple biodiversity, functional and connectivity criteria.

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DOI: 10.3897/rio.9.e110501

Authors: Konrad U. Förstner, Anke Becker, Jochen Blom, Peer Bork, Thomas Clavel, Marius Dieckmann, Alexander Goesmann, Barbara Götz, Thomas Gübitz, Franziska Hufsky, Sebastian Jünemann, Marie-Louise Körner, Manja Marz, Ulisses Nunes Da Rocha, Jörg Overmann, Alfred Pühler, Dietrich Rebholz-Schuhmann, Alexander Sczyrba, Jens Stoye, Justine Vandendorpe, Thea Van Rossum, Alice McHardy

Abstract: Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany.

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DOI: 10.3897/rio.9.e109120

Authors: Maria Lumbierres, W. Daniel Kissling

Abstract: The EuropaBON project aims to co-design a European Biodiversity Observation Network by utilising Essential Biodiversity Variables (EBVs) as the foundation for its monitoring system. To co-design the workflow steps for each EBV, the project organised a virtual workshop to engage a diverse group of experts and stakeholders. The workshop focused on describing various workflow components, identifying future needs for EBV implementation and specifying the relative importance of different monitoring techniques for each EBV. With 520 participants from 49 countries, the workshop benefited from a large stakeholder engagement and a wide range of expertise across realms, EBV classes, monitoring techniques and workflow components. During the 3-day workshop (2 hours per day), participants captured different workflows components (i.e. data collection and sampling, data integration and modelling), specified current EU or national initiatives and identified emerging tools and future needs for all 70 currently proposed EBVs. By the end of the workshop, all 70 templates of EBV workflows contained details about workflow components and future needs. Specific future needs for data collection and sampling highlighted by participants were to increase sampling efforts (e.g. number of sites, geographic coverage, sampling frequency and taxonomic scope), to develop and better incorporate novel monitoring techniques (e.g. eDNA, remote sensing and digital sensors) and to create new or improved sampling designs at a European scale. For data integration, combining and harmonising data from diverse sources and data collectors and developing standards and protocols were mentioned as key needs. For modelling, participants especially highlighted the need to develop spatially-explicit models or improve other types of existing models, ideally with open-source software and code. Next steps for designing EBV workflows are to analyse the gathered workshop information, to provide detailed descriptions of EBV workflows and to formulate specific recommendations for the development of a European Biodiversity Observation Network. Recommendations for each monitoring technique (structured in-situ monitoring, citizen science, digital sensors, genetics, satellite remote sensing and aerial remote setting) will also be identified. The gathered information will contribute to the co-design of the European Biodiversity Observation Network and to supporting the establishment of a Biodiversity Monitoring Coordination Centre in Europe.

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DOI: 10.3897/rio.9.e107220

Authors: Dimitrios Koureas, Laurence Livermore, Eva Alonso, Wouter Addink, Ana Casino

Abstract: The Distributed System of Scientific Collections (DiSSCo) is a new world-class Research Infrastructure (RI) for Natural Science Collections. The DiSSCo RI aims to create a new business model for one European collection that digitally unifies all European natural science assets under common access, curation, policies and practices that ensure that all the data is easily Findable, Accessible, Interoperable and Reusable (FAIR principles). DiSSCo represents the largest ever formal agreement between natural history museums, botanic gardens and collection-holding institutions in the world.DiSSCo entered the European Roadmap for Research Infrastructures in 2018 and launched its main preparatory phase project (DiSSCo Prepare) in 2020. DiSSCo Prepare is the primary vehicle through which DiSSCo reaches the overall maturity necessary for its construction and eventual operation. DiSSCo Prepare raises DiSSCo’s implementation readiness level (IRL) across the five dimensions: technical, scientific, data, organisational and financial. Each dimension of implementation readiness is separately addressed by specific Work Packages (WP) with distinct targets, actions and tasks that will deliver DiSSCo’s Construction Masterplan. This comprehensive and integrated Masterplan will be the product of the outputs of all of its content related tasks and will be the project’s final output. It will serve as the blueprint for construction of the DiSSCo RI, including establishing it as a legal entity.DiSSCo Prepare builds on the successful completion of DiSSCo’s design study, ICEDIG and the outcomes of other DiSSCo-linked projects such as SYNTHESYS+ and MOBILISE.This paper is an abridged version of the original DiSSCo Prepare grant proposal. It contains the overarching scientific case for DiSSCo Prepare, alongside a description of our major activities.

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DOI: 10.3897/arphapreprints.e106475

Authors: Christos Arvanitidis, Alberto Basset, Thierry Carval, Katrina Exter, Nicola Fiore, Alessandra Giorgetti, Juan Miguel González-Aranda, Mark Hebden, Georgios Kotoulas, Joaquín López Lérida, Rory Meyer, Nikos Minadakis, Matthias Obst, Nicolas Pade, Christina Pavloudi, Marc Portier, Ioulia Santi, Dick Schaap, Peter Thijsse, Lucia Vaira, Cristina Huertas Olivares

Abstract: This Science Project (SP) contributes to the estimation of the impacts of the invasive species on the European Biodiversity and Ecosystems. This topic is important for European Green Deal and the new European Biodiversity Strategy. The SP is also linked with the socio-economic issues because of the NIS implications to the local ecosystems and their services, and their societal goods and services. Since many of the above impacts may be of local scale, they may alter common practices in circular economies. The SP is implemented by: (a) Combining different sources of data and information; (b) Using a dual workflow to analyse the data; (c) Integrating its resources with core EOSC services and potentially horizontal services available; (d) Engaging the relevant scientific communities. The users will be able to: (a) Analyse distribution patterns of invasive species from different sources of data; (b) Compare the above patterns; (c) Provide managerial suggestions to relevant authorities; (d) Build on the existing infrastructure to address more complex questions (e.g. future scenarios).

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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.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.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/rio.8.e98874

Authors: Audrey Darnaude, Sophie Arnaud-Haond, Ewan Hunter, Oscar Gaggiotti, Anna Sturrock, Maria Beger, Filip Volckaert, Angel Pérez-Ruzafa, Lucía López-López, Susanne E. Tanner, Cemal Turan, Servet Ahmet Doğdu, Stelios Katsanevakis, Federica Costantini

Abstract: Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action supported by COST (European Cooperation in Science and Technology), is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policies.

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DOI: 10.3897/rio.8.e98593

Authors: Donald Hobern, Laurence Livermore, Sarah Vincent, Tim Robertson, Joseph Miller, Quentin Groom, Marie Grosjean

Abstract: Natural history collections are the foundations upon which all knowledge of natural history is constructed. Biological specimens are the best documentation of variation within each species, increasingly serve as curated sources for reference DNA, and are frequently our only evidence for historical species distribution. Collections represent an enormous multigenerational investment in research infrastructure for the biological sciences, but despite this importance most of the holdings of these institutions remain invisible on the Internet, inaccessible to taxonomists from other countries and hidden from computational biodiversity research.Although comprehensive digitisation of the complete holdings of each natural history collection is the long-term goal, this is an expensive and labor-intensive task and will not be completed in the near future for all collections. However, many benefits could quickly be achieved by publishing high-quality metadata on each collection to increase its visibility, provide the foundations for further digitisation and enable researchers to discover and communicate with collections of interest.This paper summarises the results from a consultation activity carried out in 2020 as part of the SYNTHESYS+ (Synthesys of Systematic Resources), “Developing implementation roadmaps for priority infrastructure areas as part of cooperative RI for biodiversity” project. This consultation was primed through an ideas paper, and introductory webinars and conducted as a facilitated two-week online multilingual discussion around 26 topics grouped under four broad headings (Users, Content, Technology and Governance). The results of these discussions are summarised here, along with the wider context of existing and planned initiatives.

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DOI: 10.3897/rio.8.e96274

Authors: Covadonga Orejas, Marina Carreiro-Silva, Christian Mohn, James Reimer, Toufiek Samaai, A. Louise Allcock, Sergio Rossi

Abstract: The term Marine Animal Forest (MAF) was first described by Alfred Russel Wallace in his book “The Malay Archipelago” in 1869. The term was much later re-introduced and various descriptions of MAFs were presented in great detail as part of a book series. The international research and conservation communities have advocated for the future protection of MAFs and their integration into spatial plans and, in response, there are plans to include the characteristics of MAFs into national policies and international directives and conventions (i.e. IUCN, CBD, OSPAR, HELCOM, Barcelona Convention, European directives, ABJN policies etc.). Some MAF ecosystems are already included in international and national conservation and management initiatives, for instance, shallow water coral reefs (ICRI, ICRAN) or cold-water coral reefs and gardens and sponge aggregations (classified as Vulnerable Marine Ecosystems, VMEs), but not as a group together with other ecosystems with similar ecological roles. Marine Animal Forests can be found in all oceans, from shallow to deep waters. They are composed of megabenthic communities dominated by sessile suspension feeders (such as sponges, corals and bivalves) capable of producing three-dimensional frameworks with structural complexity that provide refuge for other species.MAFs are diverse and often harbour highly endemic communities. Marine animal forests face direct anthropogenic threats and they are not protected in many regions, particularly in deep-sea environments. Even though MAFs have been already described in detail, there are still fundamental knowledge gaps regarding their geographical distribution and functioning. A workshop was dedicated to clarifying the definition of MAFs, characterising their structure and functioning, including delineating the ecosystem services that they provide and the threats upon them. The workshop was organised by Working Group 2 of the EU-COST Action “MAF-WORLD” (hereafter WG2), which is responsible for collating and promoting research on mapping, biogeography and biodiversity of MAFs, to identify and reduce these knowledge gaps. Herein, we report on this workshop and its outputs.

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DOI: 10.3897/arphapreprints.e94590

Authors: Serena Rasconi, Hans-Peter Grossart, Alena Gsell, Bastiaan Willem Ibelings, Dedmer van de Waal, Ramsy Agha, Ariola Bacu, Maija Balode, Meryem Beklioğlu, Maja Berden Zrimec, Florina Botez, Tom Butler, Slawomir Cerbin, Angela Cortina, Michael Cunliffe, Thijs Frenken, Esther Garcés, Laura Gjyli, Yonatan Golan, Tiago Guerra, Ayis Iacovides, Antonio Idà, Maiko Kagami, Veljo Kisand, Jovica Leshoski, Pini Marco, Natasa Mazalica, Takeshi Miki, Maria Iasmina Moza, Sigrid Neuhauser, Deniz Özkundakci, Kristel Panksep, Suzana Patcheva, Branka Pestoric, Maya Petrova Stoyneva, Diogo Pinto, Juergen Polle, Carmen Postolache, Joaquín Pozo Dengra, Albert Reñé, Pavel Rychtecky, Dirk S. Schmeller, Bettina Scholz, Géza Selmeczy, Télesphore Sime-Ngando, Kálmán Tapolczai, Orhideja Tasevska, Ivana Trbojevic, Blagoy Uzunov, Silke Van den Wyngaert, Ellen van Donk, Marieke Vanthoor, Elizabeta Veljanoska Sarafiloska, Susie Wood, Petr Znachor

Abstract: Zoosporic parasites (i.e. fungi and fungi-like aquatic microorganisms) constitute important drivers of natural populations, causing severe host mortality. Economic impacts of parasitic diseases are notable in the microalgae biotech industry, affecting production of food ingredients, biofuels, pharma- and nutraceuticals.While scientific research on this topic is gaining traction by increasing studies elucidating the functional role of zoosporic parasites in natural ecosystems, we are currently lacking integrated and interdisciplinary efforts for effectively detecting and controlling parasites in the microalgae industry. To fill this gap we propose to establish an innovative, dynamic European network connecting scientists, industries and stakeholders to optimize information exchange, equalize access to resources and to develop a joint research agenda. ParAqua aims at compiling and making available all information on the occurrence of zoosporic parasites and their relationship with hosts, elucidate drivers and evaluate impacts of parasitism in natural and man-made aquatic environments. We aim to implement new tools for monitoring and prevention of infections, and to create protocols and a Decision Support Tool for detecting and controlling parasites in the microalgae biotech production. Applied knowledge on zoosporic parasites can feed back from industry to ecology, and we therefore will explore whether the developed tools can be applied for monitoring lakes and reservoirs. Short-Term Scientific Missions and Training Schools will be organised specifically for early stage scientists and managers – with a specific focus on ITC – with the aim to share and integrate both scientific and applied expertise and increase exchange between basic and applied researchers and stakeholders.

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DOI: 10.3897/rio.8.e93709

Authors: Donat Agosti, Alexandros Ioannidis-Pantopikos

Abstract: Taxonomy is the science of charting and describing the worlds biodiversity. Organisms are grouped into taxa which are given a given rank building the taxonomic hierarchy. The taxa are described in taxonomic treatments, well defined sections of scientific publications (Catapano 2019). They include a nomenclatural section and one or more sections including descriptions, material citations referring to studied specimens, or notes ecology and behavior. In case the treatment does not describe a new discovered taxon, previous treatments are cited in the form of treatment citations. This citation can refer to a previous treatment and add additional data, or it can be a statement synonymizing the taxon with another taxon. This allows building a citation network, and ultimately is a constituent part of the catalogue of life. Thus treatments play an important role to understand the diversity of life on Earth by providing the scientific argument why group of organism is a new species, or a synonym, and the data provided will increasingly be important to analyze and compare whole genomes of individual genomes.Treatments have been extracted by Plazi since 2008 (Agosti and Egloff 2009), and the TaxPub schema has been described by Catapano (Catapano 2019) to complement existing vocabularies to allow annotation of legacy literature and to produce new publications including the respective annotations (Penev et al. 2010). Today, more than 750,000 treatments have been annotated by Plazi’s TreatmenBank and over 400,000 have been made FAIR digital objects in the Biodiversity Literature Repository in a collaboration of Plazi, Zenodo and Pensoft (Ioannidis-Pantopikos and Agosti 2021, Agosti et al. 2019), and are reused by the Global Biodiversity Information Facility (GBIF), Global Biotic Interaction (GloBI), and the Library System of the Swiss Institute of Bioinformatics (SIBiLS).Each treatment on the Zenodo repository is findable through its rich metadata. The insertion of custom metadata in Zenodo provides metadata referring to domain specific vocabularies such as Darwin Core (Ioannidis-Pantopikos and Agosti 2021). The treatment are accessible through its DataCite Digital Object Identifier (DOI) for the taxonomic treatment as subtype of a publication. The data is interoperable by machine actionable JSON version of the treatment. A license is provided to assure it is reusable.The richness of data and citations within a treatment provide a stepping stone to add treatments not only to knowledge systems such as Wikidata or openBioDiv, but to provide links to many of the cited objects, such as specimens through the material citations, and thus a well curated assemblage of links. Being a FAIR digital object, treatments can be cited and should ultimately linked to from a taxonomic name used in an identification of an organism.

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DOI: 10.3897/rio.8.e86985

Authors: Yuichi Kano

Abstract: Morphological data of life forms are fundamental for documenting and understanding biodiversity. I developed a photogrammetry technique for reconstructing the outer coloured morphology of various creatures and published more than 1000 models online (https://sketchfab.com/ffishAsia-and-floraZia). By suspending it with nylon fishing line(s), taking digital photos from multiple angles and analysing the photos with photogrammetry software, we can obtain a fine 3-dimensional (3D) model of a creature. I believe the challenge could contribute to various fields, such as taxonomy, museology, morphology, anatomy, ecology, education, artificial intelligence, virtual reality, metaverse and, eventually, open/citizen science. Herein, I report the idea and achievement, which I have termed “bio-photogrammetry.”

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DOI: 10.3897/rio.8.e86741

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 economic points of view. The conceptual trading system will necessarily be very 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.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/rio.8.e82597

Authors: Alessandra Pugnetti, Elisabetta Manea, Ivica Vilibić, Alessandro Sarretta, Lucilla Capotondi, Bruno Cataletto, Elisabeth De Maio, Carlo Franzosini, Ivana Golec, Marco Gottardi, Jelena Kurtović Mrčelić, Hrvoje Mihanovic, Alessandro Oggioni, Grgur Pleslic, Mariangela Ravaioli, Silvia Rova, Andrea Valentini, Caterina Bergami

Abstract: This Policy Brief succinctly presents the Ecological Observing System of the Adriatic Sea (ECOAdS), aimed at integrating the ecological and oceanographic dimensions within the conservation strategy of the Natura 2000 network, and to propose a way to go for its future development and maintenance. After a definition of marine ecological observatories, we describe the current structure of ECOAdS, its key components and potential relevance in relation to the main European strategies for biodiversity and marine observation for the next decade. Finally, we suggest some actions that could be undertaken for the future development of ECOAdS, targeting possible perspectives in different regional, macro-regional, national and European strategic contexts. This Policy Brief is one of the outcomes of the Interreg Italy-Croatia Project ECOSS (ECological Observing System in the Adriatic Sea: oceanographic observations for biodiversity; https://www.italy-croatia.eu/web/ecoss), which had the main purpose to design and carry out the first steps for the establishment of ECOAdS.

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DOI: 10.3897/rio.8.e81563

Authors: Tanya Haupt, Jamie Ceasar, Paris Stefanoudis, Charles von der Meden, Robyn Payne, Luther Adams, Darrell Anders, Anthony Bernard, Willem Coetzer, Wayne Florence, Liesl Janson, Ashley Johnson, Roxanne Juby, Alison Kock, Daniel Langenkämper, Ahmed Nadjim, Denham Parker, Toufiek Samaai, Laurenne Snyders, Leshia Upfold, Grant van der Heever, Lauren Williams

Abstract: Originating from the Second International Indian Ocean Expedition (IIOE-2), the main goal of the Western Indian Ocean (WIO) Regional Benthic Imagery Workshop, was to provide information and training on the use of various underwater imagery platforms in benthic research. To date, attempts made to explore the bottom of the ocean range from simple diving bells to more advanced camera systems, and the rapidly expanding field of underwater image-based research has supported marine exploration in many forms, from biodiversity surveys, spatial analyses and temporal studies, to monitoring schemes. Alongside the increasing use of underwater camera systems worldwide, there is an evident need to improve training and access to these techniques for students and researchers from institutes within the WIO. The week-long virtual event was conducted between 30 August and 3 September 2021 with 266 participants. Sessions consisted of lessons, practical demonstrations and interactive discussions which covered the steps required to conduct underwater imagery surveys, taking participants through elements of sampling design, data acquisition and processing, considerations for statistical analysis and, effective managment of data. The session recordings from the workshop are available online as a teaching aid which has the potential to reach marine researchers both regionally and globally. It is crucial that we build on this momentum by continuing to develop and strengthen the network established through this initiative for standardised benthic-image-based research within the WIO.

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DOI: 10.3897/rio.8.e79187

Authors: Michael Greeff, Max Caspers, Vincent Kalkman, Luc Willemse, Barry Sunderland, Olaf Bánki, Laurens Hogeweg

Abstract: Natural history collections play a vital role in biodiversity research and conservation by providing a window to the past. The usefulness of the vast amount of historical data depends on their quality, with correct taxonomic identifications being the most critical. The identification of many of the objects of natural history collections, however, is wanting, doubtful or outdated. Providing correct identifications is difficult given the sheer number of objects and the scarcity of expertise. Here we outline the construction of an ecosystem for the collaborative development and exchange of image recognition algorithms designed to support the identification of objects. Such an ecosystem will facilitate sharing taxonomic expertise among institutions by offering image datasets that are correctly identified by their in-house taxonomic experts. Together with openly accessible machine learning algorithms and easy to use workbenches, this will allow other institutes to train image recognition algorithms and thereby compensate for the lacking expertise.

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DOI: 10.3897/rio.8.e80223

Authors: Audrey Darnaude, Sophie Arnaud-Haond, Ewan Hunter, Oscar Gaggiotti, Anna Sturrock, Maria Beger, Filip Volckaert, Angel Pérez-Ruzafa, Lucía López-López, Susanne E. Tanner, Cemal Turan, Servet Ahmet Doğdu, Stelios Katsanevakis, Federica Costantini

Abstract: Truly sustainable development in a human-altered, fragmented marine environment subject to unprecedented climate change, demands informed planning strategies in order to be successful. Beyond a simple understanding of the distribution of marine species, data describing how variations in spatio-temporal dynamics impact ecosystem functioning and the evolution of species are required. Marine Functional Connectivity (MFC) characterizes the flows of matter, genes and energy produced by organism movements and migrations across the seascape. As such, MFC determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective MFC knowledge can therefore improve predictions of the impacts of environmental change and help to refine management and conservation strategies for the seas and oceans. Gathering these data are challenging however, as access to, and survey of marine ecosystems still presents significant challenge. Over 50 European institutions currently investigate aspects of MFC using complementary methods across multiple research fields, to understand the ecology and evolution of marine species. The aim of SEA-UNICORN, a COST Action within the European Union Horizon 2020 framework programme, is to bring together this research effort, unite the multiple approaches to MFC, and to integrate these under a common conceptual and analytical framework. The consortium brings together a diverse group of scientists to collate existing MFC data, to identify knowledge gaps, to enhance complementarity among disciplines, and to devise common approaches to MFC. SEA-UNICORN will promote co-working between connectivity practitioners and ecosystem modelers to facilitate the incorporation of MFC data into the predictive models used to identify marine conservation priorities. Ultimately, SEA-UNICORN will forge strong forward-working links between scientists, policy-makers and stakeholders to facilitate the integration of MFC knowledge into decision support tools for marine management and environmental policies.

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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 Bruelheide, 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/rio.7.e77750

Authors: Thibault Datry, Daniel Allen, Roger Argelich, Jose Barquin, Nuria Bonada, Andrew Boulton, Flora Branger, Yongjiu Cai, Miguel Cañedo-Argüelles, Núria Cid, Zoltán Csabai, Martin Dallimer, José Carlos de Araújo, Steven Declerck, Thijs Dekker, Petra Döll, Andrea Encalada, Maxence Forcellini, Arnaud Foulquier, Jani Heino, Franck Jabot, Patrícia Keszler, Leena Kopperoinen, Sven Kralisch, Annika Künne, Nicolas Lamouroux, Claire Lauvernet, Virpi Lehtoranta, Barbora Loskotová, Rafael Marcé, Julia Martin Ortega, Christine Matauschek, Marko Miliša, Szilárd Mogyorósi, Nabor Moya, Hannes Müller Schmied, Antoni Munné, François Munoz, Heikki Mykrä, Irina Pal, Riikka Paloniemi, Petr Pařil, Polona Pengal, Bálint Pernecker, Marek Polášek, Carla Rezende, Sergi Sabater, Romain Sarremejane, Guido Schmidt, Lisette Senerpont Domis, Gabriel Singer, Esteban Suárez, Matthew Talluto, Sven Teurlincx, Tim Trautmann, Amélie Truchy, Emmanouil Tyllianakis, Sari Väisänen, Liisa Varumo, Jean-Philippe Vidal, Annika Vilmi, Dolors Vinyoles

Abstract: River networks are among Earth’s most threatened hot-spots of biodiversity and provide key ecosystem services (e.g., supply drinking water and food, climate regulation) essential to sustaining human well-being. Climate change and increased human water use are causing more rivers and streams to dry, with devastating impacts on biodiversity and ecosystem services. Currently, more than a half of the global river networks consist of drying channels, and these are expanding dramatically. However, drying river networks (DRNs) have received little attention from scientists and policy makers, and the public is unaware of their importance. Consequently, there is no effective integrated biodiversity conservation or ecosystem management strategy of DRNs.A multidisciplinary team of 25 experts from 11 countries in Europe, South America, China and the USA will build on EU efforts to assess the cascading effects of climate change on biodiversity, ecosystem functions and ecosystem services of DRNs through changes in flow regimes and water use. DRYvER (DRYing riVER networks) will gather and upscale empirical and modelling data from nine focal DRNs (case studies) in Europe (EU) and Community of Latin American and Caribbean States (CELAC) to develop a meta-system framework applicable to Europe and worldwide. It will also generate crucial knowledge-based strategies, tools and guidelines for economically-efficient adaptive management of DRNs. Working closely with stakeholders and end-users, DRYvER will co-develop strategies to mitigate and adapt to climate change impacts in DRNs, integrating hydrological, ecological (including nature-based solutions), socio-economic and policy perspectives. The end results of DRYvER will contribute to reaching the objectives of the Paris Agreement and placing Europe at the forefront of research on climate change.

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DOI: 10.3897/rio.7.e78844

Authors: Danail Popov, Priyanka Roychoudhury, Helen Hardy, Laurence Livermore, Ken Norris

Abstract: The Natural History Museum, London has been creating digital data about collections for many years, with a formal Digital Collections Programme since 2014. Efforts to monitor the outcomes and impact of this work have focused on metrics of digital access, such as download events, and on citations of digital specimens as a measure of use. Digitisation projects and resulting research have also been used as impact case studies, highlighting areas such as human health and conservation. In 2021, the Museum decided to explore the economic impacts of collections data in more depth, and commissioned Frontier Economics to undertake modelling, resulting in this report. While the methods in this report are relevant to collections globally, this modelling focuses on benefits to the UK, and is intended to support the Museum’s own digitisation work, as well as a current scoping study funded by the Arts & Humanities Research Council about the case for digitising all UK natural science collections as a research infrastructure. This study focuses on digitisation in the round, not distinguishing between different collection types or levels of data creation at this stage. Three methods have been used: first, analysing five key thematic areas or sectors where data from natural science collections are likely to lead to benefits; secondly, analysing typical returns on investment in scientific research; and thirdly, examining the efficiency savings that can be reinvested in research if data are available freely and openly. Together, these methods confirm benefits in excess of £2 billion over 30 years, representing a seven to ten times return on investment.

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DOI: 10.3897/rio.7.e70486

Authors: Dimitra Petza, Panagiotis Anastopoulos, Marta Coll, Serge Garcia, Michel Kaiser, Stefanos Kalogirou, Irene Lourdi, Jake Rice, Marija Sciberras, Stelios Katsanevakis

Abstract: Objective: This scoping review (ScR) aims to identify and map the evidence base on the contribution of area-based fisheries management measures (ABFMs) to fisheries sustainability and marine conservation. Emphasis will be given to the research that has been conducted in terms of the methodologies applied and the key findings acknowledged.Introduction: ABFMs have been used for centuries and are present in modern fisheries management plans and regulations. Although ABFMs are commonly related to the sustainable exploitation of the target species of the managed fishery, they may also be considered as wider conservation measures, in the cases where their outcomes include the protection or reduction of impact on biodiversity or ecosystem structures and functions.Inclusion criteria: Studies that perform an assessment of the contribution of ABFMs on either fisheries sustainability or on area-based marine conservation (or both) will be considered. All types of ABFMs in the marine realm globally, which are established as management measures by any type of designation authority or jurisdiction and for any type of fishing activity, gear, target species and/or habitats will be considered. Peer-reviewed and grey literature will be included. There will be no search limitations applied by year of publication. Studies in English, French, Greek, Italian, Spanish and Swedish will be reviewed.Methods: The ScR will be conducted in accordance with the JBI (Joanna Briggs Institute) methodology. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) extension for ScRs will guide the protocol. The bibliographic databases to be searched include Scopus and Web of Science. Sources of grey literature will include databases, pre-print archives, organisational websites and web-based search engines. The design of the search strategy will be guided by a librarian/ information specialist. The Zotero software, Sysrev platform and EviAtlas tool will be used for data management, extraction and presentation. Data will be extracted by two reviewers. Tables, graphs and maps along with a narrative summary of the outcomes will be presented.

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DOI: 10.3897/arphapreprints.e70983

Authors: Blánaid White, Fiona Regan, Miguel Caetano, German Rodriguez, Iratxe Mentxaka, Joana Larreta, Maria Jesus Belzunce, Florence Menet-Nedelec, Isabelle Amouroux, Jean-Louis Gonzalez, Stephane Guesdon, Philippe Bersuder, Thi Bolam, Barbara Marras, Marco Schintu, Natalia Montero, Margarida Correia dos Santos, Craig D. Robinson, Brendan McHugh, Gary R. Fones, Hao Zhang

Abstract: This good practice guide is focused on the DGT devices, which are the most widely used passive sampler for metals, covering the following aspects:■ Principle■ Handling passive sampling devices for metals■ Estimation of appropriate field deployment time■ A Good Practice Guide for the Use of DGTs■ Passive sampling device preparation and assembly■ Selection of sampling site and safety precautions■ Passive sampling device deployment and retrieval■ Extraction of analytes from passive sampling devices■ Analysis■ Calculations

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