Christiane Werner, Ulrike Wallrabe, Andreas Christen, L. Comella, Carsten Dormann, Anna Göritz, Rüdiger Grote, S. Haberstroh, M. Jouda, Ralf Kiese, Barbara Koch, Jan Korvink, Jürgen Kreuzwieser, Friederike Lang, Julian Müller, Oswald Prucker, Alexander Reiterer, Jürgen Rühe, Stefan Rupitsch, H. Schack-Kirchner, Katrin Schmitt, Nina Stobbe, Markus Weiler, Peter Woias, Jürgen Wöllenstein
Global climate change threatens ecosystem functioning worldwide. Forest ecosystems are particularly important for carbon sequestration, thereby buffering climate change and providing socio-economic services. However, recurrent stresses, such as heat waves, droughts and floods can affect forests with potential cascading effects on their carbon sink capacity, drought resilience and sustainability. Knowledge about the stress impact on the multitude of processes driving soil-plant-atmosphere interactions within these complex forest systems is widely lacking and uncertainty about future changes extremely high. Thus, forecasting forest response to climate change will require a dramatically improved process understanding of carbon and water cycling across various temporal (minutes to seasons) and spatial (leaf to ecosystem) scales covering atmosphere, biosphere, pedosphere and hydrosphere components. Many relevant processes controlling carbon and water exchange occur at small scales (e.g. rhizosphere, single leaf) with a high spatial and temporal variability, which is poorly constrained. However, interactions and feedback loops can be key players that amplify or dampen a system’s response to stress. Moreover, spatial and temporal scaling rules for these non-linear processes in structurally and functionally diverse ecosystems are unknown. Legacy effects, for example, altered response after previous stress and retarded recovery of forests after climate extremes, are not captured in state-of-the-art models. Currently, we are lacking the appropriate and interconnected measurement, data assimilation and modelling tools allowing for a comprehensive, real-time quantification of key processes at high spatio-temporal coverage in heterogeneous environments. Moreover, since climate impacts are highly unpredictable with respect to timing and location, future research will require novel mobile, easily deployable and cost-efficient approaches. ECOSENSE, therefore, assembles expertise from environmental and engineering sciences, both being excellently paired at the University of Freiburg. Our interdisciplinary research project will investigate all relevant scales in a next-generation ecosystem research assessment (ECOSENSE). Our vision is to detect and forecast critical changes in ecosystem functioning, based on the understanding of hierarchical process interaction. In the first phase, ECOSENSE will explore these process interactions by investigating pools and fluxes of water and carbon, i.e. CO2 exchange, isotope discrimination and volatile organic compounds (VOC), as well as stress indicators by remotely and in situ sensed chlorophyll fluorescence. To address these research tasks, ECOSENSE will develop, implement and test a distributed, autonomous, intelligent sensor network, based on novel microsensors tailored to the specific needs in remote and harsh forest environments. They will measure the spatio-temporal dynamics of ecosystem pools and fluxes in a naturall
{"title":"ECOSENSE - Multi-scale quantification and modelling of spatio-temporal dynamics of ecosystem processes by smart autonomous sensor networks","authors":"Christiane Werner, Ulrike Wallrabe, Andreas Christen, L. Comella, Carsten Dormann, Anna Göritz, Rüdiger Grote, S. Haberstroh, M. Jouda, Ralf Kiese, Barbara Koch, Jan Korvink, Jürgen Kreuzwieser, Friederike Lang, Julian Müller, Oswald Prucker, Alexander Reiterer, Jürgen Rühe, Stefan Rupitsch, H. Schack-Kirchner, Katrin Schmitt, Nina Stobbe, Markus Weiler, Peter Woias, Jürgen Wöllenstein","doi":"10.3897/rio.10.e129357","DOIUrl":"https://doi.org/10.3897/rio.10.e129357","url":null,"abstract":"Global climate change threatens ecosystem functioning worldwide. Forest ecosystems are particularly important for carbon sequestration, thereby buffering climate change and providing socio-economic services. However, recurrent stresses, such as heat waves, droughts and floods can affect forests with potential cascading effects on their carbon sink capacity, drought resilience and sustainability. Knowledge about the stress impact on the multitude of processes driving soil-plant-atmosphere interactions within these complex forest systems is widely lacking and uncertainty about future changes extremely high. Thus, forecasting forest response to climate change will require a dramatically improved process understanding of carbon and water cycling across various temporal (minutes to seasons) and spatial (leaf to ecosystem) scales covering atmosphere, biosphere, pedosphere and hydrosphere components.\u0000 Many relevant processes controlling carbon and water exchange occur at small scales (e.g. rhizosphere, single leaf) with a high spatial and temporal variability, which is poorly constrained. However, interactions and feedback loops can be key players that amplify or dampen a system’s response to stress. Moreover, spatial and temporal scaling rules for these non-linear processes in structurally and functionally diverse ecosystems are unknown. Legacy effects, for example, altered response after previous stress and retarded recovery of forests after climate extremes, are not captured in state-of-the-art models. Currently, we are lacking the appropriate and interconnected measurement, data assimilation and modelling tools allowing for a comprehensive, real-time quantification of key processes at high spatio-temporal coverage in heterogeneous environments. Moreover, since climate impacts are highly unpredictable with respect to timing and location, future research will require novel mobile, easily deployable and cost-efficient approaches. ECOSENSE, therefore, assembles expertise from environmental and engineering sciences, both being excellently paired at the University of Freiburg.\u0000 Our interdisciplinary research project will investigate all relevant scales in a next-generation ecosystem research assessment (ECOSENSE). Our vision is to detect and forecast critical changes in ecosystem functioning, based on the understanding of hierarchical process interaction. In the first phase, ECOSENSE will explore these process interactions by investigating pools and fluxes of water and carbon, i.e. CO2 exchange, isotope discrimination and volatile organic compounds (VOC), as well as stress indicators by remotely and in situ sensed chlorophyll fluorescence.\u0000 To address these research tasks, ECOSENSE will develop, implement and test a distributed, autonomous, intelligent sensor network, based on novel microsensors tailored to the specific needs in remote and harsh forest environments. They will measure the spatio-temporal dynamics of ecosystem pools and fluxes in a naturall","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"80 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141652997","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Community tutelary shrines in Taiwan have been identified as excellent resources for grassroots-level heritage. As community ritual assemblages, they are able to encode data about a settlement’s social, political and economic history in their material composition, aesthetic choices, artefacts, displays and orientations. This data paper previews a first edition dataset related to 752 such shrines found throughout the greater Taipei area in northern Taiwan. It explores the basis for such a dataset, how it can be used and what has been produced. This dataset is available on the depositar research data repository, operated out of the Institute of Information Sciences at Academia Sinica in Taipei and is publicly available for download.
{"title":"Earth deity shrines of the Greater Taipei area: A first edition curated dataset","authors":"James Morris","doi":"10.3897/rio.10.e127510","DOIUrl":"https://doi.org/10.3897/rio.10.e127510","url":null,"abstract":"Community tutelary shrines in Taiwan have been identified as excellent resources for grassroots-level heritage. As community ritual assemblages, they are able to encode data about a settlement’s social, political and economic history in their material composition, aesthetic choices, artefacts, displays and orientations. This data paper previews a first edition dataset related to 752 such shrines found throughout the greater Taipei area in northern Taiwan. It explores the basis for such a dataset, how it can be used and what has been produced. This dataset is available on the depositar research data repository, operated out of the Institute of Information Sciences at Academia Sinica in Taipei and is publicly available for download.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"29 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141655063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Restoring the Lower Danube River's wetlands: a short report on the hydrological effectiveness of completed projects","authors":"G. Ioana‐Toroimac","doi":"10.3897/rio.10.e130474","DOIUrl":"https://doi.org/10.3897/rio.10.e130474","url":null,"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.\u0000 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.\u0000 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.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":" 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141673649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Steffen Neumann, Ann-Christin Andres, Felix Bach, Theo Bender, Christian Bonatto Minella, Franziska Eberl, Tillmann Fischer, Benjamin Golub, Shashank S Harivyasi, Sonja Herres‐Pawlis, Pei-Chi Huang, Johannes Hunold, John Jollife, Nicole Jung, Johannes Liermann, V. Nainala, M. Razum, Oliver Koepler, Christoph Steinbeck
The progress of the DFG-funded NFDI4Chem consortium (NFDI 4/1 - project number 441958208) in data management in chemistry is outlined in our latest report, highlighting the steps we have taken to integrate a data-centric approach within the chemistry community. This interim report offers a comprehensive overview of our data management activities, covering the reporting period from October 2020 to August 2023. The shift to digital tools in research documentation is driven by our work with Electronic Laboratory Notebooks (ELNs), such as Chemotion ELN, offering systematic data storage for easy retrieval and sharing. Additionally, we focus on developing repositories, such as Chemotion repository and RADAR4Chem, which fulfil the needs for the storage of chemical data. The NFDI4Chem Search Service ensures easy data access from our repositories. Our efforts extend to community engagement through conference visits and online presence, aimed at creating awareness for (digital) research data management and connecting to chemistry students and researchers. Our training programs have reached over 600 participants to date. Initiatives like the FAIR4Chem award and the Chemistry Data Days promote cultural change towards FAIR data. Our Editors4Chem initiative collaborates with publishers for standardised data management and the Ontologies4Chem workshops organised by our consortium promote the ontology development in the field. Apart from the consortium's engagement for chemists, NFDI4Chem members played key roles in the development of the NFDI as a whole. Being actively involved in the sections and task forces, NFDI4Chem promotes collaborative solutions across NFDI consortia.
{"title":"Interim Report NFDI4Chem 2023","authors":"Steffen Neumann, Ann-Christin Andres, Felix Bach, Theo Bender, Christian Bonatto Minella, Franziska Eberl, Tillmann Fischer, Benjamin Golub, Shashank S Harivyasi, Sonja Herres‐Pawlis, Pei-Chi Huang, Johannes Hunold, John Jollife, Nicole Jung, Johannes Liermann, V. Nainala, M. Razum, Oliver Koepler, Christoph Steinbeck","doi":"10.3897/rio.10.e124977","DOIUrl":"https://doi.org/10.3897/rio.10.e124977","url":null,"abstract":"The progress of the DFG-funded NFDI4Chem consortium (NFDI 4/1 - project number 441958208) in data management in chemistry is outlined in our latest report, highlighting the steps we have taken to integrate a data-centric approach within the chemistry community. This interim report offers a comprehensive overview of our data management activities, covering the reporting period from October 2020 to August 2023.\u0000 The shift to digital tools in research documentation is driven by our work with Electronic Laboratory Notebooks (ELNs), such as Chemotion ELN, offering systematic data storage for easy retrieval and sharing. Additionally, we focus on developing repositories, such as Chemotion repository and RADAR4Chem, which fulfil the needs for the storage of chemical data. The NFDI4Chem Search Service ensures easy data access from our repositories. Our efforts extend to community engagement through conference visits and online presence, aimed at creating awareness for (digital) research data management and connecting to chemistry students and researchers. Our training programs have reached over 600 participants to date. Initiatives like the FAIR4Chem award and the Chemistry Data Days promote cultural change towards FAIR data. Our Editors4Chem initiative collaborates with publishers for standardised data management and the Ontologies4Chem workshops organised by our consortium promote the ontology development in the field.\u0000 Apart from the consortium's engagement for chemists, NFDI4Chem members played key roles in the development of the NFDI as a whole. Being actively involved in the sections and task forces, NFDI4Chem promotes collaborative solutions across NFDI consortia.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":" 45","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141679960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mathias Dillen, Laura Abraham, Ann Bogaerts, Sofie De Smedt, H. Engledow, F. Leliaert, Maarten Trekels, Steven Dessein, Quentin Groom
This Data Management Plan outlines a comprehensive strategy for handling, storing, and sharing of data generated by digitisation projects of the herbarium at Meise Botanic Garden with Index Herbarium code BR. Its purpose is to establish clear guidelines for both staff and external users, specifying the terms governing data usage and storage. It aims to prioritise the FAIR principles (Findable, Accessible, Interoperable and Reusable), ensure responsible data management, facilitate long-term preservation, uphold legal and ethical obligations, all while aligning with the research excellence mission of Meise Botanic Garden. This plan serves as a guiding document to effectively and efficiently achieve these goals.
{"title":"The Meise Botanic Garden Herbarium Data Management Plan","authors":"Mathias Dillen, Laura Abraham, Ann Bogaerts, Sofie De Smedt, H. Engledow, F. Leliaert, Maarten Trekels, Steven Dessein, Quentin Groom","doi":"10.3897/rio.10.e124288","DOIUrl":"https://doi.org/10.3897/rio.10.e124288","url":null,"abstract":"This Data Management Plan outlines a comprehensive strategy for handling, storing, and sharing of data generated by digitisation projects of the herbarium at Meise Botanic Garden with Index Herbarium code BR. Its purpose is to establish clear guidelines for both staff and external users, specifying the terms governing data usage and storage. It aims to prioritise the FAIR principles (Findable, Accessible, Interoperable and Reusable), ensure responsible data management, facilitate long-term preservation, uphold legal and ethical obligations, all while aligning with the research excellence mission of Meise Botanic Garden. This plan serves as a guiding document to effectively and efficiently achieve these goals.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"215 S703","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141681569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Chala, E. Kusch, Claus Weiland, Carrie Andrew, Jonas Grieb, Tuomas P. Rossi, Tomas Martinovic, Dag Endresen
Amidst population growth and climate-driven crop stresses such as drought, extreme weather, fungal and insect pests, as well as various crop diseases, ensuring food security demands innovative strategies. Crop wild relatives (CWR), wild plants in the same genus as the crop as well as wild populations belonging to the same species as the crop, offer novel genetic resources crucial for enhancing crop resilience against these stress factors. Here, we introduce a prototype digital twin (pDT) to aid in searching and utilising CWR genetic resources. Using the MoDGP (Modelling the Germplasm of Interest) tool, the pDT enables mapping geographic areas where stress-tolerant CWR populations can be found. With its graphical user interface, it offers flexibility in selecting genetic resources from CWR tailored to enhance resilience of various crops against diverse stress factors.
{"title":"Prototype biodiversity digital twin: crop wild relatives genetic resources for food security","authors":"D. Chala, E. Kusch, Claus Weiland, Carrie Andrew, Jonas Grieb, Tuomas P. Rossi, Tomas Martinovic, Dag Endresen","doi":"10.3897/rio.10.e125192","DOIUrl":"https://doi.org/10.3897/rio.10.e125192","url":null,"abstract":"Amidst population growth and climate-driven crop stresses such as drought, extreme weather, fungal and insect pests, as well as various crop diseases, ensuring food security demands innovative strategies. Crop wild relatives (CWR), wild plants in the same genus as the crop as well as wild populations belonging to the same species as the crop, offer novel genetic resources crucial for enhancing crop resilience against these stress factors. Here, we introduce a prototype digital twin (pDT) to aid in searching and utilising CWR genetic resources. Using the MoDGP (Modelling the Germplasm of Interest) tool, the pDT enables mapping geographic areas where stress-tolerant CWR populations can be found. With its graphical user interface, it offers flexibility in selecting genetic resources from CWR tailored to enhance resilience of various crops against diverse stress factors.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"9 11","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141356151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vladimir Mikryukov, Kessy Abarenkov, Thomas Jeppesen, Dmitry Schigel, Tobias Frøslev
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.
{"title":"Prototype Biodiversity Digital Twin: Phylogenetic Diversity","authors":"Vladimir Mikryukov, Kessy Abarenkov, Thomas Jeppesen, Dmitry Schigel, Tobias Frøslev","doi":"10.3897/rio.10.e124988","DOIUrl":"https://doi.org/10.3897/rio.10.e124988","url":null,"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.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"125 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141360823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Prototype Biodiversity Digital Twin: prioritisation of DNA metabarcoding sampling locations","authors":"Tobias Frøslev, Robin Boyd, Dmitry Schigel","doi":"10.3897/rio.10.e124978","DOIUrl":"https://doi.org/10.3897/rio.10.e124978","url":null,"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.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"29 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141355673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jürgen Groeneveld, Tomas Martinovic, Tuomas P. Rossi, Ondrej Salamon, Kata Sara-aho, V. Grimm
Honey bees are vital to human well-being and are under multiple stresses. We need to be able to assess the viability and productivity of honey bee colonies in different landscapes and under different management and climate-change scenarios. We have developed a prototype digital twin, HONEYBEE-pDT, based on the BEEHAVE model, which simulates foraging, population dynamics and Varroa mite infestation of a single honey bee colony. The main input data are land-cover maps and daily weather data. We have developed the pDT for simulating large areas and have tested it for the whole of Germany. We have also developed a web-based GUI that users can use to run the pDT for specific sites. Hive weight data from hundreds of hives will be used for calibration and validation.
{"title":"Prototype Biodiversity Digital Twin: honey bees in agricultural landscapes","authors":"Jürgen Groeneveld, Tomas Martinovic, Tuomas P. Rossi, Ondrej Salamon, Kata Sara-aho, V. Grimm","doi":"10.3897/rio.10.e125167","DOIUrl":"https://doi.org/10.3897/rio.10.e125167","url":null,"abstract":"Honey bees are vital to human well-being and are under multiple stresses. We need to be able to assess the viability and productivity of honey bee colonies in different landscapes and under different management and climate-change scenarios. We have developed a prototype digital twin, HONEYBEE-pDT, based on the BEEHAVE model, which simulates foraging, population dynamics and Varroa mite infestation of a single honey bee colony. The main input data are land-cover maps and daily weather data. We have developed the pDT for simulating large areas and have tested it for the whole of Germany. We have also developed a web-based GUI that users can use to run the pDT for specific sites. Hive weight data from hundreds of hives will be used for calibration and validation.","PeriodicalId":92718,"journal":{"name":"Research ideas and outcomes","volume":"3 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141360578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
G. Bravo, G. Bigatti, María Bagur, E. Macaya, Nelson Valdivia, Ariel Rodriguez, Mariela Gauna, Ian Walker, J. Livore, María Mendez, Rocío Nieto Vilela, Fernando Lima, Rui Seabra, Enrique Montes
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.
美洲海洋生物多样性观测网络极点到极点（MBON Pole to Pole）于 2023 年 3 月 27-31 日和 2024 年 1 月 22-26 日在阿根廷巴塔哥尼亚举办了两期讲习班，旨在通过应用新颖易用的生物多样性观测 方法，提高对阿根廷和智利潮间带岩石群落的长期监测能力。在这些讲习班上，学员们接受了如何收集和处理底栖生物照片-四分图图像以及如何使用开源人工智能应用程序对其进行分析的培训。讲习班参与者包括公园管理员、本科生、研究生和科学家。这些培训活动涵盖了岩石海岸生态学的理论概念和实地练习。讲习班促进了生物多样性数据用户与生态学家之间的合作与知识交流，最终制定了潮间带岩石群落标准化生物多样性监测协议，该协议可在联合国教科文组织政府间海洋学委员会的海洋最佳实践系统中查阅。与会者学习了如何识别这些生境中常见的优势物种和功能类群（如大型藻类、软体动物、藤壶）及其沿海拔梯度的分区模式，如何使用由 "MBON Pole to Pole "提供的四分框架和照相机拍摄高质量的底栖照片，以及如何使用开源自动分类器计算所观察到的分类类群的百分比覆盖率估计值。新提出的建议强调了让公园护林员积极参与调查工作以及促进与管理海洋保护区的决策者沟通的重要性。这些活动得到了 "联合国十年 "的认可，被视为对 "海洋生命 2030 "计划的贡献，以提高在美洲开展协调、标准化和持续的生物多样性观测工作的能力。
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