La base de données saproxyliques : l'émergence d'un aperçu de la diversité biologique du bois mort

The Nordic countries Norway, Sweden, Finland and Denmark are developing a shared English-written database with species-specific information about the ecology of saproxylic species. The database now contains information for about 6000 species and the number is expected to approach 7000 species in the near future. The main organism groups are Ascomycetes, Basidiomycetes, Coleoptera, Diptera and Hymenoptera. This paper describes database structure, information that is entered for each species and different qualities of dead wood that the species are associated to. Furthermore, the paper describes how the database can be searched and viewed for different uses, and it gives some examples of data output. Finally, the paper describes potential uses, maintenance, and development plans including making the database accessible on InternetLes pays nordiques (Norvège, Suède, Finlande et Danemark) développent une base de données commune, en anglais, avec des informations spécifiques sur l'écologie des espèces saproxyliques. La base de données contient maintenant des informations sur environ 6000 espèces et ce nombre devrait avoisiner 7000 dans un proche avenir. Les principaux groupes d'organismes sont les Ascomycètes, les Basidiomycètes, les Coléoptères, les Diptères et les Hyménoptères. Le présent article décrit la structure de la base de données, l'information qui y est entrée pour chaque espèce et les différentes qualités de bois mort auxquelles les espèces sont associées. De plus il montre comment la base de données peut être utilisée et visualisée pour différents usages; quelques exemples de sorties de données sont fournis. Enfin l'article décrit les utilisations potentielles, la maintenance et les plans de développement de la base de données dont son accessibilité sur Internet

Erot spatiaalisissa ja ajallisissa reaktionormeissa kevään ja syksyn fenologisille tapahtumille

For species to stay temporally tuned to their environment, they use cues such as the accumulation of degree-days. The relationships between the timing of a phenological event in a population and its environmental cue can be described by a population-level reaction norm. Variation in reaction norms along environmental gradients may either intensify the envi- ronmental effects on timing (cogradient variation) or attenu- ate the effects (countergradient variation). To resolve spatial and seasonal variation in species’ response, we use a unique dataset of 91 taxa and 178 phenological events observed across a network of 472 monitoring sites, spread across the nations of the former Soviet Union. We show that compared to local rates of advancement of phenological events with the advancement of temperature-related cues (i.e., variation within site over years), spatial variation in reaction normsPeer reviewe

Phenological shifts of abiotic events, producers and consumers across a continent

Ongoing climate change can shift organism phenology in ways that vary depending on species, habitats and climate factors studied. To probe for large-scale patterns in associated phenological change, we use 70,709 observations from six decades of systematic monitoring across the former Union of Soviet Socialist Republics. Among 110 phenological events related to plants, birds, insects, amphibians and fungi, we find a mosaic of change, defying simple predictions of earlier springs, later autumns and stronger changes at higher latitudes and elevations. Site mean temperature emerged as a strong predictor of local phenology, but the magnitude and direction of change varied with trophic level and the relative timing of an event. Beyond temperature-associated variation, we uncover high variation among both sites and years, with some sites being characterized by disproportionately long seasons and others by short ones. Our findings emphasize concerns regarding ecosystem integrity and highlight the difficulty of predicting climate change outcomes. The authors use systematic monitoring across the former USSR to investigate phenological changes across taxa. The long-term mean temperature of a site emerged as a strong predictor of phenological change, with further imprints of trophic level, event timing, site, year and biotic interactions.Peer reviewe

Chronicles of nature calendar, a long-term and large-scale multitaxon database on phenology

We present an extensive, large-scale, long-term and multitaxon database on phenological and climatic variation, involving 506,186 observation dates acquired in 471 localities in Russian Federation, Ukraine, Uzbekistan, Belarus and Kyrgyzstan. The data cover the period 1890-2018, with 96% of the data being from 1960 onwards. The database is rich in plants, birds and climatic events, but also includes insects, amphibians, reptiles and fungi. The database includes multiple events per species, such as the onset days of leaf unfolding and leaf fall for plants, and the days for first spring and last autumn occurrences for birds. The data were acquired using standardized methods by permanent staff of national parks and nature reserves (87% of the data) and members of a phenological observation network (13% of the data). The database is valuable for exploring how species respond in their phenology to climate change. Large-scale analyses of spatial variation in phenological response can help to better predict the consequences of species and community responses to climate change.Peer reviewe

When Data Management Meets Project Management

Complex projects that collect, curate and analyse biodiversity data are often presented with the challenge of accommodating diverse data types, various curation and output workflows, and evolving project logistics that require rapid changes in the applications and data structures. At the same time, sustainability concerns and maintenance overheads pose a risk to the long term viability of such projects. We advocate the use of flexible, multiplatform tools that adapt to operational, day-to-day challenges while providing a robust, cost efficient, and maintainable framework that serves the needs data collectors, managers and users. EarthCape is a highly versatile platform for managing biodiversity research and collections data, associated molecular laboratory data (Fig. 1), multimedia, structured ecological surveys and monitoring schemes, and more. The platform includes a fully functional Windows client as well as a web application. The data are stored in the cloud or on-premises and can be accessed by users with various access and editing rights. Ease of customization (making changes to user interface and functionality) is critical for most environments that deal with operational research processes. For active researchers and curators, there is rarely time to wait for a cycle of development that follows a change or feature request. In EarthCape, most of the changes to the default setup can be implemented by the end users with minimum effort and require no programming skills. High flexibility and a range of customisation options is complemented with mapping to Darwin Core standard and integration with GBIF, Geolocate, Genbank, and Biodiversity Heritage Library APIs. The system is currently used daily for rapid data entry, digitization and sample tracking, by such organisations as Imperial College, University of Cambridge, University of Helsinki, University of Oxford. Being an operational data entry and retrieval tool, EarthCape sits at the bottom of Virtual Research Environments ecosystem. It is not a software or platform to build data repositories, but rather a very focused tool falling under "back office" software category. Routine label printing, laboratory notebook maintenance, rapid data entry set up, or any other of relatively loaded user interfaces make use of any industry standard relational database back end. This opens a wide scope for IT designers to implement desired integrations within their institutional infrastructure. APIs and developer access to core EarthCape libraries to build own applications and modules are under development. Basic data visualisation (charts, pivots, dashboards), mapping (full featured desktop GIS module), data outputs (report and label designer) are tailored not only to research analyses, but also for managing logistics and communication when working on (data) papers. The presentation will focus on the software platform featuring most prominent use cases from two areas: ecological research (managing complex network data digitization project) and museum collections management (herbarium and insect collections)

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The saproxylic database: an emerging overview of the biological diversity in dead wood

The Nordic countries Norway, Sweden, Finland and Denmark are developing a shared English-written database with species-specific information about the ecology of saproxylic species. The database now contains information for about 6000 species and the number is expected to approach 7000 species in the near future. The main organism groups are Ascomycetes, Basidiomycetes, Coleoptera, Diptera and Hymenoptera. This paper describes database structure, information that is entered for each species and different qualities of dead wood that the species are associated to. Furthermore, the paper describes how the database can be searched and viewed for different uses, and it gives some examples of data output. Finally, the paper describes potential uses, maintenance, and development plans including making the database accessible on Internet.La base de données saproxyliques : l’émergence d’un aperçu de la diversité biologique du bois mort. — Les pays nordiques (Norvège, Suède, Finlande et Danemark) développent une base de données commune, en anglais, avec des informations spécifiques sur l’écologie des espèces saproxyliques. La base de données contient maintenant des informations sur environ 6000 espèces et ce nombre devrait avoisiner 7000 dans un proche avenir. Les principaux groupes d’organismes sont les Ascomycètes, les Basidiomycètes, les Coléoptères, les Diptères et les Hyménoptères. Le présent article décrit la structure de la base de données, l’information qui y est entrée pour chaque espèce et les différentes qualités de bois mort auxquelles les espèces sont associées. De plus il montre comment la base de données peut être utilisée et visualisée pour différents usages ; quelques exemples de sorties de données sont fournis. Enfin l’article décrit les utilisations potentielles, la maintenance et les plans de développement de la base de données dont son accessibilité sur Internet.Stokland Jogeir N., Meyke Evgeniy. The saproxylic database: an emerging overview of the biological diversity in dead wood. In: Revue d'Écologie (La Terre et La Vie), supplément n°10, 2008. 4ème colloque sur la conservation des coléoptères saproxyliques, tenu à Vivoin (Sarthe – France) du 27 au 29 juin 2006 / Proceedings of the 4th symposium and workshop on the conservation of Saproxylic beetles, held in vivoin, sarthe department – France 27–29 June 2006. pp. 37-48

Eurasian Chronicle of Nature as a basis for large-scale analysis of changing ecosystems.

At present, the study of the consequences of global climate change on ecosystems has become particularly relevant. "Chronicles of Nature" is a unique monitoring program unmatched in geographical (former USSR) and temporal scale (from early 1900s and still ongoing in most locations), that accumulated mostly on paper until early 2000s with no coordinated attempt to compile it in a common format. It has become the basis for international cooperation since 2011 in the framework of ECN project led by the University of Helsinki. ECN: Eurasian Chronicle of Nature - Large Scale Analysis of Changing Ecosystems, it has more than 450 participants (researchers) representing 176 organizations from 12 countries including 114 PAs, 34 research institutes, 15 universities, and ministries and departments for environmental protection. The compilation of the data into a common database was conducted by the database coordinators. Large-scale and long-term dataset currently processed that can be used to examine community-level spatial variation in phenological dynamics and its climatic drivers. The database consist of 401,127 observation dates collected in 239 localities in Russia, Ukraine, Belarus, Latvia, Lithuania and Estonia, with the longest time series of 115 years - from 1899 to 2014. In addition to phenological data, we compile the long-term population data of mammals and birds and other types of surveys included "Сhronicle of nature". From the very beginning, the project had the task of forming an international network of cooperation and provided for the creation of a database for the mass counting of mammals (including small ones), birds, invertebrates, the dynamics of abundance and diversity of vascular plants and fungi, hunting statistics, meteorological factors, forest cover and phenology . The area of research is biomes of the Eurasian taiga - from Scandinavia to the Urals and further to the coast of the Pacific Ocean. It is assumed, that the database will reflect the environmental changes that have occurred in the ecosystem of boreal forests over the last 50-100 years (including taking into account the monitoring of anthropogenic dynamics of the forest structure occurring against the backdrop of climate change). Data processing is based on developments of the Group of Mathematical Biology of the University of Helsinki. The main work of the Group focuses on the interaction between theoretical and empirical research in spatial and evolutionary biology. The group developed a wide range of mathematical, statistical and computational methods for analyzing the movement of species inhabiting diverse landscapes, with special emphasis on the survival of populations. The existing experience of joint research allows us to speak about the special importance of monitoring works within the "Chronicles of nature" of PAs, and the significance of this work grows in proportion to the duration of observations.peerReviewe