A deep‐learning framework for enhancing habitat identification based on species composition

Aims The accurate classification of habitats is essential for effective biodiversity conservation. The goal of this study was to harness the potential of deep learning to advance habitat identification in Europe. We aimed to develop and evaluate models capable of assigning vegetation-plot records to the habitats of the European Nature Information System (EUNIS), a widely used reference framework for European habitat types. Location The framework was designed for use in Europe and adjacent areas (e.g., Anatolia, Caucasus). Methods We leveraged deep-learning techniques, such as transformers (i.e., models with attention components able to learn contextual relations between categorical and numerical features) that we trained using spatial k-fold cross-validation (CV) on vegetation plots sourced from the European Vegetation Archive (EVA), to show that they have great potential for classifying vegetation-plot records. We tested different network architectures, feature encodings, hyperparameter tuning and noise addition strategies to identify the optimal model. We used an independent test set from the National Plant Monitoring Scheme (NPMS) to evaluate its performance and compare its results against the traditional expert systems. Results Exploration of the use of deep learning applied to species composition and plot-location criteria for habitat classification led to the development of a framework containing a wide range of models. Our selected algorithm, applied to European habitat types, significantly improved habitat classification accuracy, achieving a more than twofold improvement compared to the previous state-of-the-art (SOTA) method on an external data set, clearly outperforming expert systems. The framework is shared and maintained through a GitHub repository. Conclusions Our results demonstrate the potential benefits of the adoption of deep learning for improving the accuracy of vegetation classification. They highlight the importance of incorporating advanced technologies into habitat monitoring. These algorithms have shown to be better suited for habitat type prediction than expert systems. They push the accuracy score on a database containing hundreds of thousands of standardized presence/absence European surveys to 88.74%, as assessed by expert judgment. Finally, our results showcase that species dominance is a strong marker of ecosystems and that the exact cover abundance of the flora is not required to train neural networks with predictive performances. The framework we developed can be used by researchers and practitioners to accurately classify habitats

Structural, ecological and biogeographical attributes of European vegetation alliances

The first comprehensive phytosociological classification of all vegetation types in Europe (EuroVegChecklist; Applied Vegetation Science, 2016, 19, 3–264) contained brief descriptions of each type. However, these descriptions were not standardized and mentioned only the most distinct features of each vegetation type. The practical application of the vegetation classification system could be enhanced if users had the option to select sets of vegetation types based on various combinations of structural, ecological, and biogeographical attributes. Based on a literature review and expert knowledge, we created a new database that assigns standardized categorical attributes of 12 variables to each of the 1106 alliances dominated by vascular plants defined in EuroVegChecklist. These variables include dominant life form, phenological optimum, substrate moisture, substrate reaction, salinity, nutrient status, soil organic matter, vegetation region, elevational vegetation belt, azonality, successional status and naturalness. The new database has the potential to enhance the usefulness of phytosociological classification for researchers and practitioners and to help understand this classification to non-specialists

Biogeographical network analysis of plant species distribution in the Mediterranean region

International audienceThe study of biotic taxa distribution on a territory represents a key step in theunderstanding, analysis and conservation of ecosystems, but often hindered by alevel of diversity and complexity that may appear overwhelming at first glance. Tobetter understand and visualize the biogeographical structure of a territory, it istherefore necessary to divide this territory into meaningful and coherentgeographical regions, minimizing the heterogeneity in taxonomic compositionwithin regions while maximizing the differences between them. While thedelineation of biogeographical regions has been based for a long time on expertknowledge of qualitative data collection, the increasing availability of species-leveldistribution data and the recent technological advances have allowed for thedevelopment of more rigorous frameworks. While limited consideration is given tonetwork approaches in biogeography, the generic nature of networks and the levelof complexity that they can capture at different scale, make it a powerful tool forinvesting the interactions among species occurring on a territory. In this work, weused a network approach to identify and characterize biogeographical regions insouthern France, based on a large database containing information on millions ofvegetation plant samples corresponding to more than 3,500 plant species

Biogeographical network analysis of plant species distribution in the French Mediterranean area

International audienc

SIMETHIS-Flore-CBNMed - Database of Southeastern France vegetation

The SIMETHIS-Flore-CBNMed database (GIVD EU-FR-006) is a regional database managed by the Conservatoire Botanique National Méditerranéen dealing with occurrence data of the vascular flora of Southeastern France. It covers the following departments: Pyrénées-Orientales, Aude, Hérault, Gard, Lozère, Vaucluse, Bouches-du-Rhône, Var and Alpes-Maritimes. It includes around 19,300 phytosociological relevés of various vegetation types from the mediterranean coastal area to the alpine vegetation belt. Vegetation plots are unpublished relevés as well as digitized data from bibliographic sources (around 310 references). Almost all relevés are geolocalized. The oldest ones date from 1915 and the most recent from 2021 and the integration of new data is done continuously. The taxonomical scheme follows the French national taxonomic repository TAXREF (currently v.15). The database is part of the European Vegetation Archive under semi-restricted regime and will be updated every year. Some of the bibliographic data featured in SIMETHIS-Flore-CBNMed may also be present in SOPHY database (EU-FR-003). All the bibliographic data of SIMETHIS-Flore-CBNMed undergo a curation process regarding georeferencing, taxonomic nomenclature updates and syntaxonomic interpretation. Abbreviations: CBNMed: Conservatoire Botanique National Méditerranéen

SIMETHIS-Flore-CBNMed - Database of Southeastern France vegetation

The SIMETHIS-Flore-CBNMed database (GIVD EU-FR-006) is a regional database managed by the Conservatoire Botanique National Méditerranéen dealing with occurrence data of the vascular flora of Southeastern France. It covers the following departments: Pyrénées-Orientales, Aude, Hérault, Gard, Lozère, Vaucluse, Bouches-du-Rhône, Var and Alpes-Maritimes. It includes around 19,300 phytosociological relevés of various vegetation types from the mediterranean coastal area to the alpine vegetation belt. Vegetation plots are unpublished relevés as well as digitized data from bibliographic sources (around 310 references). Almost all relevés are geolocalized. The oldest ones date from 1915 and the most recent from 2021 and the integration of new data is done continuously. The taxonomical scheme follows the French national taxonomic repository TAXREF (currently v.15). The database is part of the European Vegetation Archive under semi-restricted regime and will be updated every year. Some of the bibliographic data featured in SIMETHIS-Flore-CBNMed may also be present in SOPHY database (EU-FR-003). All the bibliographic data of SIMETHIS-Flore-CBNMed undergo a curation process regarding georeferencing, taxonomic nomenclature updates and syntaxonomic interpretation. Abbreviations: CBNMed: Conservatoire Botanique National Méditerranéen

Climate change impacts on Mediterranean vegetation are amplified at low altitudes

International audienceAim: In the face of ongoing climate warming, we wanted to quantify impacts on vegetation at one of the major climatic and biogeographical boundaries of Europe, the limit between the Mediterranean and Eurosiberian biogeographical regions. We analyse temperature and moisture requirements of plants along altitudinal gradients at regional scale in the period 1980–2020 and we explore if changes coincide with observedchanges in the same regions in terms of measured climatic data.Location: Southern France.Time period: 1980–2020.Taxa: Vascular plants.Methods: We calculated shifts in plants’ temperature and moisture requirements for a large floristic database from south-eastern France (SIMETHIS) during the period 1980–2020 along altitudinal gradients by using ecological indicator values (EIV). Additionally, we analysed standardized weather station data from the same area and period, to investigate whether floristic changes are synchronized with climatechanges.Results: Vegetation data suggest a linear increase in temperature requirements of plant communities from 1980 to 2020 with a greater change at low altitudes. Upward shifts in temperature requirements coincided with observed climate change although warming did not show a general trend towards greater increases at low altitudes. Data on vegetation and climate suggest an upward shift of respectively 150 and 300 m for the boundary between Mediterranean and temperate belts. Moisture requirements of vegetation indicate an increase of the frequency of dry adapted species at low altitudes but an increase towards higher moisture requirements at high altitudes. Comparing vegetation responses with climate data suggests that responses are faster at low altitudes.Main conclusions: Our analyses show that strong general changes in vegetation are underway and highlight faster responses of vegetation to warming in low altitudes compared to high altitudes and demonstrate the need for reliable data on vegetation and climate changes, especially on water balance

Monitoring snowbed vegetation in the Pyrenees: FloraPyr Interreg project

Trabajo presentado en el 26th Congress of the European Vegetation Survey, celebrado en Bilbao (España), del 13 al 16 de septiembre de 2017The FLORAPYR project (European Interreg project for years 2016-2019) is the continuation of a previous European project (2012-2014). One of our main objectives is to develop a unified monitoring protocol for snowbed vegetations within the Pyrenean range in the context of global warming, involving eight conservation and research organisations from three countries. Among the different plant communities inhabiting snowpatches, we focus on those dominated by Salix herbacea L. (Salicion herbaceae Br.-Bl. 1948). Our monitoring specifically aims at recording the floristic composition, the phenology and the environmental conditions – microclimate and soil – in the permanent plots. As accessing the different localities can be a challenging and time consuming process, the protocol was developed to ensure that the time invested in monitoring each site is limited to a few hours, thereby maximising the data collected. In addition, the response of Salix herbacea L. to warming will be assessed by means of open top chambers, set in four representative localities. We chose 14 snowbed localities distributed throughout the whole Pyrenees. In each locality, we established three permanent plots of 3 × 1 m, divided into 12 subplots of 0.5 × 0.5 m, following the snowmelt gradient and including the optimum and the margins of the Salix herbacea L. populations. Surveys are conducted four times yearly, every three weeks between the first week of July and the second week of September. We present our first results regarding the ongoing characterisation of Pyrenean Salix herbacea L. stands in terms of floristic richness, phenology and microclimatic conditions.Peer reviewe

Calibrating ecological indicator values and niche width for a Mediterranean flora

International audienceBioindication of ecological variables such as humidity, temperature or pH by ecological indicatorvalues of plants is a powerful tool for research in plant ecology, e.g. to detect early vegetationchanges. Here, we provide a data set of ecological indicator values including niche width for anentire regional flora. We used an extensive data-base with floristic relevés from Southern Franceto recalibrate indicator values for light (L), temperature (T), continentality (K), air humidity (A),soil moisture (F), pH (R), productivity (N), soil texture (G), soil organic matter content (O) andsalinity (S). Values were recalibrated using average values from co-occurring plants, enabling todevelop indicator values for species not yet evaluated previously. Recalibrated values are on acontinuous scale and we add standard deviation, median, first and third quartile for each indicatorvalue. Linear regression of average indicator values against measured factors showed highercorrelation with recalibrated values compared to original indicator values for temperature, pH andnitrogen, and comparable R 2 for moisture. Individual indicator systems performed better than acombination and applying different weighting procedures demonstrated the usefulness of inversevariance. We further illustrate graphically how recalibrated values and niche width increaseecological knowledge on plants

Calibrating ecological indicator values and niche width for a Mediterranean flora

International audienceBioindication of ecological variables such as humidity, temperature or pH by ecological indicatorvalues of plants is a powerful tool for research in plant ecology, e.g. to detect early vegetationchanges. Here, we provide a data set of ecological indicator values including niche width for anentire regional flora. We used an extensive data-base with floristic relevés from Southern Franceto recalibrate indicator values for light (L), temperature (T), continentality (K), air humidity (A),soil moisture (F), pH (R), productivity (N), soil texture (G), soil organic matter content (O) andsalinity (S). Values were recalibrated using average values from co-occurring plants, enabling todevelop indicator values for species not yet evaluated previously. Recalibrated values are on acontinuous scale and we add standard deviation, median, first and third quartile for each indicatorvalue. Linear regression of average indicator values against measured factors showed highercorrelation with recalibrated values compared to original indicator values for temperature, pH andnitrogen, and comparable R 2 for moisture. Individual indicator systems performed better than acombination and applying different weighting procedures demonstrated the usefulness of inversevariance. We further illustrate graphically how recalibrated values and niche width increaseecological knowledge on plants