Biodiversity change forecasts rely on long-term time series, but such data are often scarce in space and time. Here, we interpolated spatiotemporal changes in species richness using a new method based on machine learning that does not require temporal replication at sites. Using 698,692 one-time sampled vegetation plots, we estimated trends in vascular plant alpha diversity across Europe and validated our approach against 22,852 independent time series. We found an overall near-zero net change in species richness between 1960 and 2020. However, species richness generally declined from 1960 to 1980 and increased from 2000 to 2020 across habitats. Declines were most pronounced in forests, but trends varied across habitats and regions, with overall increases at higher latitudes and elevations, and declines or stable trends elsewhere. Our findings demonstrate how data without temporal replication can be used to reveal context-dependent biodiversity dynamics, underscoring their importance for conservation and management.

Bayreuth Center of Ecology and Environmental Research University of Bayreuth Bayreuth Germany

Biodiversity Research Institute University of Oviedo CSIC Principality of Asturias Oviedo Spain

BIOME Lab Department of Biological Geological and Environmental Sciences Alma Mater Studiorum University of Bologna Bologna Italy

Botanical Garden University of Wrocław Wrocław Poland

Center for Ecological Dynamics in a Novel Biosphere Department of Biology Aarhus University Aarhus Denmark

Conservatoire Botanique National Méditerranéen Hyères France

Departament de Biologia Evolutiva Ecologia i Ciències Ambientals Facultat de Biologia Universitat de Barcelona Barcelona Spain

Department of Biology University of Graz Graz Austria

Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic

Department of Ecoscience Aarhus University Aarhus Denmark

Department of Environmental Biology Sapienza University of Rome Rome Italy

Department of Environmental Sciences University of Basel Basel Switzerland

Department of Geobotany and Ecology M G Kholodny Institute of Botany National Academy of Sciences of Ukraine Kyiv Ukraine

Department of Plant Biology and Ecology Faculty of Science and Technology University of the Basque Country UPV EHU Bilbao Spain

Department of Spatial Sciences Faculty of Environmental Sciences Czech University of Life Sciences Prague Praha Suchdol Czech Republic

Disturbance Ecology and Vegetation Dynamics University of Bayreuth Bayreuth Germany

Division of Biodiversity Dynamics and Conservation Department of Botany and Biodiversity Research University of Vienna Vienna Austria

Division of BioInvasions Global Change and Macroecology Department of Botany and Biodiversity Research University of Vienna Vienna Austria

Egas Moniz Center for Interdisciplinary Research Egas Moniz School of Health and Science Caparica Portugal

Faculty of Natural Sciences and Mathematics Ss Cyril and Methodius University Skopje North Macedonia

Forest and Nature Lab Faculty of Bioscience Engineering Ghent University Gontrode Belgium

German Centre for Integrative Biodiversity Research Halle Jena Leipzig Leipzig Germany

Institut de Recerca de la Biodiversitat Universitat de Barcelona Barcelona Spain

Institute of Biology Geobotany and Botanical Garden Martin Luther University Halle Wittenberg Halle Germany

Institute of Botany Faculty of Biology Jagiellonian University Kraków Poland

ISIGE MINES Paris PSL Fontainebleau France

UMR CNRS 7058 Ecologie et Dynamique des Systèmes Anthropisés Université de Picardie Jules Verne Amiens France

Vegetation Ecology Research Group Institute of Natural Resource Sciences Wädenswil Switzerland

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Araújo, M. B. , Nogués‐Bravo D., Reginster I., Rounsevell M., and Whittaker R. J.. 2008. “Exposure of European Biodiversity to Changes in Human‐Induced Pressures.” Environmental Science & Policy 11: 38–45.

Bernhardt‐Römermann, M. , Baeten L., Craven D., et al. 2015. “Drivers of Temporal Changes in Temperate Forest Plant Diversity Vary Across Spatial Scales.” Global Change Biology 21: 3726–3737. PubMed PMC

Bjornstad, O. N. 2022. “Ncf: Spatial Covariance Functions.”

Blowes, S. A. , Supp S. R., Antão L. H., et al. 2019. “The Geography of Biodiversity Change in Marine and Terrestrial Assemblages.” Science 366: 339–345. PubMed

Bobbink, R. , Hicks K., Galloway J., et al. 2010. “Global Assessment of Nitrogen Deposition Effects on Terrestrial Plant Diversity: A Synthesis.” Ecological Applications 20: 30–59. PubMed

Breiman, L. 2001. “Random Forests.” Machine Learning 45: 5–32.

Chang, W. , Cheng J., Allaire J., Sievert C., Schloerke B., and Xie Y.. 2023. “shiny: Web Application Framework for R.” R Package Version 1.7.4.1.

Chen, T. , and Guestrin C.. 2016. “XGBoost: A Scalable Tree Boosting System.” In Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 785–794. ACM.

Chen, T. , He T., Benesty M., et al. 2024. “Xgboost: Extreme Gradient Boosting.” R Package Version 1.7.8.1. Accessed November 23, 2024. https://CRAN.R‐project.org/package=xgboost.

Chytrý, M. , Hennekens S. M., Jiménez‐Alfaro B., et al. 2016. “European Vegetation Archive (EVA): An Integrated Database of European Vegetation Plots.” Applied Vegetation Science 19: 173–180.

Chytrý, M. , Tichý L., Hennekens S. M., et al. 2020. “EUNIS Habitat Classification: Expert System, Characteristic Species Combinations and Distribution Maps of European Habitats.” Applied Vegetation Science 23: 648–675.

de Vries, W. , Posch M., Simpson D., et al. 2024. “Trends and Geographic Variation in Adverse Impacts of Nitrogen Use in Europe on Human Health, Climate, and Ecosystems: A Review.” Earth‐Science Reviews 253: 104789.

Dengler, J. , Matthews T. J., Steinbauer M. J., et al. 2020. “Species–Area Relationships in Continuous Vegetation: Evidence From Palaearctic Grasslands.” Journal of Biogeography 47: 72–86.

Díaz, S. , Settele J., Brondízio E. S., et al. 2019. “Pervasive Human‐Driven Decline of Life on Earth Points to the Need for Transformative Change.” Science 366: eaax3100. PubMed

Dornelas, M. , Chase J. M., Gotelli N. J., et al. 2023. “Looking Back on Biodiversity Change: Lessons for the Road Ahead.” Philosophical Transactions of the Royal Society B 378: 20220199. PubMed PMC

Dornelas, M. , Gotelli N. J., McGill B., et al. 2014. “Assemblage Time Series Reveal Biodiversity Change but Not Systematic Loss.” Science 344: 296–299. PubMed

Dornelas, M. , Magurran A. E., Buckland S. T., et al. 2013. “Quantifying Temporal Change in Biodiversity: Challenges and Opportunities.” Proceedings of the Royal Society B: Biological Sciences 280: 20121931. PubMed PMC

Dullinger, S. , Essl F., Rabitsch W., et al. 2013. “Europe's Other Debt Crisis Caused by the Long Legacy of Future Extinctions.” Proceedings of the National Academy of Sciences 110: 7342–7347. PubMed PMC

European Commission . 2012. The Common Agricultural Policy – A Partnership Between Europe and Farmers. Publications Office.

European Commission . 2017. Agri‐Environment Schemes – Impacts on the Agricultural Environment. Publications Office.

European Commission . 2023. Impact Assessment Study to Support the Development of Legally Binding EU Nature Restoration Targets – Final Report. Publications Office of the European Union.

European Economic Committee . 1992. “Council Directive 92/43/EEC of 21 May 1992 on the Conservation of Natural Habitats and of Wild Fauna and Flora.” Official Journal of the European Communities L 206: 7–50.

European Environment Agency . 2016. “Biogeographical Regions in Europe.” Accessed November 24, 2024. https://www.eea.europa.eu/en/analysis/maps‐and‐charts/biogeographical‐regions‐in‐europe‐2?activeTab=8a280073‐bf94‐4717‐b3e2‐1374b57ca99d.

Finderup Nielsen, T. , Sand‐Jensen K., and Bruun H. H.. 2021. “Drier, Darker and More Fertile: 140 Years of Plant Habitat Change Driven by Land‐Use Intensification.” Journal of Vegetation Science 32: e13066.

Friedman, J. H. , and Popescu B. E.. 2008. “Predictive Learning via Rule Ensembles.” Annals of Applied Statistics 2: 916–954.

Fuchs, R. , Herold M., Verburg P. H., Clevers J. G. P. W., and Eberle J.. 2015. “Gross Changes in Reconstructions of Historic Land Cover/Use for Europe Between 1900 and 2010.” Global Change Biology 21: 299–313. PubMed

Gonzalez, A. , Cardinale B. J., Allington G. R. H., et al. 2016. “Estimating Local Biodiversity Change: A Critique of Papers Claiming no Net Loss of Local Diversity.” Ecology 97: 1949–1960. PubMed

Gray, C. L. , Hill S. L. L., Newbold T., et al. 2016. “Local Biodiversity Is Higher Inside Than Outside Terrestrial Protected Areas Worldwide.” Nature Communications 7, no. 1: 1–7. PubMed PMC

Hédl, R. 2004. “Vegetation of Beech Forests in the Rychlebské Mountains, Czech Republic, Re‐Inspected After 60 Years With Assessment of Environmental Changes.” Plant Ecology 170: 243–265.

Hédl, R. , Kopecký M., and Komárek J.. 2010. “Half a Century of Succession in a Temperate Oakwood: From Species‐Rich Community to Mesic Forest.” Diversity and Distributions 16: 267–276.

IPBES . 2019. “Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science‐Policy Platform on Biodiversity and Ecosystem Services.”

Jandt, U. , Bruelheide H., Jansen F., et al. 2022. “More Losses Than Gains During One Century of Plant Biodiversity Change in Germany.” Nature 611, no. 7936: 512–518. PubMed

Jandt, U. , von Wehrden H., and Bruelheide H.. 2011. “Exploring Large Vegetation Databases to Detect Temporal Trends in Species Occurrences.” Journal of Vegetation Science 22: 957–972.

Johnson, T. F. , Beckerman A. P., Childs D. Z., et al. 2024. “Revealing Uncertainty in the Status of Biodiversity Change.” Nature 628, no. 8009: 788–794. PubMed PMC

Keil, P. , and Chase J.. 2022. “Interpolation of Temporal Biodiversity Change, Loss, and Gain Across Scales: A Machine Learning Approach.” EcoEvoRxiv.

Keil, P. , and Chase J. M.. 2019. “Global Patterns and Drivers of Tree Diversity Integrated Across a Continuum of Spatial Grains.” Nature Ecology & Evolution 3: 390–399. PubMed

Klinkovská, K. , Glaser M., Danihelka J., et al. 2024. “Dynamics of the Czech Flora Over the Last 60 Years: Winners, Losers and Causes of Changes.” Biological Conservation 292: 110502.

Klinkovská, K. , Sperandii M. G., Knollová I., et al. 2025. “Half a Century of Temperate Non‐Forest Vegetation Changes: No Net Loss in Species Richness, but Considerable Shifts in Taxonomic and Functional Composition.” Global Change Biology 31: e70030. PubMed PMC

Knollová, I. , Chytrý M., Bruelheide H., et al. 2024. “ReSurveyEurope: A Database of Resurveyed Vegetation Plots in Europe.” Journal of Vegetation Science 35: e13235.

Kolari, T. H. M. , Korpelainen P., Kumpula T., and Tahvanainen T.. 2021. “Accelerated Vegetation Succession but no Hydrological Change in a Boreal Fen During 20 Years of Recent Climate Change.” Ecology and Evolution 11: 7602–7621. PubMed PMC

Kuhn, M. , and Frick H.. 2024. “Dials: Tools for Creating Tuning Parameter Values.” R Package Version 1.2.1. Accessed November 23, 2024. https://CRAN.R‐project.org/package=dials.

Kuhn, M. , and Vaughan D.. 2024. “Parsnip: A Common API to Modeling and Analysis Functions.” R Package Version 1.2.1. Accessed November 23, 2024. https://CRAN.R‐project.org/package=parsnip.

Kuhn, M. , and Wickham H.. 2020. “Tidymodels: A Collection of Packages for Modeling and Machine Learning Using Tidyverse Principles.” Accessed November 23, 2024. https://www.tidymodels.org.

Legendre, P. 1993. “Spatial Autocorrelation: Trouble or New Paradigm?” Ecology 74: 1659–1673.

Lelli, C. , Nascimbene J., Alberti D., et al. 2021. “Long‐Term Changes in Italian Mountain Forests Detected by Resurvey of Historical Vegetation Data.” Journal of Vegetation Science 32: e12939.

Leroy, F. , Reif J., Vermouzek Z., et al. 2024. “Decomposing Biodiversity Change to Processes of Extinction, Colonization, and Recurrence Across Scales.” Ecography 2024: e06995.

Mahecha, M. D. , Gans F., Brandt G., et al. 2020. “Earth System Data Cubes Unravel Global Multivariate Dynamics.” Earth System Dynamics 11: 201–234.

Mayer, M. 2024. “hstats: Interaction Statistics.” Accessed November 27, 2024. https://CRAN.R‐project.org/package=hstats.

Moersberger, H. , Valdez J., Martin J. G. C., et al. 2024. “Biodiversity Monitoring in Europe: User and Policy Needs.” Conservation Letters 17: e13038.

Navrátilová, J. , Navrátil J., and Hájek M.. 2022. “Medium‐Term Changes of Vegetation Composition on Fens of the Rural Landscape, Tested Using Fixed Permanent Plots.” Folia Geobotanica 57: 151–166.

Pedrotti, E. , Rydin H., Ingmar T., Hytteborn H., Turunen P., and Granath G.. 2014. “Fine‐Scale Dynamics and Community Stability in Boreal Peatlands: Revisiting a Fen and a Bog in Sweden After 50 Years.” Ecosphere 5: 1–24.

Perring, M. P. , Bernhardt‐Römermann M., Baeten L., et al. 2018. “Global Environmental Change Effects on Plant Community Composition Trajectories Depend Upon Management Legacies.” Global Change Biology 24: 1722–1740. PubMed

Pilotto, F. , Kühn I., Adrian R., et al. 2020. “Meta‐Analysis of Multidecadal Biodiversity Trends in Europe.” Nature Communications 11: 1–11. PubMed PMC

Preislerová, Z. , Marcenò C., Loidi J., et al. 2024. “Structural, Ecological and Biogeographical Attributes of European Vegetation Alliances.” Applied Vegetation Science 27: e12766.

R Core Team . 2024. “R: A Language and Environment for Statistical Computing. Version 4.3.1.” Accessed November 23, 2024. https://www.R‐project.org/.

Roberts, D. R. , Bahn V., Ciuti S., et al. 2017. “Cross‐Validation Strategies for Data With Temporal, Spatial, Hierarchical, or Phylogenetic Structure.” Ecography 40: 913–929.

Rumpf, S. B. , Hülber K., Klonner G., et al. 2018. “Range Dynamics of Mountain Plants Decrease With Elevation.” Proceedings of the National Academy of Sciences of the United States of America 115: 1848–1853. PubMed PMC

Schöpp, W. , Posch M., Mylona S., and Johansson M.. 2003. “Long‐Term Development of Acid Deposition (1880–2030) in Sensitive Freshwater Regions in Europe.” Hydrology and Earth System Sciences 7: 436–446.

Shipley, J. R. , Frei E. R., Bergamini A., et al. 2024. “Agricultural Practices and Biodiversity: Conservation Policies for Semi‐Natural Grasslands in Europe.” Current Biology 34: R753–R761. PubMed

Sperle, T. , and Bruelheide H.. 2021. “Climate Change Aggravates Bog Species Extinctions in the Black Forest (Germany).” Diversity and Distributions 27: 282–295.

Staude, I. R. , Waller D. M., Bernhardt‐Römermann M., et al. 2020. “Replacements of Small‐ by Large‐Ranged Species Scale up to Diversity Loss in Europe's Temperate Forest Biome.” Nature Ecology & Evolution 4: 802–808. PubMed

Steinbauer, M. J. , Grytnes J. A., Jurasinski G., et al. 2018. “Accelerated Increase in Plant Species Richness on Mountain Summits Is Linked to Warming.” Nature 556, no. 7700: 231–234. PubMed

Stevens, C. J. , Dupr C., Dorland E., et al. 2010. “Nitrogen Deposition Threatens Species Richness of Grasslands Across Europe.” Environmental Pollution 158: 2940–2945. PubMed

Storch, D. 2016. “The Theory of the Nested Species–Area Relationship: Geometric Foundations of Biodiversity Scaling.” Journal of Vegetation Science 27: 880–891.

Storkey, J. , Macdonald A. J., Poulton P. R., et al. 2015. “Grassland Biodiversity Bounces Back From Long‐Term Nitrogen Addition.” Nature 528, no. 7582: 401–404. PubMed

Sutton, M. , Howard C., Erisman J., et al. 2011. The European Nitrogen Assessment. Cambridge University Press.

Thuiller, W. , Lavorel S., Araújo M. B., Sykes M. T., and Prentice I. C.. 2005. “Climate Change Threats to Plant Diversity in Europe.” Proceedings of the National Academy of Sciences 102: 8245–8250. PubMed PMC

Tobler, W. R. 1970. “A Computer Movie Simulating Urban Growth in the Detroit Region.” Economic Geography 46: 234.

Vellend, M. , Baeten L., Becker‐Scarpitta A., et al. 2017. “Plant Biodiversity Change Across Scales During the Anthropocene.” Annual Review of Plant Biology 68: 563–586. PubMed

Vellend, M. , Baeten L., Myers‐Smith I. H., et al. 2013. “Global Meta‐Analysis Reveals no Net Change in Local‐Scale Plant Biodiversity Over Time.” Proceedings of the National Academy of Sciences 110: 19456–19459. PubMed PMC

Verhoeven, J. T. A. 2014. “Wetlands in Europe: Perspectives for Restoration of a Lost Paradise.” Ecological Engineering 66: 6–9.

Vilà, M. , Espinar J. L., Hejda M., et al. 2011. “Ecological Impacts of Invasive Alien Plants: A Meta‐Analysis of Their Effects on Species, Communities and Ecosystems.” Ecology Letters 14: 702–708. PubMed

Wesche, K. , Krause B., Culmsee H., and Leuschner C.. 2012. “Fifty Years of Change in Central European Grassland Vegetation: Large Losses in Species Richness and Animal‐Pollinated Plants.” Biological Conservation 150: 76–85.

Wright, M. N. , and Ziegler A.. 2017. “Ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R.” Journal of Statistical Software 77: 1–17.