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Global impoverishment of natural vegetation revealed by dark diversity

. 2025 Apr 02 ; () : . [epub] 20250402

Status Publisher Language English Country England, Great Britain Media print-electronic

Document type Journal Article

Links

PubMed 40175550
DOI 10.1038/s41586-025-08814-5
PII: 10.1038/s41586-025-08814-5
Knihovny.cz E-resources

Anthropogenic biodiversity decline threatens the functioning of ecosystems and the many benefits they provide to humanity1. As well as causing species losses in directly affected locations, human influence might also reduce biodiversity in relatively unmodified vegetation if far-reaching anthropogenic effects trigger local extinctions and hinder recolonization. Here we show that local plant diversity is globally negatively related to the level of anthropogenic activity in the surrounding region. Impoverishment of natural vegetation was evident only when we considered community completeness: the proportion of all suitable species in the region that are present at a site. To estimate community completeness, we compared the number of recorded species with the dark diversity-ecologically suitable species that are absent from a site but present in the surrounding region2. In the sampled regions with a minimal human footprint index, an average of 35% of suitable plant species were present locally, compared with less than 20% in highly affected regions. Besides having the potential to uncover overlooked threats to biodiversity, dark diversity also provides guidance for nature conservation. Species in the dark diversity remain regionally present, and their local populations might be restored through measures that improve connectivity between natural vegetation fragments and reduce threats to population persistence.

Aerospace Information Research Institute Chinese Academy of Sciences Beijing China

Applied Plant Ecology Institute of Plant Science and Microbiology University of Hamburg Hamburg Germany

Arctic Research Centre Aarhus University Aarhus Denmark

Au Sable Institute of Environmental Studies Mancelona MI USA

Australian Tropical Herbarium James Cook University Cairns Queensland Australia

Australian Tropical Herbarium James Cook University Smithfield Queensland Australia

Biodiversity Research Institute Universitat de Barcelona Barcelona Spain

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

Biogeography and Biodiversity Lab Institute of Physical Geography Goethe University Frankfurt Frankfurt am Main Germany

Biology Education Dokuz Eylül University Buca Turkey

Bjerknes Centre for Climate Research University of Bergen Bergen Norway

Botanical Garden Center for Biological Diversity Conservation Polish Academy of Sciences Warszawa Poland

Botanical Institute of Barcelona Barcelona Spain

Center for Sustainable Landscapes Under Global Change Department of Biology Aarhus University Aarhus Denmark

Centre de Recherche sur la Biodiversité et l'Environnement UMR 5300 UPS CNRS IRD INP Université Paul Sabatier Toulouse 3 Toulouse France

Centre for Biodiversity and Taxonomy Department of Botany University of Kashmir Srinagar India

Centre for Ecosystem Science UNSW Sydney Sydney New South Wales Australia

Centre for Environmental Sciences Hasselt University Hasselt Belgium

Centre for Functional Ecology Associate Laboratory TERRA Department of Life Sciences University of Coimbra Coimbra Portugal

Centro de Investigación en Biodiversidad y Cambio Global Universidad Autónoma de Madrid Madrid Spain

Chair of Biodiversity and Nature Tourism Estonian University of Life Sciences Tartu Estonia

Chair of Plant Ecology University of Bayreuth Bayreuth Germany

Chair of Sensor based Geoinformatics Faculty of Environment and Natural Resources University of Freiburg Freiburg Germany

CIDE CSIC UV GVA Valencia Spain

CIRAD UMR Eco and Sols Montpellier France

CIRAD UMR EcoFoG Kourou French Guiana

College of Science and Engineering James Cook University Cairns Queensland Australia

Conservatoire d'espaces naturels Centre Val de Loire Orléans France

CREAF Bellaterra Spain

Deakin University Burwood Victoria Australia

Departamento de Biodiversidad Ecología y Evolución Facultad de Ciencias Biológicas Universidad Complutense de Madrid Madrid Spain

Departamento de Biología Ambiental Facultad de Ciencias Universidad de Navarra Pamplona Spain

Departamento de Biología Animal Biología Vegetal y Ecología Universidad de Jaén Jaén Spain

Departamento de Ciencias de la Vida Universidad de Alcalá Alcalá de Henares Spain

Département de biologie Université de Sherbrooke Sherbrooke Quebec Canada

Departemento Biología y Geología Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles Spain

Department of Agricultural and Food Chemistry Universidad Autónoma de Madrid Madrid Spain

Department of Agriculture and Natural Resource Sciences Namibia University of Science and Technology Windhoek Namibia

Department of Agronomy University of Almería Almería Spain

Department of Applied Ecology Faculty of Environmental Sciences Czech University of Life Sciences Prague Czech Republic

Department of Biological Chemical and Pharmaceutical Sciences and Technologies University of Palermo Palermo Italy

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

Department of Biological Sciences University of Alberta Edmonton Alberta Canada

Department of Biological Sciences University of Bergen Bergen Norway

Department of Biology Aarhus University Aarhus Denmark

Department of Biology Faculty of Science Ferdowsi University of Mashhad Mashhad Iran

Department of Biology Lund University Lund Sweden

Department of Biology National University of Mongolia Ulaanbaatar Mongolia

Department of Biology University of North Carolina at Greensboro Greensboro NC USA

Department of Biotechnology and Life Science University of Insubria Varese Italy

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

Department of Botany Faculty of Science University of South Bohemia České Budějovice Czech Republic

Department of Botany Kherson State University Kherson Ukraine

Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parma Italy

Department of Civil and Environmental Engineering University of the Andes Bogotá Colombia

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

Department of Earth and Environmental Sciences KU Leuven Leuven Belgium

Department of Ecology and Environmental Protection Faculty of Biology Sofia University St Kliment Ohridski Sofia Bulgaria

Department of Ecology and Genetics University of Oulu Oulu Finland

Department of Ecology Environment and Plant Sciences Stockholm University Stockholm Sweden

Department of Ecology University of Debrecen Debrecen Hungary

Department of Ecology University of Szeged Szeged Hungary

Department of Ecoscience Aarhus University Aarhus Denmark

Department of Ecosystem Science and Management Laramie Research and Extension Center University of Wyoming Laramie WY USA

Department of Environmental Science and Policy University of California Davis Davis CA USA

Department of Environmental Sciences Informatics and Statistics Ca' Foscari University of Venice Venice Italy

Department of Environmental Sciences University of Basel Basel Switzerland

Department of Evolutionary Biology Ecology and Environmental Sciences Universitat de Barcelona Barcelona Spain

Department of Forest Sciences Luiz de Queiroz College of Agriculture University of São Paulo Piracicaba Brazil

Department of Functional Ecology Institute of Botany Czech Academy of Sciences Třeboň Czech Republic

Department of Geography and Environmental Studies Stellenbosch University Stellenbosch South Africa

Department of Geological Biological and Environmental Sciences University of Catania Catania Italy

Department of Invasion Ecology Institute of Botany Czech Academy of Sciences Průhonice Czech Republic

Department of Life and Environmental Sciences University of Cagliari Cagliari Italy

Department of Life Health and Environmental Science University of L'Aquila Coppito L'Aquila Italy

Department of Mathematics and Science Education Faculty of Education Ordu University Ordu Turkey

Department of Molecular Biology and Genetics Faculty of Arts and Sciences Ordu University Ordu Turkey

Department of Natural Resource Sciences Thompson Rivers University Kamloops British Columbia Canada

Department of Natural Sciences Manchester Metropolitan University Manchester UK

Department of Organismal and Systems Biology University of Ovidedo Oviedo Spain

Department of Physical Geography Stockholm University Stockholm Sweden

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

Department of Plant Sciences University of Cambridge Cambridge UK

Department of Plant Sciences University of Saskatchewan Saskatoon Saskatchewan Canada

Department of Range and Watershed Management Faculty of Natural Resources and Environment Ferdowsi University of Mashhad Mashhad Iran

Department of Range and Watershed Management Faculty of Natural Resources Islamic Azad University Nour Branch Nour Iran

Department of Reclamation of Arid and Mountainous Regions University of Tehran Tehran Iran

Department of Soil Sciences Luiz de Queiroz College of Agriculture University of São Paulo Piracicaba Brazil

Department of Species Interaction Ecology Helmholtz Centre for Environmental Research UFZ Leipzig Germany

Division of BioInvasions Global Change and Macroecology University of Vienna Vienna Austria

Eco and Sols University Montpellier CIRAD INRAE Institut Agro IRD Montpellier France

École Pratique des Hautes Études Paris Sciences Lettres University Paris France

Ecology and Biodiversity Utrecht University Utrecht The Netherlands

Ecosystems and Global Change Group School of the Environment Trent University Peterborough Ontario Canada

Estación Experimental de Zonas Áridas Almería Spain

Estación Experimental del Zaidín Granada Spain

Evolution and Ecology Research Centre School of Biological Earth and Environmental Sciences UNSW Sydney Sydney New South Wales Australia

F Falz Fein Biosphere Reserve Askania Nova Kyiv Ukraine

Faculty of Agricultural and Environmental Sciences University of Rostock Rostock Germany

Faculty of Environmental Sciences and Natural Resource Management Norwegian University of Life Sciences Ås Norway

FCEFyN Universidad Nacional de Córdoba Córdoba Argentina

Future Regions Research Centre Federation University Australia Ballarat Victoria Australia

German Centre for Integrative Biodiversity Research Halle Jena Leipzig Leipzig Germany

Graduate Program in Botany Universidade Federal do Rio Grande do Sul Porto Alegre Brazil

Great Lakes Forestry Centre Canadian Forest Service Natural Resources Canada Sault Ste Marie Ontario Canada

Greenpeace España Madrid Spain

Gulbali Institute Charles Sturt University Albury New South Wales Australia

Harry Butler Institute Murdoch University Perth Western Australia Australia

Higher Technical School of Agricultural and Forestry Engineering Castilla La Mancha University Albacete Spain

HUN REN UD Biodiversity and Ecosystem Services Research Group Department of Ecology University of Debrecen Debrecen Hungary

HUN REN UD Functional and Restoration Ecology Research Group Department of Ecology University of Debrecen Debrecen Hungary

Independent reseacher Teberda Russia

Independent researcher Kazan Russia

Independent researcher Kirovsk Russia

Independent researcher Mancelona MI USA

Independent researcher Moscow Russia

Independent researcher Tehran Iran

Institute for Advanced Research in Chemical Sciences Universidad Autónoma de Madrid Madrid Spain

Institute of Agroecology and Plant Production Wrocław University of Environmental and Life Sciences Wrocław Poland

Institute of Biological Sciences University of Zielona Góra Zielona Góra Poland

Institute of Botany Czech Academy of Sciences Průhonice Czech Republic

Institute of Botany Plant Science and Biodiversity Center Slovak Academy of Sciences Bratislava Slovakia

Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia

Institute of Environmental Biology Faculty of Biology University of Warsaw Warsaw Poland

Institute of Geology Tallinn University of Technology Tallinn Estonia

Institute of Hydrobiology Biology Centre of the Czech Academy of Sciences Ceske Budejovice Czech Republic

Institute of Landscape Ecology University of Münster Münster Germany

Institute of Plant Science and Microbiology University of Hamburg Hamburg Germany

Institute of Plant Sciences University of Bern Bern Switzerland

Instituto de Biociências Lab of Vegetation Ecology Universidade Estadual Paulista Rio Claro Brazil

Instituto Interuniversitario del Sistema Tierra de Andalucía Universidad de Jaén Jaén Spain

Instituto Multidisciplinario de Biología Vegetal Córdoba Argentina

Instituto Nacional de Tecnología Agropecuaria Río Gallegos Argentina

Instituto Pirenaico de Ecologia CSIC Jaca Spain

Jilin Provincial Key Laboratory of Grassland Farming Northeast Institute of Geography and Agroecology Chinese Academy of Sciences Changchun China

Jilin Songnen Grassland Ecosystem National Observation and Research Station Northeast Institute of Geography and Agroecology Chinese Academy of Sciences Changchun China

Kalmar County Administrative Board Färjestaden Sweden

Key Laboratory of Mountain Surface Processes and Ecological Regulation Institute of Mountain Hazards and Environment Chinese Academy of Sciences Chengdu China

Key Laboratory of Soybean Molecular Design Breeding Northeast Institute of Geography and Agroecology Chinese Academy of Sciences Changchun China

KU Leuven Plant Institute KU Leuven Leuven Belgium

Laboratorio de Biodiversidad y Funcionamiento Ecosistémico Instituto de Recursos Naturales y Agrobiología de Sevilla CSIC Sevilla Spain

Lendület Seed Ecology Research Group Institute of Ecology and Botany HUN REN Centre for Ecological Research Vácrátót Hungary

National Monitoring Centre for Biodiversity Germany Leipzig Germany

Nature Conservation Agency of the Czech Republic Prague Czech Republic

Netzwerk für Angewandte Ökologie Hamburg Germany

Norwegian Institute for Nature Research Bergen Norway

Norwegian Institute for Nature Research Oslo Norway

ÖMKi Research Institute of Organic Agriculture Budapest Hungary

Plant Ecology and Nature Conservation University of Potsdam Potsdam Germany

Plant Ecology Group Institute of Evolution and Ecology University of Tübingen Tübingen Germany

Quantitative Plant Ecology and Biodiversity Research Lab Department of Biology Faculty of Science Ferdowsi University of Mashhad Mashdad Iran

Re green Rio de Janeiro Brazil

Remote Sensing Centre for Earth System Research Leipzig University Leipzig Germany

Research Group Plants and Ecosystems University of Antwerp Wilrijk Belgium

School of Agriculture Food and Ecosystem Sciences University of Melbourne Melbourne Victoria Australia

School of Biosciences and Veterinary Medicine University of Camerino Camerino Italy

School of Environmental and Rural Science University of New England Armidale New South Wales Australia

School of Grassland Science Beijing Forestry University Beijing China

School of Natural Sciences Macquarie University Sydney New South Wales Australia

Scuola di Scienze Agrarie Forestali Alimentari e Ambientali Università della Basilicata Potenza Italy

Shenzhen MSU BIT University Shenzhen China

Sichuan Academy of Forestry Chengdu China

State Key Laboratory of Black Soils Conservation and Utilization Northeast Institute of Geography and Agroecology Chinese Academy of Sciences Changchun China

State Key Laboratory of Grassland and Agro Ecosystems School of Life Sciences Lanzhou University Lanzhou China

State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China

Swedish Biodiversity Centre Department of Urban and Rural Development Swedish University of Agricultural Sciences Uppsala Sweden

Terrestrial Ecology Group Department of Ecology Universidad Autónoma de Madrid Madrid Spain

Unit of Botany Department of Animal and Plant Biology and Ecology Universitat Autònoma de Barcelona Bellaterra Spain

Univ Bordeaux CNRS Bordeaux INP EPOC UMR 5805 Pessac France

Universidad Nacional de la Patagonia Austral CONICET Río Gallegos Argentina

Universitat Autònoma de Barcelona Bellaterra Spain

University Claude Bernard Lyon 1 LEHNA UMR5023 CNRS ENTPE Villeurbanne France

Vegetation Ecology Research Group Institute of Natural Resource Sciences Wädenswil Switzerland

Yuriy Fedkovych Chernivtsi National University Chernivtsi Ukraine

See more in PubMed

Ceballos, G. et al. Accelerated modern human-induced species losses: entering the sixth mass extinction. Sci. Adv. 1, e1400253 (2015). PubMed DOI PMC

Pärtel, M., Szava-Kovats, R. & Zobel, M. Dark diversity: shedding light on absent species. Trends Ecol. Evol. 26, 124–128 (2011). PubMed DOI

Jaureguiberry, P. et al. The direct drivers of recent global anthropogenic biodiversity loss. Sci. Adv. 8, eabm9982 (2022). PubMed DOI PMC

Newbold, T. et al. Global effects of land use on local terrestrial biodiversity. Nature 520, 45–50 (2015). PubMed DOI

Williams, N. S. G. et al. A conceptual framework for predicting the effects of urban environments on floras. J. Ecol. 97, 4–9 (2009). DOI

Le Provost, G. et al. Grassland-to-crop conversion in agricultural landscapes has lasting impact on the trait diversity of bees. Landsc. Ecol. 36, 281–295 (2021). PubMed DOI

Haddad, N. M. et al. Habitat fragmentation and its lasting impact on Earth’s ecosystems. Sci. Adv. 1, e1500052 (2015). PubMed DOI PMC

Stevens, C. J., Thompson, K., Grime, J. P., Long, C. J. & Gowing, D. J. G. Contribution of acidification and eutrophication to declines in species richness of calcifuge grasslands along a gradient of atmospheric nitrogen deposition. Funct. Ecol. 24, 478–484 (2010). DOI

Chase, J. M., Blowes, S. A., Knight, T. M., Gerstner, K. & May, F. Ecosystem decay exacerbates biodiversity loss with habitat loss. Nature 584, 238–243 (2020). PubMed DOI

Barlow, J. et al. Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation. Nature 535, 144–147 (2016). PubMed DOI

Gray, C. L. et al. Local biodiversity is higher inside than outside terrestrial protected areas worldwide. Nat. Commun. 7, 12306 (2016). PubMed DOI PMC

Santangeli, A. et al. Mixed effects of a national protected area network on terrestrial and freshwater biodiversity. Nat. Commun. 14, 5426 (2023). PubMed DOI PMC

Jones, K. R. et al. One-third of global protected land is under intense human pressure. Science 360, 788–791 (2018). PubMed DOI

Cai, L. et al. Global models and predictions of plant diversity based on advanced machine learning techniques. New Phytol. 237, 1432–1445 (2022). PubMed DOI

Sabatini, F. M. et al. Global patterns of vascular plant alpha diversity. Nat. Commun. 13, 4683 (2022). PubMed DOI PMC

Fraser, L. H. et al. Coordinated distributed experiments: an emerging tool for testing global hypotheses in ecology and environmental science. Front. Ecol. Environ. 11, 147–155 (2013). DOI

Pärtel, M., Szava-Kovats, R. & Zobel, M. Community completeness: linking local and dark diversity within the species pool concept. Folia Geobot. 48, 307–317 (2013). DOI

Carmona, C. P. & Pärtel, M. Estimating probabilistic site-specific species pools and dark diversity from co-occurrence data. Glob. Ecol. Biogeogr. 30, 316–326 (2021). DOI

Whittaker, R. H. Vegetation of the Siskiyou Mountains, Oregon and California. Ecol. Monogr. 30, 279–338 (1960). DOI

Harrison, S., Vellend, M. & Damschen, E. I. ‘Structured’ beta diversity increases with climatic productivity in a classic dataset. Ecosphere 2, 1–13 (2011). DOI

Anderson, M. J. et al. Navigating the multiple meanings of beta diversity: a roadmap for the practicing ecologist. Ecol. Lett. 14, 19–28 (2011). PubMed DOI

Vellend, M. Conceptual synthesis in community ecology. Q. Rev. Biol. 85, 183–206 (2010). PubMed DOI

Salguero-Gómez, R. et al. Fast–slow continuum and reproductive strategies structure plant life-history variation worldwide. Proc. Natl Acad. Sci. USA 113, 230–235 (2016). PubMed DOI

Peco, B., Laffan, S. W. & Moles, A. T. Global patterns in post-dispersal seed removal by invertebrates and vertebrates. PLoS One 9, e91256 (2014). PubMed DOI PMC

Riibak, K. et al. Drivers of plant community completeness differ at regional and landscape scales. Agric. Ecosyst. Environ. 301, 107004 (2020). DOI

Ben-Hur, E. & Kadmon, R. Heterogeneity–diversity relationships in sessile organisms: a unified framework. Ecol. Lett. 23, 193–207 (2019). PubMed DOI

González-Trujillo, J. D., Román-Cuesta, R. M., Muñiz-Castillo, A. I., Amaral, C. H. & Araújo, M. B. Multiple dimensions of extreme weather events and their impacts on biodiversity. Clim. Change 176, 155 (2023). DOI

Gallagher, R. V. et al. High fire frequency and the impact of the 2019–2020 megafires on Australian plant diversity. Divers. Distrib. 27, 1166–1179 (2021). DOI

Outhwaite, C. L., McCann, P. & Newbold, T. Agriculture and climate change are reshaping insect biodiversity worldwide. Nature 605, 97–102 (2022). PubMed DOI

Dirzo, R. et al. Defaunation in the Anthropocene. Science 345, 401–406 (2014). PubMed DOI

Pärtel, M. et al. DarkDivNet—a global research collaboration to explore the dark diversity of plant communities. J. Veg. Sci. 30, 1039–1043 (2019). DOI

Tikhonov, G. et al. Joint species distribution modelling with the R-package HMSC. Methods Ecol. Evol. 11, 442–447 (2020). PubMed DOI PMC

Ricklefs, R. E. Community diversity: relative roles of local and regional processes. Science 235, 167–171 (1987). PubMed DOI

Gassert, F. et al. An operational approach to near real time global high resolution mapping of the terrestrial Human Footprint. Front. Remote Sens. 4, 1130896 (2023). DOI

McDonald, R. I. et al. Urban effects, distance, and protected areas in an urbanizing world. Landsc. Urban Plann. 93, 63–75 (2009). DOI

Engert, J. E. et al. Ghost roads and the destruction of Asia-Pacific tropical forests. Nature 629, 370–375 (2024). PubMed DOI PMC

Fusco, E. J., Abatzoglou, J. T., Balch, J. K., Finn, J. T. & Bradley, B. A. Quantifying the human influence on fire ignition across the western USA. Ecol. Appl. 26, 2390–2401 (2016). DOI

Lawton, R. O., Nair, U. S., Pielke, R. A. & Welch, R. M. Climatic impact of tropical lowland deforestation on nearby montane cloud forests. Science 294, 584–587 (2001). PubMed DOI

Bengtsson, J. et al. Grasslands—more important for ecosystem services than you might think. Ecosphere 10, e02582 (2019). DOI

Ellis, E. C. Land use and ecological change: a 12,000-year history. Annu. Rev. Environ. Resour. 46, 1–33 (2021). DOI

Taylor, P. D., Fahrig, L., Henein, K. & Merriam, G. Connectivity is a vital element of landscape structure. Oikos 68, 571–573 (1993). DOI

van Wees, D. et al. The role of fire in global forest loss dynamics. Glob. Chang. Biol. 27, 2377–2391 (2021). PubMed DOI PMC

Hanski, I. Habitat loss, the dynamics of biodiversity, and a perspective on conservation. Ambio 40, 248–255 (2011). PubMed DOI PMC

Aavik, T. & Helm, A. Restoration of plant species and genetic diversity depends on landscape-scale dispersal. Restor. Ecol. 26, S92–S102 (2018). DOI

Araujo, M. B. The coincidence of people and biodiversity in Europe. Glob. Ecol. Biogeogr. 12, 5–12 (2003). DOI

Oksanen, J. Is the humped relationship between species richness and biomass an artefact due to plot size? J. Ecol. 84, 293–295 (1996). DOI

Hooper, D. U. et al. Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecol. Monogr. 75, 3–35 (2005). DOI

Reich, P. B. et al. Impacts of biodiversity loss escalate through time as redundancy fades. Science 336, 589–592 (2012). PubMed DOI

Storch, D. The theory of the nested species–area relationship: geometric foundations of biodiversity scaling. J. Veg. Sci. 27, 880–891 (2016). DOI

Leibold, M. A. et al. The metacommunity concept: a framework for multi-scale community ecology. Ecol. Lett. 7, 601–613 (2004). DOI

Leclère, D. et al. Bending the curve of terrestrial biodiversity needs an integrated strategy. Nature 585, 551–556 (2020). PubMed DOI

Lewis, R. J. et al. Applying the dark diversity concept to nature conservation. Conserv. Biol. 31, 40–47 (2017). PubMed DOI

Deschênes, É., Santala, K. R., Lavigne, J. & Aubin, I. Using a trait-based dark diversity approach to evaluate natural recovery potential in forests. Restor. Ecol. 32, e14251 (2024). DOI

Moeslund, J. E. et al. Using dark diversity and plant characteristics to guide conservation and restoration. J. Appl. Ecol. 54, 1730–1741 (2017). DOI

Nathan, R. et al. Mechanisms of long-distance seed dispersal. Trends Ecol. Evol. 23, 638–647 (2008). PubMed DOI

Pollock, L. J. et al. Understanding co-occurrence by modelling species simultaneously with a Joint Species Distribution Model (JSDM). Methods Ecol. Evol. 5, 397–406 (2014). DOI

Chao, A. et al. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecol. Monogr. 84, 45–67 (2014). DOI

Hsieh, T. C., Ma, K. H. & Chao, A. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol. Evol. 7, 1451–1456 (2016). DOI

Oksanen, J. et al. vegan: Community Ecology Package. R version 4.2.2 https://CRAN.R-project.org/package=vegan (2022).

Karger, D. N. et al. Climatologies at high resolution for the earth’s land surface areas. Sci. Data 4, 170122 (2017). PubMed DOI PMC

Karger, D. N. et al. Data from: Climatologies at high resolution for the earth’s land surface areas. Dryad Digital Repository https://doi.org/10.5061/dryad.kd1d4 (2017).

Hengl, T. et al. SoilGrids250m: global gridded soil information based on machine learning. PLoS One 12, e0169748 (2017). PubMed DOI PMC

Amatulli, G., McInerney, D., Sethi, T., Strobl, P. & Domisch, S. Geomorpho90m, empirical evaluation and accuracy assessment of global high-resolution geomorphometric layers. Sci. Data 7, 162 (2020). PubMed DOI PMC

Wood, S. N. Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J. R. Stat. Soc. B 73, 3–36 (2011). DOI

Valavi, R., Elith, J., Lahoz-Monfort, J. J. & Guillera-Arroita, G. blockCV: an R package for generating spatially or environmentally separated folds for k-fold cross-validation of species distribution models. Methods Ecol. Evol. 10, 225–232 (2019). DOI

Fu, W. J., Carroll, R. J. & Wang, S. Estimating misclassification error with small samples via bootstrap cross-validation. Bioinformatics 21, 1979–1986 (2005). PubMed DOI

Breheny, P. & Burchett, W. Visualization of regression models using visreg. R J. 9, 56–71 (2017). DOI

Di Marco, M., Venter, O., Possingham, H. P. & Watson, J. E. M. Changes in human footprint drive changes in species extinction risk. Nat. Commun. 9, 4621 (2018). PubMed DOI PMC

Williams, B. A. et al. Change in terrestrial human footprint drives continued loss of intact ecosystems. One Earth 3, 371–382 (2020). DOI

Pärtel, M. et al. Supporting data for ‘Global impoverishment of natural vegetation revealed by dark diversity’. Figshare https://doi.org/10.6084/m9.figshare.25158059 (2025).

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