Global impoverishment of natural vegetation revealed by dark diversity
Status Publisher Language English Country England, Great Britain Media print-electronic
Document type Journal Article
PubMed
40175550
DOI
10.1038/s41586-025-08814-5
PII: 10.1038/s41586-025-08814-5
Knihovny.cz E-resources
- Publication type
- Journal Article MeSH
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
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
Biology Education Dokuz Eylül University Buca Turkey
Bjerknes Centre for Climate Research University of Bergen Bergen Norway
Botanical Institute of Barcelona Barcelona Spain
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
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
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
Deakin University Burwood Victoria Australia
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
Department of Agricultural and Food Chemistry Universidad Autónoma de Madrid Madrid Spain
Department of Agronomy University of Almería Almería Spain
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 Civil and Environmental Engineering University of the Andes Bogotá Colombia
Department of Earth and Environmental Sciences KU Leuven Leuven Belgium
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 Environmental Science and Policy University of California Davis Davis CA USA
Department of Environmental Sciences University of Basel Basel Switzerland
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 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 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 Reclamation of Arid and Mountainous Regions University of Tehran Tehran Iran
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
Estación Experimental de Zonas Áridas Almería Spain
Estación Experimental del Zaidín Granada Spain
F Falz Fein Biosphere Reserve Askania Nova Kyiv Ukraine
Faculty of Agricultural and Environmental Sciences University of Rostock Rostock Germany
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
Greenpeace España Madrid Spain
Gulbali Institute Charles Sturt University Albury New South Wales Australia
Harry Butler Institute Murdoch University Perth Western Australia Australia
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 Biological Sciences University of Zielona Góra Zielona Góra Poland
Institute of Botany Czech Academy of Sciences Průhonice Czech Republic
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 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
Kalmar County Administrative Board Färjestaden Sweden
KU Leuven Plant Institute KU Leuven Leuven Belgium
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
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 Biosciences and Veterinary Medicine University of Camerino Camerino Italy
School of Grassland Science Beijing Forestry University Beijing China
School of Natural Sciences Macquarie University Sydney New South Wales Australia
Shenzhen MSU BIT University Shenzhen China
Sichuan Academy of Forestry Chengdu China
Terrestrial Ecology Group Department of Ecology Universidad Autónoma de Madrid Madrid 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).