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Global impoverishment of natural vegetation revealed by dark diversity

Citation

Pärtel, M., Tamme, R., Carmona, C.P. et al. Global impoverishment of natural vegetation revealed by dark diversity. Nature 641, 917–924 (2025). https://doi.org/10.1038/s41586-025-08814-5

Abstract

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.

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Acknowledgements We thank the Estonian Research Council (PRG609, PRG1065, PSG293 and PRG2142) and the Estonian Ministry of Education and Research (Centre of Excellence AgroCropFuture, TK200) for funding the DarkDivNet steering committee, and we thank the many students and volunteers who helped with the fieldwork. Acknowledgements related to specific authors can be found in the Supplementary Notes: Additional acknowledgements • Jonathan A. Bennett: NSERC Discovery Grant (RGPIN-2018-04952) • Alessandro Chiarucci: National Recovery and Resilience Plan (NRRP), Project "National Biodiversity Future Center—NBFC" (CUP J33C22001190001) • Maarja Öpik: Estonian Research Council (1789 FUNFARM) • Vistorina Amputu: German Federal Ministry of Education and Research (BMBF; FKZ 01LC1821B) • Isabelle Aubin: K. Good, C. Zimmerman • Francisco M. Azcárate: Project REMEDINAL (TE-CM S2018/EMT-4338) • Zoltán Bátori: National Research Development and Innovation Office (FK142428), János Bolyai Research Scholarship of the Hungarian Academy of Sciences (BO/00298/21/8), New National Excellence Program of the Ministry for Culture and Innovation from the source of the National Research, Development and Innovation Fund (ÚNKP-23-5-SZTE-697) • Natalie Beenaerts: Ann Cuypers, Anne Habets, Siebe Indestege • Idoia Biurrun: Basque Government (IT1487-22) • Bazartseren Boldgiv: Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology • Francis Q. Brearley: Manchester Metropolitan University, Percy Sladen Memorial Fund • C. Guillermo Bueno: Ramon y Cajal Fellowship (RYC2021-032533-I), consolidator grant "Mycolegium" from the Spanish Ministry of Science, Innovation and University (CNS2023-143989) • James F. Cahill: NSERC Discovery Grant • Juan A. Campos: Basque Government (IT1487-22) • Christopher Carcaillet: Olivier Blarquez • Jan Čuda: Czech Academy of Sciences, long-term research development project (RVO 67985939) • Mariana Dairel: FAPESP (2019/09659-1) • John Davison: Estonian Research Council (PRG2584) • Balázs Deák: Hungarian National Research, Development and Innovation Office (NKFIH FK 135329, NKFIH KKP 144096) • Jiri Dolezal: Czech Science Foundation (24-11954S), MSMT INTER-ACTION (LUAUS24258) • Anu Eskelinen: Research Council of Finland (project no 351089) • Franz Essl: Austrian Science Foundation FWF (I 5825-B) • Fatih Fazlioglu: Ordu University Research Council (A-2028) • Arianna Ferrara: Ente Parco Nazionale Foreste Casentinesi (PhD project "Conservation of natural vegetation dynamics within the National Park of Casentinesi Forests") • Alessandra Fidelis: São Paulo Research Foundation (FAPESP 2015/06743-0), National Council for Scientific and Technological Development (CNPq 312689/2021-7), permit COTEC nº 480/2018 D67/2018 PH (SMA/SP), Heloiza Zirondi, Vagner Zanzarini, Cassy Anne Rodrigues • Markus Fischer: German Research Foundation (DFG Priority Programme 1374, "Biodiversity Exploratories") • Lauchlan H. Fraser: Natural Sciences and Engineering Research Council of Canada Industrial Research Chair in Ecosystem Reclamation • Fernando F. Furquim: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brasil (Finance code 001) • Heath W. Garris: Covenant College • Ana González-Robles: Junta de Andalucía (Delegación Territorial de Agricultura, Ganadería, Pesca y Desarrollo Sostenible en Almería), Parque Natural Cabo de Gata-Níjar and 'Playas y Cortijos family' for facilitating permits to do the field samplings, J.L. González Rebollar • Stef Haesen: FLOF fellowship (3E190655) of the KU Leuven • Martin Hejda: Czech Academy of Sciences, long-term research development project (RVO 67985939) • Ruben H. Heleno: Portuguese Foundation for Science and Technology (UIDB/04004/2020, 10.54499/LA/P/0092/2020) • Toke T. Høye: Independent Research Fund Denmark (8021-00423B) • Yingxin Huang: Strategic Priority Research Program of the Chinese Academy of Sciences (XDA28110202), project supported by the National Natural Science Foundation of China (42471071 ), China Jilin Provincial Major Science and Technology Project (20230303008SF) • John T. Hunter: Vanessa Hunter • Ricardo Ibáñez: University of Navarra (project “Red de Observatorios de la Biodiversidad de Navarra (ROBIN)”) • Borja Jiménez-Alfaro: Spanish Research Agency (PID2019-108636GA-100) • András Kelemen: János Bolyai Research Scholarship of the Hungarian Academy of Sciences (BO/00713/19) 12 • Kimberly J. Komatsu: Smithsonian Institution • Natalia Koroleva: Ekaterina Kopeina • Lauri Laanisto: Estonian Academy of Sciences (research professorship for Arctic studies), Adam Mickiewicz University Polar Station (Petuniabukta) • Vojtech Lanta: Czech Science Foundation (23-07533S) • Jonas J. Lembrechts: Research Foundation Flanders (G018919N, 12P1819N), BiodivERsA+ (The ASICS Project) • Liping Li: National Natural Science Foundation of China (82274041) • Kristin Ludewig: Harry Stöckmann, Jutta Krüger • Petr Macek: Czech Science Foundation (GA17-20839S) • Jesper Erenskjold Moeslund: Aage V. Jensen Naturfond ("Dark diversity in nature management") • Eduardo Moreno-Jiménez: Spanish Ministry of Science and Innovation (PID2020-116578RB-I00) • Ladislav Mucina: Iluka Chair at the Murdoch University, Perth, Australia • Miriam Muñoz-Rojas: Ministry of Science and Innovation, Spain (RYC2020-029255-I, TED2021-132332A-C22, PID2021-123097OA-I00) • Lena Neuenkamp: German Science Foundation (DFG Priority Programme 1374 "Biodiversity Exploratories") • Signe Normand: Independent Research Fund Denmark (7027-00133B ), Novo Nordisk Foundation Challenge Program, Matilde Mikkeline Holst Stoltze • Arkadiusz Nowak: National Science Centre, Poland (2019/35/B/NZ8/03358) • Begoña Peco: Helios Sainz • Alessandro Petraglia: COMP-HUB and COMP-R Initiatives, funded by the ‘Departments of Excellence’ program of the Italian Ministry for University and Research (MIUR, 2018-2022 and MUR, 2023-2027) • Pedro Antonio Plaza Álvarez: Regional Government of Castilla-La Mancha and the European Social Fund Plus (ESF+) • Jan Plue: Future Research Leader grant by FORMAS (2018-00961) • Triin Reitalu: Estonian Research Council (PRG874), Estonian Ministry of Education and Research, Centre of Excellence for Sustainable Land Use (TK232) • Michael Ristow: Merlin Schäfer, Marieke Bittner • Ana Belén Robles: Project Research on Forage Flora of Baetica (Ref. 201640E002) Spanish Council for Scientific Research (CSIC) Agency • Raúl Román: European Union Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie IF-GF Actions (MICROBIOCLIM, GA nr. 101028323) • Jiří Sádlo: Technology Agency of the Czech Republic, project DivLand (TACR SS02030018), Czech Academy of Sciences, long-term research development project (RVO 67985939) • Khaliun Sanchir: Taylor Family-Asia Foundation Endowed Chair in Ecology and Conservation Biology • Ute Schmiedel: German Federal Ministry of Education and Research (01LC0024, 01LC0024A, 01LC0624A2, 01LG1201A, 01LG1201N), the Soebatsfontein community (that gave permission to work on their farmland), Jona Luther-Mosebach, Inga U. Röwer, Reginald Christiaan • Josep M. Serra-Diaz: Agence Nationale de la Recherche programme Jeune Chercheur (ANR-21-CE32-0003), Remy Joly, Anna Schmidt • Hana Skálová: Technology Agency of the Czech Republic, project DivLand (TACR SS02030018), Technology Agency of the Czech Republic, BiodivClim Call 2019, project ASICS (TACR SS70010001), Czech Academy of Sciences, longterm research development project (RVO 67985939) • Judit Sonkoly: National Research, Development and Innovation Office (PD 137747), Bolyai János Scholarship of the Hungarian Academy of Sciences (BO/00587/23/8) • Kateřina Štajerová: Czech Academy of Sciences, long-term research development project (RVO 67985939), Anna Lučanová • Ivana Svitková: Scientific Grant Agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic and Slovak Academy of Sciences (VEGA 2/0031/17) • Andrew J. Tanentzap: Canada Research Chairs Program and Natural Sciences and Engineering Research Council of Canada (NSERC; RGPIN-2023-03977) • Pablo Tejero: JACA Herbarium (IPE-CSIC) • Csaba Tölgyesi: National Research Development and Innovation Office (K146137) • Enrico Tordoni: Estonian Research Council (PSG1021) • Péter Török: National Research Found of Hungary (KKP 144068) • Diego P. F. Trindade: Estonian Research Council, Estonian Research Council (PUTJD1228) • Enrique Valencia: Community of Madrid in the framework of the Multiannual Agreement with the Rey Juan Carlos University in line of action 1, “Encouragement of Young Phd students investigation” (M2165, INTRANESTI) • Mercedes Valerio: Departamento de Educación, Gobierno de Navarra (Ayudas predoctorales para la realización de programas de doctorado de interés para Navarra; Plan de Formación y de I + D 2018) • Orsolya Valkó: Hungarian National Research, Development and Innovation Office (KKP 144096) 13 • Michaela Vítková: Technology Agency of the Czech Republic, project DivLand (TACR SS02030018), Technology Agency of the Czech Republic, BiodivClim Call 2019, project ASICS (TACR SS70010001), Czech Academy of Sciences, long-term research development project (RVO 67985939) • Martin Vojík: Czech Academy of Sciences, long-term research development project (RVO 67985939), Technology Agency of the Czech Republic, project DivLand (TACR SS02030018) • Jonathan von Oppen: The Independent Research Fund of Denmark (7027-00133B) • Viktoria Wagner: Discovery Grant from the Canadian Natural Science and Engineering Research Council (RES0043426), Competitive Grant from the University of Alberta Rangeland Research Institute (RES0045021), Startup Grant from the University of Alberta • Ji-Zhong Wan: Hundred Talent Program of Chinese Academy of Sciences (No. E4K2150150) • Sajad A. Wani: University Grants Commission (UGC; 916/CSIRNET JUNE-2019)

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