More stories

  • in

    High-resolution global maps of tidal flat ecosystems from 1984 to 2019

    Murray, N. J. et al. The global distribution and trajectory of tidal flats. Nature 565, 222–225, https://doi.org/10.1038/s41586-018-0805-8 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bishop, M. J., Murray, N. J., Swearer, S. & Keith, D. A. In The IUCN Global Ecosystem Typology 2.0: Descriptive profiles for biomes and ecosystem functional groups (eds D. A. Keith, J. R. Ferrer-Paris, E. Nicholson, & R. T. Kingsford) (IUCN, 2020).Keith, D. A. et al. Earth’s ecosystems: a function-based typology for conservation and sustainability. Nature (In review).Murray, N. J., Phinn, S. R., Clemens, R. S., Roelfsema, C. M. & Fuller, R. A. Continental scale mapping of tidal flats across East Asia using the Landsat Archive. Remote Sensing 4, 3417–3426, https://doi.org/10.3390/Rs4113417 (2012).Article 

    Google Scholar 
    Murray, N. J., Clemens, R. S., Phinn, S. R., Possingham, H. P. & Fuller, R. A. Tracking the rapid loss of tidal wetlands in the Yellow Sea. Fron. Ecol. Environ. 12, 267–272, https://doi.org/10.1890/130260 (2014).Article 

    Google Scholar 
    Murray, N. J., Ma, Z. & Fuller, R. A. Tidal flats of the Yellow Sea: A review of ecosystem status and anthropogenic threats. Austral Ecol. 40, 472–481, https://doi.org/10.1111/aec.12211 (2015).Article 

    Google Scholar 
    Dhanjal-Adams, K. et al. Distribution and protection of intertidal habitats in Australia. Emu 116, 208–214 (2015).Article 

    Google Scholar 
    Murray, N. J. et al. High-resolution mapping of losses and gains of Earth’s tidal wetlands. Science 376, 744–749, https://doi.org/10.1126/science.abm9583 (2022).CAS 
    Article 
    PubMed 

    Google Scholar 
    Gong, P. et al. Finer resolution observation and monitoring of global land cover: first mapping results with Landsat TM and ETM+ data. Int. J. Remote Sens. 34, 2607–2654 (2013).Article 

    Google Scholar 
    Gorelick, N. et al. Google Earth Engine: Planetary-scale geospatial analysis for everyone. Remote Sens. Environ. 202, 18–27, https://doi.org/10.1016/j.rse.2017.06.031 (2017).Article 

    Google Scholar 
    Turner, W. et al. Free and open-access satellite data are key to biodiversity conservation. Biol. Conserv. 182, 173–176 (2015).Article 

    Google Scholar 
    Murray, N. J. et al. The role of satellite remote sensing in structured ecosystem risk assessments. Sci Total Environ 619–620, 249–257, https://doi.org/10.1016/j.scitotenv.2017.11.034 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Ying, Q. et al. Global bare ground gain from 2000 to 2012 using Landsat imagery. Remote Sens. Environ. 194, 161–176, https://doi.org/10.1016/j.rse.2017.03.022 (2017).Article 

    Google Scholar 
    Song, X.-P. et al. Global land change from 1982 to 2016. Nature 560, 639–643, https://doi.org/10.1038/s41586-018-0411-9 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Noble, S. et al. A new 30 meter resolution global shoreline vector and associated global islands database for the development of standardized ecological coastal units AU – Sayre, Roger. Journal of Operational Oceanography, 1–10, https://doi.org/10.1080/1755876X.2018.1529714 (2018).Sayre, R. et al. A global ecological classification of coastal segment units to complement marine biodiversity observation network assessments. Oceanography 34, 120–129 (2021).Article 

    Google Scholar 
    Hansen, M. C. et al. High-resolution global maps of 21st-century forest cover change. Science 342, 850–853, https://doi.org/10.1126/science.1244693 (2013).CAS 
    Article 
    PubMed 

    Google Scholar 
    Margono, B. A., Potapov, P. V., Turubanova, S., Stolle, F. & Hansen, M. C. Primary forest cover loss in Indonesia over 2000–2012. Nature Climate Change 4, 730–735, https://doi.org/10.1038/nclimate2277 (2014).Article 

    Google Scholar 
    Curtis, P. G., Slay, C. M., Harris, N. L., Tyukavina, A. & Hansen, M. C. Classifying drivers of global forest loss. Science 361, 1108–1111, https://doi.org/10.1126/science.aau3445 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Pekel, J. F., Cottam, A., Gorelick, N. & Belward, A. S. High-resolution mapping of global surface water and its long-term changes. Nature 540, 418–422, https://doi.org/10.1038/nature20584 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Pickens, A. H. et al. Mapping and sampling to characterize global inland water dynamics from 1999 to 2018 with full Landsat time-series. Remote Sens. Environ. 243, 111792, https://doi.org/10.1016/j.rse.2020.111792 (2020).Article 

    Google Scholar 
    Yamazaki, D., Trigg, M. A. & Ikeshima, D. Development of a global ~ 90 m water body map using multi-temporal Landsat images. Remote Sens. Environ. 171, 337–351, https://doi.org/10.1016/j.rse.2015.10.014 (2015).Article 

    Google Scholar 
    Fluet-Chouinard, E., Lehner, B., Rebelo, L.-M., Papa, F. & Hamilton, S. K. Development of a global inundation map at high spatial resolution from topographic downscaling of coarse-scale remote sensing data. Remote Sens. Environ. 158, 348–361, https://doi.org/10.1016/j.rse.2014.10.015 (2015).Article 

    Google Scholar 
    Bunting, P. et al. The Global Mangrove Watch—A new 2010 global baseline of mangrove extent. Remote Sensing 10, 1669 (2018).Article 

    Google Scholar 
    Worthington, T. A. et al. Harnessing Big Data to Support the Conservation and Rehabilitation of Mangrove Forests Globally. One Earth 2, 429–443, https://doi.org/10.1016/j.oneear.2020.04.018 (2020).Article 

    Google Scholar 
    Worthington, T. A. et al. A global typology of mangroves and its relevance for ecosystem services and deforestation. Scientific reports (2020).Thomas, N. et al. Distribution and drivers of global mangrove forest change, 1996–2010. PLOS ONE 12, e0179302, https://doi.org/10.1371/journal.pone.0179302 (2017).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Simard, M. et al. Mangrove canopy height globally related to precipitation, temperature and cyclone frequency. Nature Geoscience 12, 40–45, https://doi.org/10.1038/s41561-018-0279-1 (2019).CAS 
    Article 

    Google Scholar 
    Allen, G. H. & Pavelsky, T. M. Global extent of rivers and streams. Science 361, 585–588, https://doi.org/10.1126/science.aat0636 (2018).MathSciNet 
    CAS 
    Article 
    PubMed 
    MATH 

    Google Scholar 
    Lyons, M. et al. Mapping the world’s coral reefs using a global multiscale earth observation framework. Remote Sensing in Ecology and Conservation (2020).Li, J. et al. A global coral reef probability map generated using convolutional neural networks. Coral Reefs https://doi.org/10.1007/s00338-020-02005-6 (2020).Article 

    Google Scholar 
    Yang, X., Pavelsky, T. M. & Allen, G. H. The past and future of global river ice. Nature 577, 69–73, https://doi.org/10.1038/s41586-019-1848-1 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Newbold, T. et al. Has land use pushed terrestrial biodiversity beyond the planetary boundary? A global assessment. Science 353, 288–291, https://doi.org/10.1126/science.aaf2201 (2016).CAS 
    Article 
    PubMed 

    Google Scholar 
    Tittensor, D. P. et al. A mid-term analysis of progress toward international biodiversity targets. Science 346, 241–244, https://doi.org/10.1126/science.1257484 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Lee, C. K. F., Nicholson, E., Duncan, C. & Murray, N. J. Estimating changes and trends in ecosystem extent with dense time-series satellite remote sensing. Conserv Biol 35, 325–335, https://doi.org/10.1111/cobi.13520 (2021).Article 
    PubMed 

    Google Scholar 
    Deegan, L. A. et al. Coastal eutrophication as a driver of salt marsh loss. Nature 490, 388–392 (2012).CAS 
    Article 

    Google Scholar 
    Goldberg, L., Lagomasino, D., Thomas, N. & Fatoyinbo, T. Global declines in human-driven mangrove loss. Glob Chang Biol 26, 5844–5855, https://doi.org/10.1111/gcb.15275 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Brown, A. C. & McLachlan, A. Sandy shore ecosystems and the threats facing them: some predictions for the year 2025. Environ. Conserv. 29, 62–77, https://doi.org/10.1017/s037689290200005x (2002).Article 

    Google Scholar 
    Krumhansl, K. A. et al. Global patterns of kelp forest change over the past half-century. Proc. Natl. Acad. Sci. USA 113, 13785–13790, https://doi.org/10.1073/pnas.1606102113 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Hill, N. K., Woodworth, B. K., Phinn, S. R., Murray, N. J. & Fuller, R. A. Global protected-area coverage and human pressure on tidal flats. Conserv Biol, https://doi.org/10.1111/cobi.13638 (2021).Murray, N. J. et al. Myanmar’s terrestrial ecosystems: Status, threats and conservation opportunities. Biol. Conserv. 252, 108834, https://doi.org/10.1016/j.biocon.2020.108834 (2020).Article 

    Google Scholar 
    Jackson, M. V. et al. Dual threat of tidal flat loss and invasive Spartina alterniflora endanger important shorebird habitat in coastal mainland China. J Environ Manage 278, 111549, https://doi.org/10.1016/j.jenvman.2020.111549 (2021).Article 
    PubMed 

    Google Scholar 
    Davidson, N. C. & Finlayson, C. M. Updating global coastal wetland areas presented in Davidson and Finlayson (2018). Marine and Freshwater Research 70, 1195–1200, https://doi.org/10.1071/MF19010 (2019).Article 

    Google Scholar 
    Duan, H. et al. Identifying new sites of significance to waterbirds conservation and their habitat modification in the Yellow and Bohai Seas in China. Global Ecology and Conservation, e01031 (2020).Jung, M. et al. A global map of terrestrial habitat types. Scientific Data 7, 256, https://doi.org/10.1038/s41597-020-00599-8 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Keith, D. et al. The IUCN Global Ecosystem Typology v2.0: Descriptive profiles for Biomes and Ecosystem Functional Groups. (The International Union for the Conservation of Nature (IUCN), Gland, 2020).Fink, D. et al. Modeling avian full annual cycle distribution and population trends with citizen science data. Ecol. Appl. 30, e02056, https://doi.org/10.1002/eap.2056 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Convention on Biological Diversity. Indicators for the post-2020 Global Biodiversity Framework. (Convention on Biological Diversity, 2021).Murray, NJ. et al. High-resolution global maps of tidal flat ecosystems from 1984 to 2019, Figshare, https://doi.org/10.6084/m9.figshare.c.5884598.v1 (2022).Amante, C. & Eakins, B. W. ETOPO1 1 arc-minute global relief model: procedures, data sources and analysis. (US Department of Commerce, National Oceanic and Atmospheric Administration, National Environmental Satellite, Data, and Information Service, National Geophysical Data Center, Marine Geology and Geophysics Division, 2009).Farr, T. G. et al. The shuttle radar topography mission. Rev. Geophys. 45, Rg200410.1029/2005rg000183 (2007).Article 

    Google Scholar 
    Mcowen, C. et al. A global map of saltmarshes. Biodiversity Data Journal 5, https://doi.org/10.3897/BDJ.5.e11764 (2017).Giri, C. et al. Status and distribution of mangrove forests of the world using earth observation satellite data. Global Ecology and Biogeography 20, 154–159, https://doi.org/10.1111/j.1466-8238.2010.00584.x (2011).Article 

    Google Scholar 
    US Geological Survey. Product Guide: Landsat 4–7 Surface Reflectance (LEDAPS) Product (2018).US Geological Survey. Product Guide: Landsat 8 Surface Reflectance Code (LASRC) Product (2018).Foga, S. et al. Cloud detection algorithm comparison and validation for operational Landsat data products. Remote Sens. Environ. 194, 379–390 (2017).Article 

    Google Scholar 
    Breiman, L. Random forests. Machine learning 45, 5–32 (2001).Article 

    Google Scholar 
    Murray, N. J. et al. Code and data supplement to “High-resolution global maps of tidal flat ecosystems from 1984 to 2019”. Zenodo https://doi.org/10.5281/zenodo.6332960 (2020).Congalton, R. G. & Green, K. Assessing the Accuracy of Remotely Sensed Data: Principles and Practices. (CRC press, 2008).Lyons, M. B., Keith, D. A., Phinn, S. R., Mason, T. J. & Elith, J. A comparison of resampling methods for remote sensing classification and accuracy assessment. Remote Sens. Environ. 208, 145–153, https://doi.org/10.1016/j.rse.2018.02.026 (2018).Article 

    Google Scholar 
    Sagar, S., Roberts, D., Bala, B. & Lymburner, L. Extracting the intertidal extent and topography of the Australian coastline from a 28 year time series of Landsat observations. Remote Sens. Environ. 195, 153–169, https://doi.org/10.1016/j.rse.2017.04.009 (2017).Article 

    Google Scholar 
    Lee, J. et al. The first national scale evaluation of organic carbon stocks and sequestration rates of coastal sediments along the West Sea, South Sea, and East Sea of South Korea. Sci Total Environ 793, 148568, https://doi.org/10.1016/j.scitotenv.2021.148568 (2021).CAS 
    Article 
    PubMed 

    Google Scholar 
    Zhang, Z., Xu, N., Li, Y. & Li, Y. Sub-continental-scale mapping of tidal wetland composition for East Asia: A novel algorithm integrating satellite tide-level and phenological features. Remote Sens. Environ. 269, 112799, https://doi.org/10.1016/j.rse.2021.112799 (2022).Article 

    Google Scholar 
    Hooijer, A. & Vernimmen, R. Global LiDAR land elevation data reveal greatest sea-level rise vulnerability in the tropics. Nat. Commun. 12, 1–7 (2021).Article 

    Google Scholar 
    Rodríguez, J. P. et al. A practical guide to the application of the IUCN Red List of Ecosystems criteria. Philos. Trans. R. Soc. B-Biol. Sci. 370, 20140003, https://doi.org/10.1098/rstb.2014.0003 (2015).Article 

    Google Scholar 
    Keith, D. A. et al. The IUCN Red List of Ecosystems: Motivations, Challenges, and Applications. Conservation Letters 8, 214–226, https://doi.org/10.1111/conl.12167 (2015).Article 

    Google Scholar 
    Spencer, T. et al. Global coastal wetland change under sea-level rise and related stresses: The DIVA Wetland Change Model. Global and Planetary Change 139, 15–30 (2016).Article 

    Google Scholar 
    Bunting, P., Rosenqvist, A., Hilarides, L., Lucas, R. M. & Thomas, N. Global Mangrove Watch: Updated 2010 Mangrove Forest Extent (v2.5). Remote Sensing 14, 1034 (2022).Article 

    Google Scholar 
    US Geological Survey. Landsat 4–7 Collection 1 (C1) Surface Reflectance (LEDAPS) Product Guide. Version 3.0. (USGS, 2020).Xu, C. & Liu, W. Mapping and analyzing the annual dynamics of tidal flats in the conterminous United States from 1984 to 2020 using Google Earth Engine. Environmental Advances 7, 100147, https://doi.org/10.1016/j.envadv.2021.100147 (2022).Article 

    Google Scholar 
    Wang, X. X. et al. Rebound in China’s coastal wetlands following conservation and restoration. Nature Sustainability 4, 1076-+, https://doi.org/10.1038/s41893-021-00793-5 (2021).Article 

    Google Scholar 
    Fitton, J. M., Rennie, A. F., Hansom, J. D. & Muir, F. M. E. Remotely sensed mapping of the intertidal zone: a Sentinel-2 and Google Earth Engine methodology. Remote Sensing Applications: Society and Environment, 100499, https://doi.org/10.1016/j.rsase.2021.100499 (2021).Murray, N. J., Kennedy, E., Álvarez-Romero, J. G. & Lyons, M. B. Data freshness in ecology and conservation. Trends in Ecology and Evolution 36, 485–487, https://doi.org/10.1016/j.tree.2021.03.005 (2021).Article 
    PubMed 

    Google Scholar  More

  • in

    Cultivating epizoic diatoms provides insights into the evolution and ecology of both epibionts and hosts

    Zaneveld, J. R., McMinds, R. & Thurber, R. V. Stress and stability: Applying the Anna Karenina principle to animal microbiomes. Nat. Microbiol. 2, 1–8 (2017).Article 
    CAS 

    Google Scholar 
    Trevelline, B. K., Fontaine, S. S., Hartup, B. K. & Kohl, K. D. Conservation biology needs a microbial renaissance: A call for the consideration of host-associated microbiota in wildlife management practices. Proc. R. Soc. B 286, 2018–2448 (2019).Article 

    Google Scholar 
    Bennett, A. G. On the occurrence of diatoms on the skin of whales. Proc. R. Soc. Lond. B 91, 352–357 (1920).ADS 
    Article 

    Google Scholar 
    Denys, L. Morphology and taxonomy of epizoic diatoms (Epiphalaina and Tursiocola) on a sperm whale (Physeter macrocephalus) stranded on the coast of Belgium. Diatom. Res. 12, 1–18 (1997).Article 

    Google Scholar 
    Majewska, R. Tursiocola neliana sp. nov (Bacillariophyceae) epizoic on South African leatherback sea turtles (Dermochelys coriacea) and new observations on the genus Tursiocola. Phytotaxa 453, 1–15 (2020).Article 

    Google Scholar 
    Majewska, R. et al. Chelonicola and Poulinea, two new gomphonemoid genera living on marine turtles from Costa Rica. Phytotaxa 233, 236–250 (2015).Article 

    Google Scholar 
    Majewska, R. et al. Shared epizoic taxa and differences in diatom community structure between green turtles (Chelonia mydas) from distant habitats. Microb Ecol. 74, 969–978 (2017).PubMed 
    Article 

    Google Scholar 
    Majewska, R. et al. Two new epizoic Achnanthes species (Bacillariophyta) living on marine turtles from Costa Rica. Bot. Mar. 60, 303–318 (2017).Article 

    Google Scholar 
    Majewska, R., De Stefano, M. & Van de Vijver, B. Labellicula lecohuiana, a new epizoic diatom species living on green turtles in Costa Rica. Nova Hedwig Beih. 146, 23–31 (2018).Article 

    Google Scholar 
    Majewska, R. et al. Craspedostauros alatus sp. nov., a new diatom (Bacillariophyta) species found on museum sea turtle specimens. Diatom Res. 33, 229–240 (2018).Article 

    Google Scholar 
    Majewska, R. et al. Six new epibiotic Proschkinia (Bacillariophyta) species and new insights into the genus phylogeny. Eur. J. Phycol. 54, 609–631 (2019).Article 

    Google Scholar 
    Majewska, R., Robert, K., Van de Vijver, B. & Nel, R. A new species of Lucanicum (Cyclophorales, Bacillariophyta) associated with loggerhead sea turtles from South Africa. Bot. Lett. 167, 7–14 (2020).Article 

    Google Scholar 
    Frankovich, T. A., Sullivan, M. J. & Stacy, N. I. Tursiocola denysii sp. Nov. (Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta). Phytotaxa 234, 227–236 (2015).Article 

    Google Scholar 
    Frankovich, T. A., Ashworth, M. P., Sullivan, M. J., Vesela, J. & Stacy, N. I. Medlinella amphoroidea gen. et sp. Nov. (Bacillariophyta) from the neck skin of Loggerhead sea turtles (Caretta caretta). Phytotaxa 272, 101–114 (2016).Article 

    Google Scholar 
    Riaux-Gobin, C. et al. New epizoic diatom (Bacillariophyta) species from sea turtles in the Eastern Caribbean and South Pacific. Diatom Res. 32, 109–125 (2017).Article 

    Google Scholar 
    Riaux-Gobin, C., Witkowski, A., Chevallier, D. & Daniszewska-Kowalczyk, G. Two new Tursiocola species (Bacillariophyta) epizoic on green turtles (Chelonia mydas) in French Guiana and Eastern Caribbean. Fottea Olomouc 17, 150–163 (2017).Article 

    Google Scholar 
    Riaux-Gobin, C., Witkowski, A., Kociolek, J. P. & Chevallier, D. Navicula dermochelycola sp. Nov., presumably an exclusively epizoic diatom on sea turtles Dermochelys coriacea and Lepidochelys olivacea from French Guiana. Oceanol. Hydrobiol. Stud. 49, 132–139 (2020).CAS 
    Article 

    Google Scholar 
    Robert, K., Bosak, S. & Van de Vijver, B. Catenula exigua sp. nov., a new marine diatom (Bacillariophyta) species from the Adriatic Sea. Phytotaxa 414, 113–118 (2019).Article 

    Google Scholar 
    Van de Vijver, B. & Bosak, S. Planothidium kaetherobertianum, a new marine diatom (Bacillariophyta) species from the Adriatic Sea. Phytotaxa 425, 105–112 (2019).Article 

    Google Scholar 
    Robinson, N. J. et al. Epibiotic diatoms are universally present on all sea turtle species. PLoS ONE 11, e0157011 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Van de Vijver, B. et al. Diversity of diatom communities (Bacillariophyta) associated with loggerhead sea turtles. PLoS ONE 15, e0236513 (2020).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Van de Vijver, B., Robert, K., Witkowski, A. & Bosak, S. Majewskaea gen. nov. (Bacillariophyta), a new marine benthic diatom genus from the Adriatic Sea. Fottea 20, 112–120 (2020).Article 

    Google Scholar 
    Majewska, R. Nagumoea hydrophicola sp. Nov. (Bacillariophyta), the first diatom species described from sea snakes. Diatom Res. 36, 49–59 (2021).Article 

    Google Scholar 
    Frankovich, T. A., Sullivan, M. J. & Stacey, N. I. Three new species of Tursiocola (Bacillariophyta) from the skin of the West Indian manatee (Trichechus manatus). Phytotaxa 204, 33–48 (2015).Article 

    Google Scholar 
    Frankovich, T. A., Ashworth, M. P., Sullivan, M. J., Theriot, E. C. & Stacy, N. I. Epizoic and apochlorotic Tursiocola species (Bacillariophyta) from the skin of Florida manatees (Trichechus manatus latirostris). Protist 169, 539–568 (2018).PubMed 
    Article 

    Google Scholar 
    Azari, M. et al. Diatoms on sea turtles and floating debris in the Persian Gulf (Western Asia). Phycologia 59, 292–304 (2020).Article 

    Google Scholar 
    Majewska, R. & Goosen, W. E. For better, for worse: Manatee-associated Tursiocola (Bacillariophyta) remain faithful to their host. J. Phycol. 56, 1019–1027 (2020).CAS 
    PubMed 
    Article 

    Google Scholar 
    Smol, J. P. & Stoermer, E. F. The Diatoms: Applications for the Environmental and Earth Sciences (Cambridge University Press, 2010).Book 

    Google Scholar 
    Rivera, S. F. et al. DNA metabarcoding and microscopic analyses of sea turtles biofilms: Complementary to understand turtle behavior. PLoS ONE 13, e0195770 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Majewska, R. et al. On sea turtle-associated Craspedostauros with description of three novel species. J Phycol. 57, 199–208 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Holmes, R. W. The morphology of diatoms epizoic on cetaceans and their transfer from Cocconeis to two new genera, Bennettella and Epipellis. Br. Phycol. J. 20, 43–57 (1985).Article 

    Google Scholar 
    Woodworth, K. A., Frankovich, T. A. & Freshwater, D. W. Melanothamnus maniticola (Ceramiales, Rhodophyta): An epizoic species evolved for life on the West Indian Manatee. J. Phycol. 55, 1239–1245 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Vitt, L. J. & Caldwell, J. P. Herpetology: An Introductory Biology of Amphibians and Reptiles (Academic Press, 2013).
    Google Scholar 
    Pitman, L. R. et al. Skin in the game: Epidermal molt as a driver of long-distance migration in whales. Mar. Mamm. Sci. 36, 565–594 (2020).Article 

    Google Scholar 
    Pope, D. H. & Berger, L. R. Algal photosynthesis at increased hydrostatic pressure and constant pO2. Arch. Microbiol. 89, 321–325 (1973).CAS 

    Google Scholar 
    Calcagno, V., Jarne, P., Loreau, M., Mouquet, N. & David, P. Diversity spurs diversification in ecological communities. Nat. Commun. 8, 15810 (2017).ADS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Robinson, N. J. & Pfaller, J. B. Sea turtle epibiosis: Global patterns and knowledge gaps. Trends Evol. Ecol. 10, 844021 (2021).
    Google Scholar 
    Conant, T. A., Dutton, P. H., Eguchi, T., Epperly, S. P., Fahy, C. C., Godfrey, M. H., MacPherson, S. L., Possardt, E. E., Schroeder, B. A., Seminoff, J. A., Snover, M. L. Loggerhead sea turtle (Caretta caretta) 2009 status review under the US Endangered Species Act. In Report of the loggerhead biological review Team to the National Marine Fisheries Service. 222, 1–230 (2009).Evans, K. M., Wortley, A. H. & Mann, D. G. An assessment of potential diatom ‘“barcode”’ genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist 158, 349–364 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Hamsher, S. E., Evans, K. M., Mann, D. G., Poulíčková, A. & Saunders, G. W. Barcoding diatoms: Exploring alternatives to COI-5P. Protist 162, 405–422 (2011).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bowen, B. W. & Karl, S. A. Population genetics and phylogeography of sea turtles. Mol Ecol. 16, 4886–4907 (2007).CAS 
    PubMed 
    Article 

    Google Scholar 
    Shanker, K., Ramadevi, J., Choudhury, B. C., Singh, L. & Aggarwal, R. K. Phylogeography of olive ridley turtles (Lepidochelys olivacea) on the east coast of India: implications for conservation theory. Mol. Ecol. 13, 1899–1909 (2004).CAS 
    PubMed 
    Article 

    Google Scholar 
    Pinou, T. et al. Standardizing sea turtle epibiont sampling: Outcomes of the epibiont workshop at the 37th International Sea Turtle Symposium. Mar. Turt. Newsl. 157, 22–32 (2019).
    Google Scholar 
    Ehrhert L., Ogren L. H. Studies in foraging habitats: capturing and handling turtles. In Research and management techniques for the conservation of sea turtles (eds. Eckert, K. L., Bjorndal, K. A., Abreu-Grobois, F. A., Donnelly, M.). IUCN/SSC Marine Turtle Specialist Group. Publication No. 4. (1999).Guillard, R. R. Culture of phytoplankton for feeding marine invertebrates. In Culture of Marine Invertebrate Animals 29–60 (Springer, 1975).Theriot, E. C., Ashworth, M. P., Nakov, T., Ruck, E. & Jansen, R. K. Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling. Mol. Phylogenet. Evol. 89, 28–36 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Lobban, C. S., Ashworth, M. P., Calaor, J. J. & Theriot, E. C. Extreme diversity in fine-grained morphology reveals fourteen new species of conopeate Nitzschia (Bacillariophyta: Bacillariales). Phytotaxa. 401, 199–238 (2019).Article 

    Google Scholar 
    Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. PartitionFinder 2: New methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34, 772–773 (2017).CAS 
    PubMed 

    Google Scholar 
    Lanfear, R., Calcott, B., Kainer, D., Mayer, C. & Stamatakis, A. Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evol. Biol. 14, 1–14 (2014).Article 

    Google Scholar 
    Stamatakis, A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).CAS 
    PubMed 
    Article 

    Google Scholar 
    Chernomor, O., Von Haeseler, A. & Minh, B. Q. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. 65, 997–1008 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aberer, A. J., Kobert, K. & Stamatakis, A. ExaBayes: Massively parallel bayesian tree inference for the whole-genome Era. Mol. Biol. Evol. 31, 2553–2556 (2014).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar  More

  • in

    Grassland changes and adaptive management on the Qinghai–Tibetan Plateau

    Editorial Committee of Vegetation Map China. Vegetation Map of China (1:1000 000) (Geology Press, 2007).Fu, B. et al. Current condition and protection strategies of Qinghai–Tibet Plateau ecological security barrier. Bull. Chin. Acad. Sci. 36, 1298–1306 (2021).
    Google Scholar 
    Zhang, Y. et al. Spatial and temporal variability in the net primary production (NPP) of alpine grassland on Tibetan Plateau from 1982 to 2009. Acta Geogr. Sin. 68, 1197–1211 (2013).
    Google Scholar 
    Bao, C. & Liu, R. Spatiotemporal evolution of the urban system in the Tibetan Plateau. J. Geoinf. Sci. 21, 1330–1340 (2019).
    Google Scholar 
    Miehe, G. et al. The Kobresia pygmaea ecosystem of the Tibetan highlands — origin, functioning and degradation of the world’s largest pastoral alpine ecosystem: Kobresia pastures of Tibet. Sci. Total Environ. 648, 754–771 (2019). This work describes features of K. pygmaea grassland and reveals that overstocking has caused pasture degradation and soil deterioration.Article 

    Google Scholar 
    Liu, Y. et al. Grassland dynamics in responses to climate variation and human activities in China from 2000 to 2013. Sci. Total Environ. 690, 27–39 (2019).Article 

    Google Scholar 
    Cao, J. et al. Grassland degradation on the Qinghai–Tibetan Plateau: reevaluation of causative factors. Rangel. Ecol. Manag. 72, 988–995 (2019).Article 

    Google Scholar 
    Zhao, X. Restoration and Sustainable Management of Degradaded Grassland in the Three Rivers Headwater (Science Press, 2011).Gao, Q. Exploration and Study on Eoclogical Revelization Fuatures in Qiangtang Plateau (China Agriculture Press, 2015).Gu, X. et al. Soil extractable organic C and N contents, methanotrophic activity under warming and degradation in a Tibetan alpine meadow. Agric. Ecosyst. Environ. 278, 6–14 (2019).Article 

    Google Scholar 
    Li, Y. et al. Changes of soil microbial community under different degraded gradients of alpine meadow. Agric. Ecosyst. Environ. 222, 213–222 (2016).Article 

    Google Scholar 
    Wang, W., Wang, Q. & Wang, H. The effect of land management on plant community composition, species diversity, and productivity of alpine Kobersia steppe meadow. Ecol. Res. 21, 181–187 (2005).Article 

    Google Scholar 
    Xu, H., Wang, X. & Zhang, X. Alpine grasslands response to climatic factors and anthropogenic activities on the Tibetan Plateau from 2000 to 2012. Ecol. Eng. 92, 251–259 (2016).Article 

    Google Scholar 
    Yu, L., Tang, L., Wei, D., Mei, M. & Zhou, H. Characteristics and causes of changes of alpine grassland productivity in the source region of Yellow River. Int. Conf. Geoinformatics https://doi.org/10.1109/GEOINFORMATICS.2010.5567879 (2010).Article 

    Google Scholar 
    Yang, Y. et al. Responses of the functional structure of soil microbial community to livestock grazing in the Tibetan alpine grassland. Glob. Chang. Biol. 19, 637–648 (2013). This work shows that soil microbial community functional structure is very sensitive to livestock grazing.Article 

    Google Scholar 
    Gao, Y. Z. et al. Belowground net primary productivity and biomass allocation of a grassland in Inner Mongolia is affected by grazing intensity. Plant Soil 307, 41–50 (2008).Article 

    Google Scholar 
    Dlamini, A. P. et al. Controlling factors of sheet erosion under degraded grasslands in the sloping lands of KwaZulu-Natal, South Africa. Agric. Water Manag. 98, 1711–1718 (2011).Article 

    Google Scholar 
    Niemandt, C. & Greve, M. Fragmentation metric proxies provide insights into historical biodiversity loss in critically endangered grassland. Agric. Ecosyst. Environ. 235, 172–181 (2016).Article 

    Google Scholar 
    Kang, S. C. et al. Review of climate and cryospheric change in the Tibetan Plateau. Environ. Res. Lett. 5, 15101–15101 (2010).Article 

    Google Scholar 
    Shen, H. et al. Effects of simulated N deposition on photosynthesis and productivity of key plants from different functional groups of alpine meadow on Qinghai–Tibetan Plateau. Environ. Pollut. 251, 731–737 (2019).Article 

    Google Scholar 
    Yu, G. R. et al. Stabilization of atmospheric nitrogen deposition in China over the past decade. Nat. Geosci. 12, 424 (2019).Article 

    Google Scholar 
    Lu, C. & Tian, H. Spatial and temporal patterns of nitrogen deposition in China: synthesis of observational data. J. Geophys. Res. 112, D22S05 (2007).
    Google Scholar 
    National Bureau of Statistics of China. China Statistics Yearbook (China Statistics Press, 2020).Mo, X. Sustainable livestock carring capacity and overgrazing rate of grassland over Qinghai–Tibet plateau since 1980. Natl Tibetan Plateau Data Center https://doi.org/10.11888/Socioeco.tpdc.270347 (2020).Article 

    Google Scholar 
    Tian, Y. Y., Jiang, G. H., Zhou, D. Y. & Li, G. Y. Systematically addressing the heterogeneity in the response of ecosystem services to agricultural modernization, industrialization and urbanization in the Qinghai–Tibetan Plateau from 2000 to 2018. J. Clean. Prod. https://doi.org/10.1016/j.jclepro.2020.125323 (2021).Article 

    Google Scholar 
    Yao, Y. et al. Spatiotemporal pattern of gross primary productivity and its covariation with climate in China over the last thirty years. Glob. Chang. Biol. 24, 184–196 (2018).Article 

    Google Scholar 
    Li, L. et al. Current challenges in distinguishing climatic and anthropogenic contributions to alpine grassland variation on the Tibetan Plateau. Ecol. Evol. 8, 5949–5963 (2018). This work finds that large inconsistencies exist in distinguishing the respective contribution of climatic and anthropogenic forces to grassland dynamics.Article 

    Google Scholar 
    Zhong, L., Ma, Y. M., Xue, Y. K. & Piao, S. L. Climate change trends and impacts on vegetation greening over the Tibetan Plateau. J. Geophys. Res. Atmos. 124, 7540–7552 (2019). This work demonstrates that the general increasing trends in vegetation density and greening of the QTP are mainly caused by climate factors, using satellite-derived climate and vegetation data from 1999 to 2014.Article 

    Google Scholar 
    Yang, K. & He, J. China meteorological forcing dataset (1979–2018). Natl Tibetan Plateau Data Center https://doi.org/10.11888/AtmosphericPhysics.tpe.249369.file (2019).Article 

    Google Scholar 
    Xiong, Q. et al. Monitoring the impact of climate change and human activities on grassland vegetation dynamics in the northeastern Qinghai–Tibet Plateau of China during 2000–2015. J. Arid. Land 11, 637–651 (2019).Article 

    Google Scholar 
    Pan, T., Zou, X. T., Liu, Y. J., Wu, S. H. & He, G. M. Contributions of climatic and non-climatic drivers to grassland variations on the Tibetan Plateau. Ecol. Eng. 108, 307–317 (2017).Article 

    Google Scholar 
    Hou, X. 1:1 Million vegetation map of China (National Tibetan Plateau Data Center, 2019).Peng, S. S. et al. Recent change of vegetation growth trend in China. Environ. Res. Lett. 6, 044027 (2011).Article 

    Google Scholar 
    Yuan, W. et al. Increased atmospheric vapor pressure deficit reduces global vegetation growth. Sci. Adv. 5, eaax1396 (2019).Article 

    Google Scholar 
    Zhu, Z. C. et al. Greening of the earth and its drivers. Nat. Clim. Chang. 6, 791 (2016).Article 

    Google Scholar 
    Vermote, E. et al. NOAA climate data record (CDR) of normalized difference vegetation index (NDVI), version 4. NOAA Natl Cent. Environ. Inf. https://doi.org/10.7289/V5PZ56R6 (2014).Article 

    Google Scholar 
    Chen, H. et al. Attribution analyses of changes in alpine grasslands on the Qinghai–Tibetan Plateau. Chin. Sci. Bull. 65, 2406–2418 (2020). This work demonstrates that human activities play an increasingly important role in the restoration of degraded grasslands.Article 

    Google Scholar 
    Shen, M. et al. Evaporative cooling over the Tibetan Plateau induced by vegetation growth. Proc. Natl Acad. Sci. USA 112, 9299–9304 (2015).Article 

    Google Scholar 
    Cai, D. et al. Vegetation dynamics on the Tibetan Plateau (1982–2006): an attribution by ecohydrological diagnostics. J. Clim. 28, 4576–4584 (2015).Article 

    Google Scholar 
    Zhou, W. et al. Grassland degradation remote sensing monitoring and driving factors quantitative assessment in China from 1982 to 2010. Ecol. Indic. 83, 303–313 (2017).Article 

    Google Scholar 
    Liu, Z. et al. Patterns of plant species diversity along an altitudinal gradient and its effect on above-ground biomass in alpine meadows in Qinghai–Tibet Plateau. Biodivers. Sci. 23, 451–462 (2015).Article 

    Google Scholar 
    Harris, R. B. Rangeland degradation on the Qinghai–Tibetan Plateau: a review of the evidence of its magnitude and causes. J. Arid. Environ. 74, 1–12 (2010).Article 

    Google Scholar 
    Lu, S. et al. Basic characteristics of Stipa sareptana var. krylovii communities in China. Chin. J. Plant. Ecol. 44, 1087–1094 (2020).Article 

    Google Scholar 
    Qiao, X. et al. Distribution, community characteristics and classification of Stipa tianschanica var. klemenzii steppe in China. Chin. J. Plant. Ecol. 41, 231–237 (2017).Article 

    Google Scholar 
    Qiao, X., Guo, K., Zhao, L., Yang, Y. & Zhao, H. Distribution, community characteristics and classification of Stipa basiplumosa steppe on Tibetan Plateau. Geogr. Res. 36, 2432–2440 (2017).
    Google Scholar 
    Qiao, X., Guo, K., Zhao, L., Wang, Z. & Liu, C. Community characteristics of Stipa bungeana alliance in China. Chin. J. Plant Ecol. 44, 986–994 (2020).Article 

    Google Scholar 
    Zhu, Y., Qiao, X., Guo, K., Xu, R. & Zhao, L. Distribution, community characteristics and classification of Stipa tianschanica var. gobica steppe in China. Chin. J. Plant Ecol. 42, 785–792 (2018).Article 

    Google Scholar 
    Li, X. R., Jia, X. H. & Dong, G. R. Influence of desertification on vegetation pattern variations in the cold semi-arid grasslands of Qinghai–Tibet plateau, north-west China. J. Arid. Environ. 64, 505–522 (2006).Article 

    Google Scholar 
    Tang, L. et al. Changes in vegetation composition and plant diversity with rangeland degradation in the alpine region of Qinghai–Tibet Plateau. Rangel. J. 37, 107–115 (2015).Article 

    Google Scholar 
    Zhou, X. Chinese Kobresia Meadow (Science Press, 2001).Wang, B. Z. et al. Potential distribution patterns of Stipa bungeana in China and the major factors influencing distribution. Acta Prataculturae Sinica 28, 3–13 (2019).
    Google Scholar 
    Sun, H., Li, W., Zhang, M. & Han, Y. A comprehensive scientific expedition to the Qinghai–Tibet Plateau. Resour. Sci. 8, 22–30 (1986).
    Google Scholar 
    Zhu, F. X. et al. Spatiotemporal variations of annual shallow soil temperature on the Tibetan Plateau during 1983–2013. Clim. Dyn. 51, 2209–2227 (2018).Article 

    Google Scholar 
    Chen, L. T. et al. Changes of carbon stocks in alpine grassland soils from 2002 to 2011 on the Tibetan Plateau and their climatic causes. Geoderma 288, 166–174 (2017).Article 

    Google Scholar 
    Ding, J. et al. Decadal soil carbon accumulation across Tibetan permafrost regions. Nat. Geosci. 10, 420–424 (2017).Article 

    Google Scholar 
    Tian, L. M. et al. Variations in soil nutrient availability across Tibetan grassland from the 1980s to 2010s. Geoderma 338, 197–205 (2019).Article 

    Google Scholar 
    Pepin, N. et al. Elevation-dependent warming in mountain regions of the world. Nat. Clim. Chang. 5, 424–430 (2015).Article 

    Google Scholar 
    Chen, H. et al. The impacts of climate change and human activities on biogeochemical cycles on the Qinghai–Tibetan Plateau. Glob. Chang. Biol. 19, 2940–2955 (2013). This work suggests that warming enhanced NPP and soil respiration but many uncertainties remain.Article 

    Google Scholar 
    Shen, M. G. et al. Plant phenological responses to climate change on the Tibetan Plateau: research status and challenges. Natl Sci. Rev. 2, 454–467 (2015).Article 

    Google Scholar 
    Liu, X. D., Yin, Z. Y., Shao, X. M. & Qin, N. S. Temporal trends and variability of daily maximum and minimum, extreme temperature events, and growing season length over the eastern and central Tibetan Plateau during 1961–2003. J. Geophys. Res. Atmos. https://doi.org/10.1029/2005jd006915 (2006).Article 

    Google Scholar 
    Yang, K. et al. Recent climate changes over the Tibetan Plateau and their impacts on energy and water cycle: a review. Glob. Planet. Change 112, 79–91 (2014). This work reviews the main spatio-temporal characteristics of climate change on the QTP.Article 

    Google Scholar 
    Klein, J. A., Harte, J. & Zhao, X. Q. Experimental warming, not grazing, decreases rangeland quality on the Tibetan Plateau. Ecol. Appl. 17, 541–557 (2007).Article 

    Google Scholar 
    Li, C. et al. Productivity and quality of alpine grassland vary with soil water availability under experimental warming. Front. Plant. Sci. 9, 1790 (2018).Article 

    Google Scholar 
    Peng, A. H. et al. Plant community responses to warming modified by soil moisture in the Tibetan Plateau. Arct. Antarct. Alp. Res. 52, 60–69 (2020).Article 

    Google Scholar 
    Li, F. et al. Leaf area rather than photosynthetic rate determines the response of ecosystem productivity to experimental warming in an alpine steppe. J. Geophys. Res. Biogeosci. 124, 2277–2287 (2019).Article 

    Google Scholar 
    Zong, N. et al. Responses of ecosystem CO2 fluxes to short-term experimental warming and nitrogen enrichment in an alpine meadow, northern Tibet Plateau. Sci. World J. 2013, 415318 (2013).Article 

    Google Scholar 
    Chen, Q., Niu, B., Hu, Y., Luo, T. & Zhang, G. Warming and increased precipitation indirectly affect the composition and turnover of labile-fraction soil organic matter by directly affecting vegetation and microorganisms. Sci. Total Environ. 714, 136787 (2020).Article 

    Google Scholar 
    Wang, X. X. et al. Effects of short-term and long-term warming on soil nutrients, microbial biomass and enzyme activities in an alpine meadow on the Qinghai–Tibet Plateau of China. Soil. Biol. Biochem. 76, 140–142 (2014).Article 

    Google Scholar 
    Jiang, L. L. et al. Plant organic N uptake maintains species dominance under long-term warming. Plant Soil 433, 243–255 (2018).Article 

    Google Scholar 
    Li, N. et al. Short-term effects of temperature enhancement on community structure and biomass of alpine meadow in the Qinghai–Tibet Plateau. Acta Ecol. Sin. 31, 895–905 (2011).
    Google Scholar 
    Jiang, Y., Fan, M. & Zhang, Y. Effect of short-term warming on plant community features of alpine meadow in northern Tibet. Chin. J. Ecol. 36, 616–622 (2017).
    Google Scholar 
    Wang, S. et al. Effects of warming and grazing on soil N availability, species composition, and ANPP in an alpine meadow. Ecology 93, 2365–2376 (2012). This work shows the effects of asymmetric warming and moderate grazing on plant composition, diversity, productivity and their relationships.Article 

    Google Scholar 
    Liu, P. et al. Ambient climate determines the directional trend of community stability under warming and grazing. Glob. Change Biol. 27, 5198–5210 (2021). This work finds that the negative effect of warming on plant diversity disappears with experimental duration, and ambient climate modulates the effects of warming and grazing on productivity stability.Article 

    Google Scholar 
    Zhang, B. et al. Responses of soil microbial communities to experimental warming in alpine grasslands on the Qinghai–Tibet Plateau. PLoS ONE 9, e103859 (2014).Article 

    Google Scholar 
    Chen, X. et al. Effects of warming and nitrogen fertilization on GHG flux in the permafrost region of an alpine meadow. Atmos. Environ. 157, 111–124 (2017).Article 

    Google Scholar 
    Zhang, Y. et al. Effects of grazing and climate warming on plant diversity, productivity and living state in the alpine rangelands and cultivated grasslands of the Qinghai–Tibetan Plateau. Rangel. J. 37, 57–65 (2015).Article 

    Google Scholar 
    Quan, Q. et al. High-level rather than low-level warming destabilizes plant community biomass production. J. Ecol. 109, 1607–1617 (2021).Article 

    Google Scholar 
    Wang, X. et al. Response of greenhouse gases emission fluxes to long-term warming in alpine meadow of northern Tibet. Chin. J. Agrometeorol. 39, 152–161 (2018).
    Google Scholar 
    Klein, J. A., Harte, J. & Zhao, X. Q. Experimental warming causes large and rapid species loss, dampened by simulated grazing, on the Tibetan Plateau. Ecol. Lett. 7, 1170–1179 (2004).Article 

    Google Scholar 
    Zhang, C. H. et al. Recovery of plant species diversity during long-term experimental warming of a species-rich alpine meadow community on the Qinghai–Tibet Plateau. Biol. Conserv. 213, 218–224 (2017).Article 

    Google Scholar 
    Li, X. et al. Responses of biotic interactions of dominant and subordinate species to decadal warming and simulated rotational grazing in Tibetan alpine meadow. Sci. China Life Sci. 61, 849–859 (2018).Article 

    Google Scholar 
    Klein, J. A., Harte, J. & Zhao, X. Q. Dynamic and complex microclimate responses to warming and grazing manipulations. Glob. Chang. Biol. 11, 1440–1451 (2005).Article 

    Google Scholar 
    Chen, J. et al. Warming effects on ecosystem carbon fluxes are modulated by plant functional types. Ecosystems 20, 515–526 (2017).Article 

    Google Scholar 
    Zhang, Y. Q. & Welker, J. M. Tibetan alpine tundra responses to simulated changes in climate: aboveground biomass and community responses. Arct. Alp. Res. 28, 203–209 (1996).Article 

    Google Scholar 
    Liu, H. et al. Shifting plant species composition in response to climate change stabilizes grassland primary production. Proc. Natl Acad. Sci. USA 115, 4051–4056 (2018). This work demonstrates that shifting plant species composition in response to climate change may have stabilized primary production in this high-elevation ecosystem, but also causes a shift from above-ground to below-ground productivity.Article 

    Google Scholar 
    Ganjurjav, H. et al. Differential response of alpine steppe and alpine meadow to climate warming in the central Qinghai–Tibetan Plateau. Agric. For. Meteorol. 223, 233–240 (2016).Article 

    Google Scholar 
    Jiang, F., Wei, X., Kang, B. & Shao, X. Effects of warming on alpine meadow diversity and primary productivity. Acta Agrestia Sin. 27, 298–305 (2019).
    Google Scholar 
    Zong, N. et al. Responses of plant community structure and species composition to warming and N addition in an alpine meadow, northern Tibetan Plateau, China. Chin. J. Appl. Ecol. 27, 3739–3748 (2016).
    Google Scholar 
    Peng, F. et al. Warming-induced shift towards forbs and grasses and its relation to the carbon sequestration in an alpine meadow. Environ. Res. Lett. https://doi.org/10.1088/1748-9326/aa6508 (2017).Article 

    Google Scholar 
    Dorji, T. et al. Grazing and spring snow counteract the effects of warming on an alpine plant community in Tibet through effects on the dominant species. Agric. For. Meteorol. 263, 188–197 (2018).Article 

    Google Scholar 
    Xue, X., Peng, F., You, Q., Xu, M. & Dong, S. Belowground carbon responses to experimental warming regulated by soil moisture change in an alpine ecosystem of the Qinghai–Tibet Plateau. Ecol. Evol. 5, 4063–4078 (2015).Article 

    Google Scholar 
    Jing, X. et al. No temperature acclimation of soil extracellular enzymes to experimental warming in an alpine grassland ecosystem on the Tibetan Plateau. Biogeochemistry 117, 39–54 (2014).Article 

    Google Scholar 
    Yu, C. Q., Shen, Z. X., Zhang, X. Z., Sun, W. & Fu, G. Response of soil C and N, dissolved organic C and N, and inorganic N to short-term experimental warming in an alpine meadow on the Tibetan Plateau. Sci. World J. 2014, 152576 (2014).
    Google Scholar 
    Zhang, Y. et al. Simulated warming enhances the responses of microbial N transformations to reactive N input in a Tibetan alpine meadow. Environ. Int. 141, 105795 (2020).Article 

    Google Scholar 
    Jia, J. et al. Climate warming alters subsoil but not topsoil carbon dynamics in alpine grassland. Glob. Chang. Biol. 25, 4383–4393 (2019).Article 

    Google Scholar 
    Ding, X. L. et al. Warming increases microbial residue contribution to soil organic carbon in an alpine meadow. Soil. Biol. Biochem. 135, 13–19 (2019).Article 

    Google Scholar 
    Guan, S. et al. Climate warming impacts on soil organic carbon fractions and aggregate stability in a Tibetan alpine meadow. Soil. Biol. Biochem. 116, 224–236 (2018).Article 

    Google Scholar 
    Rui, Y. C. et al. Warming and grazing affect soil labile carbon and nitrogen pools differently in an alpine meadow of the Qinghai–Tibet Plateau in China. J. Soils Sediment. 11, 903–914 (2011).Article 

    Google Scholar 
    Heng, T., Wu, J., Xie, S. & Wu, M. The responses of soil C and N, microbial biomass C or N under alpine meadow of Qinghai–Tibet Plateau to the change of temperature and precipitation. Chin. Agric. Sci. Bull. 27, 425–430 (2011).
    Google Scholar 
    Li, N., Wang, G., Yang, Y., Gao, Y. & Liu, G. Plant production, and carbon and nitrogen source pools, are strongly intensified by experimental warming in alpine ecosystems in the Qinghai–Tibet Plateau. Soil. Biol. Biochem. 43, 942–953 (2011).Article 

    Google Scholar 
    Zhao, J. X. et al. Increased precipitation offsets the negative effect of warming on plant biomass and ecosystem respiration in a Tibetan alpine steppe. Agric. For. Meteorol. https://doi.org/10.1016/j.agrformet.2019.107761 (2019). This work shows that increased precipitation offsets the negative effect of warming on plant biomass and ecosystem respiration in a Tibetan alpine steppe.Article 

    Google Scholar 
    Wu, H. et al. Effects of increased precipitation combined with nitrogen addition and increased temperature on methane fluxes in alpine meadows of the Tibetan Plateau. Sci. Total Environ. 705, 135818 (2020).Article 

    Google Scholar 
    Shi, F. S., Chen, H., Chen, H. F., Wu, Y. & Wu, N. The combined effects of warming and drying suppress CO2 and N2O emission rates in an alpine meadow of the eastern Tibetan Plateau. Ecol. Res. 27, 725–733 (2012).Article 

    Google Scholar 
    Fu, G., Zhang, H. R. & Sun, W. Response of plant production to growing/non-growing season asymmetric warming in an alpine meadow of the northern Tibetan Plateau. Sci. Total Environ. 650, 2666–2673 (2019).Article 

    Google Scholar 
    Xiong, Q. L. et al. Warming and nitrogen deposition are interactive in shaping surface soil microbial communities near the alpine timberline zone on the eastern Qinghai–Tibet Plateau, southwestern China. Appl. Soil. Ecol. 101, 72–83 (2016).Article 

    Google Scholar 
    Wang, C. et al. Responses of plant leaf traits to simulated rainfall changes in alpine region. Acta Ecol. Sin. 41, 1–13 (2021).Article 

    Google Scholar 
    Zhang, K. et al. Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the Tibetan Plateau. Front. Microbiol. 7, 1032 (2016).
    Google Scholar 
    Evans, R. D. & Ehleringer, J. R. Water and nitrogen dynamics in an arid woodland. Oecologia 99, 233–242 (1994).Article 

    Google Scholar 
    Swap, R. J., Aranibar, J. N., Dowty, P. R., Gilhooly, W. P. III & Macko, S. A. Natural abundance of 13C and 15N in C3 and C4 vegetation of southern Africa: patterns and implications. Glob. Chang. Biol. 10, 350–358 (2004).Article 

    Google Scholar 
    Jia, Y. et al. Spatial and decadal variations in inorganic nitrogen wet deposition in China induced by human activity. Sci. Rep. 4, 3763–3763 (2014).Article 

    Google Scholar 
    Liu, Y. W., Xu, R., Wang, Y. S., Pan, Y. P. & Piao, S. L. Wet deposition of atmospheric inorganic nitrogen at five remote sites in the Tibetan Plateau. Atmos. Chem. Phys. 15, 11683–11700 (2015).Article 

    Google Scholar 
    Wang, W. et al. Atmospheric nitrogen deposition to a southeast Tibetan forest ecosystem. Atmosphere https://doi.org/10.3390/atmos11121331 (2020).Article 

    Google Scholar 
    Zou, X. et al. Ice-core based assessment of nitrogen deposition in the central Tibetan Plateau over the last millennium. Sci. Total Environ. https://doi.org/10.1016/j.scitotenv.2021.152692 (2022).Article 

    Google Scholar 
    Aerts, R., Wallen, B. & Malmer, N. Growth-limiting nutrients in sphagnum-dominated bogs subject to low and high amospheric nitrogen supply. J. Ecol. 80, 131–140 (1992).Article 

    Google Scholar 
    Bai, Y. F. et al. Tradeoffs and thresholds in the effects of nitrogen addition on biodiversity and ecosystem functioning: evidence from Inner Mongolia grasslands. Glob. Chang. Biol. 16, 358–372 (2010).Article 

    Google Scholar 
    Du, Y. Population statistics of Qinghai–Tibet Plateau (1952–2016) (National Tibetan Plateau Data Center, 2019).Zhang, Y. J., Zhang, X. Q., Wang, X. Y., Liu, N. & Kan, H. M. Establishing the carrying capacity of the grasslands of China: a review. Rangel. J. 36, 1–9 (2014).Article 

    Google Scholar 
    Bardgett, R. D. et al. Combatting global grassland degradation. Nat. Rev. Earth Environ. 2, 720–735 (2021). This work shows that socio-ecological solutions are needed to combat degradation and promote restoration.Article 

    Google Scholar 
    Liu, M. et al. Effects of rotational and continuous overgrazing on newly assimilated C allocation. Biol. Fertil. Soils 57, 193–202 (2021).Article 

    Google Scholar 
    Yang, X. X. et al. Different responses of soil element contents and their stoichiometry (C:N:P) to yak grazing and Tibetan sheep grazing in an alpine grassland on the eastern Qinghai–Tibetan Plateau. Agric. Ecosyst. Environ. https://doi.org/10.1016/j.agee.2019.106628 (2019).Article 

    Google Scholar 
    Lin, B., Zhao, X. R., Zheng, Y., Qi, S. & Liu, X. Z. Effect of grazing intensity on protozoan community, microbial biomass, and enzyme activity in an alpine meadow on the Tibetan Plateau. J. Soils Sediment. 17, 2752–2762 (2017).Article 

    Google Scholar 
    Ma, W. M., Ding, K. Y. & Li, Z. W. Comparison of soil carbon and nitrogen stocks at grazing-excluded and yak grazed alpine meadow sites in Qinghai–Tibetan Plateau, China. Ecol. Eng. 87, 203–211 (2016).Article 

    Google Scholar 
    Li, W. et al. Effects of grazing regime on vegetation structure, productivity, soil quality, carbon and nitrogen storage of alpine meadow on the Qinghai–Tibetan Plateau. Ecol. Eng. 98, 123–133 (2017).Article 

    Google Scholar 
    Sun, J. et al. Effects of grazing regimes on plant traits and soil nutrients in an alpine steppe, northern Tibetan Plateau. PLoS ONE 9, e108821 (2014).Article 

    Google Scholar 
    Niu, K. C., He, J. S. & Lechowicz, M. J. Grazing-induced shifts in community functional composition and soil nutrient availability in Tibetan alpine meadows. J. Appl. Ecol. 53, 1554–1564 (2016).Article 

    Google Scholar 
    Luan, J. W. et al. Different grazing removal exclosures effects on soil C stocks among alpine ecosystems in east Qinghai–Tibet Plateau. Ecol. Eng. 64, 262–268 (2014).Article 

    Google Scholar 
    Wei, D. et al. Responses of CO2, CH4 and N2O fluxes to livestock exclosure in an alpine steppe on the Tibetan Plateau, China. Plant Soil 359, 45–55 (2012).Article 

    Google Scholar 
    Shen, H. et al. Grazing enhances plant photosynthetic capacity by altering soil nitrogen in alpine grasslands on the Qinghai–Tibetan Plateau. Agric. Ecosyst. Environ. 280, 161–168 (2019).Article 

    Google Scholar 
    Jiang, L. et al. Grazing modifies inorganic and organic nitrogen uptake by coexisting plant species in alpine grassland. Biol. Fertil. Soils 52, 211–221 (2016).Article 

    Google Scholar 
    Sun, Y., Schleuss, P. M., Pausch, J., Xu, X. L. & Kuzyakov, Y. Nitrogen pools and cycles in Tibetan Kobresia pastures depending on grazing. Biol. Fertil. Soils 54, 569–581 (2018).Article 

    Google Scholar 
    Chen, B. et al. The impact of climate change and anthropogenic activities on alpine grassland over the Qinghai–Tibet Plateau. Agric. For. Meteorol. 189-190, 11–18 (2014).Article 

    Google Scholar 
    Wang, Z. Q. et al. Quantitative assess the driving forces on the grassland degradation in the Qinghai–Tibet Plateau, in China. Ecol. Inform. 33, 32–44 (2016).Article 

    Google Scholar 
    Huang, K. et al. The influences of climate change and human activities on vegetation dynamics in the Qinghai–Tibet Plateau. Remote Sens. 8, 876 (2016).Article 

    Google Scholar 
    Li, L. et al. Increasing sensitivity of alpine grasslands to climate variability along an elevational gradient on the Qinghai–Tibet Plateau. Sci. Total Environ. 678, 21–29 (2019).Article 

    Google Scholar 
    Wang, Z. et al. Vegetation expansion on the Tibetan Plateau and its relationship with climate change. Remote. Sens. https://doi.org/10.3390/rs12244150 (2020).Article 

    Google Scholar 
    Wu, J. et al. Disentangling climatic and anthropogenic contributions to nonlinear dynamics of alpine grassland productivity on the Qinghai–Tibetan Plateau. J. Environ. Manag. 281, 111875 (2021).Article 

    Google Scholar 
    Fu, G., Shen, Z. X. & Zhang, X. Z. Increased precipitation has stronger effects on plant production of an alpine meadow than does experimental warming in the northern Tibetan Plateau. Agric. For. Meteorol. 249, 11–21 (2018).Article 

    Google Scholar 
    Hu, Y. et al. Effect of increasing precipitation and warming on microbial community in Tibetan alpine steppe. Environ. Res. 189, 109917 (2020).Article 

    Google Scholar 
    Ma, Z. et al. Climate warming reduces the temporal stability of plant community biomass production. Nat. Commun. 8, 15378 (2017).Article 

    Google Scholar 
    Bai, W., Xi, J. & Wang, G. Effects of short-term warming and nitrogen addition on CO2 emission during growing season in an alpine swamp meadow ecosystem of Qinghai–Tibetan Plateau. Chin. J. Ecol. 38, 927–936 (2019).
    Google Scholar 
    Bai, W., Wang, G. X., Xi, J. Y., Liu, Y. W. & Yin, P. S. Short-term responses of ecosystem respiration to warming and nitrogen addition in an alpine swamp meadow. Eur. J. Soil Biol. 92, 16–23 (2019).Article 

    Google Scholar 
    Ge, Y. et al. Effects of warming and nitrogen addition on plant community structure and species diversity of alpine meadow in northern Tibet. Ecol. Environ. Sci. 28, 2185–2191 (2019).
    Google Scholar 
    Zong, N. et al. Effects of warming and nitrogen addition on community production and biomass allocation in an alpine meadow. Chin. J. Appl. Ecol. 29, 59–67 (2018).
    Google Scholar 
    Zhu, X. X. et al. Effects of warming, grazing/cutting and nitrogen fertilization on greenhouse gas fluxes during growing seasons in an alpine meadow on the Tibetan Plateau. Agric. For. Meteorol. 214, 506–514 (2015).Article 

    Google Scholar 
    Fu, G. et al. Clipping alters the response of biomass production to experimental warming: a case study in an alpine meadow on the Tibetan Plateau, China. J. Mt. Sci. 12, 935–942 (2015).Article 

    Google Scholar 
    Chen, S. P. et al. Plant diversity enhances productivity and soil carbon storage. Proc. Natl Acad. Sci. USA. 115, 4027–4032 (2018).Article 

    Google Scholar 
    Wu, J. S. et al. Effects of livestock exclusion and climate change on aboveground biomass accumulation in alpine pastures across the northern Tibetan Plateau. Chin. Sci. Bull. 59, 4332–4340 (2014).Article 

    Google Scholar 
    Sun, J., Cheng, G. W., Li, W. P., Sha, Y. K. & Yang, Y. C. On the variation of NDVI with the principal climatic elements in the Tibetan Plateau. Remote Sens. 5, 1894–1911 (2013).Article 

    Google Scholar 
    Sun, J. et al. Reconsidering the efficiency of grazing exclusion using fences on the Tibetan Plateau. Sci. Bull. 65, 1405–1414 (2020). This work finds that fencing enclosures lead to some negative impacts, such as hindering wildlife movement.Article 

    Google Scholar 
    Yu, C. et al. Grazing exclusion to recover degraded alpine pastures needs scientific assessments across the northern Tibetan Plateau. Sustainability https://doi.org/10.3390/su8111162 (2016).Article 

    Google Scholar 
    Wu, J. & Wang, X. Effect of enclosure ages on community characters and biomas of the degraded alpine steppe at the northern Tibet. Acta Agrestia Sin. 25, 261–266 (2017).
    Google Scholar 
    Zhao, J. X., Luo, T. X., Li, R. C., Li, X. & Tian, L. H. Grazing effect on growing season ecosystem respiration and its temperature sensitivity in alpine grasslands along a large altitudinal gradient on the central Tibetan Plateau. Agric. For. Meteorol. 218, 114–121 (2016).Article 

    Google Scholar 
    Deng, L., Sweeney, S. & Shangguan, Z. P. Grassland responses to grazing disturbance: plant diversity changes with grazing intensity in a desert steppe. Grass Forage Sci. 69, 524–533 (2014).Article 

    Google Scholar 
    Yuan, Z., Epstein, H. & Li, G. Grazing exclusion did not affect soil properties in alpine meadows in the Tibetan permafrost region. Ecol. Eng. https://doi.org/10.1016/j.ecoleng.2019.105657 (2020).Article 

    Google Scholar 
    Zhang, W. et al. Effects of banning grazing and delaying grazing on species diversity and biomass of alpine meadow in northern Tibet. J. Agric. Sci. Technol. 15, 143–149 (2013).
    Google Scholar 
    Miao, F., Guo, Y., Miao, P., Guo, Z. & Shen, Y. The northeast edge of Qinghai–Tibet Plateau area of alpine meadow community characteristics respond to nurture. Acta Prataculture Sin. 21, 11–16 (2012).
    Google Scholar 
    Lu, X. et al. Short-term grazing exclusion has no impact on soil properties and nutrients of degraded alpine grassland in Tibet, China. Solid Earth 6, 1195–1205 (2015).Article 

    Google Scholar 
    Gao, Y. H., Zeng, X. Y., Schumann, M. & Chen, H. Effectiveness of exclosures on restoration of degraded alpine meadow in the eastern Tibetan Plateau. Arid. Land. Res. Manag. 25, 164–175 (2011).Article 

    Google Scholar 
    Yao, X. X. et al. Effects of long term fencing on biomass, coverage, density, biodiversity and nutritional values of vegetation community in an alpine meadow of the Qinghai–Tibet Plateau. Ecol. Eng. 130, 80–93 (2019).Article 

    Google Scholar 
    Chen, W., Chang, H. & Liu, R. Fractal features of soil particle size distributions and their implications for indicating enclosure management in a semiarid grassland ecosystem. Pol. J. Ecol. 68, 132–144 (2020).
    Google Scholar 
    Smith, D., King, R. & Allen, B. L. Impacts of exclusion fencing on target and non-target fauna: a global review. Biol. Rev. 95, 1590–1606 (2020).Article 

    Google Scholar 
    Zhang, Y. et al. Assessment of effectiveness of nature reserves on the Tibetan Plateau based on net primary production and the large sample comparison method. J. Geogr. Sci. 26, 27–44 (2016).Article 

    Google Scholar 
    Hu, J. Research on the status quo and problems of natural reserve construction in Qinghai–Tibet Plateau. Environ. Dev. 32, 204–206 (2020).
    Google Scholar 
    Shao, Q., Fan, J., Liu, J., Cao, W. & Liu, L. Target-based assessment on effects of first-stage ecological conservation and restoration project in three-river source region, China and policy recommendations. Bull. Chin. Acad. Sci. 32, 35–44 (2017).
    Google Scholar 
    Liu, F. & Zeng, Y. N. Spatial–temporal change in vegetation net primary productivity and its response to climate and human activities in Qinghai Plateau in the past 16 years. Acta Ecol. Sin. 39, 1528–1540 (2019).
    Google Scholar 
    Zhang, Y., Wu, X., Qi, W., Li, S. & Bai, W. Characteristics and protection effectiveness of nature reserves on the Tibetan Plateau, China. Resources. Science 37, 1455–1464 (2015).
    Google Scholar 
    Buckley, M. C. & Crone, E. E. Negative off-site impacts of ecological restoration: understanding and addressing the conflict. Conserv. Biol. 22, 1118–1124 (2008).Article 

    Google Scholar 
    Cao, S. X. & Zhang, J. Political risks arising from the impacts of large-scale afforestation on water resources of the Tibetan Plateau. Gondwana Res. 28, 898–903 (2015).Article 

    Google Scholar 
    Li, Y. & Li, W. Why “Balance of Forage and Livestock” system failed to reach sustainable grassland utilization. China Agric. Univ. J. Soc. Sci. Ed. 29, 124–131 (2012).
    Google Scholar 
    Du, S. A Study on the Satisfaction Degree of Herdsmen’s Income and Grassland Ecological Compensation Policy. Master thesis, Lanzhou Univ. (2019).Yu, H., Wang, G., Yang, Y. & Lü, Y. Concept of grassland green carrying capacity and its application framework in national park. Acta Ecol. Sin. 40, 7248–7254 (2020).
    Google Scholar 
    Deng, Y. & Li, C. The investigation and research about the Farmland Retirement and Environment Project in the Yangtze River headwaters area. Ecol. Econ. 2, 77–80 (2006).
    Google Scholar 
    Zhou, Q. et al. Analysis on the relationship between grassland area and forage-livestock balance in Qinghai–Tibet Plateau. Chin. J. Grassl. 41, 110–117 (2019).
    Google Scholar 
    Li, Y. et al. Awareness and reaction of herdsmen to the policy of returning grazing land to grasslands in the Changtang Plateau,Tibet. Pratacultural Sci. 30, 788–794 (2013).
    Google Scholar 
    Fan, J. et al. Third pole national park group construction is scientific choice for implementing strategy of major function zoning and green development in Tibet, China. Bull. Chin. Acad. Sci. 32, 932–944 (2017).
    Google Scholar 
    Xu, Z., Cheng, S. & Gao, L. Impacts of herders sedentarization on regional spatial heterogeneity and grassland ecosystem change in pastoral area. J. Arid. Land. Resour. Environ. 31, 8–13 (2017).
    Google Scholar 
    Ptackova, J. Sedentarisation of Tibetan nomads in China: implementation of the Nomadic settlement project in the Tibetan Amdo area; Qinghai and Sichuan Provinces. Pastoralism https://doi.org/10.1186/2041-7136-1-4 (2011).Article 

    Google Scholar 
    Weber, K. T. & Horst, S. Desertification and livestock grazing: the roles of sedentarization, mobility and rest. Pastoralism https://doi.org/10.1186/2041-7136-1-19 (2011).Article 

    Google Scholar 
    Zhang, J. et al. Ecological consequence of nomad settlement policy in the pasture area of Qinghai–Tibetan Plateau: from plant and soil perspectives. J. Environ. Manage. https://doi.org/10.1016/j.jenvman.2020.110114 (2020).Article 

    Google Scholar 
    Li, C. X., de Jong, R., Schmid, B., Wulf, H. & Schaepman, M. E. Spatial variation of human influences on grassland biomass on the Qinghai–Tibetan Plateau. Sci. Total Environ. 665, 678–689 (2019).Article 

    Google Scholar 
    Kuang, W. Dataset of Urban Distribution, Urban Population and Built-up Area in Tibetan Plateau (2000–2015) (National Tibetan Plateau Data Center, 2021).Tian, L. & Chen, J. Urban expansion inferenced by ecosystem production on the Qinghai–Tibet plateau. Environ. Res. Lett. https://doi.org/10.1088/1748-9326/ac3178 (2022).Article 

    Google Scholar 
    Liu, Y. & Lu, C. Quantifying grass coverage trends to identify the hot plots of grassland degradation in the Tibetan Plateau during 2000–2019. Int. J. Environ. Res. Public Health https://doi.org/10.3390/ijerph18020416 (2021).Article 

    Google Scholar 
    Tang, L. et al. Warming counteracts grazing effects on the functional structure of the soil microbial community in a Tibetan grassland. Soil. Biol. Biochem. 134, 113–121 (2019).Article 

    Google Scholar 
    Zhong, L. Tourism Planning Case in Tibetan Plateau (China Tourism Press, 2018).La, M. Discussion of the coordinated development of tourism development and ecological Environment Protection in Tibetan. Soc. Sci. Res. 6, 118–120, (2013).
    Google Scholar 
    Zhuang, M. et al. Opportunities for household energy on the Qinghai–Tibet Plateau in line with United Nations’ Sustainable Development Goals. Renew. Sustain. Energy Rev. https://doi.org/10.1016/j.rser.2021.110982 (2021).Article 

    Google Scholar 
    Ruess, R. W. & Mcnaughton, S. J. Grazing and the dynamics of nutrient and energy regulated microbial processes in the serengeti grasslands. Oikos 49, 101–110 (1987).Article 

    Google Scholar 
    Li, M. et al. Changes in plant species richness distribution in Tibetan alpine grasslands under different precipitation scenarios. Glob. Ecol. Conserv. 21, 13 (2020).
    Google Scholar 
    Wang, Z. et al. Quantitative assess the driving forces on the grassland degradation in the Qinghai–Tibet Plateau, in China. Ecol. Inform. 33, 32–44 (2016).Article 

    Google Scholar 
    Muñoz Sabater, J. ERA5-Land monthly averaged data from 1981 to present, Copernicus Climate Change Service (C3S) Climate Data Store (CDS), https://doi.org/10.24381/cds.68d2bb30 (2019).Abatzoglou, J. T., Dobrowski, S. Z., Parks, S. A. & Hegewisch, K. C. Terraclimate, a high-resolution global dataset of monthly climate and climatic water balance from 1958–2015. Sci. Data 5, 170191 (2018).Article 

    Google Scholar  More

  • in

    Changes in limiting factors for forager population dynamics in Europe across the last glacial-interglacial transition

    Metcalf, C. J. & Pavard, S. Why evolutionary biologists should be demographers. Trends Ecol. Evol. 22, 205–212 (2007).PubMed 
    Article 

    Google Scholar 
    French, J. C., Riris, P., Fernandez-Lopez de Pablo, J., Lozano, S. & Silva, F. A manifesto for palaeodemography in the twenty-first century. Philos. Trans. R. Soc. Lond. B Biol. Sci. 376, 20190707 (2021).PubMed 
    Article 

    Google Scholar 
    French, J. C. Demography and the Palaeolithic archaeological record. J. Archaeol. Method Th. 23, 150–199 (2016).Article 

    Google Scholar 
    Henrich, J. Demography and cultural evolution: how adaptive cultural processes can produce maladaptive losses – The Tasmanian case. Am. Antiquity 69, 197–214 (2004).Article 

    Google Scholar 
    Powell, A., Shennan, S. & Thomas, M. G. Late Pleistocene demography and the appearance of modern human behavior. Science 324, 1298–1301 (2009).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Shennan, S. Demography and cultural innovation: a model and its implications for the emergence of modern human culture. Camb. Archaeol. J. 11, 5–16 (2001).Article 

    Google Scholar 
    Jorgensen, E. K. The palaeodemographic and environmental dynamics of prehistoric Arctic Norway: an overview of human-climate covariation. Quat. Int. 549, 36–51 (2020).Article 

    Google Scholar 
    Jorgensen, E. K. & Riede, F. Convergent catastrophes and the termination of the Arctic Norwegian Stone Age: a multi-proxy assessment of the demographic and adaptive responses of mid-Holocene collectors to biophysical forcing. Holocene 29, 1782–1800 (2019).ADS 
    Article 

    Google Scholar 
    Riede, F. Lateglacial and Postglacial Pioneers in Northern Europe (Archaeopress, 2014).Tallavaara, M. & Seppä, H. Did the mid-Holocene environmental changes cause the boom and bust of hunter-gatherer population size in eastern Fennoscandia? Holocene 22, 215–225 (2011).ADS 
    Article 

    Google Scholar 
    Kavanagh, P. H. et al. Hindcasting global population densities reveals forces enabling the origin of agriculture. Nat. Hum. Behav. 2, 478–484 (2018).PubMed 
    Article 

    Google Scholar 
    Tallavaara, M., Luoto, M., Korhonen, N., Jarvinen, H. & Seppa, H. Human population dynamics in Europe over the Last Glacial Maximum. Proc. Natl Acad. Sci. USA 112, 8232–8237 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Bliege Bird, R. & Codding, B. F. Promise and peril of ecological and evolutionary modelling using cross-cultural datasets. Nat. Ecol. Evol. 6, 1–3 (2021).Hamilton, M. J. & Tallavaara, M. Statistical inference, scale and noise in comparative anthropology. Nat. Ecol. Evol. 6, 122 (2022).PubMed 
    Article 

    Google Scholar 
    Gurven, M. D. & Davison, R. J. Periodic catastrophes over human evolutionary history are necessary to explain the forager population paradox. Proc. Natl Acad. Sci. USA 116, 12758–12766 (2019).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Tallavaara, M. & Jorgensen, E. K. Why are population growth rate estimates of past and present hunter-gatherers so different? Philos. T R Soc. B 376, 20190708 (2021).Blackman, F. F. Optima and limiting factors. With two diagrams in the text. Ann. Bot. Lond. 19, 281–296 (1905).Article 

    Google Scholar 
    Maier, A. et al. Cultural evolution and environmental change in Central Europe between 40 and 15 ka. Quat. Int. 581-582, 225–240 (2021).Article 

    Google Scholar 
    Zhu, D., Galbraith, E. D., Reyes-Garcia, V. & Ciais, P. Global hunter-gatherer population densities constrained by influence of seasonality on diet composition. Nat. Ecol. Evol. 5, 1536 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Binford, L. R. Archaeology as anthropology. Am. Antiquity 28, 217–225 (1962).Article 

    Google Scholar 
    Lowe, J. J. et al. Synchronisation of palaeoenvironmental events in the North Atlantic region during the Last Termination: a revised protocol recommended by the INTIMATE group. Quat. Sci. Rev. 27, 6–17 (2008).ADS 
    Article 

    Google Scholar 
    Bocquet-Appel, J. P., Demars, P. Y., Noiret, L. & Dobrowsky, D. Estimates of upper Palaeolithic meta-population size in Europe from archaeological data. J. Archaeol. Sci. 32, 1656–1668 (2005).Article 

    Google Scholar 
    Fort, J., Pujol, T. & Cavalli-Sforza, L. L. Palaeolithic populations and waves of advance (Human range expansions). Camb. Archaeol. J. 14, 53–61 (2004).Article 

    Google Scholar 
    Schmidt, I. et al. Approaching prehistoric demography: proxies, scales and scope of the Cologne Protocol in European contexts. Philos. Trans. R. Soc. Lond. B Biol. Sci. 376, 20190714 (2021).PubMed 
    Article 

    Google Scholar 
    de Pablo, J. F. L. et al. Palaeodemographic modelling supports a population bottleneck during the Pleistocene-Holocene transition in Iberia. Nat. Commun. 10, 1872 (2019).Binford, L. R. Constructing Frames of Reference: An Analytical Method for Archaeological Theory Building Using Ethnographic and Environmental Data Sets. (Univ. California Press, 2019).Johnson, A. L. Exploring adaptive variation among hunter-gatherers with Binford’s frames of reference. J. Archaeol. Res. 22, 1–42 (2014).Article 

    Google Scholar 
    Graham, M. H. Confronting multicollinearity in ecological multiple regression. Ecology 84, 2809–2815 (2003).Article 

    Google Scholar 
    Tallavaara, M., Eronen, J. T. & Luoto, M. Productivity, biodiversity, and pathogens influence the global hunter-gatherer population density. Proc. Natl Acad. Sci. USA 115, 1232–1237 (2018).CAS 
    PubMed 
    Article 

    Google Scholar 
    Cade, B. S. & Noon, B. R. A gentle introduction to quantile regression for ecologists. Front Ecol. Environ. 1, 412–420 (2003).Article 

    Google Scholar 
    Cade, B. S., Terrell, J. W. & Schroeder, R. L. Estimating effects of limiting factors with regression quantiles. Ecology 80, 311–323 (1999).Article 

    Google Scholar 
    Burman, P., Chow, E. & Nolan, D. A cross-validatory method for dependent data. Biometrika 81, 351–358 (1994).MathSciNet 
    MATH 
    Article 

    Google Scholar 
    Burke, K. D. et al. Differing climatic mechanisms control transient and accumulated vegetation novelty in Europe and eastern North America. Philos. Trans. R. Soc. Lond. B Biol. Sci. 374, 20190218 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Currie, D. J. Energy and large-scale patterns of animal-species and plant-species richness. Am. Nat. 137, 27–49 (1991).Article 

    Google Scholar 
    Franklin, J. Mapping Species Distributions: Spatial Inference and Prediction (Cambridge Univ. Press, 2010).Harcourt, A. Human Biogeography (Univ. California Press, 2012).Marlowe, F. W. Hunter-gatherers and human evolution. Evol. Anthropol. 14, 54–67 (2005).Article 

    Google Scholar 
    Belovsky, G. E. An optimal foraging-based model of hunter-gatherer population-dynamics. J. Anthropol. Archaeol. 7, 329–372 (1988).Article 

    Google Scholar 
    Williams, J. W. & Jackson, S. T. Novel climates, no-analog communities, and ecological surprises. Front. Ecol. Environ. 5, 475–482 (2007).Article 

    Google Scholar 
    Ohlemuller, R. Climate. Running out of climate space. Science 334, 613–614 (2011).ADS 
    PubMed 
    Article 

    Google Scholar 
    Williams, J. W., Jackson, S. T. & Kutzbach, J. E. Projected distributions of novel and disappearing climates by 2100 AD. Proc. Natl Acad. Sci. USA 104, 5738–5742 (2007).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Warren, D. L., Glor, R. E. & Turelli, M. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution 62, 2868–2883 (2008).PubMed 
    Article 

    Google Scholar 
    Broennimann, O. et al. Measuring ecological niche overlap from occurrence and spatial environmental data. Glob. Ecol. Biogeogr. 21, 481–497 (2012).Article 

    Google Scholar 
    Warren, D. L., Cardillo, M., Rosauer, D. F. & Bolnick, D. I. Mistaking geography for biology: inferring processes from species distributions. Trends Ecol. Evol. 29, 572–580 (2014).PubMed 
    Article 

    Google Scholar 
    Wobst, H. M. The archaeo-ethnology of hunter-gatherers or the tyranny of the ethnographic record in archaeology. Am Antiquity 43, 303–309 (1978).Maier, A. et al. Demographic estimates of hunter-gatherers during the Last Glacial Maximum in Europe against the background of palaeoenvironmental data. Quat. Int. 425, 49–61 (2016).Article 

    Google Scholar 
    Riede, F. Oxford Handbook of the Archaeology and Anthropology of Hunter-Gatherers (Oxford Univ. Press, 2014).Jochim, M., Herhahn, C. & Starr, H. The Magdalenian colonization of southern Germany. Am. Anthropol. 101, 129–142 (1999).Article 

    Google Scholar 
    Arts, N. & Deeben, J. On the Northwestern Border of Late Magdalenian Territory: Ecology and Archaeology of Early Late Glacial Band Societies in Northwestern Europe. In Late Glacial in Central Europe. Culture and Environment. (eds Burdukiewicz, J. M. & Kobusiewicz, M.) (Polska Akademia Nauk, Warszawa 1987).Maier, A. Population and settlement dynamics from the Gravettian to the Magdalenian. Mitteilungen der Ges. f.ür. Urgesch. 26, 83–101 (2017).
    Google Scholar 
    Maier, A., Liebermann, C. & Pfeifer, S. J. Beyond the Alps and Tatra Mountains-the 20-14 ka repopulation of the northern mid-latitudes as inferred from palimpsests deciphered with keys from Western and Central Europe. J. Paleolit. Archaeol. 3, 398–452 (2020).Article 

    Google Scholar 
    Gamble, C., Davies, W., Pettitt, P. & Richards, M., Climate change. and evolving human diversity in Europe during the last glacial. Philos. Trans. R. Soc. Lond. B Biol. Sci. 359, 243–253 (2004).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Housley, R. A., Gamble, C. S., Street, M. & Pettitt, P. Proceedings of the Prehistoric Society. (Cambridge Univ. Press).Bellwood, P. S. First Farmers: the Origins of Agricultural Societies. (Blackwell, Oxford 2005).d’Errico, F. et al. The origin and evolution of sewing technologies in Eurasia and North America. J. Hum. Evol. 125, 71–86 (2018).PubMed 
    Article 

    Google Scholar 
    Moseler, F. Brandstrukturen im späten Magdalénien: Betrieb, Nutzung und Funktion (Verlag des Römisch-Germanischen Zentralmuseums, 2020).Simova, I. & Storch, D. The enigma of terrestrial primary productivity: measurements, models, scales and the diversity-productivity relationship. Ecography 40, 239–252 (2017).Rosenzweig, M. L. Net primary productivity of terrestrial communities – prediction from climatological data. Am. Nat. 102, 67 (1968).Article 

    Google Scholar 
    Jensen, H. J. & Møberg, T. Et røgeri fra ældre stenalder ved Bølling Sø? Midtjyske Fortaellinger 2007, 51–62 (2008).Holst, D. Hazelnut economy of early Holocene hunter-gatherers: a case study from Mesolithic Duvensee, northern Germany. J. Archaeol. Sci. 37, 2871–2880 (2010).Article 

    Google Scholar 
    Boethius, A. Something rotten in Scandinavia: the world’s earliest evidence of fermentation. J. Archaeol. Sci. 66, 169–180 (2016).Article 

    Google Scholar 
    Dyson‐Hudson, R. & Smith, E. A. Human territoriality: an ecological reassessment. Am. Anthropol. 80, 21–41 (1978).Article 

    Google Scholar 
    Finlayson, C. The water optimisation hypothesis and the human occupation of the mid-latitude belt in the Pleistocene. Quat. Int 300, 22–31 (2013).Article 

    Google Scholar 
    Laland, K. N. & Brown, G. R. Niche construction, human behavior, and the adaptive-lag hypothesis. Evol. Anthropol. 15, 95–104 (2006).Article 

    Google Scholar 
    Laland, K. N. & O’Brien, M. J. Niche construction theory and archaeology. J. Archaeol. Method Th. 17, 303–322 (2010).Article 

    Google Scholar 
    Riede, F. Handbook of Evolutionary Research in Archaeology (Springer, 2019).Jöris, O. & Terberger, T. Zur Rekonstruktion eines Zeltes mit Trapezförmigem Grundriss am Magdalénien-Fundplatz Gönnersdorf/Mittelrhein: Eine» Quadratur des Kreises «? Arch.äologisches Korrespondenzblatt 31, 163–172 (2001).
    Google Scholar 
    Salomon, H., Vignaud, C., Lahlil, S. & Menguy, N. Solutrean and Magdalenian ferruginous rocks heat-treatment: accidental and/or deliberate action? J. Archaeol. Sci. 55, 100–112 (2015).CAS 
    Article 

    Google Scholar 
    Nakazawa, Y., Straus, L. G., Gonzalez-Morales, M. R., Solana, D. C. & Saiz, J. C. On stone-boiling technology in the Upper Paleolithic: behavioral implications from an Early Magdalenian hearth in El Miron Cave, Cantabria, Spain. J. Archaeol. Sci. 36, 684–693 (2009).Article 

    Google Scholar 
    Pedersen, J., Maier, A. & Riede, F. A punctuated model for the colonisation of the Late Glacial margins of northern Europe by Hamburgian hunter-gatherers. Quart.är. 65, 85–104 (2018).
    Google Scholar 
    Whallon, R. Social networks and information: non-“utilitarian” mobility among hunter-gatherers. J. Anthropol. Archaeol. 25, 259–270 (2006).Article 

    Google Scholar 
    Leal Filho, W. et al. Impacts of climate change to African indigenous communities and examples of adaptation responses. Nat. Commun. 12, 6224 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Heitz, C. F., Hinz, M., Laabs, J. & Hafner, A. Mobility as resilience capacity in northern Alpine Neolithic settlement communities. Archaeol. Rev. Camb. 36, 75–106 (2021).
    Google Scholar 
    Riede, F., Oetelaar, G. A. & VanderHoek, R. From crisis to collapse in hunter-gatherer societies. A comparative investigation of the cultural impacts of three large volcanic eruptions on past hunter-gatherers. Crisis to Collapse–The Archaeology of Social Breakdown. Louvain-la-Neuve: UCL Presses Universitaires De Louvian 23–39 (2017).Halstead, P., O’Shea, J. & O’Shea, J. M. Bad Year Economics: Cultural Responses to Risk and Uncertainty. (Cambridge Univ. Press, 2004).Brovkin, V. et al. Past abrupt changes, tipping points and cascading impacts in the Earth system. Nat. Geosci. 14, 550–558 (2021).ADS 
    CAS 
    Article 

    Google Scholar 
    Burke, A. et al. The archaeology of climate change: the case for cultural diversity. Proc Natl Acad Sci USA 118, e2108537118 (2021).Binford, L. R. Willow smoke and dogs tails – Hunter-gatherer settlement systems and archaeological site formation. Am. Antiquity 45, 4–20 (1980).Article 

    Google Scholar 
    Birdsell, J. B. Some environmental and cultural factors influencing the structuring of Australian aboriginal populations. Am. Nat. 87, 171–207 (1953).Article 

    Google Scholar 
    Kelly, R. L. The Lifeways of Hunter-Gatherers: The Foraging Spectrum (Cambridge Univ. Press, 2013).Penington, R. Hunter-gatherer demography. In Hunter-Gatherers: An Interdisciplinary Perspective. (eds. Panter-Brick, C., Layton, R. H. & Rowley-Conwy, P.) (Cambridge University Press, Cambridge, 2001).Wobst, H. M. Locational relationships in Paleolithic society. J. Hum. Evol. 5, 49–58 (1976).Article 

    Google Scholar 
    Richards, M. P., Pettitt, P. B., Stiner, M. C. & Trinkaus, E. Stable isotope evidence for increasing dietary breadth in the European mid-Upper Paleolithic. Proc. Natl Acad. Sci. USA 98, 6528–6532 (2001).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Drucker, D. & Bocherens, H. Carbon and nitrogen stable isotopes as tracers of change in diet breadth during Middle and Upper Palaeolithic in Europe. Int J. Osteoarchaeol. 14, 162–177 (2004).Article 

    Google Scholar 
    Kretschmer, I. Demographische Untersuchungen zu Bevölkerungsdichten, Mobilität und Landnutzungsmustern im späten Jungpaläolithikum (Verlag Marie Leidorf GmbH, 2015).Langley, M. C. & Street, M. Long range inland-coastal networks during the Late Magdalenian: evidence for individual acquisition of marine resources at Andernach-Martinsberg, German Central Rhineland. J. Hum. Evol. 64, 457–465 (2013).PubMed 
    Article 

    Google Scholar 
    Lanczont, M. et al. Late Glacial environment and human settlement of the Central Western Carpathians: a case study of the Nowa Biala 1 open-air site (Podhale Region, southern Poland). Quat. Int 512, 113–132 (2019).Article 

    Google Scholar 
    Cziesla, E. Robbenjagd in Brandenburg? Gedanken zur Verwendung großer Widerhakenspitzen. Ethnographisch-archaologische Z. 48, 1–48 (2007).
    Google Scholar 
    Fick, S. E. & Hijmans, R. J. WorldClim 2: new 1‐km spatial resolution climate surfaces for global land areas. Int. J. Climatol. 37, 4302–4315 (2017).Article 

    Google Scholar 
    Le Cook, B. & Manning, W. G. Thinking beyond the mean: a practical guide for using quantile regression methods for health services research. Shanghai Arch. Psychiatry 25, 55 (2013).PubMed 
    PubMed Central 

    Google Scholar 
    Yee, T. W. & Mitchell, N. D. Generalized additive-models in plant ecology. J. Veg. Sci. 2, 587–602 (1991).Article 

    Google Scholar 
    Guisan, A., Edwards, T. C. & Hastie, T. Generalized linear and generalized additive models in studies of species distributions: setting the scene. Ecol. Model 157, 89–100 (2002).Article 

    Google Scholar 
    Fewster, R. M., Buckland, S. T., Siriwardena, G. M., Baillie, S. R. & Wilson, J. D. Analysis of population trends for farmland birds using generalized additive models. Ecology 81, 1970–1984 (2000).Article 

    Google Scholar 
    Drexler, M. & Ainsworth, C. H. Generalized additive models used to predict species abundance in the Gulf of Mexico: an ecosystem modeling tool. PLos ONE 8, e64458 (2013).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Moisen, G. G. & Frescino, T. S. Comparing five modelling techniques for predicting forest characteristics. Ecol. Model 157, 209–225 (2002).Article 

    Google Scholar 
    Wood, S. N. Generalized Additive Models: An Introduction with R (CRC Press, 2006).Zuur, A. F. A Beginner’s Guide to Generalized Additive Models with R (Highland Statistics Limited, 2012).Team, R. C. R: a language and environment for statistical computing. (2013).Wood, S. N. Generalized Additive Models: An Introduction with R (CRC Press, 2017).Fasiolo, M., Wood, S. N., Zaffran, M., Nedellec, R. & Goude, Y. Fast calibrated additive quantile regression. J. Am. Stat. Assoc. 116, 1402–1412 (2021).MathSciNet 
    CAS 
    Article 

    Google Scholar 
    AlejoOrdonez/PaleoPopDen: (Version NatCommV0) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.6962693 (2022).Liu, Z. et al. Transient simulation of last deglaciation with a new mechanism for Bolling-Allerod warming. Science 325, 310–314 (2009).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Lorenz, D. J., Nieto-Lugilde, D., Blois, J. L., Fitzpatrick, M. C. & Williams, J. W. Downscaled and debiased climate simulations for North America from 21,000 years ago to 2100AD. Sci. Data 3, 160048 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Peltier, W. R., Argus, D. & Drummond, R. Space geodesy constrains ice age terminal deglaciation: the global ICE‐6G_C (VM5a) model. J. Geophys. Res. Solid Earth 120, 450–487 (2015).ADS 
    Article 

    Google Scholar 
    Vermeersch, P. M. European population changes during the Marine Isotope Stages 2 and 3. Quat. Int 137, 77–85 (2005).Article 

    Google Scholar 
    Gamble, C., Davies, W., Pettitt, P., Hazelwood, L. & Richards, M. The archaeological and genetic foundations of the European population during the late glacial: Implications for ‘agricultural thinking’. Camb. Archaeol. J. 15, 193–223 (2005).Article 

    Google Scholar 
    Steele, J. Radiocarbon dates as data: quantitative strategies for estimating colonization front speeds and event densities. J. Archaeol. Sci. 37, 2017–2030 (2010).Article 

    Google Scholar 
    Shennan, S. et al. Regional population collapse followed initial agriculture booms in mid-Holocene Europe. Nat. Commun. 4, 2486 (2013).ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 
    Surovell, T. A., Finley, J. B., Smith, G. M., Brantingham, P. J. & Kelly, R. Correcting temporal frequency distributions for taphonomic bias. J. Archaeol. Sci. 36, 1715–1724 (2009).Article 

    Google Scholar 
    Williams, A. N. The use of summed radiocarbon probability distributions in archaeology: a review of methods. J. Archaeol. Sci. 39, 578–589 (2012).Article 

    Google Scholar 
    Kelly, R. L., Surovell, T. A., Shuman, B. N. & Smith, G. M. A continuous climatic impact on Holocene human population in the Rocky Mountains. Proc. Natl Acad. Sci. USA 110, 443–447 (2013).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Hijmans, R. J. et al. Package ‘raster’. R package 734, (2015).Lewin-Koh, N. J. et al. Package ‘maptools’. Internet: http://cran.r-project.org/web/packages/maptools/maptools.pdf (2012).Thornthwaite, C. W. An approach toward a rational classification of climate. Geogr. Rev. 38, 55–94 (1948).Article 

    Google Scholar 
    Lieth, H.Primary Productivity of the Biosphere (Springer, 1975). More

  • in

    Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort

    Sample collection and metagenomic sequencingWritten informed consent was obtained prior to participation in the project. The study protocol for the Japanese (Disease, Drug, Diet, Daily life) microbiome project was approved by the medical ethics committees of the Tokyo Medical University (Approval No: T2019-0119), National Center for Global Health and Medicine (Approval No: 1690), the University of Tokyo (Approval No: 2019185NI), Waseda University (Approval No: 2018-318), and the RIKEN Center for Integrative Medical Sciences (Approval No: H30-7). We conducted a prospective cross-sectional study of 4198 individuals participating in the Japanese 4D microbiome project, which commenced in January 2015 and is ongoing20.Participants registered in the project were those who visited hospitals in the area for disease diagnosis or a health checkup. Faecal samples are collected from both healthy and diseased participants. The eligibility criteria for participants are as follows: (1) born and raised in Japan; (2) age >15 years; (3) written informed consent provided; and (4) having an endoscopic diagnosis on colonoscopy; either having undergone a colonoscopy within the last 3 years or planning to undergo colonoscopy for colorectal cancer screening, surveillance, and diagnosis of various gastrointestinal symptoms. The exclusion criteria were as follows: (1) suspected acute infectious disease based on clinical findings (e.g., acute enterocolitis, pneumonia, tuberculosis etc.); (2) acute bleeding; (3) hearing loss; (4) unable to understand written documents; (5) unable to write and (6) limited ability to perform activities of daily living. No compensation was paid to participants.Participants collected faecal samples using a Cary–Blair medium-containing tube60 at home, and the samples were refrigerated for up to 2 days before the hospital visit. Immediately after participants arrived at the hospital, their faecal samples were frozen at −80 °C until DNA extraction. We avoided collecting samples within 1 month of administering bowel preparation for colonoscopy because it has a profound effect on the gut microbiome and metabolome61. Health professionals checked that the amount of stool was sufficient for analysis. Shotgun metagenomic sequencing was performed for 4241 faecal samples and quality controls were conducted20, from which 43 samples were excluded from further analyses due to the low number of high-quality reads (130 bp. Encoded genes in the contigs were predicted by MetaGeneMark (3.38)70. Assembled contigs were defined as phages if they passed all of the following six criteria.

    1.

    A genome size threshold was applied, and contigs less than 10 Kb were excluded, as typical dsDNA phages have genomes larger than >10 Kb71.

    2.

    Viral-specific k-mer patterns were checked by DeepVirFinder (v1.0)22. Contigs with p-values >0.05 were excluded from further analysis.

    3.

    To detect viral hallmark genes (VHGs) and plasmid hallmark genes, we performed a highly sensitive HMM-HMM search against the Pfam database72. First, the encoded genes were aligned to the viral protein database, collected from complete (circular) viral genomes (n = 13,628) in the IMG/VR v2 database30 using JackHMMER. The obtained HMM profiles were searched against the Pfam database using hhblits73 with a  >95% probability cut-off. These procedures were performed using the pipeline_for_high_sensitive_domain_search script (https://github.com/yosuken/pipeline_for_high_sensitive_domain_search)74,75. Contigs with plasmid hallmark genes or those without VHGs were excluded. The hallmark genes used in this analysis are summarised in Supplementary Data 3.

    4.

    The presence of housekeeping marker genes of prokaryotic species was checked by fetchMG (v1.0)76, and ribosomal RNA genes (5 S, 16 S and 23 S) were identified by barrnap (0.9) (https://github.com/tseemann/barrnap). Contigs with the marker genes and ribosomal RNA genes were excluded from further analysis.

    5.

    The encoded genes of each contig were aligned to the viral protein database and a plasmid protein database constructed from the reference plasmids in RefSeq (n = 16,136, in April 2020) using DIAMOND (v0.9.29.130)77 with the more-sensitive option. The number of genes aligned to each database was compared, and contigs with more genes aligned to the plasmid protein database were excluded from further analysis.

    6.

    The proportion of provirus regions was assessed by CheckV (v0.7)24, and contigs estimated with 70% and 10% contamination.To evaluate the performance of this custom pipeline, we applied the pipeline to reference phage genomes (n = 2609, as positive data) and plasmid sequences (n = 16,136, as negative data) in Refseq. The true positive rate was defined as the number of phages detected as phages by the pipeline divided by the number of reference phages. The false positive rate was defined as the number of plasmids detected as phages by the pipeline divided by the number of reference plasmids. DeepVirFinder22, VirSorter (v1.0.3)23 Virsorter2 (2.2.3)25, VIBRANT (v1.2.1)26, Seeker (v1.0.3)27 and ViralVerify (v1.1)28 were also applied to the same datasets with the default parameters, and the performance was compared among them.Analysis of phage genomesViral operational taxonomic units (vOTUs) were constructed by clustering phage genomes with a  > 95% identity29 using dRep (v2.2.3)78 with the default options. Representative sequences of each vOTU selected by dRep were further clustered with reference sequences in RefSeq, IMG/VR30, gut virome database (GVD)15, gut phage database (GPD)9, and metagenomic gut virus (MGV) database31 with >95% identity and >85% length coverage using aniclust.py script in the CheckV package to identify common sequences among the databases.To further construct broader viral clusters (VC), proportions of protein clusters shared between phages were assessed. First, to define protein clusters, similarity searches of all protein sequences from all the phages identified in this study were performed using DIAMOND with the more-sensitive option (e-value 20% of clusters were grouped as a VC, which corresponds approximately to family- or subfamily-level clusters7,37. Rarefaction curves of the vOTUs and VCs were estimated with the iNEXT function in the iNEXT package (v2.0.20)80. The similarity matrix of the phages based on the percentage of shared protein clusters was further projected by tSNE using the tsne function in the Rtsne package (v0.16).Taxonomy annotation of phages was performed with a voting approach described previously16 with minor modifications. First, the protein sequences of each phage were aligned to viral proteins detected from phage genomes in RefSeq (n = 2609, in April 2020) using DIAMOND with the more-sensitive option. Then, the best-hit taxonomy of each protein (family levels) was counted, and the most common taxonomy was assigned to the phage if >20% of proteins in the phage were aligned to the same taxonomy.Phage lifestyles (i.e. virulent or temperate) were predicted by BACPHLIP40 and alignments to reference bacterial genomes in the RefSeq. Phages were defined as temperate if the BACPHLIP score was >0.8 or the phage genome was aligned to any reference genomes with >1000 bp alignment length with >95% identity.Host predictionBacterial and archaeal genomes were downloaded from the RefSeq database (in April 2019). To reduce the redundancy of genomes from closely related strains in the same species (e.g. Escherichia coli), 10 genomes were selected randomly for species with more than 10 genomes, and other genomes were excluded from the dataset. The reference dataset consisted of 33,215 bacterial and 822 archaeal genomes.Host prediction of the identified phages was performed using CRISPR spacers81. CRISPR spacers were predicted from the reference microbial genomes and assembled contigs ( >10,000 bp) from the 4198 metagenomic datasets using PILER-CR (1.06)82. Short (100 bp) spacers were discarded. In total, 679,323 and 283,619 spacers were identified from the reference microbial genomes and assembled contigs, respectively. Taxonomy information was assigned to the assembled contigs if they were aligned to the microbial reference genomes with >90% identity and >70% length coverage thresholds using MiniMap283. The CRISPR spacers were mapped to the phage genomes using BLASTN with the option for short sequences: -a20 -m9 -e1 -G10 -E2 -q1 -W7 -F F81. CRISPR spacers, which were mapped with 100% identity or 1 mismatch/indel with >95% sequence alignment, were used for host assignment at the genus level. Assignments of host species were checked manually, and if any of the following non-human intestinal species were assigned, the host was excluded: Dickeya, Anaerobutyricum, Rubellimicrobium, Eisenbergiella, Harryflintia, Leucothrix, Photorhabdus, Spirosoma, Syntrophobotulus, Thermincola, Algoriphagus, Franconibacter, Kandleria, Lawsonibacter, Methylomonas, Provencibacterium, Pseudoruminoccoccus, Rhodanobacter, Romboutsia, Sharpea, Varibaculum and Thioalkalivibrio.Quantification of viral abundance and analysis of the virome profileTo quantify the viral abundances in each sample, metagenomic reads were mapped to the gene set of VHGs (Supplementary Data 3) of each representative vOTU using Bowtie2 with a  > 95% identity threshold, and reads per kilobase million (RPKM) were calculated for each vOTU. The reason for using only VHGs in the analysis was to avoid over-counting of viral reads, which could be caused by spurious mapping of reads from horizontally transferred genes of other phages or bacterial species. The α-diversity (Shannon diversity) of the vOTU-level viral profile was calculated using the diversity function in the vegan package. The β-diversity (Bray-Curtis distance) between individuals was assessed using the vegdist function, and the average distance against other individuals was calculated for each individual. The VC-level viral profile was obtained by summing all the RPKM of vOTUs for each VC.Phylogenetic analysis of novel VCsTo construct phylogenetic trees for the vOTUs and reference genomes, protein sequences of large terminases, portal proteins, and major capsid proteins (Supplementary Data 3), which are often used to construct phage phylogenetic trees7,9, were extracted from the vOTUs in the 10 most abundant VCs (VC_19, 1, 2, 24, 12, 15, 3, 44, 18, 6), and their homologues were searched for in the reference phage genomes in RefSeq using DIAMOND with the more-sensitive option (e-value 0.01% (n = 865) and genera with average relative abundance >0.5% (n = 32) were included in the analysis.Analysis of VLPs and whole metagenomes from 24 faecal samplesQuality filtering of sequenced reads from the 24 VLPs and whole metagenomes was performed using fastp (version 0.20.1)92 with the default parameters. Contamination with human (hg38) or phiX genomes was excluded by mapping the reads to the genomes using Bowtie2.To exclude bacterial DNA contamination in the VLP dataset, we performed further filtering. First, the VLP reads were assembled into contigs using MEGAHIT and the contigs were checked for virus or not. Contigs were defined as viral contigs if they were predicted as viruses by DeepVirFinder (P-value More

  • in

    Forest vulnerability to drought controlled by bedrock composition

    Moore, J., Pope, J., Woods, M. & Ellis, A. 2018 Aerial Survey Results: California (USDA, 2018).Stephens, S. L. et al. Drought, tree mortality, and wildfire in forests adapted to frequent fire. Bioscience 68, 77–88 (2018).Article 

    Google Scholar 
    Li, S. & Banerjee, T. Spatial and temporal pattern of wildfires in California from 2000 to 2019. Sci. Rep. 11, 8779 (2021).Article 

    Google Scholar 
    Wang, D. et al. Economic footprint of California wildfires in 2018. Nat. Sustain. 4, 252–260 (2020).Article 

    Google Scholar 
    Asner, G. P. et al. Progressive forest canopy water loss during the 2012–2015 California drought. Proc. Natl Acad. Sci. USA 113, E249–E255 (2016).
    Google Scholar 
    Brodrick, P. G., Anderegg, L. D. L. & Asner, G. P. Forest drought resistance at large geographic scales. Geophys. Res. Lett. 46, 2752–2760 (2019).Article 

    Google Scholar 
    Jump, A. S. et al. Structural overshoot of tree growth with climate variability and the global spectrum of drought-induced forest dieback. Glob. Change Biol. 23, 3742–3757 (2017).Article 

    Google Scholar 
    Goulden, M. L. & Bales, R. C. California forest die-off linked to multi-year deep soil drying in 2012–2015 drought. Nat. Geosci. 12, 632–637 (2019).Article 

    Google Scholar 
    Paz-Kagan, T. et al. What mediates tree mortality during drought in the southern Sierra Nevada? Ecol. Appl. 27, 2443–2457 (2017).Article 

    Google Scholar 
    Trugman, A. T., Anderegg, L. D. L., Anderegg, W. R. L., Das, A. J. & Stephenson, N. L. Why is Tree Drought Mortality so Hard to Predict? Trends Ecol. Evol. 36, 520–532.(2021).Goodfellow, B. W. et al. The chemical, mechanical, and hydrological evolution of weathering granitoid. J. Geophys. Res. Earth Surf. 121, 1410–1435 (2016).Article 

    Google Scholar 
    Shen, X., Arson, C., Ferrier, K. L., West, N. & Dai, S. Mineral weathering and bedrock weakening: modeling microscale bedrock damage under biotite weathering. J. Geophys. Res. Earth Surf. 124, 2623–2646 (2019).Article 

    Google Scholar 
    McLaughlin, B. C. et al. Weather underground: subsurface hydrologic processes mediate tree vulnerability to extreme climatic drought. Glob. Change Biol. 26, 3091–3107 (2020).Article 

    Google Scholar 
    Hahm, W. J. et al. Low subsurface water storage capacity relative to annual rainfall decouples Mediterranean plant productivity and water use from rainfall variability. Geophys. Res. Lett. 46, 6544–6553 (2019).Article 

    Google Scholar 
    Zhang, Y., Keenan, T. F. & Zhou, S. Exacerbated drought impacts on global ecosystems due to structural overshoot. Nat. Ecol. Evol. 5, 1490–1498 (2021).Article 

    Google Scholar 
    Tague, C. & Peng, H. The sensitivity of forest water use to the timing of precipitation and snowmelt recharge in the California Sierra: implications for a warming climate. J. Geophys. Res. Biogeosci. 118, 875–887 (2013).Article 

    Google Scholar 
    Hahm, W. J., Riebe, C. S., Lukens, C. E. & Araki, S. Bedrock composition regulates mountain ecosystems and landscape evolution. Proc. Natl Acad. Sci. USA 111, 3338–3343 (2014).Article 

    Google Scholar 
    Uhlig, D., Schuessler, J. A., Bouchez, J., Dixon, J. L. & von Blanckenburg, F. Quantifying nutrient uptake as driver of rock weathering in forest ecosystems by magnesium stable isotopes. Biogeosciences 14, 3111–3128 (2017).Article 

    Google Scholar 
    Stone, E. C. Dew as an ecological factor: II. The effect of artificial dew on the survival of Pinus ponderosa and associated species. Ecology 38, 414–422 (1957).Article 

    Google Scholar 
    Wald, J. A., Graham, R. C. & Schoeneberger, P. J. Distribution and properties of soft weathered bedrock at ≤1 m depth in the contiguous United States. Earth Surf. Process. Landf. 38, 614–626 (2013).Article 

    Google Scholar 
    Klos, P. Z. et al. Subsurface plant-accessible water in mountain ecosystems with a Mediterranean climate. WIREs Water 5, e1277 (2018).Article 

    Google Scholar 
    Dawson, T. E., Hahm, W. J. & Crutchfield-Peters, K. Digging deeper: what the critical zone perspective adds to the study of plant ecophysiology. N. Phytol. 226, 666–671 (2020).Article 

    Google Scholar 
    Rempe, D. M. & Dietrich, W. E. Direct observations of rock moisture, a hidden component of the hydrologic cycle. Proc. Natl Acad. Sci. USA 115, 2664–2669 (2018).Article 

    Google Scholar 
    Holbrook, W. S. et al. Links between physical and chemical weathering inferred from a 65-m-deep borehole through Earth’s critical zone. Sci. Rep. 9, 4495 (2019).Article 

    Google Scholar 
    Krone, L. V. et al. Deep weathering in the semi-arid Coastal Cordillera, Chile. Sci. Rep. 11, 13057 (2021).Article 

    Google Scholar 
    Callahan, R. P. et al. Subsurface weathering revealed in hillslope‐integrated porosity distributions. Geophys. Res. Lett. 47, e2020GL088322 (2020).Holbrook, W. S. et al. Geophysical constraints on deep weathering and water storage potential in the Southern Sierra Critical Zone Observatory. Earth Surf. Process. Landf. 39, 366–380 (2014).Article 

    Google Scholar 
    Hayes, J. L., Riebe, C. S., Holbrook, W. S., Flinchum, B. A. & Hartsough, P. C. Porosity production in weathered rock: where volumetric strain dominates over chemical mass loss. Sci. Adv. 5, eaao0834 (2019).Article 

    Google Scholar 
    Riebe, C. S. et al. Anisovolumetric weathering in granitic saprolite controlled by climate and erosion rate. Geology 49, 551–555 (2021).Article 

    Google Scholar 
    McCormick, E. L. et al. Widespread woody plant use of water stored in bedrock. Nature 597, 225–229 (2021).Article 

    Google Scholar 
    Vitousek, P. M., Porder, S. & Houlton, B. Z. Terrestrial phosphorus limitation: mechanisms, implications, and nitrogen–phosphorus interactions. Ecol. Appl. 20, 5–15 (2010).Article 

    Google Scholar 
    Bateman, P. C., Dodge, F. C. W. & Bruggman, P. E. Major Oxide Analyses, CPIW Norms, Modes, and Bulk Specific Gravities of Plutonic Rocks from the Mariposa 1° × 2° Sheet, Central Sierra Nevada, California Open-File Report 84–162 (USGS, 1984).Amundson, R., Richter, D. D., Humphreys, G. S., Jobbagy, E. G. & Gaillardet, J. Coupling between biota and earth materials in the critical zone. Elements 3, 327–332 (2007).Article 

    Google Scholar 
    Tune, A. K., Druhan, J. L., Wang, J., Bennett, P. C. & Rempe, D. M. Carbon dioxide production in bedrock beneath soils substantially contributes to forest carbon cycling. J. Geophys. Res. Biogeosci. 125, e2020JG005795 (2020).Gabet, E. J. & Mudd, S. M. Bedrock erosion by root fracture and tree throw: a coupled biogeomorphic model to explore the humped soil production function and the persistence of hillslope soils. J. Geophys. Res. 115, F04005 (2010).Bateman, P. C. Plutonism in the Central Part of the Sierra Nevada Batholith, California (USGS, 1992); http://pubs.er.usgs.gov/publication/pp1483Callahan, R. P. et al. Arrested development: erosional equilibrium in the southern Sierra Nevada, California, maintained by feedbacks between channel incision and hillslope sediment production. GSA Bull. 131, 1179–1202 (2019).Article 

    Google Scholar 
    Flinchum, B. A. et al. Estimating the water holding capacity of the critical zone using near-surface geophysics. Hydrol. Process. 32, 3308–3326 (2018).Article 

    Google Scholar 
    St. Clair, J. Geophysical Investigations of Underplating at the Middle American Trench, Weathering in the Critical Zone, and Snow Water Equivalent in Seasonal Snow. PhD thesis, Univ. Wyoming (2015).Dvorkin, J. & Nur, A. Elasticity of high‐porosity sandstones: theory for two North Sea data sets. Geophysics 61, 1363–1370 (1996).Article 

    Google Scholar 
    Gu, X. et al. Seismic refraction tracks porosity generation and possible CO2 production at depth under a headwater catchment. Proc. Natl Acad. Sci. USA 117, 18991–18997 (2020).Article 

    Google Scholar 
    Pasquet, S., Holbrook, W. S., Carr, B. J. & Sims, K. W. W. Geophysical imaging of shallow degassing in a Yellowstone hydrothermal system. Geophys. Res. Lett. 43, 12,027–12,035 (2016).Article 

    Google Scholar 
    Dahlgren, R. A., Boettinger, J. L., Huntington, G. L. & Amundson, R. G. Soil development along an elevational transect in the western Sierra Nevada, California. Geoderma 78, 207–236 (1997).Article 

    Google Scholar 
    Stone, E. L. & Kalisz, P. J. On the maximum extent of tree roots. For. Ecol. Manage. 46, 59–102 (1991).Article 

    Google Scholar 
    Carlson, T. N. & Ripley, D. A. On the relation between NDVI, fractional vegetation cover, and leaf area index. Remote Sens. Environ. 62, 241–252 (1997).Article 

    Google Scholar 
    Goulden, M. L. et al. Evapotranspiration along an elevation gradient in California’s Sierra Nevada. J. Geophys. Res. 117, G03028 (2012).Ma, Q. et al. Wildfire controls on evapotranspiration in California’s Sierra Nevada. J. Hydrol. 590, 125364 (2020).Article 

    Google Scholar 
    Roche, J. W., Goulden, M. L. & Bales, R. C. Estimating evapotranspiration change due to forest treatment and fire at the basin scale in the Sierra Nevada, California. Ecohydrology 11, e1978 (2018).Bales, R. C. et al. Mechanisms controlling the impact of multi-year drought on mountain hydrology. Sci. Rep. 8, 690 (2018).Article 

    Google Scholar 
    Roy, D. P. et al. Characterization of Landsat-7 to Landsat-8 reflective wavelength and normalized difference vegetation index continuity. Remote Sens. Environ. 185, 57–70 (2016).Article 

    Google Scholar 
    Su, Y. et al. Emerging stress and relative resiliency of giant sequoia groves experiencing multiyear dry periods in a warming climate. J. Geophys. Res. Biogeosci. 122, 3063–3075 (2017).Article 

    Google Scholar 
    Moore, J., McAfee, L. & Iaccarino, J. 2016 Aerial Survey Results: California (USDA, 2017).Budyko, M. I., Miller, D. H. & Miller, D. H. Climate and Life (Academic Press, 1974).Hargreaves, G. H. & Samani, Z. A. Reference crop evapotranspiration from temperature. Appl. Eng. Agric. 1, 96–99 (1985).Article 

    Google Scholar 
    PRISM Climate Group PRISM Climate Data (Oregon State Univ., 2019).Bales, R. et al. Spatially distributed water-balance and meteorological data from the rain–snow transition, southern Sierra Nevada, California. Earth Syst. Sci. Data 10, 1795–1805 (2018).Article 

    Google Scholar 
    Callahan, R. P. Supplement for “Forest vulnerability to drought controlled by bedrock composition”. Hydroshare https://doi.org/10.4211/hs.edbb6ebfbc744186b5800932cd00b507 (2022).Earth Resources Observation and Science (EROS) Center USGS EROS Archive—Aerial Phorography—National Agriculture Imagery Program (NAIP) (USGS, 2017); https://doi.org/10.5066/F7QN651G More

  • in

    Hinfluences severe disease-mediated population declines in two of the most common garden bird species in Great Britain

    Gregory, R. D. & van Strien, A. Wild bird indicators: Using composite population trends of birds as measures of environmental health. Ornithol. Sci. 9, 3–22 (2010).Article 

    Google Scholar 
    Cox, D. T. C. & Gaston, K. J. Urban bird feeding: Connecting people with nature. PLoS ONE 11, e0158717 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Anderson, R. M. & May, R. M. Population biology of infectious diseases: Part I. Nature 280, 361–367 (1979).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Keesing, F. et al. Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature 468, 647–652 (2010).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Smith, K. F., Acevedo-Whitehouse, K. & Pedersen, A. B. The role of infectious diseases in biological conservation. Anim. Conserv. 12, 1–12 (2009).Article 

    Google Scholar 
    Han, B. A., Kramer, A. M. & Drake, J. M. Global patterns of zoonotic disease in mammals. Trends Parasitol. 32, 565–577 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Estrada-Peña, A., Ostfeld, R. S., Peterson, A. T., Poulin, R. & de la Fuente, J. Effects of environmental change on zoonotic disease risk: An ecological primer. Trends Parasitol. 30, 205–214 (2014).PubMed 
    Article 

    Google Scholar 
    Daszak, P., Cunningham, A. A. & Hyatt, A. D. Emerging infectious diseases of wildlife–threats to biodiversity and human health. Science 287(5452), 443–449 (2000).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Pedersen, A. B., Jones, K. E., Nunn, C. L. & Altizer, S. Infectious diseases and extinction risk in wild mammals. Conserv. Biol. 21, 1269–1279 (2007).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Atkinson, C. T. & Samuel, M. D. Avian malaria Plasmodium relictum in native Hawaiian forest birds: Epizootiology and demographic impacts on àapapane Himatione sanguinea. J. Avian Biol. 41, 357–366 (2010).Article 

    Google Scholar 
    George, T. L. et al. Persistent impacts of West Nile virus on North American bird populations. Proc. Natl. Acad. Sci. USA. 112, 14290–14294 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Dhondt, A. A., Tessaglia, D. L. & Slothower, R. L. Epidemic mycoplasmal conjunctivitis in house finches from Eastern North America. J. Wildl. Dis. 34, 265–280 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Monterroso, P. et al. Disease-mediated bottom-up regulation: An emergent virus affects a keystone prey, and alters the dynamics of trophic webs. Sci. Rep. 6, 36072 (2016).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Cheng, T. L. et al. The scope and severity of white-nose syndrome on hibernating bats in North America. Conserv. Biol. 35, 1586–1597 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Rushton, S. P. et al. Disease threats posed by alien species: The role of a poxvirus in the decline of the native red squirrel in Britain. Epidemiol. Infect. 134, 521–533 (2006).CAS 
    PubMed 
    Article 

    Google Scholar 
    Scheele, B. C. et al. Amphibian fungal panzootic causes catastrophic and ongoing loss of biodiversity. Science 363(6434), 1459–1463 (2019).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Bradley, C. A. & Altizer, S. Urbanization and the ecology of wildlife diseases. Trends Ecol. Evol. 22, 95–102 (2007).PubMed 
    Article 

    Google Scholar 
    Murray, M. H. et al. City sicker? A meta-analysis of wildlife health and urbanization. Front. Ecol. Environ. 17, 575–583 (2019).Article 

    Google Scholar 
    Giraudeau, M., Mousel, M., Earl, S. & McGraw, K. Parasites in the city: Degree of urbanization predicts poxvirus and coccidian infections in house finches (Haemorhous mexicanus). PLoS ONE 9, e86747 (2014).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Shutt, J. D. & Lees, A. C. Killing with kindness: Does widespread generalised provisioning of wildlife help or hinder biodiversity conservation efforts? Biol. Conserv. 261, 109295 (2021).Article 

    Google Scholar 
    Van Doren, B. M. et al. Human activity shapes the wintering ecology of a migratory bird. Glob. Chang. Biol. 27, 2715–2727 (2021).PubMed 
    Article 
    CAS 

    Google Scholar 
    Plummer, K. E., Risely, K., Toms, M. P. & Siriwardena, G. M. The composition of British bird communities is associated with long-term garden bird feeding. Nat. Commun. 10, 2088 (2019).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Lawson, B. et al. Health hazards to wild birds and risk factors associated with anthropogenic food provisioning. Philos. Trans. R. Soc. B Biol. Sci. 373, 20170091 (2018).Galbraith, J. A., Stanley, M. C., Jones, D. N. & Beggs, J. R. Experimental feeding regime influences urban bird disease dynamics. J. Avian Biol. 48, 700–713 (2017).Article 

    Google Scholar 
    Siriwardena, G. M. et al. The effect of supplementary winter seed food on breeding populations of farmland birds: Evidence from two large-scale experiments. J. Appl. Ecol. 44, 920–932 (2007).Article 

    Google Scholar 
    Kubasiewicz, L. M., Bunnefeld, N., Tulloch, A. I. T., Quine, C. P. & Park, K. J. Diversionary feeding: An effective management strategy for conservation conflict? Biodivers. Conserv. 25, 1–22 (2016).Article 

    Google Scholar 
    Lawson, B. et al. A clonal strain of Trichomonas gallinae is the aetiologic agent of an emerging avian epidemic disease. Infect. Genet. Evol. 11, 1638–1645 (2011).PubMed 
    Article 

    Google Scholar 
    Robinson, R. A. et al. Emerging infectious disease leads to rapid population declines of common British birds. PLoS ONE 5, e12215 (2010).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Forrester, D. J. & Foster, G. W. Trichomonosis. In: Parasitic Diseases of Wild Birds 120–153 (Wiley-Blackwell, 2008).Lawson, B. et al. Evidence of spread of the emerging infectious disease, finch trichomonosis, by migrating birds. EcoHealth 8, 143–153 (2011).PubMed 
    Article 

    Google Scholar 
    Lawson, B. et al. The emergence and spread of finch trichomonosis in the British Isles. Philos. Trans. R. Soc. B Biol. Sci. 367, 2852–2863 (2012).Article 

    Google Scholar 
    Woodward, I. D. et al. BirdTrends 2020: Trends in numbers, breeding success and survival for UK breeding birds. Research Report 732. BTO, Thetford. (2020).Enoksson, B. Age- and sex-related differences in dominance and foraging behaviour of nuthatches Sitta europaea. Anim. Behav. 36, 231–238 (1988).Article 

    Google Scholar 
    Tarvin, K. A. & Woolfenden, G. E. Patterns of dominance and aggressive behavior in blue jays at a feeder. Condor 99, 434–444 (1997).Article 

    Google Scholar 
    Brittingham, M. C. & Temple, S. A. Use of winter feeders by black-capped chickadees. Wildl. Soc. 56, 103–110 (1992).
    Google Scholar 
    Woodward, I. et al. Population estimates of birds in Great Britain and the United Kingdom. Br. Birds 113, 69–104 (2020).
    Google Scholar 
    Musgrove, A. J. et al. Population estimates of birds in Great Britain and the United Kingdom. Br. Birds 106, 64–100 (2013).
    Google Scholar 
    Wernham, C. et al. The Migration Atlas: Movements of the Birds of Britain and Ireland. (T & AD Poyser, 2002).Main, I. G. The partial migration of Fennoscandian Greenfinches Carduelis chloris. Ringing Migr. 20, 167–180 (2000).Article 

    Google Scholar 
    Lack, P. C. The Atlas of Wintering Birds in Britain and Ireland. (T. & A.D. Poyser, 1986).Robinson, R. A. BirdFacts: profiles of birds occurring in Britain & Ireland. BTO, Thetford (2005). Available at: http://www.bto.org/birdfacts. Accessed: 15 May 2022.Tratalos, J. et al. Bird densities are associated with household densities. Glob. Chang. Biol. 13, 1685–1695 (2007).ADS 
    Article 

    Google Scholar 
    Gregory, R. D. Broad-scale habitat use of sparrows, finches and buntings in Britain. Die Vogelwelt 120, 47–57 (1999).
    Google Scholar 
    Newton, I. Finches. New Naturalist Series, Volume: 55. (HarperCollins, 1972).Robinson, R. A., Baillie, S. R. & Crick, H. Q. P. Weather-dependent survival: Implications of climate change for passerine population processes. Ibis. 149, 357–364 (2007).Article 

    Google Scholar 
    Crick, H. Q. P. A bird-habitat coding system for use in Britain and Ireland incorporating aspects of land-management and human activity. Bird Study 39, 1–12 (1992).Article 

    Google Scholar 
    Davies, Z. G. et al. A national scale inventory of resource provision for biodiversity within domestic gardens. Biol. Conserv. 142, 761–771 (2009).Article 

    Google Scholar 
    Balmer, D. E. et al. Bird Atlas 2007–11: The breeding and wintering birds of Britain and Ireland. (BTO Books, 2013).Lawson, B. et al. Epidemiology of salmonellosis in garden birds in England and Wales, 1993 to 2003. EcoHealth 7, 294–306 (2010).CAS 
    PubMed 
    Article 

    Google Scholar 
    Svensson, L. Identification guide to European passerines, 4th edition. (BTO, 1992).Jenni, L. & Winkler, R. Moult and ageing of European passerines, 2nd edition. (Helm, 2020).Baillie, S. R. The contribution of ringing to the conservation and management of bird populations: A review. Ardea 89, 167–184 (2001).
    Google Scholar 
    Kéry, M. & Schaub, M. Bayesian Population Analysis using WinBUGS: A hierarchical perspective (Academic Press, 2012).
    Google Scholar 
    R Core Team. R: A language and environment for statistical computing. (2020).Plummer, M. JAGS: A program for analysis of Bayesian graphical models using Gibbs sampling. in Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003) (eds. Hornik, K., Leisch, F. & Zeileis, A.) (2003).Su, Y.-S. & Yajima, M. R2jags: Using R to Run ‘JAGS’. R package version 0.6–1. (2020).Robinson, R. A., Morrison, C. A. & Baillie, S. R. Integrating demographic data: Towards a framework for monitoring wildlife populations at large spatial scales. Methods Ecol. Evol. 5, 1361–1372 (2014).Article 

    Google Scholar 
    Newson, S. E., Evans, K. L., Noble, D. G., Greenwood, J. J. D. & Gaston, K. J. Use of distance sampling to improve estimates of national population sizes for common and widespread breeding birds in the UK. J. Appl. Ecol. 45, 1330–1338 (2008).Article 

    Google Scholar 
    Newson, S. E., Massimino, D., Johnston, A., Baillie, S. R. & Pearce-Higgins, J. W. Should we account for detectability in population trends? Bird Study 60, 384–390 (2013).Article 

    Google Scholar 
    Crick, H. Q. P., Baillie, S. R. & Leech, D. I. The UK Nest Record Scheme: its value for science and conservation. Bird Study 50, 254–270 (2003).Article 

    Google Scholar 
    Abadi, F., Gimenez, O., Arlettaz, R. & Schaub, M. An assessment of integrated population models: Bias, accuracy, and violation of the assumption of independence. Ecology 91, 7–14 (2010).PubMed 
    Article 

    Google Scholar 
    Plard, F., Turek, D., Grüebler, M. U. & Schaub, M. IPM2: Toward better understanding and forecasting of population dynamics. Ecol. Monogr. 89, e01364 (2019).Article 

    Google Scholar 
    Weegman, M. D., Arnold, T. W., Clark, R. G. & Schaub, M. Partial and complete dependency among data sets has minimal consequence on estimates from integrated population models. Ecol. Appl. 31, e02258 (2021).Article 

    Google Scholar 
    Koons, D. N., Iles, D. T., Schaub, M. & Caswell, H. A life-history perspective on the demographic drivers of structured population dynamics in changing environments. Ecol. Lett. 19, 1023–1031 (2016).PubMed 
    Article 

    Google Scholar 
    Koons, D. N., Arnold, T. W. & Schaub, M. Understanding the demographic drivers of realized population growth rates. Ecol Appl. 27, 2102–2115 (2017).PubMed 
    Article 

    Google Scholar 
    Caswell, H. Matrix population models: Construction, analysis and interpretation. (Sinauer Associates, 2001).Stubben, C. & Milligan, B. Estimating and analyzing demographic models using the popbio package in R. J. Stat. Softw. 22, 1–23 (2007).Article 

    Google Scholar 
    Stanbury, A. et al. The status of our bird populations: The fifth Birds of Conservation Concern in the United Kingdom, Channel Islands and Isle of Man and second IUCN Red List assessment of extinction risk for Great Britain. Br. Birds 114, 723–747 (2021).
    Google Scholar 
    Lehikoinen, A., Lehikoinen, E., Valkama, J., Väisänen, R. A. & Isomursu, M. Impacts of trichomonosis epidemics on greenfinch Chloris chloris and chaffinch Fringilla coelebs populations in Finland. Ibis 155, 357–366 (2013).Article 

    Google Scholar 
    PECBMS. EBCC/BirdLife/RSPB/CSO’ Pan-European Common Bird Monitoring Scheme. (2021). Available at: https://pecbms.info/. (Accessed: 14th July 2022)Keller, V. et al. European Breeding Bird Atlas 2: Distribution, Abundance and Change. (European Bird Census Council and Lynx Edicions, 2020).Rijks, J. M. et al. Trichomonosis in greenfinches (Chloris chloris) in the Netherlands 2009–2017: A concealed threat. Front. Vet. Sci. 6, 425 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Boele, A. et al. Broedvogels in Nederland in 2020. Sovonrapport 2022/05. (Sovon Vogelonderzoek Nederland, Nijmegen., 2022).Jones, D. The Birds at My Table: Why We Feed Wild Birds and Why It Matters. (Cornell University Press, 2018).Pennycott, T. W. et al. Causes of death of wild birds of the family fringillidae in Britain. Vet. Rec. 143, 155–158 (1998).CAS 
    PubMed 
    Article 

    Google Scholar 
    Bouwman, K. M. & Hawley, D. M. Sickness behaviour acting as an evolutionary trap? Male house finches preferentially feed near diseased conspecifics. Biol. Lett. 6, 462–465 (2010).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Lawson, B. et al. Acute necrotising pneumonitis associated with Suttonella ornithocola infection in tits (Paridae). Vet. J. 188, 96–100 (2011).PubMed 
    Article 

    Google Scholar 
    Clewley, G. D., Robinson, R. A. & Clark, J. A. Estimating mortality rates among passerines caught for ringing with mist nets using data from previously ringed birds. Ecol. Evol. 8, 5164–5172 (2018).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Francis, M. L. et al. Effects of supplementary feeding on interspecific dominance hierarchies in garden birds. PLoS ONE 13, e0202152 (2018).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Wojczulanis-Jakubas, K., Kulpińska, M. & Minias, P. Who bullies whom at a garden feeder? Interspecific agonistic interactions of small passerines during a cold winter. J. Ethol. 33, 159–163 (2015).Article 

    Google Scholar 
    Cramp, S. Handbook of the Birds of Europe, the Middle East and North Africa. Volume VIII: Crows to Finches. (Oxford University Press, 1994).Brook, B. W. & Bradshaw, C. J. A. Strength of evidence for density dependence in abundance time series of 1198 species. Ecology 87, 1445–1451 (2006).PubMed 
    Article 

    Google Scholar 
    Hochachka, W. M. & Dhondt, A. A. Density-dependent decline of host abundance resulting from a new infectious disease. Proc. Natl. Acad. Sci. USA. 97, 5303–5306 (2000).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Hochachka, W. M., Dobson, A. P., Hawley, D. M. & Dhondt, A. A. Host population dynamics in the face of an evolving pathogen. J. Anim. Ecol. 90, 1480–1491 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Chi, J. F. et al. The finch epidemic strain of Trichomonas gallinae is predominant in British non-passerines. Parasitology 140, 1234–1245 (2013).PubMed 
    Article 

    Google Scholar 
    Orros, M. E. & Fellowes, M. D. E. Wild bird feeding in an urban area: Intensity, economics and numbers of individuals supported. Acta Ornithol. 50, 43–58 (2015).Article 

    Google Scholar 
    Dirren, S., Borel, S., Wolfrum, N. & Korner-Nievergelt, F. Trichomonas gallinae infections in the naïve host Montifringilla nivalis subsp nivalis. J. Ornithol. 163, 333–337 (2022).Article 

    Google Scholar 
    Tulloch, A. I. T., Possingham, H. P., Joseph, L. N., Szabo, J. & Martin, T. G. Realising the full potential of citizen science monitoring programs. Biol. Conserv. 165, 128–138 (2013).Article 

    Google Scholar 
    Silvertown, J., Buesching, C., Jacobson, S. & Rebelo, T. Citizen science and nature conservation. in Key Topics in Conservation Biology 2 (eds. Macdonald, D. W. & Willis, K. J.) 127–142 (John Wiley & Sons, 2013).Dickinson, J. L., Zuckerberg, B. & Bonter, D. N. Citizen science as an ecological research tool: Challenges and benefits. Annu. Rev. Ecol. Evol. Syst. 41, 149–172 (2010).Article 

    Google Scholar 
    Baillie, S. R., Wernham, C. V. & Clark, J. A. Development of the British and Irish ringing scheme and its role in conservation biology. Ringing Migr. 19, S5–S19 (1999).Article 

    Google Scholar 
    Greenwood, J. J. D. Citizens, science and bird conservation. J. Ornithol. 148, S77–S124 (2007).Article 

    Google Scholar 
    Horns, J. J., Adler, F. R. & Şekercioğlu, Ç. H. Using opportunistic citizen science data to estimate avian population trends. Biol. Conserv. 221, 151–159 (2018).Article 

    Google Scholar 
    Ryan, R. L., Kaplan, R. & Grese, R. E. Predicting volunteer commitment in environmental stewardship programmes. J. Environ. Plan. Manag. 44, 629–648 (2001).Article 

    Google Scholar 
    Maund, P. R. et al. What motivates the masses: Understanding why people contribute to conservation citizen science projects. Biol. Conserv. 246, 108587 (2020).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Martin, V. Y. & Greig, E. I. Young adults’ motivations to feed wild birds and influences on their potential participation in citizen science: An exploratory study. Biol. Conserv. 235, 295–307 (2019).Article 

    Google Scholar 
    Cox, D. T. C. & Gaston, K. J. Human–nature interactions and the consequences and drivers of provisioning wildlife. Philos.Trans. R. Soc. B Biol. Sci. 373, 20170092 (2018).Article 

    Google Scholar 
    Murray, M. H., Becker, D. J., Hall, R. J. & Hernandez, S. M. Wildlife health and supplemental feeding: A review and management recommendations. Biol. Conserv. 204, 163–174 (2016).Article 

    Google Scholar 
    Rocha, G. & Quillfeldt, P. Effect of supplementary food on age ratios of European turtle doves (Streptopelia turtur L.). Anim. Biodivers. Conserv. 38, 11–21 (2015).Article 

    Google Scholar  More

  • in

    Assessing mammal trapping standards in wild boar drop-net capture

    Dubois, S. et al. International consensus principles for ethical wildlife control. Conserv. Biol. 31(4), 753–760 (2017).PubMed 
    Article 

    Google Scholar 
    Frank, B. & Glikman, J. A. Human–wildlife conflicts and the need to include coexistence. In Human–Wildlife Interactions (eds Frank, B. et al.) 1–19 (Cambridge University Press, 2019).
    Google Scholar 
    Meng, X. J., Lindsay, D. S. & Sriranganathan, N. Wild boars as sources for infectious diseases in livestock and humans. Philos. Trans. R. Soc. B Biol. Sci. 364, 2697–2707 (2009).CAS 
    Article 

    Google Scholar 
    Massei, G., Roy, S. & Bunting, R. Too many hogs? A review of methods to mitigate impact by wild boar and feral hogs. Hum. Wildl. Interact. 5, 79–99 (2011).
    Google Scholar 
    Carpio, A. J., Apollonio, M. & Acevedo, P. Wild ungulate overabundance in Europe: Contexts, causes, monitoring and management recommendations. Mamm. Rev. 51, 95–108 (2021).Article 

    Google Scholar 
    Stillfried, M. et al. Secrets of success in a landscape of fear: Urban wild boar adjust risk perception and tolerate disturbance. Front. Ecol. Evol. 5, 157 (2017).Article 

    Google Scholar 
    Castillo-Contreras, R. et al. Urban wild boars prefer fragmented areas with food resources near natural corridors. Sci. Total Environ. 615, 282–288 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Keuling, O., Strauß, E. & Siebert, U. Regulating wild boar populations is ‘somebody else’s problem’!—Human dimension in wild boar management. Sci. Total Environ. 554–555, 311–319 (2016).ADS 
    PubMed 
    Article 
    CAS 

    Google Scholar 
    Vajas, P. et al. Many, large and early: Hunting pressure on wild boar relates to simple metrics of hunting effort. Sci. Total Environ. 698, 134251. https://doi.org/10.1016/j.scitotenv.2019.134251 (2020).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Licoppe, A. et al. Wild boar/feral pig in (peri-)urban areas. Managing wild boar in human-dominated landscapes. in International Union of Game Biologists (IUGB)—Congress IUGB 2013, 1–31 (2013).Torres-Blas, I. et al. Assessing methods to live-capture wild boars (Sus scrofa) in urban and peri-urban environments. Vet. Rec. 187, e85. https://doi.org/10.1136/vr.105766 (2020).Article 
    PubMed 

    Google Scholar 
    Adams, C. E. Urban Wildlife Management (CRC Press, 2016).
    Google Scholar 
    Conejero, C. et al. Past experiences drive citizen perception of wild boar in urban areas. Mamm. Biol. 96, 68–72 (2019).Article 

    Google Scholar 
    Lewis, J. S., VerCauteren, K. C., Denkhaus, R. M. & Mayer, J. J. Wild pig populations along the urban gradient. In Invasive Wild Pigs in North America (eds VerCauteren, K. C. et al.) 439–463 (CRC Press, 2019).Chapter 

    Google Scholar 
    Massei, G. et al. Effect of the GnRH vaccine GonaCon on the fertility, physiology and behaviour of wild boar. Wildl. Res. 35, 540–547 (2008).CAS 
    Article 

    Google Scholar 
    Náhlik, A. et al. Wild boar management in Europe: Knowledge and practice. In Ecology, Conservation and Management of Wild Pigs and Peccaries (eds Melletti, M. & Meijaard, E.) 339–353 (Cambridge University Press, 2017).Chapter 

    Google Scholar 
    Croft, S., Franzetti, B., Gill, R. & Massei, G. Too many wild boar? Modelling fertility control and culling to reduce wild boar numbers in isolated populations. PLoS One 15, e0238429. https://doi.org/10.1371/journal.pone.0238429 (2020).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    González-Crespo, C. et al. Stochastic assessment of management strategies for a Mediterranean peri-urban wild boar population. PLoS One 13, e0202289. https://doi.org/10.1371/journal.pone.0202289 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Schemnitz, S. D., Batcheller, G. R., Lovallo, M. J., White, H. B. & Fall, M. W. Capturing and handling wild animals. In Research and Management Techniques for Wildlife and Habitats (ed. Silvy, N. J.) 232–269 (John Hopkins University Press, 2009).
    Google Scholar 
    ECGCGRF (European Community, Government of Canada, and Government of the Russian Federation). Agreement on international humane trapping standards. Off. J. Eur. Communities 42, 43–57 (1997).
    Google Scholar 
    Anonymous. International agreement in the form of an agreed minute between the European Community and the United States of America on humane trapping standards. Off. J. Eur. Communities L219, 26–37 (1998).
    Google Scholar 
    ISO 10990-4. Methods for testing killing trap systems used on land and underwater. in Animal (Mammal) Traps—Part 4 (International Organization for Standardization, 1999).ISO 10990-5. Methods for testing restraining traps. in Animal (Mammal) Traps—Part 5 (International Organization for Standardization, 1999).Proulx, G., Cattet, M., Serfass, T. L. & Baker, S. E. Updating the AIHTS trapping standards to improve animal welfare and capture efficiency and selectivity. Animals 10, 1–26 (2020).Article 

    Google Scholar 
    Proulx, G. Mammal Trapping—Wildlife Management, Animal Welfare and International Standards (Alpha Wildlife Publications, 2022).
    Google Scholar 
    Iossa, G., Soulsbury, C. & Harris, S. Mammal trapping: A review of animal welfare standards of killing and restraining traps. Anim. Welf. 16, 335–352 (2007).CAS 

    Google Scholar 
    Muñoz-Igualada, J., Shivik, J. A., Domínguez, F. G., Lara, J. & González, L. M. Evaluation of cage-traps and cable restraint devices to capture red foxes in Spain. J. Wildl. Manag. 72, 830–836 (2008).Article 

    Google Scholar 
    Trap Research and Development Committee. Best Trapping Practices (Fur Institute of Canada, 2018).
    Google Scholar 
    Virgós, E. et al. A poor international standard for trap selectivity threatens global carnivore and biodiversity conservation. Biodivers. Conserv. 25, 1409–1419 (2016).Article 

    Google Scholar 
    Barasona, J. A., López-Olvera, J. R., Beltrán-Beck, B., Gortázar, C. & Vicente, J. Trap-effectiveness and response to tiletamine-zolazepam and medetomidine anaesthesia in Eurasian wild boar captured with cage and corral traps. BMC Vet. Res. 9, 107 (2013).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Shury, T. Physical capture and restraint. In Zoo Animal and Wildlife Immobilization and Anesthesia (eds West, G. et al.) 109–124 (Wiley Blackwell, 2015).
    Google Scholar 
    Webb, S. L., Lewis, J. S., Hewitt, D. G., Hellickson, M. W. & Bryant, F. C. Assessing the helicopter and net gun as a capture technique for white-tailed deer. J. Wildl. Manag. 72, 310–314 (2008).Article 

    Google Scholar 
    López-Olvera, J. R. et al. Comparative evaluation of effort, capture and handling effects of drive nets to capture roe deer (Capreolus capreolus), Southern chamois (Rupicapra pyrenaica) and Spanish ibex (Capra pyrenaica). Eur. J. Wildl. Res. 55, 193–202 (2009).Article 

    Google Scholar 
    Breed, D. et al. Conserving wildlife in a changing world: Understanding capture myopathy—A malignant outcome of stress during capture and translocation. Conserv. Physiol. 7, 1–21 (2019).Article 
    CAS 

    Google Scholar 
    Mentaberre, G. et al. Azaperone and sudden death of drive net-captured southern chamois. Eur. J. Wildl. Res. 58, 489–493 (2012).Article 

    Google Scholar 
    Gaskamp, J. A., Gee, K. L., Campbell, T. A., Silvy, N. J. & Webb, S. L. Effectiveness and efficiency of corral traps, drop nets and suspended traps for capturing wild pigs (Sus scrofa). Animals 11, 1565 (2021).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Baker, S. E., Macdonald, D. W. & Ellwood, S. A. Double standards in spring trap welfare. In Proceedings of the Ninth International Conference on Urban Pests (eds Daivies, C. & Pfeiffer, W. H.) 139–145 (Pureprint Group, 2017).
    Google Scholar 
    López-Olvera, J. R., Castillo-Contreras, R., González-Crespo, C., Conejero, C. & Mentaberre, G. Wild boar is not welcome in the city. Barcelona Metròpolis 103, 22–23 (2017).
    Google Scholar 
    Conejero, C. et al. Conflicto o habituación: las dos caras de la percepción social del jabalí urbano. in Proceedings of XIV Congreso de la Sociedad Española para la Conservación y Estudio de los Mamíferos (SECEM, 2019).Conferencia Sectorial de Medio Ambiente. Directrices Técnicas para la Captura de Especies Cinegéticas Predadoras: Homologación de Métodos y Acreditación de Usuarios (Ministerio para la Transición Ecológica y el Reto Demográfico de España, 2011).Generalitat de Catalunya—Government of Catalonia. Decret 56/2014 relatiu a l’homologació de mètodes de captura en viu d’espècies cinegètiques depredadores i d’espècies exòtiques invasores depredadores i l’acreditació de les persones que en són usuàries. Diari Oficial de la Generalitat de Catalunya 6609 (2014).Fahlman, Å. et al. Wild boar behaviour during live-trap capture in a corral-style trap: Implications for animal welfare. Acta Vet. Scand. 62, 1–11 (2020).Article 

    Google Scholar 
    Sharp, T. & Saunders, G. A Model for Assessing the Relative Humaneness of Pest Animal Control Methods (Australian Government—Department of Agriculture, Fisheries and Forestry [New Millennium Print], 2011).
    Google Scholar 
    Ziegler, L., Fischer, D., Nesseler, A. & Lierz, M. Validation of the live trap ‘Krefelder Fuchsfalle’ in combination with electronic trap sensors based on AIHTS standards. Eur. J. Wildl. Res. 64, 17 (2018).Article 

    Google Scholar 
    Marco, I. et al. Capture myopathy in little bustards after trapping and marking. J. Wildl. Dis. 42, 889–891 (2006).ADS 
    PubMed 
    Article 

    Google Scholar 
    Rideout, C. B. Comparison of techniques for capturing mountain goats. J. Wildl. Manag. 38, 573 (1974).Article 

    Google Scholar 
    Jedrzejewski, W. & Kamler, J. F. Modified drop-net for capturing ungulates. Wildl. Soc. Bull. 32, 1305–1308 (2004).Article 

    Google Scholar 
    Gaskamp, J. A. Use of drop-nets for wild pig damage and disease abatement. Master’s thesis, available electronically from https://hdl.handle.net/1969.1/148198 (Texas A&M University, 2012).Lavelle, M. J. et al. When pigs fly: Reducing injury and flight response when capturing wild pigs. Appl. Anim. Behav. Sci. 215, 21–25 (2019).Article 

    Google Scholar 
    Masilkova, M. et al. Observation of rescue behaviour in wild boar (Sus scrofa). Sci. Rep. 11, 16217 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Podgórski, T. et al. Spatiotemporal behavioral plasticity of wild boar (Sus scrofa) under contrasting conditions of human pressure: Primeval forest and metropolitan area. J. Mammal. 94, 109–119 (2013).Article 

    Google Scholar 
    Manfredo, M., Teel, T. & Bright, A. Why are public values toward wildlife changing?. Hum. Dimens. Wildl. 8, 287–306 (2003).Article 

    Google Scholar 
    Cahill, S., Llimona, F., Cabañeros, L. & Calomardo, F. Characteristics of wild boar (Sus scrofa) habituation to urban areas in the Collserola Natural Park (Barcelona) and comparison with other locations. Anim. Biodivers. Conserv. 35, 221–233 (2012).Article 

    Google Scholar  More